scholarly journals The Microbiota of Edam Cheeses Determined by Cultivation and High-Throughput Sequencing of the 16S rRNA Amplicon

2020 ◽  
Vol 10 (12) ◽  
pp. 4063
Author(s):  
Beata Nalepa ◽  
Sławomir Ciesielski ◽  
Marek Aljewicz
Keyword(s):  
High Throughput ◽  
High Throughput Sequencing ◽  
Starter Culture ◽  
Lactobacillus Rhamnosus ◽  
Streptococcus Thermophilus ◽  
Genus Clostridium ◽  
Lactobacillus Kefiri ◽  
Spore Forming Bacteria ◽  
Generation Sequencing

The aim of this study was to evaluate the microbiome of industrially produced ripened Edam cheeses by next-generation sequencing. The samples for analyses were collected in spring and autumn. Spring samples were characterized by significantly higher Lactococcus and Bacillus counts and lower counts of Enterobacteriaceae, Enterococcus, and yeasts than autumn samples. The predominant microorganisms identified by the Illumina high-throughput sequencing technology belonged to four phyla: Firmicutes, Actinobacteria, Proteobacteria and Bacteroidetes. The dominant species were starter culture bacteria. Lactobacillus rhamnosus, Lactobacillus kefiri, Lactobacillus kefiranofaciens, Lactobacillus casei, Streptococcus thermophilus, and Bifidobacterium had the highest share of microbial cheese communities. The number of γ-Proteobacteria reads was higher in autumn cheese samples. A high number of reads was also noted in the genus Clostridium. The counts of spore-forming bacteria of the genus Bacillus were higher in cheeses produced in spring. The study revealed highly similar relationships between the analyzed production periods. The present results contribute to the existing knowledge of cheese microbiota, and they can be used to improve and modify production processes based on the composition of microbial communities, as well as to improve the quality of the final product.

scholarly journals Great differences in performance and outcome of high-throughput sequencing data analysis platforms for fungal metabarcoding

MycoKeys ◽  
2018 ◽  
Vol 39 ◽  
pp. 29-40 ◽  
Author(s):  
Sten Anslan ◽  
R. Henrik Nilsson ◽  
Christian Wurzbacher ◽  
Petr Baldrian ◽  
Leho Tedersoo ◽  
...  
Keyword(s):  
High Throughput ◽  
High Throughput Sequencing ◽  
Computation Time ◽  
Potential Effect ◽  
Data Sets ◽  
Sequencing Data ◽  
Operational Taxonomic Units ◽  
High Throughput Sequencing Data ◽  
Recent Developments

Along with recent developments in high-throughput sequencing (HTS) technologies and thus fast accumulation of HTS data, there has been a growing need and interest for developing tools for HTS data processing and communication. In particular, a number of bioinformatics tools have been designed for analysing metabarcoding data, each with specific features, assumptions and outputs. To evaluate the potential effect of the application of different bioinformatics workflow on the results, we compared the performance of different analysis platforms on two contrasting high-throughput sequencing data sets. Our analysis revealed that the computation time, quality of error filtering and hence output of specific bioinformatics process largely depends on the platform used. Our results show that none of the bioinformatics workflows appears to perfectly filter out the accumulated errors and generate Operational Taxonomic Units, although PipeCraft, LotuS and PIPITS perform better than QIIME2 and Galaxy for the tested fungal amplicon dataset. We conclude that the output of each platform requires manual validation of the OTUs by examining the taxonomy assignment values.

Screening and Identification of PLK1-Polo Box Binding Peptides by High-Throughput Sequencing of Phage-Selected Libraries

2019 ◽  
Vol 26 (8) ◽  
pp. 620-633 ◽  
Author(s):  
Nousheen Bibi ◽  
Hafsa Niaz ◽  
Ted Hupp ◽  
Mohammad Amjad Kamal ◽  
Sajid Rashid
Keyword(s):  
Next Generation Sequencing ◽  
Phage Display ◽  
High Throughput ◽  
High Throughput Sequencing ◽  
B Lymphocyte ◽  
Fluorescent Protein ◽  
Next Generation ◽  
Peptide Phage Display ◽  
Binding Peptides ◽  
Generation Sequencing

Background: Human proteome contains a plethora of short linear peptide motifs that is crucial for signaling and other cellular processes. These motifs are difficult to identify due to lack of systematic approach for their detection. Objective: Here we demonstrate the use of peptide phage display in combination with high throughput next generation sequencing to identify enriched peptide sequences through biopanning process against polo box domain (PBD) of mitotic polo like kinase 1 (Plk1). Methods: Purified recombinant Plk1 and two unrelated controls namely B-lymphocyte antigen (CD20) and fluorescent protein (mCherry) were subjected to peptide phage display analysis. Bacterially-propagated phage DNA was amplified by PCR using triplet bar coded primers to tag the pool from each amplicon. Results: Proteomic peptide phage display along with next generation sequencing and Bioinformatics analysis demonstrated several known and putative novel interactions which were potentially related to Plk1-PBD. With our strategy, we were able to identify and characterize several Plk1-PBD binding peptides, as well as define more precisely, consensus sequences. Conclusion: We believe that this information could provide valuable tools for exploring novel interaction involved in Plk1 signaling as well as to choose peptides for Plk1 specific drug development.

scholarly journals An integrated pipeline for next generation sequencing and annotation of the complete mitochondrial genome of the giant intestinal fluke, Fasciolopsis buski (Lankester,1857) Looss, 1899

2013 ◽  
Author(s):  
Devendra Kumar Biswal ◽  
Sudeep Ghatani ◽  
Jollin A Shylla ◽  
Ranjana Sahu ◽  
Nandita Mullapudi ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Mitochondrial Genome ◽  
High Throughput ◽  
High Throughput Sequencing ◽  
Next Generation ◽  
Genome Sequences ◽  
Fasciolopsis Buski ◽  
Mt Genome ◽  
Generation Sequencing ◽  
Control Regions

Helminths include both parasitic nematodes (roundworms) and platyhelminths (trematode and cestode flatworms) that are abundant, and are of clinical importance. The genetic characterization of parasitic flatworms using advanced molecular tools is central to the diagnosis and control of infections. Although the nuclear genome houses suitable genetic markers (e.g., in ribosomal (r) DNA) for species identification and molecular characterization, the mitochondrial (mt) genome consistently provides a rich source of novel markers for informative systematics and epidemiological studies. In the last decade, there have been some important advances in mtDNA genomics of helminths, especially lung flukes, liver flukes and intestinal flukes. Fasciolopsis buski, often called the giant intestinal fluke, is one of the largest digenean trematodes infecting humans and found primarily in Asia, in particular the Indian subcontinent. Next-generation sequencing (NGS) technologies now provide opportunities for high throughput sequencing, assembly and annotation within a short span of time. Herein, we describe a high-throughput sequencing and bioinformatics pipeline for mt genomics for F. buski that emphasizes the utility of short read NGS platforms such as Ion Torrent and Illumina in successfully sequencing and assembling the mt genome using innovative approaches for PCR primer design as well as assembly. We took advantage of our NGS whole genome sequence data (unpublished so far) for F. buski and its comparison with available data for the Fasciola hepatica mtDNA as the reference genome for design of precise and specific primers for amplification of mt genome sequences from F. buski. A long-range PCR was carried out to create a NGS library enriched in mt DNA sequences. Two different NGS platforms were employed for complete sequencing, assembly and annotation of the F. buski mt genome. The complete mt genome sequences of the intestinal fluke comprise 14,118 bp and is thus the shortest trematode mitochondrial genome sequenced to date. The noncoding control regions are separated into two parts by the tRNA-Gly gene and donot contain either tandem repeats or secondary structures, which are typical for trematode control regions. The gene content and arrangement are identical to that of F. hepatica. The F. buski mtDNA genome has a close resemblance with F. hepatica and has a similar gene order tallying with that of other trematodes. The mtDNA for the intestinal fluke is reported herein for the first time by our group that would help invesigate Fasciolidae taxonomy and systematics with the aid of mtDNA NGS data. More so, it would serve as a resource for comparative mitochondrial genomics and systematic studies of trematode parasites.

scholarly journals An integrated pipeline for next generation sequencing and annotation of the complete mitochondrial genome of the giant intestinal fluke, Fasciolopsis buski (Lankester,1857) Looss, 1899

2013 ◽  
Author(s):  
Devendra Kumar Biswal ◽  
Sudeep Ghatani ◽  
Jollin A Shylla ◽  
Ranjana Sahu ◽  
Nandita Mullapudi ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Mitochondrial Genome ◽  
High Throughput ◽  
High Throughput Sequencing ◽  
Next Generation ◽  
Genome Sequences ◽  
Fasciolopsis Buski ◽  
Mt Genome ◽  
Generation Sequencing ◽  
Control Regions

Helminths include both parasitic nematodes (roundworms) and platyhelminths (trematode and cestode flatworms) that are abundant, and are of clinical importance. The genetic characterization of parasitic flatworms using advanced molecular tools is central to the diagnosis and control of infections. Although the nuclear genome houses suitable genetic markers (e.g., in ribosomal (r) DNA) for species identification and molecular characterization, the mitochondrial (mt) genome consistently provides a rich source of novel markers for informative systematics and epidemiological studies. In the last decade, there have been some important advances in mtDNA genomics of helminths, especially lung flukes, liver flukes and intestinal flukes. Fasciolopsis buski, often called the giant intestinal fluke, is one of the largest digenean trematodes infecting humans and found primarily in Asia, in particular the Indian subcontinent. Next-generation sequencing (NGS) technologies now provide opportunities for high throughput sequencing, assembly and annotation within a short span of time. Herein, we describe a high-throughput sequencing and bioinformatics pipeline for mt genomics for F. buski that emphasizes the utility of short read NGS platforms such as Ion Torrent and Illumina in successfully sequencing and assembling the mt genome using innovative approaches for PCR primer design as well as assembly. We took advantage of our NGS whole genome sequence data (unpublished so far) for F. buski and its comparison with available data for the Fasciola hepatica mtDNA as the reference genome for design of precise and specific primers for amplification of mt genome sequences from F. buski. A long-range PCR was carried out to create a NGS library enriched in mt DNA sequences. Two different NGS platforms were employed for complete sequencing, assembly and annotation of the F. buski mt genome. The complete mt genome sequences of the intestinal fluke comprise 14,118 bp and is thus the shortest trematode mitochondrial genome sequenced to date. The noncoding control regions are separated into two parts by the tRNA-Gly gene and donot contain either tandem repeats or secondary structures, which are typical for trematode control regions. The gene content and arrangement are identical to that of F. hepatica. The F. buski mtDNA genome has a close resemblance with F. hepatica and has a similar gene order tallying with that of other trematodes. The mtDNA for the intestinal fluke is reported herein for the first time by our group that would help invesigate Fasciolidae taxonomy and systematics with the aid of mtDNA NGS data. More so, it would serve as a resource for comparative mitochondrial genomics and systematic studies of trematode parasites.

scholarly journals Effect of Lactic Acid Bacteria Starter Cultures on Vitamin and Oligosaccharide Composition of Milk Extracted from Three Common Bean (Phaselous Vulgaris L) Varieties

2019 ◽  
Vol 8 (3) ◽  
pp. 103
Author(s):  
Calvince Anino ◽  
Arnold Onyango ◽  
Samuel Imathiu ◽  
Julius Maina
Keyword(s):  
Common Bean ◽  
Starter Culture ◽  
Lactobacillus Rhamnosus ◽  
Vitamin B1 ◽  
Streptococcus Thermophilus ◽  
Starter Cultures ◽  
Lactobacillus Bulgaricus ◽  
Fermented Foods ◽  
Raffinose Oligosaccharides ◽  
B Complex Vitamins

Fermented foods have in recent times attracted consumer interest mainly due to perceived health benefits of probiotic microorganisms. This study characterized changes in the concentrations of selected B-complex vitamins and oligosaccharides of common bean milk during fermentation by a common dairy starter culture, YF L-903 (Streptococcus thermophilus + Lactobacillus Bulgaricus subs Debulgaricus), and three probiotic cultures namely ABT (Lactobacillus acidophilus La-5 + Bifidobacterium animalis Bb-12 + Streptococcus thermophilus), Yoba (Lactobacillus rhamnosus yoba + Streptococcus thermophilus), and Yoba Fiti (Lactobacillus rhamnosus GR1 + Streptococcus thermophilus). Bean milk was prepared from three common bean varieties. It was found that, apart from thiamine (vitamin B1) and riboflavin (vitamin B2), fermentation with each of the mixed cultures caused significant increase in the vitamin B complex. Significant reductions (p<0.05) in the oligosaccharides concentration of the bean milks were observed upon fermentation. Highest reduction in the oligosaccharide sugars of 77.8% was found in milk from pinto bean variety fermented with ABT culture. These findings suggest that LAB probiotic cultures have a potential for improving biosynthesis of vitamins and removal of the verbascose, stachyose and raffinose oligosaccharides, thus making the product more digestible and the nutrients more bioavailable.

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