Microencapsulation of a Pseudomonas Strain (VUPF506) in Alginate–Whey Protein–Carbon Nanotubes and Next-Generation Sequencing Identification of This Strain

Alginate is a common agent used for microencapsulation; however, the formed capsule is easily damaged. Therefore, alginate requires blending with other biopolymers to reduce capsule vulnerability. Whey protein is one polymer that can be incorporated with alginate to improve microcapsule structure. In this study, three different encapsulation methods (extrusion, emulsification, and spray drying) were tested for their ability to stabilize microencapsulated Pseudomonas strain VUPF506. Extrusion and emulsification methods enhanced encapsulation efficiency by up to 80% and gave the best release patterns over two months. A greenhouse experiment using potato plants treated with alginate–whey protein microcapsules showed a decrease in Rhizoctonia disease intensity of up to 70%. This is because whey protein is rich in amino acids and can serve as a resistance induction agent for the plant. In this study, the use of CNT in the ALG–WP system increased the rooting and proliferation and reduced physiological complication. The results of this study showed that the technique used in encapsulation could have a significant effect on the efficiency and persistence of probiotic bacteria. Whole genome sequence analysis of strain VUPF506 identified it as Pseudomonas chlororaphis and revealed some genes that control pathogens.

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The effectiveness of a new biological product Spud on the basis of Bacillus subtilis in the cultivation of potatoes

The Agrarian Scientific Journal ◽

10.28983/asj.y2019i5pp8-14 ◽

2019 ◽

pp. 8-14

Author(s):

Marina Konstantinovna Derevyagina ◽

Svetlana Viktorovna Vasilyeva ◽

Grigory Leonidovich Belov ◽

Vladimir Nikolaevich Zeyruk ◽

Irina Igorevna Novikova

Keyword(s):

Late Blight ◽

Disease Development ◽

Dry Rot ◽

Potato Blight ◽

Potato Plants ◽

Moderate Disease ◽

Rhizoctonia Disease ◽

The Impact ◽

Fungistatic Effect ◽

New Crop

It is shown the efficiency of the application of preparative forms (dry and liquid) of Kartofin during the growing season 2016-2018 years against major diseases of potatoes and the impact on the growth and development of culture. Biopreparation possesses high fungistatic effect, protecting potato plants against rhizoctonia disease, potato blight and late blight under field conditions and tubers of the new crop from dry rot. In years of low and moderate disease development, the effectiveness of the studied Potato biopreparation on the Sante variety was at the level of the reference chemical variant, equally reducing the distribution and degree of disease development. In the years of epiphytotic disease development fungistatic effect of the biopreparation was inferior in efficiency to chemical fungicides, but had a significant protective effect compared to the control, reducing the distribution of rhizoctonia disease by 22.5%, potato blightby 20.7%, late blight by 12.8% on average. The results of tuberous analyses after harvesting showed a decrease in the percentage of tuber damage by dry rot in variants with Kartofin (1.7 and 1.4%). The yield of the standard potatoes after application of Kartofin was slightly higher than in the control – by 5.1–7.7%.

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Complete Genome Sequence of Matlo Bat Lyssavirus

Microbiology Resource Announcements ◽

10.1128/mra.00241-21 ◽

2021 ◽

Vol 10 (20) ◽

Author(s):

Colyn S. Grobler ◽

Jessica Coertse ◽

Wanda Markotter

Keyword(s):

South Africa ◽

Next Generation Sequencing ◽

Genome Sequence ◽

Complete Genome Sequence ◽

Complete Genome ◽

Novel Species ◽

Whole Genome Sequence ◽

Whole Genome ◽

Sequencing Technologies ◽

Generation Sequencing

ABSTRACT The genus Lyssavirus includes rabies virus as well as multiple diverse and recently described novel species. Using next-generation sequencing technologies, we have obtained the whole-genome sequence of Matlo bat lyssavirus, which was isolated from a Natal long-fingered bat (Miniopterus natalensis) in South Africa.

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Genome Assessment of Antibiotic Resistance Genes in Probiotic Bacteria and a Literature Review

10.21203/rs.3.rs-254514/v1 ◽

2021 ◽

Author(s):

Mehdi Fatahi-Bafghi ◽

Sara Naseri ◽

Ali Alizehi

Keyword(s):

Antibiotic Resistance ◽

Genome Sequence ◽

Resistance Genes ◽

Pathogenic Bacteria ◽

Antibiotic Resistance Genes ◽

Probiotic Bacteria ◽

Whole Genome Sequence ◽

Probiotic Properties ◽

Antibiotic Resistant ◽

To Come

Abstract Having various clinical applications, probiotic bacteria are currently used in the diet. There are reports of antibiotic resistance genes (ARGs) in these bacteria that can be transferred to other microflora and pathogenic bacteria. The aim of the study is to examine whole-genome sequence analysis in bacteria with probiotic properties. Moreover, this study follows existing issues about the importance and presence of ARGs in these bacteria the dangers of which may affect human health in the years to come. In the present study, 126 complete probiotic bacterial genomes were collected and analysed for ARGs. The results of the study shows there are various antibiotic resistant genes of in these bacteria some of which can be transmitted to other bacteria. We propose microorganisms be applied as a probiotic element in various types of products, antibiogram be conducted for a large number of antibiotics and analysis of complete genome sequence for ARGs prediction.

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Preparation and Characterization of Alginate and Psyllium Beads ContainingLactobacillus acidophilus

The Scientific World JOURNAL ◽

10.1100/2012/680108 ◽

2012 ◽

Vol 2012 ◽

pp. 1-8 ◽

Cited By ~ 23

Author(s):

Farzaneh Lotfipour ◽

Shahla Mirzaeei ◽

Maryam Maghsoodi

Keyword(s):

Lactobacillus Acidophilus ◽

Encapsulation Efficiency ◽

Alginate Beads ◽

Probiotic Bacteria ◽

Partial Substitution ◽

Narrow Size Distribution ◽

Acidic Conditions ◽

Ph Conditions

This paper describes preparation and characterization of beads of alginate and psyllium containing probiotic bacteria ofLactobacillus acidophilusDMSZ20079. Twelve different formulations containing alginate (ALG) and alginate-psyllium (ALG-PSL) were prepared using extrusion technique. The prepared beads were characterized in terms of size, morphology and surface properties, encapsulation efficiency, viabilities in acid (pH 1.8, 2 hours) and bile (0.5% w/v, 2 hours) conditions, and release in simulated colon pH conditions. The results showed that spherical beads with narrow size distribution ranging from1.59±0.04to1.67±0.09 mm for ALG and from1.61±0.06to1.80±0.07mm for ALG-PSL with encapsulation efficiency higher than 98% were achieved. Furthermore, addition of PSL into ALG enhanced the integrity of prepared beads in comparison with ALG formulations. The results indicated that incorporation of PSL into alginate beads improved viability of the bacteria in acidic conditions as well as bile conditions. Also, stimulating effect of PSL on the probiotic bacteria was observed through 20-hour incubation in simulated colonic pH solution. According to ourin vitrostudies, PSL can be a suitable polymer candidate for partial substitution with ALG for probiotic coating.

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Whole-Genome Sequencing of Six Borrelia miyamotoi Clinical Strains Isolated in Russia

Genome Announcements ◽

10.1128/genomea.01424-17 ◽

2018 ◽

Vol 6 (1) ◽

Cited By ~ 3

Author(s):

Konstantin V. Kuleshov ◽

Joris Koetsveld ◽

Irina A. Goptar ◽

Mikhail L. Markelov ◽

Nadezhda M. Kolyasnikova ◽

...

Keyword(s):

Next Generation Sequencing ◽

Genome Sequencing ◽

Russian Federation ◽

Complete Sequence ◽

Whole Genome Sequence ◽

Borrelia Miyamotoi ◽

Whole Genome ◽

The Russian Federation ◽

Sequencing Platforms ◽

Generation Sequencing

ABSTRACT Here, we report the whole-genome sequence of six clinical Borrelia miyamotoi isolates from the Russian Federation. Using two independent next-generation sequencing platforms, we determined the complete sequence of the chromosome and several plasmids. All strains have an Asian genotype with 99.8% chromosome nucleotide similarity with B. miyamotoi strain FR64b.

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Comparative Genomic Analysis of Pseudomonas chlororaphis PCL1606 Reveals New Insight into Antifungal Compounds Involved in Biocontrol

Molecular Plant-Microbe Interactions ◽

10.1094/mpmi-10-14-0326-fi ◽

2015 ◽

Vol 28 (3) ◽

pp. 249-260 ◽

Cited By ~ 21

Author(s):

Claudia E. Calderón ◽

Cayo Ramos ◽

Antonio de Vicente ◽

Francisco M. Cazorla

Keyword(s):

Genome Sequence ◽

Genomic Analysis ◽

Comparative Genomic Analysis ◽

Whole Genome Sequence ◽

Comparative Genomic ◽

Antifungal Compound ◽

Antifungal Compounds ◽

Pseudomonas Chlororaphis ◽

Biosynthetic Genes ◽

Biocontrol Activity

Pseudomonas chlororaphis PCL1606 is a rhizobacterium that has biocontrol activity against many soilborne phytopathogenic fungi. The whole genome sequence of this strain was obtained using the Illumina Hiseq 2000 sequencing platform and was assembled using SOAP denovo software. The resulting 6.66-Mb complete sequence of the PCL1606 genome was further analyzed. A comparative genomic analysis using 10 plant-associated strains within the fluorescent Pseudomonas group, including the complete genome of P. chlororaphis PCL1606, revealed a diverse spectrum of traits involved in multitrophic interactions with plants and microbes as well as biological control. Phylogenetic analysis of these strains using eight housekeeping genes clearly placed strain PCL1606 into the P. chlororaphis group. The genome sequence of P. chlororaphis PCL1606 revealed the presence of sequences that were homologous to biosynthetic genes for the antifungal compounds 2-hexyl, 5-propyl resorcinol (HPR), hydrogen cyanide, and pyrrolnitrin; this is the first report of pyrrolnitrin encoding genes in this P. chlororaphis strain. Single-, double-, and triple-insertional mutants in the biosynthetic genes of each antifungal compound were used to test their roles in the production of these antifungal compounds and in antagonism and biocontrol of two fungal pathogens. The results confirmed the function of HPR in the antagonistic phenotype and in the biocontrol activity of P. chlororaphis PCL1606.

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Finding functional disease-associated non-coding variation using next-generation sequencing

10.1101/060285 ◽

2016 ◽

Author(s):

Paolo Devanna ◽

Xiaowei Sylvia Chen ◽

Joses Ho ◽

Dario Gajewski ◽

Alessandro Gialluisi ◽

...

Keyword(s):

Next Generation Sequencing ◽

Binding Sites ◽

Large Scale ◽

Sequence Data ◽

Whole Genome Sequence ◽

Next Generation Sequencing Data ◽

Whole Genome ◽

Next Generation ◽

Whole Exome ◽

Generation Sequencing

ABSTRACTNext generation sequencing has opened the way for the large scale interrogation of cohorts at the whole exome, or whole genome level. Currently, the field largely focuses on potential disease causing variants that fall within coding sequences and that are predicted to cause protein sequence changes, generally discarding non-coding variants. However non-coding DNA makes up ~98% of the genome and contains a range of sequences essential for controlling the expression of protein coding genes. Thus, potentially causative non-coding variation is currently being overlooked. To address this, we have designed an approach to assess variation in one class of non-coding regulatory DNA; the 3′UTRome. Variants in the 3'UTR region of genes are of particular interest because 3'UTRs are responsible for modulating protein expression levels via their interactions with microRNAs. Furthermore they are amenable to large scale analysis as 3′UTR-microRNA interactions are based on complementary base pairing and as such can be predicted in silico at the genome-wide level. We report a strategy for identifying and functionally testing variants in microRNA binding sites within the 3'UTRome and demonstrate the efficacy of this pipeline in a cohort of language impaired children. Using whole exome sequence data from 43 probands, we extracted variants that lay within 3'UTR microRNA binding sites. We identified a common variant (SNP) in a microRNA binding site and found this SNP to be associated with an endophenotype of language impairment (non-word repetition). We showed that this variant disrupted microRNA regulation in cells and was linked to altered gene expression in the brain, suggesting it may represent a risk factor contributing to SLI. This work demonstrates that biologically relevant variants are currently being under-investigated despite the wealth of next-generation sequencing data available and presents a simple strategy for interrogating non-coding regions of the genome. We propose that this strategy should be routinely applied to whole exome and whole genome sequence data in order to broaden our understanding of how non-coding genetic variation underlies complex phenotypes such as neurodevelopmental disorders.

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Isolation and characterization of Pseudomonas chlororaphis strain ST9 and its potential as a bioinoculant for agriculture

10.1101/2020.12.23.424151 ◽

2020 ◽

Author(s):

Iris Bertani ◽

Elisa Zampieri ◽

Cristina Bez ◽

Andrea Volante ◽

Vittorio Venturi ◽

...

Keyword(s):

Plant Growth ◽

Crop Yields ◽

Whole Genome Sequence ◽

Pseudomonas Chlororaphis ◽

Plant Tolerance ◽

Biotic Stresses ◽

Isolation And Characterization ◽

Plant Growth Promoting ◽

Plant Genes

AbstractThe development of biotechnologies based on beneficial microorganisms for improving soil fertility and crop yields could help addressing many current agriculture challenges, such as food security, climate change, pests control, soil depletion while decreasing the use of chemical fertilizers and pesticides. Plant Growth Promoting (PGP) microbes can be used as probiotics in order to increase plant tolerance/resistance to abiotic/biotic stresses and in this context strains belonging to the Pseudomonas chlororaphis group have shown to have potential as PGP candidates. In this work a new P. chlororaphis isolate is reported and tested for (i) in vitro PGP features, (ii) whole genome sequence analysis, and (iii) its effects on root microbiome, plant growth and on the expression of different plant genes in greenhouse experiments. The potential use of this P. chlororaphis strain as a plant probiotic is discussed.

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Transcriptomics-Based Approach Identifies Spinosad-Associated Targets in the Colorado Potato Beetle, Leptinotarsa decemlineata

Insects ◽

10.3390/insects11110820 ◽

2020 ◽

Vol 11 (11) ◽

pp. 820

Author(s):

Pierre Bastarache ◽

Gabriel Wajnberg ◽

Pascal Dumas ◽

Simi Chacko ◽

Jacynthe Lacroix ◽

...

Keyword(s):

Colorado Potato Beetle ◽

Leptinotarsa Decemlineata ◽

Insect Pest ◽

Molecular Targets ◽

Primary Method ◽

Juvenile Hormone Esterase ◽

Potato Plants ◽

Potato Beetle ◽

Potato Crops ◽

Generation Sequencing

The Colorado potato beetle Leptinotarsa decemlineata is an insect pest that threatens potato crops globally. The primary method to control its damage on potato plants is the use of insecticides, including imidacloprid, chlorantraniliprole and spinosad. However, insecticide resistance has been frequently observed in Colorado potato beetles. The molecular targets and the basis of resistance to imidacloprid and chlorantraniliprole have both been previously quantified. This work was undertaken with the overarching goal of better characterizing the molecular changes associated with spinosad exposure in this insect pest. Next-generation sequencing was conducted to identify transcripts that were differentially expressed between Colorado potato beetles exposed to spinosad versus control insects. Results showed several transcripts that exhibit different expression levels between the two conditions, including ones coding for venom carboxylesterase-6, chitinase 10, juvenile hormone esterase and multidrug resistance-associated protein 4. In addition, several microRNAs, such as miR-12-3p and miR-750-3p, were also modulated in the investigated conditions. Overall, this work reveals a molecular footprint underlying spinosad response in Colorado potato beetles and provides novel leads that could be targeted as part of RNAi-based approaches to control this insect pest.

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Isolation and Characterization of Pseudomonas chlororaphis Strain ST9; Rhizomicrobiota and in Planta Studies

Plants ◽

10.3390/plants10071466 ◽

2021 ◽

Vol 10 (7) ◽

pp. 1466

Author(s):

Iris Bertani ◽

Elisa Zampieri ◽

Cristina Bez ◽

Andrea Volante ◽

Vittorio Venturi ◽

...

Keyword(s):

Plant Growth ◽

Crop Yields ◽

Whole Genome Sequence ◽

Pseudomonas Chlororaphis ◽

Plant Tolerance ◽

In Planta ◽

Biotic Stresses ◽

Isolation And Characterization ◽

Plant Genes

The development of biotechnologies based on beneficial microorganisms for improving soil fertility and crop yields could help to address many current agriculture challenges, such as food security, climate change, pest control, soil depletion while decreasing the use of chemical fertilizers and pesticides. Plant growth-promoting (PGP) microbes can be used as probiotics in order to increase plant tolerance/resistance to abiotic/biotic stresses and in this context strains belonging to the Pseudomonas chlororaphis group have shown to have potential as PGP candidates. In this study a new P. chlororaphis isolate is reported and tested for (i) in vitro PGP features, (ii) whole-genome sequence analysis, and (iii) its effects on the rhizosphere microbiota composition, plant growth, and different plant genes expression levels in greenhouse experiments. Results showed that P. chlororaphis ST9 is an efficient rice root colonizer which integrates into the plant resident-microbiota and affects the expression of several plant genes. The potential use of this P. chlororaphis strain as a plant probiotic is discussed.

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