Whole-Genome Sequencing of Lactobacillus helveticus D75 and D76 Confirms Safety and Probiotic Potential

Whole-genome DNA sequencing of Lactobacillus D75 and D76 strains (Vitaflor, Russia) was determined using the PacBio RS II platform, which was followed by de novo assembly with SMRT Portal 2.3.0. The average nucleotide identity (ANI) test showed that both strains belong to the Lactobacillus helveticus, but not to the L. acidophilus, as previously assumed. In addition, 31 exopolysaccharide (EPS) production genes (nine of which form a single genetic cluster), 13 adhesion genes, 38 milk protein and 11 milk sugar utilization genes, 13 genes for and against specific antagonistic activity, eight antibiotic resistance genes, and also three CRISPR blocks and eight Cas I-B system genes were identified in the genomes of both strains. The expression of bacteriocin helveticin J genes was confirmed. In fact, the presence of identified genes suggests that L. helveticus D75 and D76 are able to form biofilms on the outer mucin layer, inhibit the growth of pathogens and pathobionts, utilize milk substrates with the formation of digestible milk sugars and bioactive peptides, resist bacteriophages, show some genome-determined resistance to antibiotics, and stimulate the host’s immune system. Pathogenicity genes have not been identified. The study results confirm the safety and high probiotic potential of the strains.

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Whole-Genome Sequencing of Lactobacillus Helveticus D75 and D76 Confirms Safety and Probiotic Potential

10.20944/preprints201912.0354.v1 ◽

2019 ◽

Author(s):

Vyacheslav Toropov ◽

Elena Demyanova ◽

Olga Shalaeva ◽

Stanislav Sitkin ◽

Timur Vakhitov

Keyword(s):

Milk Protein ◽

De Novo ◽

Antibiotic Resistance Genes ◽

Antagonistic Activity ◽

Lactobacillus Helveticus ◽

Whole Genome ◽

Probiotic Potential ◽

Pacbio Rs Ii ◽

Study Results ◽

Mucin Layer

Whole-genome DNA sequencing of Lactobacillus D75 and D76 strains (Vitaflor, Russia) was performed using the PacBio RS II platform, followed by de novo assembly with SMRT Portal 2.3.0. The average nucleotide identity (ANI) test showed that both strains belong to the Lactobacillus helveticus, but not the L. acidophilus as previously assumed. 31 exopolysaccharide (EPS) production genes (nine of which form a single genetic cluster), 13 adhesion genes, 38 milk protein and 11 milk sugar utilization genes, 13 genes for and against specific antagonistic activity, aight antibiotic resistance genes, and also three CRISPR blocks and eight Cas I-B system genes were identified in the genomes of the both strains. The expression of some genes was confirmed. In fact, the presence of identified genes suggests that L. helveticus D75 and D76 are able to form biofilms on the outer mucin layer, inhibit the growth of pathogens and pathobionts, utilize milk substrates with the formation of digestible milk sugars and bioactive peptides, resist bacteriophages and show some genome-determined resistance to antibiotics, stimulate the host’s immune system. Pathogenicity genes have not been identified. The study results confirm the safety and high probiotic potential of the strains.

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The use of whole-genome sequencing for molecular epidemiology and antimicrobial surveillance: identifying the role of IncX3 plasmids and the spread of blaNDM-4-like genes in the Enterobacteriaceae

Journal of Clinical Pathology ◽

10.1136/jclinpath-2015-203044 ◽

2015 ◽

Vol 68 (10) ◽

pp. 835-838 ◽

Cited By ~ 32

Author(s):

Björn A Espedido ◽

Borce Dimitrijovski ◽

Sebastiaan J van Hal ◽

Slade O Jensen

Keyword(s):

Antibiotic Resistance ◽

Whole Genome Sequencing ◽

Resistance Gene ◽

Genome Sequencing ◽

De Novo ◽

Antibiotic Resistance Genes ◽

Whole Genome ◽

Antimicrobial Surveillance ◽

Metropolitan Hospital ◽

Genetic Context

AimsTo characterise the resistome of a multi-drug resistant Klebsiella pneumoniae (Kp0003) isolated from an Australian traveller who was repatriated to a Sydney Metropolitan Hospital from Myanmar with possible prosthetic aortic valve infective endocarditis.MethodsKp0003 was recovered from a blood culture of the patient and whole genome sequencing was performed. Read mapping and de novo assembly of reads facilitated in silico multi-locus sequence and plasmid replicon typing as well as the characterisation of antibiotic resistance genes and their genetic context. Conjugation experiments were also performed to assess the plasmid (and resistance gene) transferability and the effect on the antibiotic resistance phenotype.ResultsImportantly, and of particular concern, the carbapenem-hydrolysing β-lactamase gene blaNDM-4 was identified on a conjugative IncX3 plasmid (pJEG027). In this respect, the blaNDM-4 genetic context is similar (at least to some extent) to what has previously been identified for blaNDM-1 and blaNDM-4-like variants.ConclusionsThis study highlights the potential role that IncX3 plasmids have played in the emergence and dissemination of blaNDM-4-like variants worldwide and emphasises the importance of resistance gene surveillance.

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Comparative Genome Analysis Reveals Human Pathogenic Potential of ESBL-Escherichia coli Isolated from Swine Microbiomes

10.1101/2021.07.15.452468 ◽

2021 ◽

Author(s):

Luria L Founou ◽

Raspail Carrel Founou ◽

Mushal Allam ◽

Arshad Ismael ◽

Sabiha Yusuf Essack

Keyword(s):

South Africa ◽

Virulence Genes ◽

De Novo ◽

Antibiotic Resistance Genes ◽

Whole Genome ◽

Comparative Genome Analysis ◽

Pathogenic Potential ◽

E Coli ◽

Effective Strategies ◽

Sequence Types

Background: Extended-spectrum β-lactamase-producing E. coli (ESBL-Ec) harbouring virulence genes in the microbiome of food animals could likely threaten human health but is poorly understood in Cameroon and South Africa. Here, we assessed the resistome, virulome and mobilome of ESBL-Ec isolated from swine microbiomes in these countries, using whole genome sequencing (WGS). Materials/methods: Eleven clonally-related phenotypic ESBL-Ec isolates were subjected to WGS. The isolates were de novo assembled using the CLC Genomics Workbench and SPAdes while RAST and PROKKA were used for annotation of the assembled contigs. Prediction of antibiotic resistance genes, virulence factors and plasmids was performed using ResFinder, VirulenceFinder and PlasmidFinder, respectively. Results: Diverse STs were detected with sequence types ST2144 and ST88 predominating and blaCTX-M-15 (55%) as principal ESBL genes. Although the isolates belonged mainly to commensal phylogroups A/B1 (45/28.3%) and C (18.18%), all harboured at least three extraintestinal pathogenic E. coli (ExPEC) VFs with one isolate harbouring up to 18 ExPEC VFs. Conclusion: The resistance and pathogenic potential of ESBL-Ec colonizing the gut microbiota of swine in both countries demonstrate the urgent need to implement effective strategies to contain the dissemination of virulent ESBL-Ec through the food chain in Cameroon and South Africa.

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Whole-Genome Shotgun Sequencing of an Indian-Origin Lactobacillus helveticus Strain, MTCC 5463, with Probiotic Potential

Journal of Bacteriology ◽

10.1128/jb.05449-11 ◽

2011 ◽

Vol 193 (16) ◽

pp. 4282-4283 ◽

Cited By ~ 12

Author(s):

J. B. Prajapati ◽

C. D. Khedkar ◽

J. Chitra ◽

S. Suja ◽

V. Mishra ◽

...

Keyword(s):

Shotgun Sequencing ◽

Whole Genome Shotgun ◽

Lactobacillus Helveticus ◽

Whole Genome ◽

Probiotic Potential ◽

Whole Genome Shotgun Sequencing ◽

Indian Origin

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Penatalaksanaan IMD pada Ibu Postpartum Sectio Caesarea Mempengaruhi Status Gizi dan Kecepatan Produksi ASI

Jurnal Bidan Cerdas (JBC) ◽

10.33860/jbc.v2i2.68 ◽

2020 ◽

Vol 2 (2) ◽

pp. 112-120

Author(s):

Nursari Abdul Syukur ◽

Susi Purwanti

Keyword(s):

Breast Milk ◽

Nutritional Status ◽

Milk Production ◽

Quantitative Research ◽

Milk Protein ◽

Sectio Caesarea ◽

Control Group ◽

P Value ◽

Study Results

Many mothers who give birth to Sectio Caesarea (SC) do not Initiate Early Breastfeeding (IMD), which fails exclusive breastfeeding. This study aimed to determine the effect of IMD management in postpartum SC mothers on nutritional status, speed of milk production, and quality of breast milk protein. Method: quantitative research with quasi approach experiment. The research design used was a pre-post-test control non-equivalent control group. A sampling of this study used the Consecutive method sampling with a sample of 20 mothers who gave birth by cesarean section (SC). Hypothesis testing uses the independent t-test and the Mann-Whitney test. The study results showed an influence on the management of IMD in postpartum SC mothers on the speed of ASI production (p-value=0.004) and nutritional status (p-value=0.028). There was no effect of IMD management on postpartum SC mothers on the quality of breast milk protein (p-value = 0.543). This study recommends that the hospital implement an IMD promotion program before the abdominal wall is closed as a form of intervention to increase milk production and maternal nutritional status

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Effective variant filtering and expected candidate variant yield in studies of rare human disease

npj Genomic Medicine ◽

10.1038/s41525-021-00227-3 ◽

2021 ◽

Vol 6 (1) ◽

Author(s):

Brent S. Pedersen ◽

Joe M. Brown ◽

Harriet Dashnow ◽

Amelia D. Wallace ◽

Matt Velinder ◽

...

Keyword(s):

Whole Genome Sequencing ◽

Rare Disease ◽

Genome Sequencing ◽

Autosomal Dominant ◽

De Novo ◽

Autosomal Dominant Inheritance ◽

Compound Heterozygous ◽

Whole Genome ◽

Dominant Inheritance ◽

Family Based

AbstractIn studies of families with rare disease, it is common to screen for de novo mutations, as well as recessive or dominant variants that explain the phenotype. However, the filtering strategies and software used to prioritize high-confidence variants vary from study to study. In an effort to establish recommendations for rare disease research, we explore effective guidelines for variant (SNP and INDEL) filtering and report the expected number of candidates for de novo dominant, recessive, and autosomal dominant modes of inheritance. We derived these guidelines using two large family-based cohorts that underwent whole-genome sequencing, as well as two family cohorts with whole-exome sequencing. The filters are applied to common attributes, including genotype-quality, sequencing depth, allele balance, and population allele frequency. The resulting guidelines yield ~10 candidate SNP and INDEL variants per exome, and 18 per genome for recessive and de novo dominant modes of inheritance, with substantially more candidates for autosomal dominant inheritance. For family-based, whole-genome sequencing studies, this number includes an average of three de novo, ten compound heterozygous, one autosomal recessive, four X-linked variants, and roughly 100 candidate variants following autosomal dominant inheritance. The slivar software we developed to establish and rapidly apply these filters to VCF files is available at https://github.com/brentp/slivar under an MIT license, and includes documentation and recommendations for best practices for rare disease analysis.

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A study of transposable element-associated structural variations (TASVs) using a de novo-assembled Korean genome

Experimental & Molecular Medicine ◽

10.1038/s12276-021-00586-y ◽

2021 ◽

Author(s):

Seyoung Mun ◽

Songmi Kim ◽

Wooseok Lee ◽

Keunsoo Kang ◽

Thomas J. Meyer ◽

...

Keyword(s):

Genome Sequencing ◽

Genome Assembly ◽

De Novo ◽

Personal Genome ◽

Human Populations ◽

Whole Genome ◽

Structural Variations ◽

Insert Size ◽

Human Genomes ◽

Next Generation Sequencing Ngs

AbstractAdvances in next-generation sequencing (NGS) technology have made personal genome sequencing possible, and indeed, many individual human genomes have now been sequenced. Comparisons of these individual genomes have revealed substantial genomic differences between human populations as well as between individuals from closely related ethnic groups. Transposable elements (TEs) are known to be one of the major sources of these variations and act through various mechanisms, including de novo insertion, insertion-mediated deletion, and TE–TE recombination-mediated deletion. In this study, we carried out de novo whole-genome sequencing of one Korean individual (KPGP9) via multiple insert-size libraries. The de novo whole-genome assembly resulted in 31,305 scaffolds with a scaffold N50 size of 13.23 Mb. Furthermore, through computational data analysis and experimental verification, we revealed that 182 TE-associated structural variation (TASV) insertions and 89 TASV deletions contributed 64,232 bp in sequence gain and 82,772 bp in sequence loss, respectively, in the KPGP9 genome relative to the hg19 reference genome. We also verified structural differences associated with TASVs by comparative analysis with TASVs in recent genomes (AK1 and TCGA genomes) and reported their details. Here, we constructed a new Korean de novo whole-genome assembly and provide the first study, to our knowledge, focused on the identification of TASVs in an individual Korean genome. Our findings again highlight the role of TEs as a major driver of structural variations in human individual genomes.

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