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Assignment Task

Original title: Beneficial bacteria in dairy products: identification and analysis using metagenomics and comparative genomics
Modified title: Analysis of the Genome Sequence of [bacterial and strain names]
Aim: identify and analyse specific genetic traits related to beneficial and relevant properties of probiotic bacteria
Objectives (see methods):
• Literature searches
• Gene detection and analysis
• Analysis of amino acid sequences of specific products
• Genome analysis: detection of gene clusters, mobile elements etc
• Comparative genomics 

Mohamed Ali
Analysis of the Genome Sequence of Streptococcus thermophilus strain 
Nadia Elahi
Analysis of the Genome Sequence of Lactobacillus delbrueckii strain 
Maneesha Injeti
Analysis of the Genome Sequence of Lactococcus lactis strain 
Laskhmi Syamala Uppaluru
Analysis of the Genome Sequence of Lactobacillus plantarum strain

Methods and work plan

Methods

1.Search literature and genome sequencing data to identify strains of the allocated bacterium used in food industry

2.Select a strain with full genome sequence (e.g. from Genome Announcements, etc)

3.Extract complete genome sequence from GenBank, view it using CLC Genomics Workbench (limited functionality, to be provided)

4.Perform search for genes involved in probiotic properties by keywords in GenBank and using RAST (compare)

5.As above, but by doing similarity searches using query sequences from other bacteria (Blast)

6.Search for presence/absence of genes related to probiotic and other properties of these bacteria (such as those involved in production of adhesins, bacteriocins - BAGEL3, CRISPR, toxins, antib. resistance) and speculate on their advantages / disadvantages and/or beneficial effects of dairy products

7.Analyse sequences of these genes and products (Blast) – best hits, justification of annotation based on similarity

8.Organisation of the regions containing these genes. i.e. as gene clusters, and their possible origin – HGT (GC content difference from surrounding regions, possible location in prophages or transposons or on plasmids; possible horizontal transfer

9.Comparative genomics (presence of these traits in other species). Use Mauve and other whole genome analysis and comparison tools e.g. to draw and compare circular maps; identification of and comparison with the most closely related genomes

10.Comparative analysis of aa acid sequences of some specific proteins (multiple sequence comparison tool ClustalW)

11.Discussion. How these results may 1) explain probiotic properties 2) help with construction of improved strains 3) address antimicrobial resistance problems, etc. (indicative, extend as necessary).

Literature search
1.Current methods or bacterial identification
2.Properties and usage (in industry) or different strains of the species (indicating essential factors)
Report: should be structures with sections to include Introduction, Methods, Results (data analysis), Discussion and
Conclusion/Summary

Notes:
1.Date range during which the milestones should be achieved.
2.This needs to involve some preliminary literature searches, to confirm that appropriate data is available
3.This needs to involve some preliminary literature and data searches and trying out analysis tools, to confirm that
appropriate data and data analysis tools are available.

Notes from supervisor: the dates and milestones shown above are copied from the module guide and are indicative, and should be only used as a general guidance.

Some of these are not relevant to these projects, e.g. you’re expected to start working on your projects (both literature and data analysis) according to the plan provided (see methods above) straight after introductory lectures 1-3 June; formulation of hypothesis until “12-06” is not applicable, as the hypothesis has already been discussed on 29 May.

 

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  • Uploaded By : Alon 
  • Posted on : September 24th, 2018

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