Information Package / Course Catalogue
Metagenomic Analysis of Microbiome
Course Code: MİK668
Course Type: Area Elective
Couse Group: Third Cycle (Doctorate Degree)
Education Language: Turkish
Work Placement: N/A
Theory: 2
Prt.: 2
Credit: 3
Lab: 0
ECTS: 4
Objectives of the Course

The objective of this course is to give information about the metagenomic analysis of microbiome

Course Content

It is necessary to learn and practice whole laboratory steps of microbiome analysis, to be able to transfer the knowledge on microbiota and microbiome to the field and clinical application. Fort his reason, this course contains the main methods used in the laboratory analysis of microbiota and microbiome; laboratory steps of microbiome analysis by new generation sequencing; determination of target genes, library construction; wet lab steps on the basis of different NGS systems; use of bioinformatic tools and databases; bioinformatic analysis, filtering and quality control of data; sampling and proceesing of microbiome material; statistical analysis and presentation of microbiome data.

Name of Lecturer(s)
Learning Outcomes
1.1. To know sampling and pre-processing steps for microbiome analysis
2.2. To know and be able to perform NGS steps
3.3. To know and be able to perform bioinformatic tools
4.4. To be able to control and evaluate microbiome data
5.5. To be able to perform Metagenomic analysis by him/her self
Recommended or Required Reading
1.A Beginner's Guide for Metagenome Analysis
2.Metagenomics for Microbiology
Weekly Detailed Course Contents
Week 1 - Theoretical & Practice
Laboratory analysis of microbiota and microbiome: general principles - Introduction of equipment
Week 2 - Theoretical & Practice
Microbiota analysis by bacteriological culturing - Microbiota analysis by bacteriological culturing
Week 3 - Theoretical & Practice
Microbiome analysis by real-time PCR - Microbiome analysis by real-time PCR
Week 4 - Theoretical & Practice
Microbiome analysis by new generation sequencing (NGS) - Microbiome analysis by new generation sequencing (NGS)
Week 5 - Theoretical & Practice
Target genes used in microbiome analysis - Target genes used in microbiome analysis
Week 6 - Theoretical & Practice
Library construction for microbiome analysis - Library construction for microbiome analysis
Week 7 - Theoretical & Practice
Laboratory protocols for microbiome analysis with NGSs - Laboratory protocols for microbiome analysis with NGSs
Week 8 - Theoretical & Practice
Bioinformatic tools for microbiome analysis
Week 9 - Theoretical & Practice
Processing of sequence data for microbiome analysis
Week 10 - Theoretical & Practice
Processing of sequence data for microbiome analysis
Week 11 - Theoretical & Practice
The use of reference database in microbiome analysis
Week 12 - Theoretical & Practice
Filtering and taxonomic control of microbiome data
Week 13 - Theoretical & Practice
Determination of uncultured microorganism by shot-gun sequencing
Week 14 - Theoretical & Practice
Sampling and proceesing of microbome material, Statistical analysis and presentation of microbiome data
Assessment Methods and Criteria
Type of AssessmentCountPercent
Attending Lectures1%5
Laboratory1%5
Midterm Examination1%20
Final Examination1%70
Workload Calculation
ActivitiesCountPreparationTimeTotal Work Load (hours)
Lecture - Theory140228
Lecture - Practice140228
Laboratory115116
Reading1527
Quiz1112
Midterm Examination1527
Final Examination110212
TOTAL WORKLOAD (hours)100
Contribution of Learning Outcomes to Programme Outcomes
PÇ-1
PÇ-2
PÇ-3
PÇ-4
PÇ-5
PÇ-6
PÇ-7
OÇ-1
3
5
4
4
4
5
3
OÇ-2
5
5
3
4
4
3
4
OÇ-3
4
5
5
4
4
5
5
OÇ-4
4
5
5
4
3
3
4
OÇ-5
4
5
4
4
4
5
4
Adnan Menderes University - Information Package / Course Catalogue
2026