Science

Master of Science in Applied Microbiology

The Master of Science in Applied Microbiology is a postgraduate programme that prepares professionals for advanced practice in microbiology, biotechnology, and microbial applications. The programme combines microbiological theory with practical laboratory and industrial application.

Core areas include medical microbiology, industrial microbiology, food microbiology, environmental microbiology, microbial genetics, immunology, virology, mycology, research methods, and thesis. Students engage with both microbiological theory and practical laboratory work through coursework and research.

The programme is offered by the University of Nairobi, Kenyatta University, JKUAT, Pwani University, and several other public universities. Programmes are offered over two academic years through full-time and part-time modes of study.

Students develop competencies in medical microbiology, industrial microbiology, food microbiology, environmental microbiology, microbial genetics, immunology, virology, mycology, and research methods. The programme includes coursework, examinations, laboratory work, and a supervised research thesis.

JKUAT charges approximately KES 178,500/year (KES 357,000 total) for microbiology programmes. KU charges KES 326,400/year for science programmes. UoN charges approximately KES 433,500/year for science programmes. Entry requires a Bachelor's degree with Second Class Honours Upper Division in microbiology, biochemistry, biology, biotechnology, or related fields from a recognised university.

Graduates pursue careers as microbiologists, quality control officers, laboratory managers, research scientists, food safety officers, and lecturers in microbiology across hospitals, pharmaceutical companies, food industry, research institutions, regulatory bodies, and universities.

Skills Required

Medical Microbiology and Pathogen Identification
Industrial Microbiology and Fermentation Technology
Food Microbiology and Food Safety
Environmental Microbiology and Bioremediation
Microbial Genetics and Molecular Biology
Immunology and Serological Techniques
Virology and Viral Diagnostic Methods
Mycology and Fungal Biotechnology
Research Methods in Microbiology
Academic Writing and Thesis Research

Key Subjects

Medical Microbiology and Pathogen Identification
Industrial Microbiology and Fermentation Technology
Food Microbiology and Food Safety
Environmental Microbiology and Bioremediation
Microbial Genetics and Molecular Biology
Immunology and Serological Techniques
Virology and Viral Diagnostic Methods
Mycology and Fungal Biotechnology
Research Methods in Microbiology
Thesis Research

Certifications

KEMRI Research Certification
KEBS Laboratory Certification

Specializations

Medical Microbiology

Focuses on medical microbiology, covering pathogen identification, antimicrobial resistance, diagnostic methods, infectious disease, and managing medical microbiology.

Industrial Microbiology

Examines industrial microbiology, covering fermentation, bioproducts, enzyme technology, bioprocessing, and managing industrial microbiology.

Food Microbiology

Covers food microbiology, covering foodborne pathogens, food fermentation, food safety, quality control, and managing food microbiology.

Environmental Microbiology

Focuses on environmental microbiology, covering bioremediation, waste treatment, environmental monitoring, and managing environmental microbiology.

Virology

Examines virology, covering viral structure, replication, pathogenesis, diagnostic methods, antivirals, and managing virology.

Mycology

Covers mycology, covering fungal biology, fungal pathogens, fungal biotechnology, antifungals, and managing mycology.

Duration: 2 years
Public, up to: Ksh 395,000
Job market: High

The programme

What you study, how long it takes, and how it is delivered.

Practicalities

Study mode: Full-time, Part-time
Attachment: 0 months
Average class: 20 students
Award: Masters

What you study

10 subjects

Medical Microbiology and Pathogen Identification
Industrial Microbiology and Fermentation Technology
Food Microbiology and Food Safety
Environmental Microbiology and Bioremediation
Microbial Genetics and Molecular Biology
Immunology and Serological Techniques
Virology and Viral Diagnostic Methods
Mycology and Fungal Biotechnology
Research Methods in Microbiology
Thesis Research

Modules

12 in the programme

Medical Microbiology and Pathogen Identification
Year 1Semester 13 creditsCore
Examines pathogen identification, antimicrobial resistance, diagnostic methods, infectious disease, and managing medical microbiology.
Industrial Microbiology and Fermentation Technology
Year 1Semester 13 creditsCore
Covers fermentation, bioproducts, enzyme technology, bioprocessing, industrial applications, and managing industrial microbiology.
Research Methods in Microbiology
Year 1Semester 13 creditsCore
Covers research design, data collection, analysis, laboratory methods, and conducting microbiology research, preparing students for their thesis.
Food Microbiology and Food Safety
Year 1Semester 23 creditsCore
Examines foodborne pathogens, food fermentation, food safety, quality control, shelf-life, and managing food microbiology.
Environmental Microbiology and Bioremediation
Year 1Semester 23 creditsCore
Covers bioremediation, waste treatment, environmental monitoring, microbial ecology, and managing environmental microbiology.
Microbial Genetics and Molecular Biology
Year 1Semester 23 creditsCore
Examines gene expression, plasmids, transformation, conjugation, molecular techniques, and managing microbial genetics.
Immunology and Serological Techniques
Year 1Semester 23 creditsCore
Covers immune response, antibodies, serological techniques, immunodiagnostics, vaccine development, and managing immunology.
Virology and Viral Diagnostic Methods
Year 2Semester 13 creditsCore
Examines viral structure, replication, pathogenesis, diagnostic methods, antivirals, emerging viruses, and managing virology.
Mycology and Fungal Biotechnology
Year 2Semester 13 creditsCore
Covers fungal biology, fungal pathogens, fungal biotechnology, antifungals, mycotoxins, and managing mycology.
Antimicrobial Resistance and Stewardship
Year 2Semester 13 creditsCore
Examines resistance mechanisms, surveillance, stewardship, drug development, and managing antimicrobial resistance.
Biosafety and Biosecurity in Microbiology
Year 2Semester 13 creditsCore
Covers biosafety levels, biosecurity, risk assessment, laboratory safety, regulations, and managing biosafety.
Research Thesis
Year 2Semester 29 creditsCore
Original supervised research thesis on a microbiology topic, demonstrating mastery of research methods and microbiology knowledge, assessed through written submission and oral defence.

Specialisations

Medical Microbiology
Focuses on medical microbiology, covering pathogen identification, antimicrobial resistance, diagnostic methods, infectious disease, and managing medical microbiology.
Industrial Microbiology
Examines industrial microbiology, covering fermentation, bioproducts, enzyme technology, bioprocessing, and managing industrial microbiology.
Food Microbiology
Covers food microbiology, covering foodborne pathogens, food fermentation, food safety, quality control, and managing food microbiology.
Environmental Microbiology
Focuses on environmental microbiology, covering bioremediation, waste treatment, environmental monitoring, and managing environmental microbiology.
Virology
Examines virology, covering viral structure, replication, pathogenesis, diagnostic methods, antivirals, and managing virology.
Mycology
Covers mycology, covering fungal biology, fungal pathogens, fungal biotechnology, antifungals, and managing mycology.

A day as a student

A typical day during the MSc in Applied Microbiology programme combines lectures, laboratory sessions, practical workshops, seminars, and independent study. Sessions cover medical microbiology, industrial microbiology, food microbiology, environmental microbiology, and microbial genetics. Medical microbiology sessions examine pathogen identification, antimicrobial resistance, diagnostic methods, infectious disease, and managing medical microbiology. Industrial microbiology sessions cover fermentation, bioproducts, enzyme technology, bioprocessing, and managing industrial microbiology. Food microbiology sessions cover foodborne pathogens, food fermentation, food safety, quality control, and managing food microbiology. Environmental microbiology sessions cover bioremediation, waste treatment, environmental monitoring, and managing environmental microbiology. Microbial genetics sessions cover gene expression, plasmids, transformation, conjugation, molecular biology, and managing microbial genetics. Immunology sessions cover immune response, antibodies, serological techniques, immunodiagnostics, and managing immunology. Virology sessions cover viral structure, replication, pathogenesis, diagnostic methods, antivirals, and managing virology. Mycology sessions cover fungal biology, fungal pathogens, fungal biotechnology, antifungals, and managing mycology. Research methods sessions prepare students for their thesis, covering research design, data collection, and analysis. Laboratory sessions provide hands-on experience with microbial culture, staining, identification, antimicrobial testing, molecular techniques, and fermentation. Practical workshops provide hands-on experience with food microbiology testing, environmental sampling, industrial fermentation, and diagnostic methods. Seminars and discussion groups provide opportunities for debating current issues in microbiology. Guest lectures from experienced microbiologists, researchers, and industry professionals provide practical insights. The programme culminates in a supervised research thesis on a microbiology topic.

The trade offs

In its favour

High demand for microbiology professionals with growing pharmaceutical industry, food safety regulation, biotechnology, and infectious disease research in Kenya.
Programme offered by four public universities (UoN, KU, JKUAT, Pwani), providing wide institutional choice with different fee levels.
JKUAT offers competitive fees at approximately KES 178,500/year for microbiology programmes.
Strong industry links with KEMRI, KEBS, and pharmaceutical companies providing research collaboration and career opportunities.

Against it

UoN fees are higher at approximately KES 433,500/year for science programmes.
The exact programme name may vary across institutions, potentially causing confusion for prospective students.
No private university confirmed offering this exact programme, limiting options.
Programme requires microbiology, biochemistry, biology, or biotechnology background, which limits access for non-related graduates.

What it costs

Tuition at both ends of the market, and how to pay for it.

What it costs, and where

Against 243 science courses

Public179k to 395k

179k at Jomo Kenyatta University of Agriculture and Technology395k at University of Nairobi

Annual tuition in Kenyan shillings, rounded. The upright tick is the median for this field, so a bar sitting entirely to its right is an expensive programme by the standards of its own subject.

The fine print

UoN ~395K/yr (biochemistry.uonbi.ac.ke). JKUAT 178.75K/yr. Private unverified.

HELB postgraduate loans are available for Kenyan students. KU may offer postgraduate bursaries for eligible students. KEMRI and medical research organisations may provide research support. Some pharmaceutical and food companies may sponsor staff for postgraduate study.

Funding options

HELB Postgraduate Loan
KU Postgraduate Bursary
KEMRI Research Support

Scholarships

3 recorded

HELB Postgraduate Loan
LoanKsh 200,000Kenyan
Kenyan students pursuing postgraduate studies at recognised universities.
KU Postgraduate Bursary
ScholarshipKsh 100,000Kenyan
Kenyatta University offers postgraduate bursaries for eligible students.
KEMRI Research Support
GrantKsh 250,000Kenyan
KEMRI and partner organisations may provide research support for microbiology and medical research professionals.

Getting in

The grades, the alternatives, and who accredits the award.

What you need

KCSE mean grade: N/A (Postgraduate)
Alternative entry: Most universities require Upper Second Class Honours in microbiology, biochemistry, biology, or biotechnology. Lower Second Division holders with relevant experience or postgraduate diplomas are considered. Contact respective universities for specific admission requirements.

How you are assessed

4 components

Coursework and Continuous Assessment
Coursework30% of the mark
Continuous assessment through coursework assignments, laboratory reports, practical tests, seminar presentations, and class participation.
Written Examinations
Examination70% of the mark
Written examinations covering medical microbiology, industrial microbiology, food microbiology, environmental microbiology, and microbial genetics.
Laboratory and Practical Assessment
Practical30% of the mark
Practical assessment through laboratory exercises, microbial culture, identification, antimicrobial testing, molecular techniques, and demonstrating microbiology skills.
Research Thesis
Research100% of the mark
Original supervised research thesis on a microbiology topic, demonstrating mastery of research methods and microbiology knowledge, assessed through written submission and oral defence.

Accreditation

The programme is accredited by the Commission for University Education (CUE). University of Nairobi, Kenyatta University, JKUAT, and Pwani University (all public) offer MSc in Applied Microbiology or related microbiology programmes. All programmes meet CUE standards for postgraduate training in microbiology. Graduates are eligible for KEMRI research certification and KEBS laboratory certification.

Accredited by

Commission for University Education (CUE)
Academic accreditationRequired
Programme accredited by CUE. University of Nairobi, Kenyatta University, JKUAT, and Pwani University (all public) offer MSc in Applied Microbiology or related microbiology programmes. All programmes meet CUE standards for postgraduate training in microbiology. Graduates are eligible for KEMRI research certification and KEBS laboratory certification.

Where it leads

The roles it opens, and what you leave with.

Where graduates go

6 roles

Microbiologist
High demandKsh 130,000 to Ksh 550,000
Conducts microbiology work, overseeing microbial analysis, identification, quality control, and managing microbiology.
Quality Control Officer
High demandKsh 120,000 to Ksh 500,000
Manages quality control, overseeing microbiology testing, standards compliance, quality assurance, and managing quality control.
Laboratory Manager
Moderate demandKsh 140,000 to Ksh 600,000
Manages laboratory operations, overseeing testing, equipment, staff, quality, safety, and managing laboratory operations.
Research Scientist
High demandKsh 130,000 to Ksh 550,000
Conducts scientific research, overseeing research design, experimentation, analysis, publication, and managing scientific research.
Food Safety Officer
High demandKsh 120,000 to Ksh 500,000
Manages food safety, overseeing microbiology testing, HACCP, compliance, inspection, and managing food safety.
Microbiology Lecturer
Moderate demandKsh 120,000 to Ksh 500,000
Teaches microbiology at university or college level, overseeing instruction, research, laboratory supervision, and academic supervision.

Graduate outcomes

Where these fields lead

8 careers

Tools you will learn

BLAST
SoftwarePrimary
BLAST for sequence analysis, covering microbial identification, sequence alignment, phylogenetics, and managing molecular data.
SPSS
Software
SPSS for statistical analysis, covering experimental data, microbial counts, and managing research data.
R
Software
R for statistical analysis, covering microbial data, bioinformatics, and managing research data.
MEGA
Software
MEGA for molecular evolutionary analysis, covering phylogenetics, sequence analysis, evolutionary genetics, and managing molecular data.

Industry links

Common misconceptions

Microbiology is just about studying bacteria.
Applied microbiology covers comprehensive medical, industrial, food, environmental microbiology, virology, mycology, and microbial genetics beyond just bacteria.
This programme is only for those who want to work in hospitals.
Microbiology skills are valuable for pharmaceuticals, food industry, agriculture, environment, biotechnology, and academia beyond just hospitals.
Microbiology has limited career prospects in Kenya.
With growing pharmaceutical industry, food safety regulation, biotechnology, and infectious disease research, demand for microbiology professionals is high in Kenya.
Industrial microbiology is just about brewing beer.
Industrial microbiology covers comprehensive fermentation, bioproducts, enzymes, antibiotics, vaccines, and bioprocessing.
Food microbiology is just about testing for spoilage.
Food microbiology covers comprehensive foodborne pathogens, fermentation, food safety, quality control, and shelf-life studies.
Environmental microbiology is just about testing water.
Environmental microbiology covers comprehensive bioremediation, waste treatment, environmental monitoring, and microbial ecology.