Department of Microbiology

About Us


The Department of Microbiology is part of School of Pure and Applied Sciences and offers courses to students from the School of Agriculture and Enterprise Development, School of Applied Human Sciences, School of Education, School of Environmental Studies and School of Medicine.


External links
The Department has established research collaborations with institutions such as Kenya Medical Research institute (KEMRI), Kenya Agricultural Research Institute (KARI), Kenya Forestry Research Institute (KEFRI), International Livestock Research Institute (ILRI), Institute of Primate Research (IPR), World Agroforestry Centre (ICRAF) and other Universities in Kenya.


The Department trains graduate students at both MSc. and PhD levels in the following areas of specialization: - Agricultural and Soil Microbiology, Industrial Microbiology, Environmental Microbiology and Medical Microbiology.
Moreover, the Department offers a B.Sc. course in Microbiology.


Career Prospects

 Our graduates are marketable in National and international Research institutions, Pharmaceutical firms, Biotechnology industries, Food industries, Institutions of Higher Learning and Health services laboratories.



Research activities
Members of staff  are currently involved in research in the following areas:-

  • Agricultural and Soil Microbiology
  • Bacteriology, Mycology and Virology
  • Environmental Microbiology
  • Evolutionary studies in infectious agents
  • Food Microbiology
  • Immunological aspects of tropical diseases
  • Industrial Microbiology
  • Infectious diseases
  • Molecular Biology
  • Plant extracts and their microbial properties
  • Plant-microbe interactions


Publications 2013

  1. Beatrice Mukami Muriuki, Michael Muita Gicheru, Dorcas Wachira, Anthony Kebira Nyamache andSamoel Ashimosi Khamadi.Prevalence of hepatitis B and C viral co-infections among HIV-1 infected individuals in Nairobi, Kenya. BMC Research notes 2013, 6:363 doi:10.1186/1756-0500-6-363
  2. Gicharu, G.K., Gitonga, N.M, Boga H, Cheruiyot R.C., and Maingi (2013): Effect of inoculating selected climbing bean cultivars with different rhizobia strains on nitrogen fixation. Online International Journal of Microbiology Research 1(2), 25-31.
  3. Gicharu G. K., Gitonga N.M., Boga H., Cheruiyot R.C. and Maingi J.M (2013): Variation in Nitrogen Fixation among Three Bush Bean Cultivars Grown in Kenya when Inoculated with Three Rhizobia Strains. Greener Journal of Agricultural Sciences, 3 (11) 748-754.
  4. Kago E.K, Kinyua Z.M, Okemo P.O and Maingi J.M. (2013). Efficacy of Brassica Tissue and ChalimTM on Control of Plant Parasitic Nematodes. Journal of Biology , 01, (01) 25-32.
  5. Kemoi, E K, Okemo, P, and Bii C, (2013). Presence of Cryptococcus species in domestic chicken (Gallus gallus) droppings and the possible risk it posed to humans in Kabigeriet Village, Nakuru County, Kenya. East African Medical Journal (89):277-280
  6. Kemoi E. K. Okemo, P. O, and Bii, C. C (2013). Isolation of Candida Species in domestic chicken (Gallus gallus) droppings in Kabigeriet Village, Nakuru County, Kenya. European Scientific Journal 9 (36): 309-318.
  7. Kemoi E. K. Okemo P.O and Bii, C. C (2013). Pathogenic Cryptococol species Co-presence with Salmonella in rectal swabs of domestic chicken (Gallus gallus) at Kabigeriet Village, Nakuru County, Kenya. East African Medical Journal 90(1): 116-120.
  8. Luvanda M.K., Maingi J., Okemo P., and Yang E (2013). Analysis of the effects of di-electric heating on common food bacterial pathogens: Evaluation based on antibiotic susceptibility and infective doses. Greener Journal of Biological Sciences 3(6), 220-228.
  9. Margaret Githiri, Judith Kimiywe and Paul Okemo (2013). Knowledge in food hygiene and hygienic practices differ-in food handlers at a hospital in Nairobi, Kenya. African Journal of food Science and Technology 4(1):19-24.
  10. Musyoki A.M, Suleiman M.A, Mbithi J.N., and Maingi J.M. (2013). Water-borne bacterial pathogens in surface waters of Nairobi River and health implication to communities downstream Athi River. International Journal of Life Science and Pharma Research 3(1), 4-9.
  11. Musyoki A.M, Suleiman M.A, Mbithi J.N., and Maingi J.M. (2013). Diurnal and seasonal variations of pathogenic bacteria in Dandora Sewage Treatment Plant wastewater, Nairobi, Kenya. Journal of Research in Environmental Science and Toxicology 2(2), 36-41.
  12. Njeru, E.M. (2013) Crop diversification:a potential strategyto mitigate food insecurity by smallholdersin sub Saharan Africa. Journal of Agriculture, Food Systems,and Community Development pp. 1–7 ISSN: 2152-0801 online
  13. Njeru, E.M., Maingi, J.M., Cheruiyot, R. and Gitonga, N.M.(2013) Managing soybean for enhanced food production and soil bio-fertility insmallholdersystems throughmaximized fertilizer use efficiency. International Journalof Agriculture and Forestry 3(5):191-197.
  14. Njeru E.M., Avio L., Sbrana C., Turrini A., Bocci G., Bàrberi P., Giovannetti M. (2013) First evidence fora major cover cropeffect on arbuscular mycorrhizal fungi and organic maize growth. Agronomy for Sustainable Development: 1-8. DOI: 10.1007/s13593-013-0197-y.
  15. Njeru, E.M. (2013) Crop diversification:a potential strategyto mitigate food insecurity by smallholdersin sub Saharan Africa. Journal of Agriculture, Food Systems,and Community Development pp. 1–7 ISSN: 2152-0801 online
  16. Nyamboya Rosemary Atieno, Okemo Paul Owuor, and Ombori Omwoyo (2013). Heavy metal and associated antibiotic resistance of fecal coloforms, fecal streptococii and pathogens isolated from wastewaters of abattoirs in Nairobi, Kenya. Journal of Applied Biosciences 64:4858-4866.
  17. Nyamboya R. A, Okemo P. O, and Omwoyo O. (2013). Isolation of High antibiotic resistant Fecal Bacteria indicators, Salmonella and Vibrio spicies fromraw Abbattoirs sewage in Peri-Urban locations of Nairobi.Greener Journal of Biological Sciences 3(5):172-178.
  18. Nyamboya R. A. Okemo P.O, Ombori O.(2013).Antibiotic Resistance of Fecael Bacterial indicators and pathogens isolated from sludge and wastewaters of Abottoirs in Nairobi, Kenya. Journal of Biology 1(5)
  19. Nyamache A.K, Muigai A.W, Khamadi S.A.: Profile of HIV-1 Co-Receptor Tropism among Kenyan patients from 2009 to 2010. Journal of AIDS Research and Human Retroviruses. 2013; 29, 8, 1105-1109 
  20. Nyamache AK, A.W Muigai, SA Khamadi. Circulating Trends of non B HIV type 1 subtypes among Kenyan individuals. Journal of AIDS Research and Human Retroviruses Journal of AIDS Research and Human Retroviruses 2013, 29(2): 400-403 
  21. Erick M Bosire, A.K Nyamache, Michael M Gicheru, Raphael W Lihana,Vincent Okoth and Samoel A Khamadi. Population specific reference ranges of CD3, CD4 and CD8 lymphocyte subsets among healthy Kenyans.1929235879995082. AIDS Res Ther. 2013 Nov 7: 10(1):24.
  22. Omari A, Okemo P.O. Machocho A. Mbugua P. Njagi. N.M. and Nyamache A K. (2013).The Role of Phytomedicine in the Challenges of Emerging, Re-Emerging Diseases; and pathogens Resistance to Antibiotics. International Journal of Herbal Medicine1(4):92-101.

Publications 2014

  1. A.E. Alakonya, S.M. Runo E. O. Monda, N.R. Sinha (2014). Application and intercropping of maize and sorghum with Lupinus albus inhibits Striga hermonthica emergence and arbuscular mycorrhiza fungal colonization.Agricultural. Science Research Journal 4:1-9, January 2014.
  2. Caroline N.W , Paul O. Okemo and Kebira A. N. (2014). Microbial quality and Antibiotic Reseistant Bacterial pathogens isolated from Groundwater Used by Residents of Ongata Rongai, Kajiado North County, Kenya. International Biological and Biochemical Sciences 8(1): 134-143
  3. Kago E.K, Kinyua Z.M., Okemo P.O. and Maingi J.M. (2014): Effects of Cabbage Tissue and Calcium Hypochlorite on Soil Fertility and Yields of Selected Solanaceous Crops. Annual Research and Review in Biology, 4(3) 547-559.
  4. Menge D. S., Makobe M., Monda E.O., and Okemo P.O. (2014). Effects of crude extracts on some selected physiological parameters of French beans) Phaseolus vulgaris) infected with rust (Uromyces appendiculatus). African Journal of Plant Science 8 (7) 356-363.
  5. Muthini M., Maingi J.M., Muoma J.O., Amoding A., Mukaminega D., Osoro N., Mgutu A. And Ombori O. (2014): Morphological Assessment and Effectiveness of Indigenous Rhizobia Isolates that Nodulate P. vulgaris in Water Hyacinth Compost Testing Field in Lake Victoria Basin. British Journal of Applied Science & Technology, 4(5) 718-738
  6. Mutuku, C. Okemo P. O. and Boga H. (2014). Association of Metal Tolerance with Multidrug Resistance among Environmental Bacteria from wetlands of Lake Victoria Basin. Agriculture and Biology Journal of North America 5(1):24-32
  7. Mutuku, C. Okemo P. O, and Boga H., (2014). Metal pollutants distribution within Lake Victoria Basin and their influence on the Native and TransientMicrobial Flora.Journal of Agricultural and Biological Sciences, 9(4): 127-133.
  8. Mutuiri S. P. M., Chege G., Mwaengo D., Ochola L., Elephas W. Munene, Maria Kiio, Peter G. Mwethera and Kariuki T.M. (2014) Serial in vivo Passage of CXCR4-Tropic Simian/Human Immunodeficiency Chimeric Virus (SHIV89.6P) in Papio Anubis; A Preclinical Disease Model AIDS Research and Human Retroviruses.October 2014: A183-A183.
  9. Moto J. N., Maingi J.M. and Nyamache A. K. (2015). Prevalence of Tinea capitis in school going children from Mathare, informal settlement in Nairobi, Kenya. BMC Research Notes 8: 274-279
  10. Naluyange V., Ochieno D.M.W, Maingi J.M., Ombori O., Mukaminega D., Amoding A., Odendo M., Okoth S.A, Shivoga W.A. and Muoma J.V.O (2014). Compatibility of Rhizobium inoculant and water hyacinth compost formulations in Rosé coco bean and consequences on Aphis fabae and Colletotrichum lindemuthianum infestations. Applied Soil Ecology 76, 68– 77
  11. Omari A. Machocho A. Okemo P.O. and Mbugua P.K (2014). Profiling of Antimicrobial properties of Rubus keniensis Standl. Crude methanol root bark extracts against selected human pathogenic bacteri. Journal of Pharmacognosy and Phytochemistry 2(5)20-23
  12. Omari A., Okemo P. O. Machocho A and Mbugua P. K. (2014). Ethnobotanical Survey of selected Medicinal Plants used by Ogiek Community in Kenya against Microbial Infections. Ethnobotany Research and Applications12:1547-1565
  13. Omari Amuka, Alex K. Machocho, Paul O. Okemo, and Paul K. Mbugua ( 2014). Antibacterial and Antifungal activities of Essential oils from Satureia biflora D. Don, Berth, Speng (Chepsagitiet). Lippia javanica Burm. F. (Labotuet) and Toddalia asiatica (L) Lam. Rutaceae (Chepindoruet). Global Journal of Science frontier Research. B. Chemistry 14(4): 2249-4626.
  14. Osborn Yamakhakha Khasabuli and Anthony Kebira Nyamache. Isolation, characterization and primary screening of soil actinomycetes from Kenyatta University arboretum grounds for antibacterial activities. Journal of Applied Biosciences 2014 74:6072– 6079
  15. Osoro N., Muoma J.O, Amoding A., Mukaminega D., Muthini M., Ombori O. and Maingi J.M. (2014): Effects of Water Hyacinth (Eichhornia crassipes [mart.] solms) Compost on Growth and Yield Parameters of Maize (Zea mays). British Journal of Applied Science and Technology, 4(4): 617-633.
  16. Paul Njenga Waithaka, John Muthini Maingi, A. K. Nyamache (2014): Physico-chemical and Salmonella isolates in community taps and river Kandutura in Nakuru North Sub-county, Kenya. International Journal of Microbiology and Epidemiological Research 2(4): 29-37.
  17. Paul Njenga Waithaka, J. Maingi, A. K Nyamache (2014): Microbial contamination ofenvironmental, food and treated water samples in Nakuru North Sub-county, Kenya International Journal of Microbiology and Allied Sciences 1(2):78-9
  18. P.N. Waithaka, J.M. Maingi, A.K. Nyamache (2014): Isolation of microorganismsscreening of heavy metals from Municipal Council’s treated sewage from Nakuru sewage treatment plant in Nakuru County, Kenya. Scientific Journal of Microbiology 3(12), 118-125.
  19. Schifra Uwamungu, Florence Masaisa, Sarah Kaggia Njoki, Anthony Kebira Nyamache. Coagulation factors level in fresh frozen plasma in Rwanda.submiitted under Review. East Africa Medical Journal March 2014
  20. Theddeus M. Kiswii, Ethel O. Monda, Paul Okemo, Christine Bii and E. Alakonya (2014). Efficacy of selected medicinal plants from Eastern Kenya against Aspergillus flavus. Journal of Plant Science 2(5): 226-231

Publications 2015

  1. Karanja A., Kotut K. and Gitonga N.M. (2015). Assessment of Physico-chemical parameters on the Kasarani section of River Thome, Nairobi. Journal of Geography, Environment and Earth Science International, 3(4).
  2. Amuka, o, Machocho A. K. Okemo, P. O. and Mbugua, P.K( 2015). Antifungal and Antibacterial activity of crude stem Bark Extracts of Bersama abysinicca Verdc. And Faurea saligna Harr. Research Journal of Medicinal Plants 9 (4): 160-169
  3. Joel Masanga, Jonathan Matheka, Rasha Omer Sheila Ommeh, Ethel Monda and Amos Alakonyab (2015). Downregulation of transcription factor aflR in aflatoxin accumulation in transgenic maize with alteration of host plant architecture. Plant Cell reports Springer DOI 10.1007/s00299-015-1794-9.
  4. Kirui J.K, Kotut K, Okemo, P.O (2015). Efficacy of acqueous plant extracts in disinfecting water of different physicochemical properties. Journal of water and Health 13(3): 848-852.
  5. Mathenge J.M. Okemo P.O, Nganga P.M, and Gicheru M.M, (2015). Identification of Enterotoxigenic staphylococcus aureus strains from meat and dairy products by multiplex PCR and reverse passive latex agglutination test in Nairobi, Kenya. The East and Central Africa Medical Journal 2(2):97-103.
  6. Moto J. N., Maingi J.M. and Nyamache A. K. (2015). Prevalence of Tinea capitis in school going children from Mathare, informal settlement in Nairobi, Kenya. BMC Research Notes 8: 274-279
  7. Rossmassler K., Dietrich C., Thompson C., Mikaelyan A., Nonoh J.O., Scheffrahn R.H., Sillam-Dussès D. and Brune A. (2015). Metagenomic analysis of the microbiota in the highly compartmented hindguts of six wood- or soil-feeding higher termites. Microbiome 3:56.

Publications 2016

  1. Alessandra Turrini A., Sbrana C., Avio L., Njeru E.M, Bocci G., Bàrberi P., Giovannetti M. (2016). Changes in the composition of native root arbuscular mycorrhizal fungal communities during a short-term cover crop-maize succession. Biology and Fertility of Soils52, (5) 543-553.
  2. Ernest Wandera Ouma, Anne Mercy Asango, John Maingi, and Ezekiel Mugendi Njeru (2016): Elucidating the Potential of Native Rhizobial Isolates to Improve Biological Nitrogen Fixation and Growth of Common Bean and Soybean in Smallholder Farming Systems of Kenya. International Journal of Agronomy, 2016, Article ID 4569241, 7 pages
  3. Kariko Elizabeth Kago, Murimi Zacharia Kinyua, Owuor Paul Okemo , Maingi John Muthini (2016): Bacterial Wilt, A Challenge in Solanaceous Crops Production At Kenyan Highlands and Lowlands. World Journal of Research and Review, 3(1), 6-11.
  4. Maryanne Betsy Usagi M. B, Odilla G.A., Maingi J.M. and Kebira A. (2016): Isolation, Identification and Determination of the Prevalence of Mycobacterium tuberculosis Complex among People Living with HIV in Kisumu County, Kenya. Science Journal of Public Health 4(4), 359-365.
  5. Monda E.O and Alakonya A.E. (2016): A Review of Agricultural Aflatoxin Management Strategies and Emerging Innovations in sub –Sahara Africa, African Journal of Agriculture Nutrition and Development 16:11126-11138.
  6. Naluyange V., Ochieno D.M.W, Wandahwa P., Odendo M., Maingi J.M., Amoding A., Ombori O., Mukaminega D. and Muoma J (2016): Belowground Influence of Rhizobium Inoculant and Water Hyacinth Composts on Yellow Bean Infested by Aphis fabae and Colletotrichum lindemuthianum under Field Conditions. Journal of Plant Studies 5 (2), 32-46.
  7. Oruru M.B. and Njeru E.M (2016): Upscaling Arbuscular Mycorrhizal Symbiosis and Related Agroecosystems Services in Smallholder Farming Systems. BioMed Research International2016, Article ID 4376240, 12 pages.
  8. Simon Wambui Mburu, Gilbert Koskey, Jacinta Malia Kimiti, Omwoyo Ombori, John M. Maingi and Ezekiel Mugendi Njeru (2016): Agrobiodiversity conservation enhances food security in subsistence-based farming systems of Eastern Kenya. Agriculture & Food Security (2016) 5:19, 1-10

On-going Research

  • Ochratoxin contamination and molecular characterization of Penicillium sp. from cereals in eastern province of Kenya
  • Incidence of Aspergillus flavus in dried fish and fish feeds, aflatoxin levels and characterization of isolated A. flavus in Kisii county, Kenya
  • Distribution and molecular characterization of toxigenic and atoxigenic strains of Fusarium verticillioides in selected maize genotypes in Nakuru county, Kenya
  • Diversity of collectotrichum gloeosporioides (penz.) penz. & sacc. and management of anthracnose disease of avocado in Kenya
  • Essential oils of Lippiaand Ocimum species as potential post-harvest protectants against selected fungi and associated mycotoxins in maize
  • Synthesis, Characterization, DFT and Antitubercular studies on Organometallic complexes of Pyrazine-2-carboxamide and Isonicotinohydrazide
  • Increasing Soybeans and Climbing Beans production in smallholders` farms in Eastern Kenya


Academic Staff
The academic staff have qualifications in the following areas:-

  • Microbial biotechnology
  • Environmental Microbiology
  • Virology
  • Bacteriology
  • Mycology
  • Bioinformatics
  • Microbial ecology
  • Industrial Microbiology
  • Immunology
  • Agricultural and Soil Microbiology
  • Food Microbiology

Staff Profiles

Last Updated on Tuesday, 09 January 2018 07:39


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