http://erepository.uonbi.ac.ke/handle/11295/82041 Mon, 18 May 2026 20:36:22 GMT 2026-05-18T20:36:22Z http://erepository.uonbi.ac.ke/handle/11295/163980 Diversity and functional analysis of rumen and fecal microbial communities associated with dietary changes in crossbreed dairy cattle Kibegwa, Felix M; Bett, Rawlynce C; Gachuiri, Charles K; Machuka, Eunice; Stomeo, Francesca; Mujibi, Fidalis D The objective of this study was to investigate the effect of varying roughage and concentrate proportions, in diet of crossbreed dairy cattle, on the composition and associated functional genes of rumen and fecal microbiota. We also explored fecal samples as a proxy for rumen liquor samples. Six crossbred dairy cattle were reared on three diets with an increasing concentrate and reducing roughage amount in three consecutive 10-day periods. After each period, individual rumen liquor and fecal samples were collected and analyzed through shotgun metagenomic sequencing. Average relative abundance of identified Operational Taxonomic Units (OTU) and microbial functional roles from all animals were compared between diets and sample types (fecal and rumen liquor). Results indicated that dietary modifications significantly affected several rumen and fecal microbial OTUs. In the rumen, an increase in dietary concentrate resulted in an upsurge in the abundance of Proteobacteria, while reducing the proportions of Bacteroidetes and Firmicutes. Conversely, changes in microbial composition in fecal samples were not consistent with dietary modification patterns. Microbial functional pathway classification identified that carbohydrate metabolism and protein metabolism pathways dominated microbial roles. Assessment of dietary effects on the predicted functional roles of these microbiota revealed that a high amount of dietary concentrate resulted in an increase in central carbohydrate metabolism and a corresponding reduction in protein synthesis. Moreover, we identified several microbial stress-related responses linked to dietary changes. Bacteroides and Clostridium genera were the principal hosts of these microbial functions. Therefore, the roughage to concentrate proportion has more influence on the microbial composition and microbial functional genes in rumen samples than fecal samples. As such, we did not establish a significant relationship between the rumen and fecal metagenome profiles, and the rumen and fecal microbiota from one animal did not correlate more than those from different animals. Sun, 01 Jan 2023 00:00:00 GMT http://erepository.uonbi.ac.ke/handle/11295/163980 2023-01-01T00:00:00Z http://erepository.uonbi.ac.ke/handle/11295/163910 Spatio-temporal epidemiology of livestock diseases in the variable semi-arid rangelands of northern Kenya Lelenguyah, Geoffrey L; Nyangito, Moses M; Wasonga, Oliver V; Bett, Rawlynce C Diseases affecting livestock can have significant impacts on the animal, humans and the economy. Participatory epidemiology and spatial analysis were conducted to assess livestock disease problems in Samburu County, northern Kenya. Key informants were selected purposively with the help of local leaders. Among the livestock, goats were identified to have the most economic importance. On the other hand Pestes des Petits Ruminants (PPR), Foot and Mouth Disease (FMD) and Camel Trypanosomiasis diseases were identified to have the highest impact on pastoral livelihood. Spatial analysis indicated that all the disease hotspots were closely related to the distribution of herds during different seasons of the year. Correlations between the mean annual rainfall and selected livestock diseases were significant for East Coast Fever (ECF) (r = - 0.767, p = 0.001, N = 15), Cattle Helminthiasis (r = 0.639, p = 0.010, N = 15), Cattle Anaplasmosis (r = 0.631, p = 0.012, N = 15) and Camel Pox (r = - 0.646, p = 0.044, N = 10). There was a strong relationship between seasonality and livestock disease epidemiology. Disease control efforts should be focused towards the hotspots in the wet season and dry season grazing areas. Sun, 01 Jan 2023 00:00:00 GMT http://erepository.uonbi.ac.ke/handle/11295/163910 2023-01-01T00:00:00Z http://erepository.uonbi.ac.ke/handle/11295/161405 Assessment of Milk Quality and Food Safety Challenges in the Complex Nairobi Dairy Value Chain Kiambi, Stella; Fèvre, Eric M; Alarcon, Pablo; Gitahi, Nduhiu; Masinde, Johnstone; Kang'ethe, Erastus; Aboge, Gabriel; Jonathan, Rushton Food networks present varying food safety concerns because of the complexity of interactions, production, and handling practices. We investigated total bacteria counts (TBCs) and total coliform counts (TCCs) in various nodes of a Nairobi dairy value chain and identified practices that influence food safety. A value chain analysis framework facilitated qualitative data collection through 23 key informant interviews and 20 focus group discussions. Content thematic analysis identified food safety challenges. Cow milk products (N = 290) were collected from farms (N = 63), collection centers (N = 5), shops/kiosks (N = 37), milk bars (N = 17), roadside vendors (N = 14), restaurants (N = 3), milk vending machines (N = 2), mobile traders (N = 2) and a supermarket (N = 1). Mean values of colony-forming units for TBC and TCC were referenced to East African Standards (EAS). Logistic regression analysis assessed differences in milk acceptability based on EAS. The raw milk from farms and collection centers was relatively within acceptable EAS limits in terms of TBC (3.5 × 105 and 1.4 × 106 respectively) but TCC in the milk from farms was 3 times higher than EAS limits (1.5 × 105). Compared to farms, the odds ratio of milk acceptability based on TBC was lower on milk bars (0.02), restaurants (0.02), roadside vendors (0.03), shops/kiosks (0.07), and supermarkets (0.17). For TCC, the odds that milk samples from collection centers, milk bars, restaurants, roadside vendors, and shops/kiosks were acceptable was less than the odds of samples collected from farms (0.18, 0.03, 0.06, 0.02, and 0.12, respectively). Comparison of raw milk across the nodes showed that the odds of milk samples from restaurants, roadside vendors, and shops/kiosks being acceptable were less than the odds of samples collected the farm for TBC (0.03, 0.04, and 0.04, respectively). For TCC, the odds of raw milk from collection centers, restaurants, roadside vendors, milk bars, and shops/kiosks being acceptable were lower than the odds of acceptability for the farm samples (0.18, 0.12, 0.02, 0.04, and 0.05, respectively). Practices with possible influence on milk bacterial quality included muddy cowsheds, unconventional animal feed sources, re-use of spoilt raw milk, milk adulteration, acceptance of low-quality milk for processing, and lack of cold chain. Therefore, milk contamination occurs at various points, and the designing of interventions should focus on every node. Wed, 01 Jun 2022 00:00:00 GMT http://erepository.uonbi.ac.ke/handle/11295/161405 2022-06-01T00:00:00Z http://erepository.uonbi.ac.ke/handle/11295/155547 Consumer perceptions of food safety in animal source foods choice and consumption in Nairobi's informal settlements Bukachi, Salome A; Ngutu, Mariah; Muthiru, Ann W; Lépine, Aurélia; Kadiyala, Suneetha; Paula, Domínguez-Salas Background: Animal-source foods (ASFs) are high-quality nutrient-dense products key to reducing stunting and micronutrient deficiencies. However, their consumption among the poorest households in urban informal settlements is low. Several drivers beyond price, including health considerations have been reported to drive ASF choice and consumption among consumers. This current study explores consumer perceptions of food safety associated with animal source foods (ASFs) consumption in urban informal settlements with a view to unpacking the health considerations driving their choice and consumption. Methods: Coupled households with children 6-59 months formed the study sample. The Food Environments Working Group (FEWG) Framework of the Agriculture and Nutrition for Health academy (ANH) was used to guide the study which utilized qualitative methods namely, 60 in-depth interviews (IDIs), 19 focus group discussions, and 19 key informant interviews (KIIs) complemented by unstructured observations. Data were transcribed and analysed according to emerging themes. Results: Consumer perceptions of food safety are driven by concerns about food production, processing, handling, storage and the health risks associated with consumption of the ASFs. For all the ASFs, lack of traceability of source, unhygienic environments in which they were sold and health risks around consuming too much or improperly cooked products were key perceptions from the community. To mitigate against food safety risks, consumers used strategies such as boiling the ASFs, purchasing their products from trusted retailers, avoiding vendors in unhygienic environments and reducing the amount and frequency of consumption of ASFs or totally avoiding their consumption. These consumer perceptions are increasingly influencing the ASFs choice and consumption in low-income populations besides other drivers. Notably, given limited incomes that influence their purchasing power and the need for nutritious diets that included ASFs, the dilemma of quality vis-a-vis quantity persists and consumers still accessed and consumed these ASF products to supplement their diets. Conclusions: To enhance food safety for ASFs, as well as assure consumer access to safe ASFs from informal markets, there is need to contextualize the value chain as informed by consumer perceptions on food safety as these influence their ASFs choice and consumption. Fri, 01 Jan 2021 00:00:00 GMT http://erepository.uonbi.ac.ke/handle/11295/155547 2021-01-01T00:00:00Z