Factors associated with strongylida infections in sheep on farms in peri-urban Nairobi, Kenya.

Gastrointestinal parasite infections are among the major limitations to production in sheep in many parts of the world. It is important to continually assess their levels of infection in order to institute control measures and reduce the impact. This study determined the factors associated with the strongylida egg counts in sheep on selected farms in peri-urban Nairobi, Kenya. This was a cross-sectional study in which farm and animal-level data, including faecal samples, were collected from 1640 sheep from 30 purposively selected farms in Ruai, and Kamulu wards in Kasarani sub-county and Utawala and Mihango wards in Embakasi East Sub-County, in Nairobi County Kenya. The faecal samples were subjected to coprological examination using a modified McMaster technique to determine counts of strongylida eggs and coccidia oocysts with a detection level of 100 egg or oocyst per gram (EPG or OPG) of faeces. The positive faecal samples for strongylida eggs were pooled per farm and cultured for morphological identification of larval stage three. Descriptive statistics and multilevel mixed-effect logistic regression analyses were used to determine factors associated with strongylida egg count ≥600 EPG (p < 0.05). The receiver operating characteristics curve was used to assess the overall diagnostic performance in the final model. Strongylida eggs were detected in 45.5% (746/1640) of the sheep, and the mean EPG was 486.0± 858.9 with a median of 200 and a range of 0-16,700. The coccidia oocysts were detected in 49.4% (810/1640) of the sheep with a mean OPG was 341.7± 1782.4, a median of 0 and a range of 0-60,000. In the coprocultures, the nematode genera identified (% differential count of L3) were Haemonchus (90%), Trichostrongylus (5%) and Oesophagostomum (5%). In the final multivariable regression model, the odds of detecting EPG ≥ 600 was 1.44 times higher for sheep shedding coccidia oocysts than those that did not. The odds for detecting EPG ≥ 600 was 4.01 times for sheep in Ruai ward compared with those in the combined Kamulu, Utawala and Mihango wards. The receiver operating characteristic curve area was 73.1%, suggestive of good model performance. The results suggest that gastrointestinal strongylida and coccidia infections are common in sheep and farmers should be educated on the importance of appropriate control measures.

Effects of pretreating wheat middlings and sunflower meal with fiber degrading enzymes on components solubilization and utilization in broiler chickens.

Pretreating fibrous feedstuffs with exogenous enzymes may improve their utilization in broiler chickens. Pretreatment of wheat middlings (WM) and sunflower meal (SM) with fiber degrading enzymes (FDE) was investigated for 1) in vitro solubilization of crude protein (CP) and fiber-degrading (experiment 1), and 2) apparent retention (AR) of CP, neutral detergent fiber (NDF), nitrogen corrected apparent metabolizable energy (AMEn), as well as the concentration of ceca digesta metabolites in broiler chickens (experiment 2). In experiment 1, WM was pretreated with FDE and SM with FDE ±â€…protease and incubated in a shaker for 24 or 48 h at 40°C and 200 rpm. Samples were centrifuged, and the supernatant used for assay of sugars and organic acids and pellet processed for determination of apparent disappearance (AD) of dry matter (DM), fiber, and CP solubilization. In experiment 2, WM and SM were pretreated with FDE for 24 h, oven-dried, and incorporated in iso-caloric and iso-nitrogenous experimental diets. Diets were: 1) a corn-soybean meal positive control (PC); 2) PC plus untreated WM and SM (negative control, NC), and diets 3, 4, 5, and 6 test diets, in which the untreated WM and SM in NC were replaced with pretreated WM and SM at 25% (N25), 50% (N50), 75% (N75), and 100% (N100), respectively. Diets were prepared in mash form in two phases (starter, days 0 to 21 and finisher, days 22 to 42) and had TiO2 (0.3%) as an indigestible marker. A total of 288 Ross708 d-old male broiler chicks were placed in cages based on body weights (6 birds/cage) and allocated diets (n = 8). Birds had free access to feed and water. Samples of excreta for AR and AMEn, and of ceca digesta for the concentration of short-chain fatty acids (SCFA) were collected at the end of each phase. Pretreatment with FDE increased (P < 0.001) solubilization of CP, AD of NDF, and release of sugars and organic acids in the supernatant. The mixture of FDE and protease further increased (P < 0.001) CP solubilization in SM. Feeding pretreated WM and SM had a linear response (P ≤ 0.038) on AMEn, and gross energy (GE) (day 21) and a quadratic response (P < 0.05) on AR of components and AMEn (day 42) and concentration of total SCFA on day 42. On day 42, N25 and N50 had higher AR of DM, CP, NDF, and GE than N75 and N100. In conclusion, pretreatment of WM and SM with enzymes increased CP and fiber degradation. Incorporating moderate amounts (N25 and N50) of pretreated WM and SM in a corn-soybean meal diet fed to broiler chickens improved nutrient and energy utilization.

Comparative growth performance, gizzard weight, ceca digesta short chain fatty acids and nutrient utilization in broiler chickens and turkey poults in response to cereal grain type, fiber level, and multienzyme supplement fed from hatch to 28 days of life.

Growth performance, gizzard weight, ceca digesta short-chain fatty acids (SCFA), and apparent retention (AR) of components were investigated in broilers and turkeys in response to cereal grain type, fiber level, and multienzyme supplement (MES) fed from hatch to 28 d of life. 480-day-old male broiler chicks and equal number of turkeys were placed separately in metabolism cages (10 birds/cage) and allocated to 8 diets. The species-specific diets were a corn or wheat-based basal diet without (LF) or with 10% corn DDGS or wheat middlings (HF) and fed without or with MES. This effectively created a 2 (grain types) × 2 (fiber levels) × 2 (MES) factorial arrangement of treatments. The diets had TiO2 as an indigestible marker. Body weight, feed intake, and mortalities were recorded to calculate body weight gain (BWG) and feed conversion ratio (FCR). Excreta samples were collected on d 25 to 27 for AR, and all birds were necropsied for gizzard weight and ceca digesta on d 28. The interaction between grain and MES in broilers was such that wheat diets with MES had the lowest (P = 0.005) FCR. In broilers, LF diets had better (P = 0.010) FCR than HF diets. The wheat diets had the highest (P = 0.006) concentration of butyric acid in broilers. Broilers fed HF and corn diets had heavier gizzard than broilers-fed LF and wheat diets. The MES improved (P < 0.05) AMEn in HF, corn, and wheat diets in broilers. The turkeys fed wheat diets had the lowest (P = 0.019) FCR. Turkeys fed HF wheat diets had the heaviest (P < 0.001) gizzard. In turkeys, the MES improved AMEn in HF and LF corn diets, and only in LF wheat diets compared to respective controls. Treatments had no effect on turkeys cecal SCFA. In conclusion, grain type, fiber, and MES did not affect growth in both species. However, species exhibited differing FCR, gizzard, and energy utilization to fiber and MES.

Diversity and functional analysis of rumen and fecal microbial communities associated with dietary changes in crossbreed dairy cattle.

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.

Diversity of gut methanogens and functional enzymes associated with methane metabolism in smallholder dairy cattle.

Methane is a greenhouse gas with disastrous consequences when released to intolerable levels. Ruminants produce methane during gut fermentation releasing it through belching and/or flatulence. To better understand the diversity of methanogens and functional enzymes associated with methane metabolism in dairy cows, 48 samples; 6 rumen fluid and 42 dung samples were collected from Kenyan and Tanzanian farms and were analyzed using shotgun metagenomic approach. Statistical analysis for species frequency, relative abundance, percentages, and P values were undertaken using MS Excel and IBM SPSS statistics 20. The results showed archaea from 5 phyla, 9 classes, 16 orders, 25 families, 59 genera, and 87 species. Gut sites significantly contributed to the presence and distribution of various methanogens (P < 0.01). The class Methanomicrobia was abundant in the rumen samples (~ 39%) and dung (~ 44%). The most abundant (~ 17%) methanogen species identified was Methanocorpusculum labreanum. However, some taxonomic class data were unclassified (~ 6% in the rumen and ~ 4% in the dung). Five functional enzymes: Glycine/Serine hydroxymethyltransferase, Formylmethanofuran-tetrahydromethanopterin N-formyltransferase, Formate dehydrogenase, anaerobic carbon monoxide dehydrogenase, and catalase-peroxidase associated with methane metabolism were identified. KEGG functional metabolic analysis for the enzymes identified during this study was significant (P < 0.05) for five metabolism processes. The methanogen species abundances from this study in numbers/kind can be utilized exclusively or jointly as indirect selection criteria for methane mitigation. When targeting functional genes of the microbes/animal for better performance, the concern not to affect the host animal's functionality should be undertaken. Future studies should consider taxonomically categorizing unclassified species.

Characterization of dairy innovations in selected milksheds in Kenya using a categorical principal component analysis.

To enhance milk quantity and quality which have continued to decrease in Kenya, various stakeholders have intervened through promotion of technical dairy innovations at the farm level including improved cow feeding, health management, promotion of exotic breeds, and milking hygiene. At the milkshed level, stakeholders' focus has been on organizational innovations, specifically milk sale by farmers through groups. This study sought to characterize dairy innovations that have been adopted by farmers in the milkshed of three milk processors including New Kenya Co-operative Creameries Sotik (NKCC Sotik), Happy Cow Limited (HCL), and Mukurweini Wakulima Dairy Limited (MWDL), representing one state, private, and farmer-owned processor, respectively. Data were collected using a structured questionnaire from a sample of 1146 farmers (410, 382, and 354 in MWDL, HCL, and NKCC Sotik, respectively). A categorical principal components analysis was used to reduce 32 variables into four sets of uncorrelated components. Four categories were identified including principal component (PC) 1 (technical capacity), PC 2 (animal health management), PC 3 (organizational capacity), and PC 4 (milk hygiene). More farmers in the milkshed of MWDL adopted technical and organizational dairy innovations such as use of artificial insemination and milk sale through groups, respectively, than farmers in milkshed of NKCC and HCL. The county governments in the milkshed of HCL and NKCC Sotik need to strengthen cooperative societies to boost adoption of artificial insemination through arrangement in which milk is sold and payment of services offered on credit is settled from milk sale and ensure milk market availability throughout the year.

A Comparison of Two DNA Metagenomic Bioinformatic Pipelines While Evaluating the Microbial Diversity in Feces of Tanzanian Small Holder Dairy Cattle.

Analysis of shotgun metagenomic data generated from next generation sequencing platforms can be done through a variety of bioinformatic pipelines. These pipelines employ different sets of sophisticated bioinformatics algorithms which may affect the results of this analysis. In this study, we compared two commonly used pipelines for shotgun metagenomic analysis: MG-RAST and Kraken 2, in terms of taxonomic classification, diversity analysis, and usability using their primarily default parameters. Overall, the two pipelines detected similar abundance distributions in the three most abundant taxa Proteobacteria, Firmicutes, and Bacteroidetes. Within bacterial domain, 497 genera were identified by both pipelines, while an additional 694 and 98 genera were solely identified by Kraken 2 and MG-RAST, respectively. 933 species were detected by the two algorithms. Kraken 2 solely detected 3550 species, while MG-RAST identified 557 species uniquely. For archaea, Kraken 2 generated 105 and 236 genera and species, respectively, while MG-RAST detected 60 genera and 88 species. 54 genera and 72 species were commonly detected by the two methods. Kraken 2 had a quicker analysis time (~4 hours) while MG-RAST took approximately 2 days per sample. This study revealed that Kraken 2 and MG-RAST generate comparable results and that a reliable high-level overview of sample is generated irrespective of the pipeline selected. However, Kraken 2 generated a more accurate taxonomic identification given the higher number of "Unclassified" reads in MG-RAST. The observed variations at the genus level show that a main restriction is using different databases for classification of the metagenomic data. The results of this research indicate that a more inclusive and representative classification of microbiomes may be achieved through creation of the combined pipelines.

Risk factors of gastrointestinal nematode parasite infections in small ruminants kept in smallholder mixed farms in Kenya.

BACKGROUND: Helminth infections in small ruminants are serious problems in the developing world, particularly where nutrition and sanitation are poor. This study investigated the burden and risk factors of gastrointestinal nematode parasite infections in sheep and goats kept in smallholder mixed farms in the Kenyan Central Highlands. Three hundred and seven small ruminants were sampled from 66 smallholder mixed farms in agro-ecological zones 1 (humid) and 3 (semi-humid) in the Kenyan Central highlands. The farms were visited once a month for eight months during which a health and production survey questionnaire was administered. Fecal samples were collected at each visit from each animal. Fecal egg counts (FEC) were performed using the modified McMaster technique. Associations between potential risk factors and FEC were assessed using 3-level Poisson models fit in SAS using GLIMMIX macro. Correlations among repeated observations were adjusted for using three different correlation structures. RESULTS: A rise in FEC was observed two months after the onset of rains. Farmer education, age category, de-worming during the preceding month and grazing system were significant predictors of FEC. Additionally, there were significant interactions between grazing system and both de-worming and age category implying that the effect of grazing system is dependent on both de-worming status and age category; and that the effect of de-worming depends on the grazing system. The most important predictors of FEC in the study area were grazing system, de-worming status and education of the farmers. CONCLUSION: Since several factors were important predictors of FEC, controlling gastrointestinal helminths of small ruminants in these resource-poor smallholder mixed farms requires a sustainable integrated helminth control strategy that includes adoption of zero-grazing and more farmer education probably through extension services. Achieving improved helminth controls in these resource-poor farming systems offers an opportunity to increase small ruminant productivity and hence has a potential of improving the livelihood of the resource-poor farmers.