Whole genome sequencing on next-generation instruments provides an unbiased way to identify the organisms present in complex metagenomic samples. However, the time-to-result can be protracted because of fixed-time sequencing runs and cumbersome bioinformatics workflows. This limits the utility of the approach in settings where rapid species identification is crucial, such as in the quality control of food-chain components, or in during an outbreak of an infectious disease. Here we present What′s in my Pot? (WIMP), a laboratory and analysis workflow in which, starting with an unprocessed sample, sequence data is generated and bacteria, viruses and fungi present in the sample are classified to subspecies and strain level in a quantitative manner, without prior knowledge of the sample composition, in approximately 3.5 hours. This workflow relies on the combination of Oxford Nanopore Technologies′ MinION ™ sensing device with a real-time species identification bioinformatics application.

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What's in my pot? Real-time species identification on the MinION

Human and animal faeces present persistent threats to global public health and also opportunities for recovery of resources. We present the first global-scale accounting of recoverable faeces (livestock animal and human) from 2003 to 2030 using country-specific human and animal population estimates and estimated species-specific faeces production by human or animal body mass. We also examine global coverage of domestic livestock animals and sanitation facilities to describe the distribution of onsite versus offsite hazards from animal and human faeces. In 2014, the total mass of faeces was 3.9 × 1012 kg per year, increasing by >52 × 109 kg per year since 2003 and anticipated to reach at least 4.6 × 1012 kg in 2030. Annual global production of faeces from animals (primarily cattle, chickens and sheep) was about four times that from humans. Ratios of animal faeces to human faeces continue to increase (geometric mean of 4.2:1 for 2003 versus 5.0:1 for 2014 versus a projected 6.0:1 for 2030). Low-income populations bear the greatest burden of onsite faeces, mostly from animals in or near the domestic environment. This analysis highlights the challenges of resource recovery from concentrated and dispersed sources of faeces, and the global public health policy needed for safe management of animal faeces. Human and animal faeces simultaneously threaten global health and provide resources for recovery. This study presents the first global-scale analysis of recoverable faeces from 2003 projected to 2030 and of associated burdens. Production from domestic animals is about four times that of humans, emphasizing the need for better onsite management.

Estimation of global recoverable human and animal faecal biomass

Seasonal variations in the composition of ram seminal plasma and its effect on frozen-thawed ram sperm

Seasonal thyroidal activity and reproductive characteristics of Iranian fat-tailed rams.

BackgroundMastitis prevalence, milking procedures and management practices were investigated in 25 big dairy herds supplying milk to an Estonian dairy company. The aim of the study was to provide information for the company to be used in their new udder health improvement program to be set up after the completion of this study.MethodsQuarter milk samples were collected from 3,166 cows for bacterial analysis and SCC (somatic cell counting). During the farm visit the veterinarian filled in a questionnaire about milking procedures and management practices with the help of farm managers. If the milk SCC of a cow or of a quarter exceeded 200,000/ml, the cow was defined as having mastitis.ResultsThe percentage of cows having inflammation in one or more quarters measured by SCC (200,000/ml) was 52.7%. Corynebacterium bovis, Staphylococcus aureus and coagulase negative staphylococci were the most common bacterial isolates. Women as farm owners, and participating in the milking, were associated with lower mastitis prevalence on the farm. Peat bedding was associated with higher mastitis prevalence.ConclusionWe demonstrated relatively high mastitis prevalence in this study. Contagious bacteria (eg. S. aureus, C. bovis, S. agalactiae and coagulase negative staphylococci) caused most of the infections. These infections are usually spread from cow to cow at milking if the milking hygiene is not good enough. The mastitis situation could be improved by improving milking procedures and hygiene.

A study of bovine mastitis, milking procedures and management

Seasonal variation in semen characteristics, scrotal circumference and libido of Persian Karakul rams

Estrous response to synchronization of estrus using different progesterone treatments outside the natural breeding season in ewes

This study was designed to evaluate the efficiency of five different hormonal treatments of oestrous synchronization in Karakul ewes reared in southern Iran. During mid- to late spring, (outside the natural breeding season), 180 Karakul ewes were stratified based on age and body weight and then randomly allocated to six groups (n = 30/group). The oestrous cycles of the ewes in each group were synchronized using one of the following hormonal treatments: T1 - intramuscular (im) administration of 20 mg progesterone acetate in oil every second day for a 12-day period and an im administration of 500 IU equine chorionic gonadotrophin (eCG) on day 12; T2 - insertion of a controlled intravaginal drug releasing device (CIDR) containing 0.3 g progesterone for 12 days; T3 - administrating an intravaginal sponge containing 60 mg medroxyprogesterone acetate (MAP) for 12 days; T4 - a double injection (im) of 10 mg prostaglandin F2α nine days apart; T5 - a double injection (im) of 10 mg prostaglandin F2α nine days apart plus an im injection of 500 IU eCG on the day of the second prostaglandin F2α administration; T6 - control group. The ewes in Treatments 2 and 3 were intramuscularly injected with a 500 IU eCG at CIDR or sponge withdraw. Twenty-four hours after the last hormonal treatment, three fertile Karakul rams were introduced to the ewes in each experimental group and remained there for five days for oestrous detection and mating. Significant differences in oestrous response, number of ewes that lambed within the 152 ± 7 day period, fecundity and fertility rate were recorded between treatment groups. The oestrous response was comparable in Treatments 2 (93%) and 3 (100%), and significantly higher than the other treatments (T1 = 80; T4 = 37; T5 = 30 and T6 = 20%). The highest and the lowest number of ewes that lambed within 152 ± 7 days were 27 (90%) in Treatments 3 and 4 and 13% in Treatments 4 and 5, respectively. The highest recorded fecundity rate was 133% in Treatment 3 and the lowest, 75% in Treatment 4. Furthermore, the fertility rate was 90% in Treatment 3 that was significantly higher than in Treatments 4 (36%) and 5 (44%). The results of the present study indicated that oestrous synchronisation with progestagens plus eCG induced a synchronized oestrus in a higher percentage of Iranian fat-tailed Karakul ewes than prostaglandin F2α (with or without eCG) outside the breeding season. Furthermore, the administration of an impregnated intravaginal sponge for a 12-day period plus a dose of 500 IU eCG resulted in higher fertility, fecundity and lambing rates compared to the other hormonal treatments considered. Keywords : Karakul ewes, oestrous synchronization, reproductive performance South African Journal of Animal Science Vol. 36 (4) 2006: pp. 229-234

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Reproductive performance of Karakul ewes following different oestrous synchronisation treatments outside the natural breeding season

Summary Mastitis continues to be one of the economically most important diseases in dairy farming. Forty-six licensed dairy farms in the central region of Fars province were randomly selected in order to participate in a seasonal prevalence study. A cross-sectional study was designed to determine prevalence at cow and quarter level based on clinical signs for clinical mastitis and indirect tests for subclinical mastitis. 6180 quarters from 1545 dairy cows were tested by clinical examination and California mastitis test (CMT). Milk samples from both clinical and subclinical quarters were collected for bacteriological culture. 4714 (76.28%) quarters were healthy, 1335 (21.6%) quarters were positive by results of CMT (as indicated to subclinical mastitis), 44 (0.71%) quarters showed clinical mastitis signs and 87 (1.41%) quarters were blind. The clinical and subclinical mastitis prevalence at cow level was 2.2 and 42.5%, respectively. There was no significant difference in the prevalence of mastitis between different quarters, seasons and cities. The most prevalent isolated bacteria were coagulase positive staphylococci followed by Streptococci, Escherichia coli and coagulase negative staphylococci. Insufficient control measures such as pre and post milking hygiene and dry cow therapy in dairy farms and limited knowledge of farmers on the importance, identification and control of mastitis, especially subclinical forms, can be the main causes for the high prevalence of mastitis in Fars province.

M. Safdarian

Papers

Seasonal variation in semen characteristics, scrotal circumference and libido of Persian Karakul rams

Estrous response to synchronization of estrus using different progesterone treatments outside the natural breeding season in ewes

Reproductive performance of Karakul ewes following different oestrous synchronisation treatments outside the natural breeding season

The prevalence of clinical and subclinical mastitis in dairy cows in the central region of Fars province, south of Iran