BackgroundThe caecal microbiota plays a key role in chicken health and performance, influencing digestion and absorption of nutrients, and contributing to defence against colonisation by invading pathogens. Measures of productivity and resistance to pathogen colonisation are directly influenced by chicken genotype, but host driven variation in microbiome structure is also likely to exert a considerable indirect influence.MethodsHere, we define the caecal microbiome of indigenous Indian Aseel and Kadaknath chicken breeds and compare them with the global commercial broiler Cobb400 and Ross 308 lines using 16S rDNA V3-V4 hypervariable amplicon sequencing.ResultsEach caecal microbiome was dominated by the genera Bacteroides, unclassified bacteria, unclassified Clostridiales, Clostridium, Alistipes, Faecalibacterium, Eubacterium and Blautia. Geographic location (a measure recognised to include variation in environmental and climatic factors, but also likely to feature varied management practices) and chicken line/breed were both found to exert significant impacts (p < 0.05) on caecal microbiome composition. Linear discriminant analysis effect size (LEfSe) revealed 42 breed-specific biomarkers in the chicken lines reared under controlled conditions at two different locations.ConclusionChicken breed-specific variation in bacterial occurrence, correlation between genera and clustering of operational taxonomic units indicate scope for quantitative genetic analysis and the possibility of selective breeding of chickens for defined enteric microbiota.Electronic supplementary materialThe online version of this article (10.1186/s40168-018-0501-9) contains supplementary material, which is available to authorized users.

Lumpy skin disease (LSD), sheeppox (SP), and goatpox (GP) are contagious viral infections, affecting cattle (LSD), sheep and goats (SP and GP) with highly characteristic clinical signs affecting multiple body systems. All three diseases are widely reported to reduce meat, milk, wool and cashmere production although few studies have formally evaluated their economic impact on affected farms. This study aimed to estimate the economic impact and epidemiological parameters of LSD, SP, and GP among backyard and transhumance farmers in northeast Nigeria. A retrospective study was conducted on herds and flocks affected between August 2017 and January 2018 in Bauchi, Nigeria. Herds and flocks were diagnosed based on clinical signs and information was collected once the outbreak concluded using a standardized questionnaire. Data were collected from 99 farmers (87 backyard and 12 transhumance). The median incidence risk and fatality rate were 33 and 0% in cattle, 53 and 34 % in sheep; 50 and 33% in goats, respectively, with young stock having higher incidence risk and fatality rates than adults. Almost all farmers (94%) treated affected animals with antibiotics, spending a median of US$1.96 (min US$0.19-max US$27.5) per herd per day. Slaughtering or selling affected animals at low prices were common coping strategies. Farmers sold live cattle for 47% less than would have been sold if the animal was healthy, while sheep and goats were sold for 58 and 57% less, respectively. Milk production dropped 65% when cows were clinically affected and 35% after they recovered. Cattle lost a median of 10% of their live weight and sheep and goats lost 15%. Overall economic losses at farm level range from US$9.6 to US$6,340 depending on species affected and production system. Most of the farmers (72%) had not replaced all affected animals at the time of the study. Livestock markets were the most common place to sell affected animals and buy replacements, suggesting these are likely hubs for spreading infections. This study confirms the immediate and long-lasting impact of these diseases on subsistence farmers' livelihoods in NorthEast Nigeria and suggests potential mechanisms for targeted control.

HighlightsMultivariate analysis revealed comparable poultry clusters in north and south India.Eimeria species occurrence varied between system clusters.E. tenella occurrence across systems may underpin region-specific genetic diversity.E. necatrix was found to be more common in north than south India.

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The lungworm, Angiostrongylus vasorum, was first reported in indigenous dogs in southwestern England in 1980 and has since been recorded in Wales, southeastern England and, more recently, in the West Midlands, northern England and Scotland. The nationwide distribution of the parasite was evaluated using a postal questionnaire sent to 3950 small animal practices during 2009. Information was sought on the location of each practice, awareness of the parasite locally, number of cases diagnosed over the past year and whether diagnosis was based on clinical signs alone or supported by additional tests. 1419 practices returned a usable response, the majority being located in a city/town. Nearly one-third of responding practices were aware of the parasite locally, 20.7 per cent had seen at least one confirmed case and 0.3 per cent >20 confirmed cases over the past year. The most widely used tests were faecal examination and any type of imaging. Existing clusters of infection were detected in southeastern England and south Wales; infection was also found to be widespread in central England, though patchy in northern England and Scotland. Using distribution of clinical cases as an indicator of parasite distribution, this study confirmed that A. vasorum has spread beyond traditional UK endemic foci.