SciCombinator

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Concept: Ruminant

173

Schmallenberg virus was detected in cattle and sheep in northwestern Europe in 2011. To determine whether wild ruminants are also susceptible, we measured antibody seroprevalence in cervids (roe deer and red deer) in Belgium in 2010 and 2011. Findings indicated rapid spread among these deer since virus emergence ≈250 km away.

Concepts: Deer, Elk, Ruminant, Antler, Red Deer, Roe Deer

140

The bacterial community plays important roles in the gastrointestinal tracts (GITs) of animals. However, our understanding of the microbial communities in the GIT of Bactrian camels remains limited. Here, we describe the bacterial communities from eight different GIT segments (rumen, reticulum, abomasum, duodenum, ileum, jejunum, caecum, colon) and faeces determined from 11 Bactrian camels using 16S rRNA gene amplicon sequencing. Twenty-seven bacterial phyla were found in the GIT, with Firmicutes, Verrucomicrobia and Bacteroidetes predominating. However, there were significant differences in microbial community composition between segments of the GIT. In particular, a greater proportion of Akkermansia and Unclassified Ruminococcaceae were found in the large intestine and faecal samples, while more Unclassified Clostridiales and Unclassified Bacteroidales were present in the in forestomach and small intestine. Comparative analysis of the microbiota from different GIT segments revealed that the microbial profile in the large intestine was like that in faeces. We also predicted the metagenomic profiles for the different GIT regions. In forestomach, there was enrichment associated with replication and repair and amino acid metabolism, while carbohydrate metabolism was enriched in the large intestine and faeces. These results provide profound insights into the GIT microbiota of Bactrian camels.

Concepts: Bacteria, Microbiology, Digestive system, 16S ribosomal RNA, Small intestine, Abdomen, Digestion, Ruminant

68

Sivatherium giganteum is an extinct giraffid from the Plio-Pleistocene boundary of the Himalayan foothills. To date, there has been no rigorous skeletal reconstruction of this unusual mammal. Historical and contemporary accounts anecdotally state that Sivatherium rivalled the African elephant in terms of its body mass, but this statement has never been tested. Here, we present a three-dimensional composite skeletal reconstruction and calculate a representative body mass estimate for this species using a volumetric method. We find that the estimated adult body mass of 1246 kg (857-1812 kg range) does not approach that of an African elephant, but confirms that Sivatherium was certainly a large giraffid, and may have been the largest ruminant mammal that has ever existed. We contrast this volumetric estimate with a bivariate scaling estimate derived from Sivatherium’s humeral circumference and find that there is a discrepancy between the two. The difference implies that the humeral circumference of Sivatherium is greater than expected for an animal of this size, and we speculate this may be linked to a cranial shift in centre of mass.

Concepts: Mathematics, Mass, Estimation, Giraffe, Giraffidae, Elephant, Ruminant, Ruminantia

28

A total of 10,818 domestic ruminants (3913 cattle, 2722 sheep, 3779 goats, 404 dromedaries) slaughtered in various abattoirs in Tunisia between 2003 and 2010 were examined for the presence of Echinococcus granulosus hydatid cysts. The prevalence of cystic echinococcosis (CE) was 16.42% in sheep, 8.56% in cattle, 5.94% in dromedaries and 2.88% in goats. CE prevalence increased with age according to an asymptotic model and there was evidence of variation in infection pressure depending on the region of Tunisia where the animals were slaughtered. Cattle appeared to have the highest infection pressure of the species examined. The mean intensity of hepatic cysts was higher than that of pulmonary cysts in all species. The highest mean intensity of infection with E. granulosus larvae was observed in cattle (18.14) followed by sheep (9.58), goats (2.31) and dromedaries (2.12). The abundance of infection increased in a linear fashion with age in all animal species. Cyst abundance varied with species of animal and district of Tunisia. Cysts from dromedaries were more fertile (44.44%) than those from sheep (30.25%), goats (30.32%) and cattle (0.95%). The viability of the protoscoleces from fertile cysts from cattle (78.45%) was higher than those from sheep (70.71%) and camels (69.57%). The lowest protoscolex viability was recorded for hydatid cysts from goats (20.21%). This epidemiological study confirms the importance of CE in all domestic ruminant species, particularly in sheep, throughout Tunisia and emphasizes the need to interrupt parasite transmission by preventive integrated approaches in a CE control programme.

Concepts: Epidemiology, Mammal, Cyst, Livestock, Ruminant, Goat, Camel, Herbivorous animals

27

This study sought to describe the morphological changes taking place in the goat reticulum during prenatal development, using histomorphometric and immunohistochemical techniques. A total of 140 goat embryos and foetuses were used, from the first stages of prenatal life until birth. Differentiation of the reticulum as a separate compartment of the primitive gastric tube was observed at 35 days of prenatal life (23% gestation). By 38 days (25% gestation) the reticular wall comprised three layers: an internal epithelial layer, a middle layer of pluripotential blastemic tissue and an external layer or serosa. Primary reticular crests were visible at 59 days (38% gestation) as evaginations of the epithelial stratum basale, marking the earliest histological differentiation of future reticular cells. Secondary reticular crests were observed at 87 days (61% gestation). Corneum papillae first became apparent on the lateral surface of primary reticular crests at 101 days (64% gestation). The muscularis mucosae was visible by 101 days (64% gestation) in primary reticular crests. Neuroendocrine cells were detected by synaptophysin at 64 days (43% gestation), while glial cell markers (glial fibrillary acidic protein and vimentin) were observed at 64 days (43% gestation) and 38 days (25% gestation), respectively. The peptidergic innervation markers such as neuropeptide Y and vasoactive intestinal polypeptide were detected at 75 days (50% gestation). In conclusion, prenatal development of the reticulum - like that of the rumen - appears to take place somewhat earlier in goats than in sheep or cattle, but at a similar rate to that reported in deer.

Concepts: Protein, Pregnancy, Embryo, Stomach, Skin, Glial fibrillary acidic protein, Ruminant, Goat

23

Small ruminant lentivirus infections in goats affect both production and animal welfare. This represents a threat to the qualitative and quantitative growth of goat farming, recently observed in mountainous regions such as the Autonomous Province of Bolzano - South Tyrol (Italy). To monitor and eradicate the caprine arthritis encephalitis virus in this goat population, a compulsory eradication campaign was launched, based on a strict census of small ruminants and yearly serological testing of all animals, followed by the consequent culling of seropositive individuals. The campaign succeeded in completely eliminating cases of clinical disease in goats, while drastically reducing the seroprevalence at the herd as well as individual animal level. The serological outcome of the introduced control measures was determined using commercially available ELISA kits, demonstrating their suitability for use in this type of campaign, aimed at reducing seroprevalence as well as clinical manifestations of these infections. However, this clear success is diminished by the failure to achieve a complete eradication of these viruses. The reasons leading to the observed tailing phenomenon and the occurrence of new infections in already sanitised flocks are discussed and implementation of further measures are proposed.

Concepts: RNA interference, Qualitative research, Ruminant, Goat, Autonomous area, Province of Bolzano-Bozen, Trentino-Alto Adige/Südtirol, Province of Trento

10

The moose (Alces alces) is a ruminant that harvests energy from fiber-rich lignocellulose material through carbohydrate-active enzymes (CAZymes) produced by its rumen microbes. We applied shotgun metagenomics to rumen contents from six moose to obtain insights into this microbiome. Following binning, 99 metagenome-assembled genomes (MAGs) belonging to 11 prokaryotic phyla were reconstructed and characterized based on phylogeny and CAZyme profile. The taxonomy of these MAGs reflected the overall composition of the metagenome, with dominance of the phyla Bacteroidetes and Firmicutes. Unlike in other ruminants, Spirochaetes constituted a significant proportion of the community and our analyses indicate that the corresponding strains are primarily pectin digesters. Pectin-degrading genes were also common in MAGs of Ruminococcus, Fibrobacteres and Bacteroidetes and were overall overrepresented in the moose microbiome compared with other ruminants. Phylogenomic analyses revealed several clades within the Bacteriodetes without previously characterized genomes. Several of these MAGs encoded a large numbers of dockerins, a module usually associated with cellulosomes. The Bacteroidetes dockerins were often linked to CAZymes and sometimes encoded inside polysaccharide utilization loci, which has never been reported before. The almost 100 CAZyme-annotated genomes reconstructed in this study provide an in-depth view of an efficient lignocellulose-degrading microbiome and prospects for developing enzyme technology for biorefineries.The ISME Journal advance online publication, 21 July 2017; doi:10.1038/ismej.2017.108.

Concepts: Bacteria, Organism, Microbiology, Deer, Ruminant, Rumen, Moose

9

The decrease in sequencing cost and increased sophistication of assembly algorithms for short-read platforms has resulted in a sharp increase in the number of species with genome assemblies. However, these assemblies are highly fragmented, with many gaps, ambiguities, and errors, impeding downstream applications. We demonstrate current state of the art for de novo assembly using the domestic goat (Capra hircus) based on long reads for contig formation, short reads for consensus validation, and scaffolding by optical and chromatin interaction mapping. These combined technologies produced what is, to our knowledge, the most continuous de novo mammalian assembly to date, with chromosome-length scaffolds and only 649 gaps. Our assembly represents a ∼400-fold improvement in continuity due to properly assembled gaps, compared to the previously published C. hircus assembly, and better resolves repetitive structures longer than 1 kb, representing the largest repeat family and immune gene complex yet produced for an individual of a ruminant species.

Concepts: DNA, Milk, Mammal, Livestock, Ruminant, Goat, Capra, Goats

7

The goal of this review was to analyze published data related to mitigation of enteric methane (CH4) emissions from ruminant animals to document the most effective and sustainable strategies. Increasing forage digestibility and digestible forage intake was one of the major recommended CH4 mitigation practices. Although responses vary, CH4 emissions can be reduced when corn silage replaces grass silage in the diet. Feeding legume silages could also lower CH4 emissions compared to grass silage due to their lower fiber concentration. Dietary lipids can be effective in reducing CH4 emissions, but their applicability will depend on effects on feed intake, fiber digestibility, production, and milk composition. Inclusion of concentrate feeds in the diet of ruminants will likely decrease CH4 emission intensity (Ei; CH4 per unit animal product), particularly when inclusion is above 40% of dietary dry matter and rumen function is not impaired. Supplementation of diets containing medium to poor quality forages with small amounts of concentrate feed will typically decrease CH4 Ei. Nitrates show promise as CH4 mitigation agents, but more studies are needed to fully understand their impact on whole-farm GHG emissions, animal productivity, and animal health. Through their effect on feed efficiency and rumen stoichiometry, ionophores are likely to have a moderate CH4 mitigating effect in ruminants fed high-grain or mixed grain-forage diets. Tannins may also reduce CH4 emissions, although in some situations intake and milk production may be compromised. Some direct-fed microbials, such as yeast-based products, might have a moderate CH4-mitigating effect through increasing animal productivity and feed efficiency, but the effect is likely to be inconsistent. Vaccines against rumen archaea may offer mitigation opportunities in the future, although the extent of CH4 reduction is likely to be small, and adaptation by ruminal microbes and persistence of the effect is unknown. Overall, improving forage quality and the overall efficiency of dietary nutrient use is an effective way of decreasing CH4 Ei. Several feed supplements have a potential to reduce CH4 emission from ruminants, although their long-term effect has not been well-established and some are toxic or may not be economically feasible.

Concepts: Carbon dioxide, Archaea, Nutrition, Methane, Ruminant, Greenhouse gas, Greenhouse gases, Rumen

4

Future growth in demand for meat and milk, and the socioeconomic and environmental challenges that farmers face, represent a “grand challenge for humanity”. Improving the digestibility of crop residues such as straw could enhance the sustainability of ruminant production systems. Here, we investigated if transfer of rumen contents from bison to cattle could alter the rumen microbiome and enhance total tract digestibility of a barley straw-based diet. Beef heifers were adapted to the diet for 28 days prior to the experiment. After 46 days, ~70 percent of rumen contents were removed from each heifer and replaced with mixed rumen contents collected immediately after slaughter from 32 bison. This procedure was repeated 14 days later. Intake, chewing activity, total tract digestibility, ruminal passage rate, ruminal fermentation, and the bacterial and protozoal communities were examined before the first and after the second transfer. Overall, inoculation with bison rumen contents successfully altered the cattle rumen microbiome and metabolism, and increased protein digestibility and nitrogen retention, but did not alter fiber digestibility.

Concepts: Protein, Metabolism, Nutrition, Cattle, Meat, Digestion, Ruminant, Rumen