Epimural bacterial community structure in the rumen of Holstein cows with different responses to a long-term subacute ruminal acidosis diet challenge.

Subacute ruminal acidosis (SARA) is a prevalent metabolic disorder in cattle, characterized by intermittent drops in ruminal pH. This study investigated the effect of a gradual adaptation and continuously induced long-term SARA challenge diet on the epimural bacterial community structure in the rumen of cows. Eight rumen-cannulated nonlactating Holstein cows were transitioned over 1 wk from a forage-based baseline feeding diet (grass silage-hay mix) to a SARA challenge diet, which they were fed for 4 wk. The SARA challenge diet consisted of 60% concentrates (dry matter basis) and 40% grass silage-hay mix. Rumen papillae biopsies were taken at the baseline, on the last day of the 1-wk adaptation, and on the last day of the 4-wk SARA challenge period; ruminal pH was measured using wireless sensors. We isolated DNA from papillae samples for 16S rRNA gene amplicon sequencing using Illumina MiSeq. Sequencing results of most abundant key phylotypes were confirmed by quantitative PCR. Although they were fed similar amounts of concentrate, cows responded differently in terms of ruminal pH during the SARA feeding challenge. Cows were therefore classified as responders (n = 4) and nonresponders (n = 4): only responders met the SARA criterion of a ruminal pH drop below 5.8 for longer than 330 min/d. Data showed that Proteobacteria, Firmicutes, and Bacteroidetes were the most abundant phyla, and at genus level, Campylobacter and Kingella showed highest relative abundance, at 15.5 and 7.8%, respectively. Diversity analyses revealed a significant increase of diversity after the 1-wk adaptation but a decrease of diversity and species richness after the 4-wk SARA feeding challenge, although without distinction between responders and nonresponders. At the level of the operational taxonomic unit, we detected diet-specific shifts in epimural community structure, but in the overall epimural bacterial community structure, we found no differences between responders and nonresponders. Correlation analysis revealed significant associations between grain intake and operational taxonomic unit abundance. The study revealed major shifts in the 3 dominating phyla and, most importantly, a loss of diversity in the epimural bacterial communities during a long-term SARA diet challenge, in which 60% concentrate supply for 4 wk was instrumental rather than the magnitude of the drop of ruminal pH below 5.8.

High diversity of viable bacteria isolated from lymph nodes of slaughter pigs and its possible impacts for food safety.

AIMS: Ileocaecal lymph nodes (ICLNs) of pigs, the key immune inductive site for bacterial systemic invasion, were examined in this study with emphasis on viable and cultivable bacteria. METHODS AND RESULTS: Asymptomatic and pathologically altered ICLNs of slaughter pigs (n = 16) with hyperplasia, purulence or granulomatous formations were aerobically and anaerobically cultivated. In total, 209 isolates were collected and the near full-length 16S rRNA gene from each isolate was sequenced. Taxonomic classification revealed that 68% of the isolates belonged to Proteobacteria, 27% to Firmicutes and 5% to Actinobacteria. Purulent and granulomatous ICLNs generally tended to contain more Proteobacteria than asymptomatic and enlarged ICLNs (P = 0·061). The isolates could be assigned to 25 species belonging to 17 genera including Escherichia, Carnobacterium, Lactobacillus, Staphylococcus and Acinetobacter. Furthermore, pathogens such as Streptococcus suis and Salmonella enterica were detected. The most abundant isolate (57%) was most similar (>99%) to Escherichia coli. Random amplified polymorphic DNA (RAPD) profiling revealed a high genetic diversity among E. coli isolates and 24% of these isolates were positive for at least one gene associated with enterohemorrhagic disease (eae, fliC, stx1 or hlyA). Compared with a recently published DNA-based high-throughput sequencing data set including the same ICLNs, 4% of species detected were cultivable. CONCLUSIONS: The presence of viable, commensal and pathogenic bacterial phylotypes could be proven in ICLNs with Proteobacteria being dominant. SIGNIFICANCE AND IMPACT OF THE STUDY: This is the first study that broadly characterizes viable bacteria from ICLNs of pigs. The presence of bacteria in lymph nodes of farm animals has practical relevance for host colonization and possible chronic infection. It is also of great interest for basic research investigating translocation of bacteria from the gastrointestinal tract to ICLNs.

The trade network in the dairy industry and its implication for the spread of contamination.

In case of an outbreak of a foodborne disease, administrative decisions in the context of crisis management are only efficient if they follow standard practices and are specifically adapted to the outbreak situation in a timely manner. These goals are hard to achieve. The complexity of national and global trade structures obscures a clear view of trade flows and, consequently, it is often impossible to unravel complex trade links quickly. Furthermore, increasing public concerns about possible health hazards caused by global trade put additional pressure on decision makers. The aim of this paper was to unveil the specific trade structures of the German milk supply chain, to highlight how these structures could affect the spatial spread of a hypothetical contaminant, and to quantify the risk of the contaminant reaching the consumer. To achieve this goal, the vertical and horizontal trade links between milk producers, dairies, and consumers were taken into account. The horizontal flow of milk between dairies (inter-dairy trade), which is intended to compensate a temporary over- or undersupply of milk, is of special importance in this respect. We hypothesized that the extent of inter-dairy trade would significantly influence the spatial spread of contaminated milk and the contamination risk. This hypothesis was tested using a computer simulation model that predicts the hypothetical spread of a contaminant via trade of milk. The model parameters were estimated using trade data collected in 2004 and 2010. The results of our study indicate that inter-dairy trade significantly influenced the contamination risk. Compared with a scenario with no inter-dairy trade, the risk that contaminated milk will reach the consumer was up to 4 times higher, even with moderate inter-dairy trade. The contamination risk depended on the extent of inter-dairy trade in a nonlinear way and reached its maximum asymptotically when inter-dairy trade increased. The contamination risk exhibited considerable spatial variation, which could be utilized to implement more accurate food control interventions in times of crisis caused by a foodborne disease.

Gut microbiota of the European Brown Hare (Lepus europaeus).

Diseases of the gastrointestinal tract due to changes in the bacterial flora have been described with increasing incidence in the European brown hare. Despite extensive demographic and phylogeographic research, little is known about the composition of its gut microbiota and how it might vary based on potential environmental or host factors. We analysed the intestinal and faecal microbiota of 3 hare populations by Illumina MiSeq 16S rRNA gene amplicon sequencing. The phyla and OTU abundance composition differed significantly between intestinal and faecal samples (PERMANOVA: P = 0.002 and P = 0.031, respectively), but in both sample types Firmicutes and Bacteroidetes dominated the microbial community composition (45.51% and 19.30% relative abundance). Intestinal samples contained an enrichment of Proteobacteria compared with faecal samples (15.71-fold change, P < 0.001). At OTU level, a significant enrichment with best BLAST hits to the Escherichia-Shigella group, Eubacterium limosum, Sphingomonas kyeonggiensis, Flintibacter butyricus and Blautia faecis were detected in intestinal samples (P < 0.05). In our statistical model, geographic location and possibly associated environmental factors had a greater impact on the microbiota composition than host factors. Population had a significant effect on the composition of abundant intestinal and faecal OTUs, and on the abundance of potential pathogenic bacteria of the family Enterobacteriaceae, regularly associated with intestinal dysbiosis in hares, in faecal samples. Our study is the first to describe the microbiota in brown hares and provides a foundation to generate hypothesis aiming to test the role of gut health in population fluctuations of the species.

A cost-benefit analysis and the potential trade effects of the bovine viral diarrhoea eradication programme in Styria, Austria.

This study evaluated the voluntary and compulsory implementation of a bovine viral diarrhoea virus (BVDV) eradication programme in the Austrian Federal State of Styria, Austria, from an economic point of view using ex-post assessment of costs and benefits (disease losses avoided). An economic net benefit (benefit:cost ratio, BCR=1.18) of the programme was demonstrated during the voluntary programme phase (January 1998-July 2004). The break-even point was reached in 2003. If investments in the compulsory programme (August 2004-December 2016) were taken into account, a net economic loss (BCR=0.16) was demonstrated. In contrast to on-going annual testing of all cattle herds, annual testing in accordance with a revised sampling scheme could reduce total surveillance costs by more than 77%. A Bayesian structural time series model was applied to analyse a hypothesised positive impact of the compulsory BVDV programme on the Styrian cattle export market. The average number of exported cows and bulls increased significantly by 42% (P=0.03) and 47% (P=0.01), respectively, and the producer price increased by 14% (P=0.00) and 5% (P=0.16), respectively, during the compulsory programme period compared with the period prior to intervention. This equates to an average revenue increase of €29,754 for cows and €137,563 for bulls per month. These results justify the implementation of eradication programmes, which initially may not appear to be economically viable, particularly if trade effects are not included in the calculations.

Economic comparison of the monitoring programmes for bluetongue vectors in Austria and Switzerland.

With the bluetongue virus serotype 8 (BTV-8) outbreak in 2006, vector monitoring programmes (according to EU regulation 1266/2007) were implemented by European countries to obtain information on the spatial distribution of vectors and the vector-free period. This study investigates the vector monitoring programmes in Austria and Switzerland by performing a retrospective cost analysis for the period 2006-2010. Two types of costs were distinguished: costs financed directly via the national bluetongue programmes and costs contributed in-kind by the responsible institutions and agricultural holdings. The total net costs of the monitoring programme in Austria amounted to €1,415,000, whereby in Switzerland the costs were valued at €94,000. Both countries followed the legislation complying with requirements, but differed in regard to sampling frequency, number of trap sites and sampling strategy. Furthermore, the surface area of Austria is twice the area of Switzerland although the number of ruminants is almost the same in both countries. Thus, for comparison, the costs were normalised with regard to the sampling frequency and the number of trap sites. Resulting costs per trap sample comprised €164 for Austria and €48 for Switzerland. In both countries, around 50 per cent of the total costs can be attributed to payments in-kind. The benefit of this study is twofold: first, veterinary authorities may use the results to improve the economic efficiency of future vector monitoring programmes. Second, the analysis of the payment in-kind contribution is of great importance to public authorities as it makes the available resources visible and demonstrates how they have been used.