Livestock microbial landscape patterns: Retail poultry microbiomes significantly vary by region and season.

Microbes play key roles in animal welfare and food safety but there is little understanding of whether microbiomes associated with livestock vary in space and time. Here we analysed the bacteria associated with the carcasses of the same breed of 28 poultry broiler flocks at different stages of processing across two climatically similar UK regions over two seasons with 16S metabarcode DNA sequencing. Numbers of taxa types did not differ by region, but did by season (P = 1.2 × 10-19), and numbers increased with factory processing, especially in summer. There was also a significant (P < 1 × 10-4) difference in the presences and abundances of taxa types by season, region and factory processing stage, and the signal for seasonal and regional differences remained highly significant on final retail products. This study therefore revealed that both season and region influence the types and abundances of taxa on retail poultry products. That poultry microbiomes differ in space and time should be considered when testing the efficacy of microbial management interventions designed to increase animal welfare and food safety: these may have differential effects on livestock depending on location and timing.

Separate and combined Hanseniaspora uvarum and Metschnikowia pulcherrima metabolic volatiles are attractive to Drosophila suzukii in the laboratory and field.

Drosophila suzukii flies cause economic losses to fruit crops globally. Previous work shows various Drosophila species are attracted to volatile metabolites produced by individual fruit associated yeast isolates, but fruits naturally harbour a rich diversity of yeast species. Here, we report the relative attractiveness of D. suzukii to yeasts presented individually or in combinations using laboratory preference tests and field trapping data. Laboratory trials revealed four of 12 single yeast isolates were attractive to D. suzukii, of which Metschnikowia pulcherrima and Hanseniaspora uvarum were also attractive in field trials. Four out of 10 yeast combinations involving Candida zemplinina, Pichia pijperi, M. pulcherrima and H. uvarum were attractive in the laboratory. Whilst a combination of M. pulcherrima + H. uvarum trapped the greatest number of D. suzukii in the field, the efficacy of the M. pulcherrima + H. uvarum combination to trap D. suzukii was not significantly greater than traps primed with volatiles from only H. uvarum. While volatiles from isolates of M. pulcherrima and H. uvarum show promise as baits for D. suzukii, further research is needed to ascertain how and why flies are attracted to certain baits to optimise control efficacy.

[Assessment of the inter- and intraobserver variability for sonographical measurement of intestinal wall thickness in dogs without gastrointestinal diseases]. / Inter- und Intraobserver-Variabilität bei der sonographischen Bestimmung der Darmwanddicke von Hunden ohne gastrointestinale Erkrankungen.

OBJECTIVE: The aim of the present study was to determine inter- and intraobserver agreement for transabdominal ultrasonographic measurements of the intestinal wall in dogs without gastrointestinal diseases. MATERIAL AND METHODS: This prospective study included 30 dogs diagnosed with a non-gastrointestinal disease and were evaluated using a transabdominal ultrasound scan in our clinic. Transverse ultrasonographic images for each segment (duodenum, jejunum, colon descendens) were obtained. These images were masked, randomized and imported as DICOM files in the OsiriX® version 5.0 program for Mac Os X. Two observers independently determined the intestinal wall thicknesses using the software inherent measurement tools. The measurements were repeated five times for each segment in all patients on 4 consecutive days. Therefore, each observer performed 1800 measurements, and 3600 measurements in total were analyzed. RESULTS: The mean values for each intestinal segment were comparable to those in the literature. The statistical analyses showed a significant positive correlation (p  <  0.01) for the inter- and intraobserver measurements at all intestinal locations. There was very high intraobserver repeatability for the measurements, with deviations of <  10%. In addition, the study displayed good interobserver reproducibility for the measurements of all intestinal segments, with variances of <  20% for the duodenum and jejunum, and <  50% for the colonic wall thickness. Even with these variances the interobserver variability for all segments was much less than the mean deviance between normal and diseased dogs. CONCLUSION AND CLINICAL RELEVANCE: Transabdominal ultrasonography is a practicable tool to assess intestinal wall thickness and integrity in small animal medicine. Our results are comparable to established reference ranges for the normal canine intestinal wall thickness. In addition, we found a good inter- and intraobserver agreement for the measurements of the canine wall thicknesses in dogs without gastrointestinal diseases.

Characterizing the relationship between protein-fusion and gene co-expression.

A pair of distinct proteins in one organism may most closely match different parts of the same protein in another organism. A comparison of all proteins from the genome of Saccharomyces cerevisiae and all proteins from 24 prokaryotic genomes yields 1010 pairs of yeast proteins whose homologs are parts of one protein from a prokaryotic genome. Marcotte et al. (Science 285:751-3) showed that proteins related in this manner are more likely to interact than proteins chosen at random. In this paper, we investigated whether genes coding for such proteins are also likely to be concurrently transcribed. We identified 1010 fused pairs of proteins encoded in the yeast genome and analyzed expression of the corresponding genes at the transcriptional level. We found that the transcriptional profiles of fused gene pairs are significantly closer than those of randomly selected pairs. This finding is reproducible and established by multiple distance metrics. Moreover, such pairs frequently share additional biologically relevant properties. Thus, while protein fusion patterns are not predictive of co-expression, they are an important element in explaining co-expression. This justifies the use of curated protein fusion events to help characterize gene co-expression clusters.

Genetic analyses of NFKB1 and OCA-B function: defects in B cells, serum IgM level, and antibody responses in Nfkb1-/-Oca-b-/- mice.

Defined patterns of gene expression during cell differentiation are likely to be ensured by multiple factors playing redundant roles. By generating mice deficient in both NFKB1 and OCA-B, we show here that the two transcription factors are required for B-1 cell differentiation and serum IgM production. In addition, relative to Nfkb1(-/-) or Oca-b(-/-) mice, the Nfkb1(-/-)Oca-b(-/-) mice show a decrease in conventional B cell frequencies in the spleen and augmented reductions in T-independent and T-dependent Ab responses. These results suggest that NFKB1 and OCA-B play compensatory roles in multiple aspects of B cell differentiation.