Effects of seasonality and previous logging on faecal helminth-microbiota associations in wild lemurs.

Gastrointestinal helminth-microbiota associations are shaped by various ecological processes. The effect of the ecological context of the host on the bacterial microbiome and gastrointestinal helminth parasites has been tested in a number of ecosystems and experimentally. This study takes the important step to look at these two groups at the same time and to start to examine how these communities interact in a changing host environment. Fresh faecal samples (N = 335) from eight wild Eulemur populations were collected over 2 years across Madagascar. We used 16S ribosomal RNA gene sequencing to characterise the bacterial microbiota composition, and faecal flotation to isolate and morphologically identify nematode eggs. Infections with nematodes of the genera Callistoura and Lemuricola occurred in all lemur populations. Seasonality significantly contributed to the observed variation in microbiota composition, especially in the dry deciduous forest. Microbial richness and Lemuricola spp. infection prevalence were highest in a previously intensely logged site, whereas Callistoura spp. showed no such pattern. In addition, we observed significant correlations between gastrointestinal parasites and bacterial microbiota composition in these lemurs, with 0.4-0.7% of the variation in faecal bacterial microbiota composition being explained by helminth infections. With this study, we show effects of environmental conditions on gastrointestinal nematodes and bacterial interactions in wild lemurs and believe it is essential to consider the potential role of microbiome-parasite associations on the hosts' GI stability, health, and survival.

An observational field study of the cloacal microbiota in adult laying hens with and without access to an outdoor range.

BACKGROUND: Laying hens with access to outdoor ranges are exposed to additional environmental factors and microorganisms, including potential pathogens. Differences in composition of the cloacal microbial community between indoor- and outdoor-housed layers may serve as an indicator for exposure to the outdoor environment, including its pathogens, and may yield insights into factors affecting the chickens' microbiota community dynamics. However, little is known about the influence of outdoor housing on microbiota community composition in commercial layer flocks. We performed a cross-sectional field study to evaluate differences in the cloacal microbiota of indoor- vs outdoor-layers across farms. Eight layer flocks (four indoor, four outdoor) from five commercial poultry farms were sampled. Indoor and outdoor flocks with the same rearing flock of origin, age, and breed were selected. In each flock, cloacal swabs were taken from ten layers, and microbiota were analysed with 16S rRNA gene amplicon sequencing. RESULTS: Housing type (indoor vs outdoor), rearing farm, farm and poultry house within the farm all significantly contributed to bacterial community composition. Poultry house explained most of the variation (20.9%), while housing type only explained 0.2% of the variation in community composition. Bacterial diversity was higher in indoor-layers than in outdoor-layers, and indoor-layers also had more variation in their bacterial community composition. No phyla or genera were found to be differentially abundant between indoor and outdoor poultry houses. One amplicon sequence variant was exclusively present in outdoor-layers across all outdoor poultry houses, and was identified as Dietzia maris. CONCLUSIONS: This study shows that exposure to an outdoor environment is responsible for a relatively small proportion of the community variation in the microbiota of layers. The poultry house, farm, and rearing flock play a much greater role in determining the cloacal microbiota composition of adult laying hens. Overall, measuring differences in cloacal microbiota of layers as an indicator for the level of exposure to potential pathogens and biosecurity seems of limited practical use. To gain more insight into environmental drivers of the gut microbiota, future research should aim at investigating community composition of commercial layer flocks over time.

Genetic consequences of breaking migratory traditions in barnacle geese Branta leucopsis.

Cultural transmission of migratory traditions enables species to deal with their environment based on experiences from earlier generations. Also, it allows a more adequate and rapid response to rapidly changing environments. When individuals break with their migratory traditions, new population structures can emerge that may affect gene flow. Recently, the migratory traditions of the Barnacle Goose Branta leucopsis changed, and new populations differing in migratory distance emerged. Here, we investigate the population genetic structure of the Barnacle Goose to evaluate the consequences of altered migratory traditions. We used a set of 358 single nucleotide polymorphism (SNP) markers to genotype 418 individuals from breeding populations in Greenland, Spitsbergen, Russia, Sweden and the Netherlands, the latter two being newly emerged populations. We used discriminant analysis of principal components, FST , linkage disequilibrium and a comparison of geneflow models using migrate-n to show that there is significant population structure, but that relatively many pairs of SNPs are in linkage disequilibrium, suggesting recent admixture between these populations. Despite the assumed traditions of migration within populations, we also show that genetic exchange occurs between all populations. The newly established nonmigratory population in the Netherlands is characterized by high emigration into other populations, which suggests more exploratory behaviour, possibly as a result of shortened parental care. These results suggest that migratory traditions in populations are subject to change in geese and that such changes have population genetic consequences. We argue that the emergence of nonmigration probably resulted from developmental plasticity.

Genome-wide single nucleotide polymorphism analysis reveals recent genetic introgression from domestic pigs into Northwest European wild boar populations.

Present-day genetic introgression from domestic pigs into European wild boar has been suggested in various studies. However, no hybrids have been identified beyond doubt mainly because available methods were unable to quantify the extent of introgression and rule out natural processes. Genetic introgression from domestic pigs may have far-reaching ecological consequences by altering traits like the reproduction rate or immunology of wild boar. In this study, we demonstrate a novel approach to investigate genetic introgression in a Northwest (NW) European wild boar data set using a genome-wide single nucleotide polymorphism (SNP) assay developed for domestic pigs. We quantified the extent of introgression using allele frequency spectrum analysis, in silico hybridization simulations and genome distribution patterns of introgressed SNPs. Levels of recent introgression in the study area were expected to be low, as pig farming practices are prevailingly intensive and indoors. However, evidence was found for geographically widespread presence of domestic pig SNPs in 10% of analysed wild boar. This was supported by the identification of two different pig mitochondrial DNA haplotypes in three of the identified hybrid wild boar, suggesting that introgression had occurred from multiple sources (pig breeds). In silico hybridization simulations showed that the level of introgression in the identified hybrid wild boar is equivalent to first-generation hybrids until fifth-generation backcrosses with wild boar. The distribution pattern of introgressed SNPs supported these assignments in four of nine hybrids. The other five hybrids are considered advanced-generation hybrids, resulting from interbreeding among hybrid individuals. Three of nine hybrids were genetically associated with a different wild boar population than the one in which they were sampled. This discrepancy suggests that genetic introgression has occurred through the escape or release of an already hybridized farmed wild boar stock. We conclude that genetic introgression from domestic pigs into NW European wild boar populations is more recent and more common than expected and that genome-wide SNP analysis is a promising tool to quantify recent hybridization in free-living populations.

Solid-phase synthesis of polymyxin B1 and analogues via a safety-catch approach.

As part of a program towards the development of novel antibiotics, a convenient method for solid-phase synthesis of the cyclic cationic peptide polymyxin B1 and analogues thereof is described. The methodology, based on cleavage-by-cyclization using Kenner's safety-catch linker, yields crude products with purities ranging from 37-67%. Antibacterial assays revealed that analogues 23-26, in which the (S)-6-methyloctanoic acid moiety is replaced with shorter acyl chains, exhibit distinct antimicrobial activity. The results suggest that the length of the acyl chain is rather critical for antimicrobial activity. On the other hand, substitution of the hydrophobic ring-segment D-Phe-6/Leu-7 in polymyxin B1 with dipeptide mimics (i.e. analogues 27-33) resulted in almost complete loss of antimicrobial activity.

Stereoselective transformations on D-glucose-derived eight-membered ring carbocycles.

[structure: see text]. The cyclooctenol derivative 1 can be transformed into the nine-membered ring lactone 3, as well as the amino-containing carbocycles 4 and 5. The corresponding ketone 2 gives access to the conformationally locked azasugar 6.

Construction of a full three-dimensional model of the transpeptidase domain of Streptococcus pneumoniae PBP2x starting from its Calpha-atom coordinates.

A new method is described for generating all-atom protein structures from Calpha-atom information. The method, which combines both local structural trace alignments and comparative side chain modeling with ab initio side chain modeling, makes use of both the virtual-bond and the dipole-path methods. Provided that 3D structures of structurally and functionally related proteins exist, the method presented here is highly suitable for generating all-atom coordinates of partly solved, low-resolution crystal structures. Particularly the active site region can be modeled accurately with this procedure, which enables investigation of the binding modes of different classes of ligands with molecular dynamics simulations. The method is applied to the trace of Streptococcus pneumoniae, in order to construct an all-atom structure of the transpeptidase domain. Since after generation of full coordinates of the transpeptidase domain the structure had been solved to 2.4 A resolution, new X-ray coordinates for the worst modeled loop (residues T370 to M386; 17 out of a total number of 351 residues constituting the transpeptidase domain) were incorporated, as kindly provided by Dr. Dideberg. The structure was relaxed with molecular dynamics simulations and simulated annealing methods. The RMS deviation between the 144 aligned Calpha-atoms and the corresponding ones in the originally solved 3.5 A resolution crystal structure was 0.98. The 351 Calpha-atoms of the whole transpeptidase domain of the final model showed an RMS deviation of 1.58. The Ramachandran plot showed that 79.3% of the residues are in the most favored regions, with only 1.0% occurring in disallowed regions. The model presented here can be used to investigate the three-dimensional influences of mutations around the active site of PBP2x.

Preparation of spacer-containing di-, tri-, and tetrasaccharide fragments of the circulating anodic antigen of Schistosoma mansoni for diagnostic purposes.

The chemical synthesis of beta-D-GlcpA-(1-->3)-beta-D-GalpNAc-(1-->O)CH2CH = CH2, beta-D-Galp-NAc-(1-->6)-[beta-D-GlcpA-(1-->3)]-beta-D-GalpNAc-(1-- >O)CH2CH = CH2, and beta-D-GlcpA-(1-->3)-beta-D-GalpNAc-(1-->6)-[beta-D-GlcpA-(1 -->3)] -beta-D-GalpNAc-(1-->O)CH2CH = CH2 is described. These oligosaccharides represent fragments of th circulating anodic antigen, secreted by the parasite Schistosoma mansoni in the circulatory system of the host. The applied synthesis strategy includes the preparation of a non-oxidised backbone oligosaccharide, with a levulinoyl group at O-6 of the beta-D-glucose residue. After the selective removal of the levulinoyl group, the obtained hydroxyl functions were converted into carboxyl groups, using pyridinium dichromate and acetic anhydride in dichloromethane, to afford the desired glucuronic-acid-containing oligosaccharides. Subsequently, the allyl glycosides have been elongated with cysteamine to give the corresponding amine-spacer-containing oligosaccharides.