Characterization and comparison of the bacterial community between complete intensive and extensive feeding patterns in pigs

To investigate and compare the gut microbiota structures in complete intensive feeding pattern (CP) and extensive feeding pattern (EP) groups, a total of 20 pigs were divided into two groups and fed the same diet. The fecal microbial composition was profiled using 16S rRNA gene sequencing. Our results showed that seventeen predominant genera were present in each pig sample and constituted the phylogenetic core of the microbiota at the class level. The abundance of most of the core microbial flora were significantly higher in the CP group than in the EP group (P < 0.05), while the abundance of Gammaproteobacteria was significantly lower in the CP group than in the EP group (P < 0.05). The CP group had significantly greater community diversity, richness, and evenness than the EP group (P < 0.05). Functional prediction analysis indicated that intestinal microbial species potentially led to faster growth and an increased fat accumulation capacity in the CP group; however, disease resistance was weaker in the CP group than in the EP group. In conclusion, EP pigs have a wider range of activity and better animal welfare than CP pigs, which helps reduce the occurrence of diseases and neurological symptoms. To explore the effect of intestinal flora on disease resistance in pigs at the molecular level, Coprococcus, which is a key gut bacterium in the intestine, was selected for isolation and purification and cocultured with intestinal epithelial cells. qPCR was performed to determine the effect of Coprococcus on SLA-DRB gene expression in intestinal epithelial cells. The results showed that Coprococcus enhanced SLA-DRB gene expression in intestinal epithelial cells. The results provide useful reference data for further study on the relationship between intestinal flora and pig disease resistance.

Characterization and comparison of the bacterial community between complete intensive and extensive feeding patterns in pigs

To investigate and compare the gut microbiota structure in complete intensive feeding pattern (CP) and extensive feeding pattern (EP) groups, a total of 20 pigs were divided into two groups and fed the same diet. The fecal microbial composition was profiled using 16S rRNA gene sequencing. Our results showed that seventeen predominant genera were present in each pig sample and constituted a phylogenetic core microbiota at the class level. Most of the core microbial flora was significantly higher in the CP group than the EP group ( P < 0.05), while Gammaproteobacteria was significantly lower in the CP group than in the EP group ( P < 0.05). The CP group had significantly higher community diversity, richness, and evenness than the EP group ( P < 0.05). Functional prediction indicated that intestinal microbial species might lead to higher growth and an increased fat accumulation capacity in the CP group; however, disease resistance was weaker in the CP group than the EP group. In conclusion, EP pigs have a wider range of sports venues and better animal welfare than CP pigs, which helps reduce the occurrence of diseases and neurological symptoms. To explore the effect of intestinal flora on the disease resistance of pigs at the molecular level, Coprococcus, which has the key gut bacterium in the intestine, was selected for isolation and purification, and co-cultured with intestinal epithelial cells. The qPCR was used to determine the effect of Coprococcus on SLA-DRB gene expression in intestinal epithelial cells. The results showed that Coprococcus enhance SLA-DRB gene expression in intestinal epithelial cells. The results provided useful references for further study on the relationship between intestinal flora and pig disease resistance.

MHC Genetic Variation Influences both Olfactory Signals and Scent Discrimination in Ring-Tailed Lemurs

ABSTRACTDiversity at the Major Histocompatibility Complex (MHC) is critical to health and fitness, such that MHC genotype may predict an individual’s quality or compatibility as a competitor, ally, or mate. Moreover, because MHC products can influence the components of bodily secretions, an individual’s body odor may signal its MHC and influence partner identification or mate choice. To investigate MHC-based signaling and recipient sensitivity, we test for odor-gene covariance and behavioral discrimination of MHC diversity and pairwise dissimilarity, under the good genes and good fit paradigms, in a strepsirrhine primate, the ring-tailed lemur (Lemur catta). First, we coupled genotyping with gas chromatography-mass spectrometry to investigate if diversity of the MHC-DRB gene is signaled by the chemical diversity of lemur genital scent gland secretions. We also assessed if the chemical similarity between individuals correlated with their MHC similarity. Next, we assessed if lemurs discriminated this chemically encoded, genetic information in opposite-sex conspecifics. We found that both sexes signaled overall MHC diversity and pairwise MHC similarity via genital secretions, but in a sex- and season-dependent manner. Additionally, both sexes discriminated absolute and relative MHC-DRB diversity in the genital odors of opposite-sex conspecifics, supporting previous findings that lemur genital odors function as advertisement of genetic quality. In this species, genital odors provide honest information about an individual’s absolute and relative MHC quality. Complementing evidence in humans and Old World monkeys, our results suggest that reliance on scent signals to communicate MHC quality may be important across the primate lineage.

Application of computational algorithms to assess the functionality of non-synonymous substitutions in MHC DRB gene of Nigerian goats

The Major Histocompatibility Complex (MHC) contains highly variable multi-gene families, which play a key role in the adaptive immune response within vertebrates. Among the Capra MHC class II genes, the expressed DRB locus is highly polymorphic, particularly in exon 2, which encodes the antigen-binding site. Models of variable non-synonymous/synonymous rate ratios among sites may provide important insights into functional constraints at different amino acid sites and may be used to detect sites under positive selection. Many non-synonymous single nucleotide polymorphisms (nsSNPs) at the DRB locus in goats are suspected to impact protein function. This study, therefore, aimed at comparing the efficiency of six computational approaches to predict the likelihood of a particular non-synonymous (amino acid change) coding SNP to cause a functional impact on the protein. This involved the use of PANTHER, SNAP, SIFT, PolyPhen-2, PROVEAN and nsSNPAnalyzer bioinformatics analytical tools in detecting harmful and beneficial effects at H57G, Y89R, V104D and Y112I substitutions in the peptide binding region of the DRB gene of Nigerian goats. The results from PANTHER analysis revealed that H57G, Y89R and Y112I substitutions (Pdeleterious= 0.113, 0.204 and 0.472, respectively) were beneficial; while that of V104D was deleterious (Pdeleterious= 0.756), an indication that it was non-neutral. As regards the SNAP approach, H57G and Y89R substitutions were returned neutral with expected accuracy of 53 and 69%, respectively while V104D and Y112I substitutions were harmful. H57G and Y89R substitutions were also found harmless in the SIFT analysis. However, only H57G (PROVEAN) and V104D (nsSNPAnalyzer) amino acid substitutions were found to be beneficial. Interestingly, the predicted 3D structures of both native and mutant DRB protein appeared similar as validated by Ramachandran plots. The consensus reached by PANTHER, SNAP, SIFT and PolyPhen-2 approaches on the neutrality especially of H57G (PROVEAN inclusive) and Y89R amino acid substitutions may be used in search of disease resistant genotypes at the DRB locus of Nigerian goats.