In recent years, Luchuan pigs in southern China have been used to produce high-quality meat by crossbreeding them with Duroc boars; however, PSE (pale, soft and exudative) meat was frequently reported in the crossbred pigs, and the underlying reason remains unknown. We excluded the possibility of the well-known causative mutations in RYR1 and PRKAG3 but identified the existence of an unfavorable allele of a splicing mutation (g.8283C>A) in PHKG1 in two Duroc boars and three Duroc 9 Luchuan crossbred pigs with PSE meat. An association analysis with 425 Duroc 9 Luchuan crossbred pigs revealed that the polymorphism of the splicing site of PHKG1 has significant association with the ultimate meat pH value (P = 0.035) and color score (P = 0.004). In addition, a strong cis-eQTL (expression QTL) signal for the expression of PHKG1 was identified in 189 Duroc 9 Luchuan crossbred pigs, and the splicing mutation was proven to be significantly associated with the expression of PHKG1 (P = 4.01e-11). Furthermore, RNA-sequencing data analysis confirmed that 131 CC homozygotes had only one transcript (T1), with FPKM (fragments per kilobase of transcript per million) of 35.40 AE 7.28, and 58 CA heterozygotes had two types of transcripts (T1 and T2), with FPKM of 19.63 AE 5.11 and 9.20 AE 2.39 respectively. Based on the association and eQTL analysis results, we concluded that PSE meat in Duroc 9 Luchuan crossbred pigs is caused by the splicing mutation in PHKG1. Our findings further support the effect of the causative mutation in PHKG1 on meat quality. The GEO accession number for the data is GSE124315.

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The emergence and worldwide spread of Methicillin-resistant Staphylococcus aureus (MRSA) poses a threat to human health. While bacteriophages are recognized as an effective alternative to treat infections caused by drug resistant pathogens, some bacteriophages in particular the temperate bacteriophage may also influence the virulence of the host bacteria in distinct ways. In this study, we isolated a bacteriophage vB_Saus_PHB21 from an epidermal sample of Siberian tiger (Panthera tigris altaica) using a MRSA strain SA14 as the indicator. Our following laboratory tests and whole genome sequencing analyses revealed that vB_Saus_PHB21 was a temperate bacteriophage belonging to the Siphoviridae family, and this bacteriophage did not contain any virulence genes. However, the integration of PHB21 genome into the host MRSA increased the bacterial capacities of cell adhesion, cell invasion, anti-phagocytosis and biofilm formation. Challenge of the lysogenic strain (SA14+) caused severer mortalities in both Galleria mellonella and mouse models. Mice challenged with SA14+ showed more serious organ lesions and produced higher inflammatory cytokines (IL-8, IFN-γ and TNF-α) compared to those challenged with SA14. In mechanism, we found the integration of PHB21 genome caused the upregulated expression of many genes encoding products involved in bacterial biofilm formation, adherence and invasion to host cells, anti-phagocytosis, and virulence. This study may provide novel knowledge of “bacteria-phage-interactions” in MRSA.IMPORTANCEThe interaction between bacteriophage and bacteria is like a “double-edged sword”: phages can either kill bacteria, or they may contribute to the bacterial fitness and virulence. In general, phages have positive impacts on bacterial fitness and virulence mainly because they carry antimicrobial resistance genes (ARGs) and/or virulence factors encoding genes (VFGs) and they can spread these harmful genes to the host bacteria. However, we found those phages which do not harbor ARGs and/or VFGs may also enhance the bacterial fitness and virulence. In addition, we also found the integration of phage genomes may lead to the upregulated expression of virulence associated genes in bacteria. Our study may provide new insights to redefine the relationship between phage and bacteria, and the results may also remind a cautious way to set phage-therapy for bacterial infections, before which the safety of a phage intends to be used should be fully evaluated.

Mycobacteria would encounter a number of environment changes during infection, and respond to it using different mechanisms. sRNA is a posttranscriptionally regulatory system for the function of genes and has been investigated in many other bacteria. Here, we used Mycobacterium tuberculosis and Mycobacterium bovis BCG infection models and sequenced the whole bacterial RNAs before and after host cells infection. Comparison of differential expressed sRNAs, by using GO and KEGG, and target predication, was carried out. Six pathogenically relevant stresses, drug resistance test, growth rate and morphology were used for screening and identify sRNAs. From these data, we identified a subset of sRNAs that are differentially expressed in multiple infection groups and stress conditions. We found that many of them were associated with lipid metabolism. Among them, ncBCG427, was significantly down-regulated when BCG entered into macrophages, and was associated with increase of biofilm formation and changed in drug susceptibility. Then, reduction of virulence possibility depends on regulating lipid metabolism.