Studies on the Characterisation and Utilisation of a New Phytase-Producing Bacterium Isolated from the Rumen of Cattle

Five phytase-producing bacterial strains isolated from the rumen of cattle were identified to be a new bacterial species based on their morphological, physiological, biochemical and molecular characters. The new species is named Mitsuokella jalaludinii. Mitsuokella jalaludinii hydrolysed sodium phytate rapidly and the phytase production was strongly induced by phytate present in the medium. Rice bran (RB) and soybean milk (SM) were found to be the best carbon and nitrogen sources, respectively, for phytase production by M. jalaludinii. Phosphate at a level of 0.05 - 0.5% in RB -SM medium had no effect on phytase production. Glucose added to RB-SM medium had a negative effect on phytase production of M jalaludinii. The optimum temperature and optimum initial pH for phytase production of M jalaludinii were 3 9 °C and about 7.0, respectively. The activity of M jalaludinii phytase was highest at 55 - 60°C and pH 4.0 - 5.0. It was specific to phytate as a substrate, significantly stimulated by Ba2+, Mn2+, and Ca2+ and significantly inhibited by Zn2+, Cu2+, Fe2+ and Fe3+. The metal ion chelators and phosphate were not the inhibitors of M jalaludinii phytase activity. Acute pathogenicity tests indicated that M jalaludinii was non-pathogenic to chickens and mice. Supplementation of M jalaludinii culture to corn soybean meal feed for chickens significantly increased P released from the feed in vitro and P, DM and CP digestibilities in vivo. About 70% of in vivo response in P digestibility and 90% of in vivo response in DM and CP digestibilities or AME value could be predicted by the P released in vitro. Mitsuokellajalaludinii phytase was most active in the crop of broiler chickens and was inactivated in the stomach. Supplementation of either fresh active M jalaludinii culture (AMJC) or freezedried active M jalaludinii culture (FD-AMJC) or Natuphos® phytase to 10w-aP diet significantly improved the feed intake, body weight gain and feed conversion ratio of broilers. The digestibilities of DM, CP, P , Ca, and Cu and the AME value of diet were significantly increased by the supplementation of AMJC. S upplementation of AMJC or FD-AMJC or Natuphos® phytase to 10w-aP diet significantly increased the tibia ash content and serum P concentration but significantly reduced Mn concentration in tibia ash of broiler chickens. Chicks receiving FD-AMJC had better (P<0.05) feed conversion rate as compared to those receiving Natuphos® phytase. FD-AMJC supplementation to 1 0w-aP diet significantly (P<O.OS) increased the AME value of diet and the digestibilities of DM, CP, P, Ca and Cu ( 1 1 to 1 3 - day-old and 1 8 to 20-day-old chicks) but Natuphos® phytase supplementation only significantly improved the digestibilities of DM, P ( 1 1 to 1 3 -day-old and ] 8 to 20- day-old chicks) and Ca ( 1 1 to 1 3 -day-old chicks). Chicks receiving 10w-aP diet added with AMJC or FD-AMJC or Natuphos® phytase had similar (P>0 .05) performance as those receiving normal-aP diet but excreted less (P<0.05) phosphorus

Systematic Identification and Comparison of the Expressed Profiles of lncRNAs, miRNAs, circRNAs, and mRNAs with Associated Co-Expression Networks in Pigs with Low and High Intramuscular Fat

Intramuscular fat (IMF) content is a complex trait that affects meat quality and determines pork quality. In order to explore the potential mechanisms that affect the intramuscular fat content of pigs, a Large white × Min pigs F2 resource populations were constructed, then whole-transcriptome profile analysis was carried out for five low-IMF and five high-IMF F2 individuals. In total, 218 messenger RNA (mRNAs), 213 long non-coding RNAs (lncRNAs), 18 microRNAs (miRNAs), and 59 circular RNAs (circRNAs) were found to be differentially expressed in the longissimus dorsi muscle. Gene ontology analysis and Kyoto Encyclopedia of Genes and Genomes annotations revealed that these differentially expressed (DE) genes or potential target genes (PTGs) of DE regulatory RNAs (lncRNAs, miRNAs, and circRNAs) are mainly involved in cell differentiation, fatty acid synthesis, system development, muscle fiber development, and regulating lipid metabolism. In total, 274 PTGs were found to be differentially expressed between low- and high-IMF pigs, which indicated that some DE regulatory RNAs may contribute to the deposition/metabolism of IMF by regulating their PTGs. In addition, we analyzed the quantitative trait loci (QTLs) of DE RNAs co-located in high- and low-IMF groups. A total of 97 DE regulatory RNAs could be found located in the QTLs related to IMF. Co-expression networks among different types of RNA and competing endogenous RNA (ceRNA) regulatory networks were also constructed, and some genes involved in type I diabetes mellitus were found to play an important role in the complex molecular process of intramuscular fat deposition. This study identified and analyzed some differential RNAs, regulatory RNAs, and PTGs related to IMF, and provided new insights into the study of IMF formation at the level of the genome-wide landscape

miR-423-5p Regulates Skeletal Muscle Growth and Development by Negatively Inhibiting Target Gene SRF

The process of muscle growth directly affects the yield and quality of pork food products. Muscle fibers are created during the embryonic stage, grow following birth, and regenerate during adulthood; these are all considered to be phases of muscle development. A multilevel network of transcriptional, post-transcriptional, and pathway levels controls this process. An integrated toolbox of genetics and genomics as well as the use of genomics techniques has been used in the past to attempt to understand the molecular processes behind skeletal muscle growth and development in pigs under divergent selection processes. A class of endogenous noncoding RNAs have a major regulatory function in myogenesis. But the precise function of miRNA-423-5p in muscle development and the related molecular pathways remain largely unknown. Using target prediction software, initially, the potential target genes of miR-423-5p in the Guangxi Bama miniature pig line were identified using various selection criteria for skeletal muscle growth and development. The serum response factor (SRF) was found to be one of the potential target genes, and the two are negatively correlated, suggesting that there may be targeted interactions. In addition to being strongly expressed in swine skeletal muscle, miR-423-5p was also up-regulated during C2C12 cell development. Furthermore, real-time PCR analysis showed that the overexpression of miR-423-5p significantly reduced the expression of myogenin and the myogenic differentiation antigen (p SRF expression (p SRF, confirming that SRF is a target gene of miR-423-5p. Taken together, miR-423-5p’s involvement in skeletal muscle differentiation may be through the regulation of SRF

Assessment of M. longissimus fibre types and metabolic enzymes in Bama miniature pigs and Landrace swine

Overt differences exist between Chinese local pigs and exotic pig breeds, especially in muscle growth rate and meat quality. However, the underlying molecular mechanisms remain unclear. This study aimed to assess muscle fibre types and metabolic enzymes in Bama miniature pigs and Landrace swine. Meat quality traits, including intramuscular fat content, and muscle colour, conductivity, and tenderness, were assessed in these pig breeds. Then, muscle fibre types were classified, and mRNA amounts and activities of lactate dehydrogenase (LDH), succinate dehydrogenase (SDH), and malate dehydrogenase (MDH) assessed, in M. longissimus from the two pig breeds, at various ages. Our data showed significantly higher back fat thickness, muscle conductivity, and intramuscular fat content in samples from Bama miniature pigs compared with the values obtained for Landrace pigs (p < .05). In addition, SDH activity was significantly higher, and LDH activity overtly lower in Bama pigs compared with Landrace swine (p < .05). Furthermore, myosin heavy-chain (MyHC) II A, II B, and II X mRNA levels in Bama miniature pigs at 180 were significantly higher than values obtained for Landrace pigs of the same age. Although MyHC I gene expression levels were similar in Bama miniature and Landrace pigs at 180 days of age, significantly higher amounts were obtained in 300 day old Bama miniature pigs compared with 180 day old Landrace pigs (p < .05). Collectively, these preliminary findings indicated that skeletal muscles from Bama miniature pigs may contain more oxidative fibres compared with those from Landrace pigs, which might explain the meat quality differences between the two pig breeds

Integrated Analysis of the Transcriptome and Microbial Diversity in the Intestine of Miniature Pig Obesity Model

Obesity, a key contributor to metabolic disorders, necessitates an in-depth understanding of its pathogenesis and prerequisites for prevention. Guangxi Bama miniature pig (GBM) offers an apt model for obesity-related studies. In this research, we used transcriptomics and 16S rRNA gene sequencing to discern the differentially expressed genes (DEGs) within intestinal (jejunum, ileum, and colon) tissues and variations in microbial communities in intestinal contents of GBM subjected to normal diets (ND) and high-fat, high-carbohydrate diets (HFHCD). After a feeding duration of 26 weeks, the HFHCD-fed experimental group demonstrated notable increases in backfat thickness, BMI, abnormal blood glucose metabolism, and blood lipid levels alongside the escalated serum expression of pro-inflammatory factors and a marked decline in intestinal health status when compared to the ND group. Transcriptomic analysis revealed a total of 1669 DEGs, of which 27 had similar differences in three intestinal segments across different groups, including five immune related genes: COL6A6, CYP1A1, EIF2AK2, NMI, and LGALS3B. Further, we found significant changes in the microbiota composition, with a significant decrease in beneficial bacterial populations within the HFHCD group. Finally, the results of integrated analysis of microbial diversity with transcriptomics show a positive link between certain microbial abundance (Solibacillus, norank_f__Saccharimonadaceae, Candidatus_Saccharimonas, and unclassified_f__Butyricicoccaceae) and changes in gene expression (COL6A6 and NMI). Overall, HFHCD appears to co-contribute to the initiation and progression of obesity in GBM by aggravating inflammatory responses, disrupting immune homeostasis, and creating imbalances in intestinal flora

The Landscape of Accessible Chromatin and Developmental Transcriptome Maps Reveal a Genetic Mechanism of Skeletal Muscle Development in Pigs

The epigenetic regulation mechanism of porcine skeletal muscle development relies on the openness of chromatin and is also precisely regulated by transcriptional machinery. However, fewer studies have exploited the temporal changes in gene expression and the landscape of accessible chromatin to reveal the underlying molecular mechanisms controlling muscle development. To address this, skeletal muscle biopsy samples were taken from Landrace pigs at days 0 (D0), 60 (D60), 120 (D120), and 180 (D180) after birth and were then analyzed using RNA-seq and ATAC-seq. The RNA-seq analysis identified 8554 effective differential genes, among which ACBD7, TMEM220, and ATP1A2 were identified as key genes related to the development of porcine skeletal muscle. Some potential cis-regulatory elements identified by ATAC-seq analysis contain binding sites for many transcription factors, including SP1 and EGR1, which are also the predicted transcription factors regulating the expression of ACBD7 genes. Moreover, the omics analyses revealed regulatory regions that become ectopically active after birth during porcine skeletal muscle development after birth and identified 151,245, 53,435, 30,494, and 40,911 peaks. The enriched functional elements are related to the cell cycle, muscle development, and lipid metabolism. In summary, comprehensive high-resolution gene expression maps were developed for the transcriptome and accessible chromatin during postnatal skeletal muscle development in pigs

Effects of the Probiotic, <i>Lactobacillus delbrueckii</i> subsp. <i>bulgaricus</i>, as a Substitute for Antibiotics on the Gastrointestinal Tract Microbiota and Metabolomics Profile of Female Growing-Finishing Pigs

Lactobacillus delbrueckii subsp. bulgaricus (LDB) is an approved feed additive on the Chinese ‘Approved Feed Additives’ list. However, the possibility of LDB as an antibiotic replacement remains unclear. Particularly, the effect of LDB on microbiota and metabolites in the gastrointestinal tract (GIT) requires further explanation. This study aimed to identify the microbiota and metabolites present in fecal samples and investigate the relationship between the microbiota and metabolites to evaluate the potential of LDB as an antibiotic replacement in pig production. A total of 42 female growing-finishing pigs were randomly allocated into the antibiotic group (basal diet + 75 mg/kg aureomycin) and LDB (basal diet + 3.0 × 109 cfu/kg LDB) groups. Fecal samples were collected on days 0 and 30. Growth performance was recorded and assessed. 16S rRNA sequencing and liquid chromatography-mass spectrometry-based non-targeted metabolomics approaches were used to analyze the differences in microbiota and metabolites. Associations between the differences were calculated using Spearman correlations with the Benjamini–Hochberg adjustment. The LDB diet had no adverse effect on feed efficiency but slightly enhanced the average daily weight gain and average daily feed intake (p > 0.05). The diet supplemented with LDB increased Lactobacillus abundance and decreased that of Prevotellaceae_NK3B31_group spp. Dietary-supplemented LDB enhanced the concentrations of pyridoxine, tyramine, D-(+)-pyroglutamic acid, hypoxanthine, putrescine and 5-hydroxyindole-3-acetic acid and decreased the lithocholic acid concentration. The Lactobacillus networks (Lactobacillus, Peptococcus, Ruminococcaceae_UCG-004, Escherichia-Shigella, acetophenone, tyramine, putrescine, N-methylisopelletierine, N1-acetylspermine) and Prevotellaceae_NK3B31_group networks (Prevotellaceae_NK3B31_group, Treponema_2, monolaurin, penciclovir, N-(5-acetamidopentyl)acetamide, glycerol 3-phosphate) were the most important in the LDB effect on pig GIT health in our study. These findings indicate that LDB may regulate GIT function through the Lactobacillus and Prevotellaceae_NK3B31_group networks. However, our results were restrained to fecal samples of female growing-finishing pigs; gender, growth stages, breeds and other factors should be considered to comprehensively assess LDB as an antibiotic replacement in pig production