Deciphering Estrus Expression in Gilts: The Role of Alternative Polyadenylation and LincRNAs in Reproductive Transcriptomics.

The fertility rate and litter size of female pigs are critically affected by the expression of estrus. The objective of this study was to elucidate the regulatory mechanisms of estrus expression by analyzing the differential expression of genes and long intergenic non-coding RNAs (lincRNA), as well as the utilization of alternative polyadenylation (APA) sites, in the vulva and vagina during the estrus and diestrus stages of Large White and indigenous Chinese Mi gilts. Our study revealed that the number of differentially expressed genes (DEG) in the vulva was less than that in the vagina, and the DEGs in the vulva were enriched in pathways such as "neural" pathways and steroid hormone responses, including the "Calcium signaling pathway" and "Oxytocin signaling pathway". The DEGs in the vagina were enriched in the "Metabolic pathways" and "VEGF signaling pathway". Furthermore, 27 and 21 differentially expressed lincRNAs (DEL), whose target genes were enriched in the "Endocrine resistance" pathway, were identified in the vulva and vagina, respectively. Additionally, we observed that 63 and 618 transcripts of the 3'-untranslated region (3'-UTR) were lengthened during estrus in the vulva and vagina, respectively. Interestingly, the genes undergoing APA events in the vulva exhibited species-specific enrichment in neural or steroid-related pathways, whereas those in the vagina were enriched in apoptosis or autophagy-related pathways. Further bioinformatic analysis of these lengthened 3'-UTRs revealed the presence of multiple miRNAs binding sites and cytoplasmic polyadenylation element (CPE) regulatory aspects. In particular, we identified more than 10 CPEs in the validated lengthened 3'-UTRs of the NFIX, PCNX4, CEP162 and ABHD2 genes using RT-qPCR. These findings demonstrated the involvement of APA and lincRNAs in the regulation of estrus expression in female pigs, providing new insights into the molecular mechanisms underlying estrus expression in pigs.

Occurrence of Aflatoxin M1 in Three Types of Milk from Xinjiang, China, and the Risk of Exposure for Milk Consumers in Different Age-Sex Groups.

Aflatoxin M1 (AFM1), a group 1 carcinogen, is a risk factor to be monitored in milk. This study aimed to investigate the occurrence of AFM1 in milk in Xinjiang, China, and to assess the risk of exposure for milk consumers in different age-sex groups. A total of 259 milk samples including pasteurized milk (93 samples), extended-shelf-life (ESL) milk (96), and raw donkey milk (70) were collected in Xinjiang from January to March in 2022. The AFM1 content of the milk samples was detected using a validated ELISA method. Of the 259 total samples analyzed for AFM1, 84 (32.4%) samples were contaminated at levels greater than the detection limit of 5 ng/L, with the maximum level of 16.5 ng/L. The positive rates of AFM1 in pasteurized milk and ESL milk were 43.0% (n = 40) and 45.8% (n = 44), respectively, and AFM1 was undetectable in donkey milk. The estimated daily intakes of AFM1 in each age group were lower than the hazard limits and were similar between male and female milk consumers. Therefore, the AFM1 contamination of milk in Xinjiang is low but still needs to be continuously monitored considering that children are susceptible to AFM1.

Bacterial colonisation of reeds and cottonseed hulls in the rumen of Tarim red deer (Cervus elaphus yarkandensis).

The rumen microbiome contributes greatly to the degradation of plant fibres to volatile fatty acids and microbial products, affecting the health and productivity of ruminants. In this study, we investigated the dynamics of colonisation by bacterial communities attached to reeds and cottonseed hulls in the rumen of Tarim red deer, a native species distributed in the desert of the Tarim Basin. The reed and cottonseed hull samples incubated in nylon bags for 1, 6, 12, and 48 h were collected and used to examine the bacterial communities by next-generation sequencing of the bacterial 16S rRNA gene. Prevotella1 and Rikenellaceae RC9 were the most abundant taxa in both the reed and cottonseed hull groups at various times, indicating a key role of these organisms in rumen fermentation in Tarim red deer. The relative abundances of cellulolytic bacteria, such as members of Fibrobacter, Treponema 2, Ruminococcaceae NK4A214 and Succiniclasticum increased, while that of the genus Prevotella 1 decreased, with increasing incubation time in both reeds and cottonseed hulls. Moreover, the temporal changes in bacterial diversity between reeds and cottonseed hulls were different, as demonstrated by the variations in the taxa Ruminococcaceae UCG 010 and Papillibacter in the reed group and Sphaerochaeta and Erysipelotrichaceae UCG 004 in the cottonseed hull group; the abundances of these bacteria first decreased and then increased. In conclusion, our results reveal the dynamics of bacterial colonisation of reeds and cottonseed hulls in the rumen of Tarim red deer.

Lower dietary concentrate level increases bacterial diversity in the rumen of Cervus elaphus yarkandensis.

The ruminal microbiota plays major roles in feed digestion. The composition and fermentation of the bacterial communities in 3 important ruminant species have been studied previously. Here, we extended this research to the effect of concentrate-to-forage ratios on ruminal bacterial communities in Tarim red deer (Cervus elaphus yarkandensis). Different concentrate-to-forage ratios (2:8, 3:7, 4:6, and 5:5) were fed to Tarim red deer for 20 days. Ruminal bacterial communities were elucidated by 16S ribosomal RNA gene sequencing on an Illumina HiSeq 2500 platform. The microbial composition and biodiversity at the different concentrate-to-forage ratio levels were analyzed using clustering of operational taxonomic units based on 97% sequence identity, taxonomic classification at the phylum and genus levels, α diversity, and ß diversity. Rumen microorganisms of deer fed a diet with a concentrate-to-forage ratio of 2:8 had the highest species diversity, followed by ratios of 3:7, 4:6, and 5:5. The community structure of the A1 and A2 samples and the A3 and A4 samples was similar. The bacterial composition appeared to be affected by diet, with a lower dietary concentrate level tending to increase the richness and diversity of ruminal bacteria in the rumen of Tarim red deer.

Bacterial community composition and fermentation in the rumen of Xinjiang brown cattle (Bos taurus), Tarim red deer (Cervus elaphus yarkandensis), and Karakul sheep (Ovis aries).

The rumen microbiota plays a major role in the metabolism and absorption of indigestible food sources. Xinjiang brown cattle (Bos taurus), Tarim red deer (Cervus elaphus yarkandensis), and Karakul sheep (Ovis aries) are important ruminant species for animal husbandry in the Tarim Basin. However, the microbiota and rumen fermentation of these animals are poorly understood. Here, we apply high-throughput sequencing to examine the bacterial community in the rumen of cattle, red deer, and sheep and measured rumen fermentation products. Overall, 548 218 high-quality sequences were obtained and then classified into 6034 operational taxonomic units. Prevotella spp., Succiniclasticum spp., and unclassified bacteria within the families Succinivibrionaceae, Lachnospiraceae, and Veillonellaceae were the dominant bacteria in the rumen across the 3 hosts. Principal coordinate analysis identified significant differences in the bacterial communities across the 3 hosts. Pseudobutyrivibrio spp., Oscillospira spp., and Prevotella spp. were more prevalent in the rumen of the cattle, red deer, and sheep, respectively. Among the 3 hosts, the red deer rumen had the greatest amounts of acetate and butyrate and the lowest pH value. These results showed that Prevotella spp. are the dominant bacteria in the rumen of the cattle, red deer, and sheep, providing new insight into the rumen fermentation of ruminants distributed in the Tarim Basin.