Multi-omic Analyses Shed Light on The Genetic Control of High-altitude Adaptation in Sheep.

Sheep were domesticated in the Fertile Crescent and then spread globally, where they have been encountering various environmental conditions. The Tibetan sheep has adapted to high altitudes on the Qinghai-Tibet Plateau over the past 3000 years. To explore genomic variants associated with high-altitude adaptation in Tibetan sheep, we analyzed Illumina short-reads of 994 whole genomes representing ∼ 60 sheep breeds/populations at varied altitudes, PacBio High fidelity (HiFi) reads of 13 breeds, and 96 transcriptomes from 12 sheep organs. Association testing between the inhabited altitudes and 34,298,967 variants was conducted to investigate the genetic architecture of altitude adaptation. Highly accurate HiFi reads were used to complement the current ovine reference assembly at the most significantly associated ß-globin locus and to validate the presence of two haplotypes A and B among 13 sheep breeds. The haplotype A carried two homologous gene clusters: (1) HBE1, HBE2, HBB-like, and HBBC, and (2) HBE1-like, HBE2-like, HBB-like, and HBB; while the haplotype B lacked the first cluster. The high-altitude sheep showed highly frequent or nearly fixed haplotype A, while the low-altitude sheep dominated by haplotype B. We further demonstrated that sheep with haplotype A had an increased hemoglobin-O2 affinity compared with those carrying haplotype B. Another highly associated genomic region contained the EGLN1 gene which showed varied expression between high-altitude and low-altitude sheep. Our results provide evidence that the rapid adaptive evolution of advantageous alleles play an important role in facilitating the environmental adaptation of Tibetan sheep.

16S rRNA Gene Sequencing Revealed Changes in Gut Microbiota Composition during Pregnancy and Lactation in Mice Model.

The gut microbiota play a vital role in regulating endocrine-mediated metabolism, immunity, and energy metabolism. However, little is known about the gut microbiota and metabolite composition and development throughout pregnancy and lactation. Here, we used amplicon sequencing to analyze the gut microbiota composition of 35 female mice in five stages of pregnancy and lactation, namely, non-receptive (NR) stages, sexually-receptive (SR) stages, at day 15 of pregnancy (Pre_D15), at the day of birth (Del), and at day 10 of lactation (Lac_D10). The results revealed that the α diversity of gut microbiota was significantly increased during pregnancy and lactation. In addition, the principal coordinate analysis (PCoA) conducted on the amplicon sequence variants' (ASVs') distribution of the 16S rRNA amplicons indicated that the microbiota composition was significantly different among the five groups. Based on a random forest analysis, Oscillospira, Dehalobacterium, and Alistipes were the most important microbiota. The abundance of Allobaculum, Oscillospira, and Ruminococcus were negatively correlated with the serum progesterone concentration, while the abundance of Oscillospira was positively correlated with the propionate and valerate concentration in the caecal contents. Moreover, the concentration of acetate and propionate in the Del and Lac_D10 stages was significantly lower than in the SR and Pre_D15 stages. Our findings indicate that some gut microbes and metabolites vary considerably at the different stages of pregnancy and during lactation stages, which can potentially be used as microbial biomarkers. These results provide information on the potential use of the identified microbes as probiotics to maintain a healthy pregnancy and lactation.

Diversity and Composition of Rumen Bacteria, Fungi, and Protozoa in Goats and Sheep Living in the Same High-Altitude Pasture.

Environmental adaptation of ruminants was highly related to microbiota in the rumen. To investigate the diversity and composition of bacteria, fungi, and protozoa in the rumen of high-altitude animals, amplicon gene sequencing was performed using rumen fluid samples derived from both Tibetan goats and sheep at the same pasture in a highland (altitude > 4800 m). Between these two species, the ruminal bacteria and fungi were significantly different at multiple taxonomic levels. The alpha diversity of bacteria was significantly high in goats (p < 0.05). One hundred and sixty-four and 29 Operational Taxonomy Units (OTUs) with significant differences were detected in bacteria and fungi, respectively. The abundance of bacteria, fungi, and protozoa in the rumen was characterized at multiple taxonomic levels, and we determined that Firmicutes, Bacteroidetes, Neocallimastigomycota, and Ciliophora were the most abundant bacteria, fungi, and protozoa. The family Neocallimastigaceae and the genus Metadinium had cellulose degradation capacity in the rumen with high abundance, thereby, suggesting that fungi and protozoa played an essential role in rumen fermentation. In addition, by comparing microbiota in the rumen of goats and sheep it was found, that the fiber-degrading fungi genus (Cyllamyces) was increased in the rumen of sheep (p < 0.05) whereas VFA-producing bacteria (Saccharofermentans and Lachnospiraceae_XPB1014) were increased in the rumen of goats (p < 0.05). Interestingly, in the rumen, no differences in protozoa were observed between goats and sheep (p > 0.05). Furthermore, when compared to sheep, level of acetic acid, propionic acid, and total volatile fatty acid (TVFA) were significantly increased in the rumen of goats (p < 0.05). Taken together, these results suggested microbiota in the rumen drive goats to better adapt to high-altitude grazing conditions.