High-altitude hypoxia acclimatization requires whole-body physiological regulation in highland immigrants, but the underlying genetic mechanism has not been clarified. Here we use sheep as an animal model for low-to-high altitude translocation. We generate multi-omics data including whole-genome sequences, time-resolved bulk RNA-Seq, ATAC-Seq and single-cell RNA-Seq from multiple tissues as well as phenotypic data from 20 bio-indicators. We characterize transcriptional changes of all genes in each tissue, and examine multi-tissue temporal dynamics and transcriptional interactions among genes. Particularly, we identify critical functional genes regulating the short response to hypoxia in each tissue (e.g., PARG in the cerebellum and HMOX1 in the colon). We further identify TAD-constrained cis-regulatory elements, which suppress the transcriptional activity of most genes under hypoxia. Phenotypic and transcriptional evidence indicate that antenatal hypoxia could improve hypoxia tolerance in offspring. Furthermore, we provide time-series expression data of candidate genes associated with human mountain sickness (e.g., BMPR2) and high-altitude adaptation (e.g., HIF1A). Our study provides valuable resources and insights for future hypoxia-related studies in mammals. The mechanisms underlying high-altitude acclimatization remain unclear. Here authors use the sheep model to reveal multi-tissue temporal dynamics of gene transcription and regulation during acclimatization, and provide resources for hypoxia-related studies.

ABSTRACT Lactobacilli bacteria, as probiotics, show significant potential for lipid reduction. Current research into their lipid‐lowering effects is in the early stages, with mechanisms largely unexplored. In this study, mice were induced with a high‐fat diet (HFD) and treated with Lactiplantibacillus plantarum R2‐5 (LPR2‐5) via oral gavage. After 12 weeks, the LPR2‐5‐treated group exhibited substantial improvements in body weight and lipid abnormalities, with significant reductions in liver and abdominal fat accumulation. (LPR2‐5 can reduce serum total cholesterol [TC] by 25.7%, lower triglycerides [TG] by 45%, decrease low‐density lipoprotein cholesterol [LDL‐C] by 30%, and double high‐density lipoprotein cholesterol [HDL‐C].) Analysis of gut microbiota diversity demonstrated that LPR2‐5 intervention altered the gut microbiome, increasing the abundance of short‐chain fatty acid (SCFA)‐producing bacteria (Lactobacillus, Roseburia) and potentially beneficial microbes (Turicibacter, Christensenella), while inhibiting obesity‐associated bacteria (Alistipes, Bilophila), thus altering metabolic activity in the gut. Using multi‐omics techniques, key metabolic pathways and metabolites were identified. The lipid‐lowering mechanism involved a notable increase in N6,N6‐dimethyl‐l‐lysine, a precursor for carnitine synthesis, enhancing carnitine production in the liver and promoting β‐oxidation of long‐chain fatty acids, thereby effectively reducing early stage adipose accumulation.

The acidic thermostable xylanase (AT-xynA) has great potential in the feed industry, but its low activity is not conductive to large-scale production, and its application in poultry diets still needs to be further evaluated. In Experiment1, AT-xynA activity increased 3.10 times by constructing multi-copy strains, and the highest activity reached 10,018.29 ± 91.18 U/mL. AT-xynA showed protease resistance, high specificity for xylan substrates, xylobiose and xylotriose were the main hydrolysates. In Experiment2, 192 broilers were assigned into 3 treatments including a wheat-based diet, and the diets supplemented with AT-xynA during the entire period (XY-42) or exclusively during the early stage (XY-21). AT-xynA improved growth performance, while the performance of XY-21 and XY-42 was identical. To further clarify the mechanism underlying the particular effectiveness of AT-xynA during the early stage, 128 broilers were allotted into 2 treatments including a wheat-based diet and the diet supplemented with AT-xynA for 42 d in Experiment3. AT-xynA improved intestinal digestive function and microbiota composition, the benefits were stronger in younger broilers than older ones. Overall, the activity of AT-xynA exhibiting protease resistance and high xylan degradation ability increased by constructing multi-copy strains, and AT-xynA was particularly effective in improving broiler performance during the early stage.

The laccase gene (Lac1) was cloned from Coriolopsis trogii strain Mafic-2001. Full-length sequence of Lac1 containing 11 exons and 10 introns is composed of 2140 nucleotides (nts). mRNA of Lac1 encoded for a protein of 517 aa. Nucleotide sequence of the laccase was optimized and expressed in Pichia pastoris X-33. SDS-PAGE analysis showed that the molecular weight of the purified recombinant laccase rLac1 was about 70 kDa. The optimum temperature and pH of rLac1 were 40 ℃ and 3.0, respectively. rLac1 showed high residual activity (90%) in the solutions after 1 h incubation at the pH ranging from 2.5 to 8.0. rLac1 maintained over 60% of laccase activity at the temperatures ranging from 20 to 60 °C, and kept higher than 50% of its activity at 40 °C for 2 h. The activity of rLac1 was promoted by Cu2+ and inhibited by Fe2+. Under optimal conditions, lignin degradation rates of rLac1 on the substrates of rice straw, corn stover, and palm kernel cake were 50.24%, 55.49%, and 24.43% (the lignin contents of substrates untreated with rLac1 were 100%), respectively. Treated with rLac1, the structures of agricultural residues (rice straw, corn stover, and palm kernel cake) were obviously loosened which was reflected by the analysis of scanning electron microscopy and Fourier transform infrared spectroscopy. Based on the specific activity of rLac1 on the degradation of lignin, rLac1 from Coriolopsis trogii strain Mafic-2001 has the potential for in-depth utilization of agricultural residues.

The rumen undergoes developmental changes during maturation. To characterize this understudied dynamic process, we profiled single-cell transcriptomes of about 308,000 cells from the rumen tissues of sheep and goats at 17 time points. We built comprehensive transcriptome and metagenome atlases from early embryonic to rumination stages, and recapitulated histomorphometric and transcriptional features of the rumen, revealing key transitional signatures associated with the development of ruminal cells, microbiota, and core transcriptional regulatory networks. In addition, we identified and validated potential cross-talk between host cells and microbiomes and revealed their roles in modulating the spatiotemporal expression of key genes in ruminal cells. Cross-species analyses revealed convergent developmental patterns of cellular heterogeneity, gene expression, and cell-cell and microbiome-cell interactions. Finally, we uncovered how the interactions can act upon the symbiotic rumen system to modify the processes of fermentation, fiber digestion, and immune defense. These results significantly enhance understanding of the genetic basis of the unique roles of rumen.

The fat tail of sheep is an important organ that has evolved to adapt to extreme environments. However, the genetic mechanisms underlying the fat tail phenotype remain poorly understood. Here, we characterize transcriptome and lipidome profiles and morphological changes in 250 adipose tissues from two thin-tailed and three fat-tailed sheep populations in summer and winter. We implement whole-genome selective sweep tests to identify genetic variants related to fat-tails. We identify a set of functional genes that show differential expression in the tail fat of fat-tailed and thin-tailed sheep in summer and winter. These genes are significantly enriched in pathways, such as lipid metabolism, extracellular matrix (ECM) remodeling, molecular transport, and inflammatory response. In contrast to thin-tailed sheep, tail fat from fat-tailed sheep show slighter changes in adipocyte size, ECM remodeling, and lipid metabolism, and had less inflammation in response to seasonal changes, indicating improved homeostasis. Whole-genome selective sweep tests identify genes involved in preadipocyte commitment (e.g., BMP2, PDGFD ) and terminal adipogenic differentiation (e.g., VEGFA ), which could contribute to enhanced adipocyte hyperplasia. Altogether, we establish a model of regulatory networks regulating adipose homeostasis in sheep tails. These findings improve our understanding of how adipose homeostasis is maintained, in response to extreme environments in animals.

BACKGROUND Western flower thrips are considered the major insect pest of horticultural crops worldwide, causing economic and yield loss to Solanaceae crops. The eggplant (Solanum melongena L.) resistance against thrips remains largely unexplored. This work aims to identify thrips-resistant eggplants and dissect the molecular mechanisms underlying this resistance using the integrated metabolomic and transcriptomic analyses of thrips-resistant and -susceptible cultivars. RESULTS We developed a micro-cage thrips bioassay to identify thrips-resistant eggplant cultivars, and highly resistant cultivars were identified from wild eggplant relatives. Metabolomic profiles of thrips-resistant and -susceptible eggplant were compared using the gas chromatography-mass spectrometry (GC-MS)-based approach, resulting in the identification of a higher amount of quinic acid in thrips-resistant eggplant compared to the thrips-susceptible plant. RNA-sequencing analysis identified differentially expressed genes (DEGs) by comparing genome-wide gene expression changes between thrips-resistant and -susceptible eggplants. Consistent with metabolomic analysis, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis of DEGs revealed that the starch and sucrose metabolic pathway in which quinic acid is a metabolic by-product was highly enriched. External application of quinic acid enhances the resistance of susceptible eggplant to thrips. CONCLUSION Our results showed that quinic acid plays a key role in the resistance to thrips. These findings highlight a potential application of quinic acid as a biocontrol agent to manage thrips and expand our knowledge to breed thrips-resistant eggplant. © 2022 Society of Chemical Industry.

A total of 240 1-day-old Arbor Acres male broilers were randomly divided into five dietary treatments (control feed (CON), supplemented with 75 mg/kg aureomycin (ANT), supplemented with 7.5 × 108 CFU/kg (Ba1) and 2.5 × 109 CFU/kg (Ba1), and 7.5 × 109 CFU/kg (Ba3) Bacillus amyloliquefaciens TL106, respectively) to investigate the probiotic effect of TL106 instead of antibiotics in broilers. On days 1–21, the average daily gain of broilers in the Ba groups was increased compared with the CON group (p < 0.05). In addition, the feed/gain ratio of broilers in the Ba groups was lower than that of broilers in the CON and ANT groups on days 22–42 and days 1–42 (p < 0.05). Compared with the CON group, dietary TL106 increased the digestibility of crude fiber and crude protein (p < 0.05), and the effect was similar to that of the ANT group. The levels of IL-1β, IFN-γ, and IL-6 in serum, jejunum, and ileum of broilers fed TL106 were decreased compared with the control group (p < 0.05). The mRNA expression of tight junction proteins in broilers of ANT and Ba groups was higher than the control group (p < 0.05). After 21 days, villus height and the ratio of villus height to crypt depth of duodenum and jejunum of broilers fed TL106 were higher than the control group (p < 0.05). The concentrations of short-chain fatty acids such as lactate, acetate, propionate, and butyrate in cecal digesta of broilers dietary TL106 were higher than the control group (p < 0.05). The supplementation with TL106 altered the compositions and diversity of the cecal microbiota of broilers. Moreover, supplementation with TL106 improved the ratio of Firmicutes to Bacteroidetes and decreased the relative abundance of Proteobacteria on days 21 and 28, while the abundance of Peptostreptococcaceae, Ruminococcaceae and Lactobacillaceae was increased. On days 35 and 42, broilers fed TL106 had an increased total abundance of Firmicutes and Bacteroidetes and decreased abundances of Lactobacillaceae, while the abundance of Barnesiellaceae was increased. In conclusion, dietary supplementation with TL106 improved the broiler’s growth performance, immune response capacity, gut health, modulated development, and composition of the gut microbiota in broilers. It is suggested that Bacillus amyloliquefaciens TL106 may be a suitable alternative to in-feed antibiotics to improve broiler health and performance.

Xylanase has been demonstrated to improve growth performance of broilers fed wheat- or corn-based diets due to its ability to degrade arabinoxylans (AX). However, content and structure of AX in corn and wheat are different, comparing effects of xylanase on cecal microbiota of broilers fed corn- or wheat-based diets could further elaborate the mechanism of the specificity of xylanase for different cereal grains. Thus, a total of 192 one-day-old broilers were randomly allotted into four dietary treatments, including wheat-soybean basal diet, wheat-soybean basal diet with 4,000U/kg xylanase, corn-soybean basal diet, and corn-soybean basal diet with 4,000U/kg xylanase to evaluate interactive effects of xylanase in corn- or wheat-based diets on broilers cecal microbiota during a 6-week production period. The results indicated that bacterial community clustering was mainly due to cereal grains rather than xylanase supplementation. Compared with broilers fed wheat-based diets, corn-based diets increased alpha-diversity and separated from wheat-based diets (p<0.05). Xylanase modulated the abundance of specific bacteria without changing overall microbial structure. In broilers fed wheat-based diets, xylanase increased the abundance of Lactobacillus, Bifidobacterium, and some butyrate-producing bacteria, and decreased the abundance of non-starch polysaccharides-degrading (NSP) bacteria, such as Ruminococcaceae and Bacteroidetes (p<0.05). In broilers fed corn-based diets, xylanase decreased the abundance of harmful bacteria (such as genus Faecalitalea and Escherichia-Shigella) and promoted the abundance of beneficial bacteria (such as Anaerofustis and Lachnospiraceae_UCG_010) in the cecum (p<0.05). Overall, xylanase supplementation to wheat- or corn-based diets improved broilers performance and cecal microbiota composition. Xylanase supplementation to wheat-based diets increased the abundance of butyrate-producing bacteria and decreased the abundance of NSP-degrading bacteria. Moreover, positive effects of xylanase on cecal microbiota of broilers fed corn-based diets were mostly related to the inhibition of potentially pathogenic bacteria, and xylanase supplementation to corn-based diets slightly affected the abundance of butyrate-producing bacteria and NSP-degrading bacterium, the difference might be related to lower content of AX in corn compared to wheat.

A study was carried out to investigate the characterization of a novel Aspergillus sulphureus JCM01963 xylanase (AS-xyn10A) with a carbohydrate binding module (CBM) and its application in degrading alkali pretreated corncob, rapeseed meal and corn stover alone and in combination with a commercial cellulase. In this study, the 3D structure of AS-xyn10A, which contained a CBM at C-terminal. AS-xyn10A and its CBM-truncated variant (AS-xyn10A-dC) was codon-optimized and over-expressed in Komagaella phaffii X-33 (syn. Pichia pastoris) and characterized with optimal condition at 70 °C and pH 5.0, respectively. AS-xyn10A displayed high activity to xylan extracted from corn stover, corncob, and rapeseed meal. The concentration of hydrolyzed xylo-oligosaccharides (XOSs) reached 1592.26 μg/mL, 1149.92 μg/mL, and 621.86 μg/mL, respectively. Xylobiose was the main product (~70%) in the hydrolysis mixture. AS-xyn10A significantly synergized with cellulase to improve the hydrolysis efficiency of corn stover, corncob, and rapeseed meal to glucose. The degree of synergy (DS) was 1.32, 1.31, and 1.30, respectively. Simultaneously, XOSs hydrolyzed with AS-xyn10A and cellulase was improved by 46.48%, 66.13% and 141.45%, respectively. In addition, CBM variant decreased the yields of xylo-oligosaccharide and glucose in rapeseed meal degradation. This study provided a novel GH10 endo-xylanase, which has potential applications in hydrolysis of biomass.

Copy number variations (CNVs) are a major source of structural variation in mammalian genomes. Here, we characterized the genome-wide CNV in 2059 sheep from 67 populations all over the world using the Ovine Infinium HD (600K) SNP BeadChip. We tested their associations with distinct phenotypic traits by conducting multiple independent genome-wide tests. In total, we detected 7547 unique CNVs and 18,152 CNV events in 1217 non-redundant CNV regions (CNVRs), covering 245 Mb (∼10%) of the whole sheep genome. We identified seven CNVRs with frequencies correlating to geographical origins and 107 CNVRs overlapping 53 known quantitative trait loci (QTLs). Gene ontology and pathway enrichment analyses of CNV-overlapping genes revealed their common involvement in energy metabolism, endocrine regulation, nervous system development, cell proliferation, immune, and reproduction. For the phenotypic traits, we detected significantly associated (adjusted P < 0.05) CNVRs harboring functional candidate genes, such as SBNO2 for polycerate; PPP1R11 and GABBR1 for tail weight; AKT1 for supernumerary nipple; CSRP1 , WNT7B , HMX1 , and FGFR3 for ear size; and NOS3 and FILIP1 in Wadi sheep; SNRPD3 , KHDRBS2 , and SDCCAG3 in Hu sheep; NOS3 , BMP1 , and SLC19A1 in Icelandic; CDK2 in Finnsheep; MICA in Romanov; and REEP4 in Texel sheep for litter size. These CNVs and associated genes are important markers for molecular breeding of sheep and other livestock species.

The α-galactosidase gene (galC) was cloned from Aspergillus oryzae YZ1 and expressed in Pichia pastoris. The galC (2319 bp) containing two introns encoded a protein of 726 amino acids. The activity of the α-galactosidase (GalC) increased 1-fold after coding sequence optimization. Purified GalC exhibited a single protein band (100 kDa) in SDS-PAGE. The optimum pH and temperature of GalC were pH 4.66 and 50 °C, respectively. Like many GH36 family α-galactosidases, GalC displayed its activities towards raffinose and stachyose. The Km values for pNPG, raffinose and stachyose were 2.16, 4.63 and 8.54 mM, respectively. The GalC retained about 90% activity within the pH range 3.0-8.0. The activity of GalC was inhibited by Cu2+, while Ca2+ increased the enzyme activity. Different concentrations of glucose, mannose, galactose, xylose and sucrose slightly affected the activity of GalC. The GalC displayed strong resistance to trypsin, α-chymotrypsin, and proteinase K. Under simulated gastric conditions, GalC maintained most of its native activity after pepsin treatment for 3 h. The GalC could also effectively degrade raffinose and stachyose in soymilk. The GalC with high hydrolysis efficiency towards raffinose family oligosaccharides (RFOs) and strong resistance to proteases is considered to have great potential in food and feed industries.

A Galactomyces geotrichum strain with lipolytic activity was isolated and identified by the analysis of internal transcribed spacer (ITS) sequence of 18 s rDNA. Full-length lipase gene of this stain is composed of 1692 base pairs (bp) without intron, which encodes a 563-amino-acid protein. A catalytic triad (Ser217–Glu354–His463) was found by constructing the three-dimensional structure of the lipase. In shake flasks, the lipase (LIP) catalytic activity in the supernatant of the recombinant Pichia pastoris increased 48.7% by codon optimization. LIP purified by anion exchange column showed a single protein band on 12% SDS-PAGE. The molecular weight (MW) of LIP was approximately 62 kDa. The specific activity of purified LIP reached 1257.9 U/mg. The optimum temperature and pH of LIP catalysis were 45 °C and pH 8.2, respectively. LIP was stable over the pH range of 4.2–11.2. LIP maintained its activity constantly at 40 °C and 50 °C for 120 min. Zn2+ inhibited LIP activity; Ba2+, Mn2+, Ca2+ and EDTA increased the enzyme activity. Referring the amount of hydrolyzed olive oil by LIP as 100%, various oils including lard, peanut oil, rapeseed oil, sunflower oil, soybean oil and linseed oil were efficiently hydrolyzed by 17.24 ± 1.34%, 40.34 ± 2.56%, 105.86 ± 2.78%, 115.51 ± 2.32%, 116.21 ± 2.15%, 120.69 ± 1.98%, respectively. The characteristics allow LIP as a potential biocatalyst in various fields of industry.

Objective In this study, two glycosidases (XMosidases), β-xylosidase and β-mannosidase, were investigated on their in vitro hydrolysis activities of feed and on the improvement of growth performance in vivo in weanling pigs. Methods Enzyme activities of XMosidases in vitro were evaluated in test tubes and simulation of gastric and small intestinal digestion, respectively, in the presence of NSPase. In vivo study was performed in 108 weaned piglets in a 28-d treatment. Pigs were allotted to one of three dietary treatments with six replicate pens in each treatment. The three treatment groups were as follows: i) Control (basal diet); ii) CE (basal diets+CE); iii) CE-Xmosidases (basal diets+ CE+β-xylosidase at 800 U/kg and β-mannosidase at 40 U/kg). CE was complex enzymes (amylase, protease, xylanase, and mannanase). Results In vitro XMosidases displayed significant activities on hydrolysis of corn and soybean meal in the presence of non-starch polysaccharide degrading enzymes (xylanase and β-mannanase). In vitro simulation of gastric and small intestinal digestion by XMosidases showed XMosidases achieved 67.89%±0.22% of dry matter digestibility and 63.12%±0.21% of energy digestibility at 40°C for 5 hrs. In weanling pigs, additional XMosidases to CE in feed improved average daily gain, feed conversion rate (p<0.05), and apparent total tract digestibility of crude protein (p = 0.01) and dry matter (p = 0.02). XMosidases also altered the gut bacterial diversity and composition by increasing the proportion of beneficial bacteria. Conclusion Addition of a complex enzyme supplementation (contained xylanase, β-mannanase, protease and amylase), XMosidases (β-xylosidase and β-mannosidase) can further improve the growth performance and nutrient digestion of young pigs.

An acidic thermostable xylanase (AT-xynA) which was stable at low pH and high temperature was considered to have great potential in animal feed. For large-scale production, AT-xynA activity was enhanced about 1-fold in Pichia pastoris by constructing a double-copy expression strain in this study. Furthermore, impacts of different AT-xynA levels on growth performance, nutrient digestibility, short-chain fatty acids, and bacterial community in weaned piglets were determined. Compared with the control group, ADFI and ADG were higher for the pigs fed 4,000 or 6,000 U/kg AT-xynA (P < 0.05). AT-xynA supplementation also significantly increased the digestibility of OM, GE, and DM (P < 0.05). AT-xynA supplementation increased the concentrations of acetate in ileal (P < 0.01) and cecal digesta (P < 0.05). Isobutyrate (P < 0.05) and valerate (P < 0.05) concentrations in colonic digesta also significantly increased compared with the control group. AT-xynA supplementation increased the abundance of Lactobacillus in the ileal, cecal, and colonic digesta of weaned piglets (P < 0.05). AT-xynA alleviated anti-nutritional effects of nonstarch polysaccharides (NSP) by preventing the growth of Pateurella and Leptotrichia in the ileum (P < 0.05). AT-xynA increased the abundance of NSP-degrading bacteria, such as Ruminococcaceae, Prevotella in the cecum and colon (P < 0.05). In summary, AT-xynA addition could improve the growth performance of weaned piglets by altering gut microbiota.

Objective: The objective of this study was to investigate effects of supplementation of culture media from solid-state fermented Isaria cicadae (I. cicadae) on performance, serum biochemical parameters, serum immune indexes, antioxidant capacity and meat quality of broiler chickens.Methods: A total of 648 Arbor Acres male broiler chickens(1 d; average body weight, 42.93± 0.47 g) were randomly assigned to 6 treatments, each with six replicates and 18 broiler chickens per replicate. Broiler chickens were fed phase I (d 1 to 21) and phase II (d 22 to 42) diets. The phase I diets were corn and soybean-meal based diets supplemented with 0%, 2%, 4%, 6%, 8%, or 10% culture media from solid-state fermented I. cicadae respectively. The phase II diets were corn and soybean-meal based diets supplemented with 0%, 1.33%, 2.67%, 4.00%, 5.32%, or 6.67% culture media from solid-state fermented I. cicadae respectively.Results: In phase I, the broiler chickens with the supplementation of culture media had increased body weight gain and feed intake (linear and quadratic, p<0.05) with increasing inclusion of culture media. The levels of serum total antioxidant capacity (T-AOC), glutathione (GSH) and superoxide dismutase (SOD) increased linearly (p<0.05). In phase II, levels of serum T-AOC and interleukin-1β increased linearly (p<0.05), and GSH increased (p<0.05). In the kidney, GSH and glutathione peroxidase (GSH-Px) concentrations increased (linear and quadratic, p<0.05) and SOD concentration increased linearly (p<0.05). Compared to the control, shear force and drip loss of breast muscle decreased (linear and quadratic, p<0.05). Drip loss of leg muscle decreased linearly and quadratically (p<0.05).Conclusion: Dietary supplementation of culture media from solid-state fermented I.cicadae which was enriched in both wheat and residual bioactive components of I. cicadae enhanced the growth performance of broiler chickens. It also improved body anti-oxidative status and contributed to improve broiler meat quality.