40 results on '"Yimin Zhuang"'
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2. Maternal gastrointestinal microbiome shapes gut microbial function and resistome of newborns in a cow-to-calf model
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Yimin Zhuang, Shuai Liu, Duo Gao, Yiming Xu, Wen Jiang, Guobin Hou, Sumin Li, Xinjie Zhao, Tianyu Chen, Shangru Li, Siyuan Zhang, Yanting Huang, Jingjun Wang, Jianxin Xiao, Mengmeng Li, Wei Wang, Shengli Li, and Zhijun Cao
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Enterotype ,Microbiome ,Multi-omics ,Vertical transmission ,Resistome ,Microbial ecology ,QR100-130 - Abstract
Abstract Background The maternal gut microbiome is the direct and important source of early colonization and development of the neonatal gut microbiome. However, differences in unique and shared features between mothers with different physiological phenotypes and their newborns still lack exhaustive investigation. Here, using a cow-to-calf model, a comprehensive investigation was conducted to elucidate the pattern and characterization of microbial transfer from the maternal source to the offspring. Results The microbiota in the rumen and feces of dairy cows were divided into two clusters via enterotype analysis. The cows from the enterotype distinguished by Prevotella in the rumen had better production performance, whereas no difference was observed in the cows classified by feces enterotype. Furthermore, through a pairwise combination of fecal and ruminal enterotypes, we screened a group of dairy cows with excellent phenotypes. The gastrointestinal microbiomes of cows with different phenotypes and their offspring differed significantly. The rumen was a more important microbial source for meconium than feces. Transmission of beneficial bacteria from mother to offspring was observed. Additionally, the meconium inherits advantageous metabolic functions of the rumen. The resistome features of the rumen, feces, and meconium were consistent, and resistome abundance from cows to calves showed an expanding trend. The interaction between antibiotic-resistance genes and mobile genetic elements from the rumen to meconium was the most remarkable. The diversity of core metabolites from cows to calves was stable and not affected by differences in phenotypes. However, the abundance of specific metabolites varied greatly. Conclusions Our study demonstrates the microbial taxa, metabolic function, and resistome characteristics of maternal and neonatal microbiomes, and reveals the potential vertical transmission of the microbiome from a cow-to-calf model. These findings provide new insights into the transgenerational transmission pattern of the microbiome. Video Abstract
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- 2024
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3. Seven hundred and ninety-seven metagenome-assembled genomes from the goat rumen during early life
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Tao Ma, Yimin Zhuang, Wei Lu, Yan Tu, Qiyu Diao, Xia Fan, and Naifeng Zhang
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Science - Abstract
Abstract The rumen microbiome plays an important role in providing energy and protein to the host. Manipulation of rumen microbiome during early life may have a long-term beneficial effect on the health, growth performance, and feed efficiency of ruminants. To better understand the profiles and functional potentials of rumen microbiome in young ruminants, metagenomic binning was performed to investigate the rumen microbiome of goat kids from one to 84 days of age. A total of 797 metagenome-assembled genomes (MAGs) were recovered from the rumen of 42 Laiwu black goat kids. Our findings provide fundamental knowledge of the rumen microbiome during early life based on metagenomic binning, which may provide insights into effective strategies to achieve long-term beneficial effects on animal health and production.
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- 2024
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4. The Bifidobacterium-dominated fecal microbiome in dairy calves shapes the characteristic growth phenotype of host
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Yimin Zhuang, Shuai Liu, Duo Gao, Yiming Xu, Wen Jiang, Tianyu Chen, Jianxin Xiao, Jingjun Wang, Guobin Hou, Sumin Li, Xinjie Zhao, Yanting Huang, Shangru Li, Siyuan Zhang, Mengmeng Li, Wei Wang, Shengli Li, and Zhijun Cao
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Microbial ecology ,QR100-130 - Abstract
Abstract The dominant bacteria in the hindgut of calves play an important role in their growth and health, which could even lead to lifelong consequences. However, the identification of core probiotics in the hindgut and its mechanism regulating host growth remain unclear. Here, a total of 1045 fecal samples were analyzed by 16S rRNA gene sequencing from the 408 Holstein dairy calves at the age of 0, 14, 28, 42, 56, and 70 days to characterize the dynamic changes of core taxa. Moreover, the mechanisms of nutrient metabolism of calf growth regulated by core bacteria were investigated using multi-omics analyses. Finally, fecal microbiota transplantation (FMT) in mice were conducted to illustrate the potential beneficial effects of core bacteria. Four calf enterotypes were identified and enterotypes dominated by Bifidobacterium and Oscillospiraceae_UCG-005 were representative. The frequency of enterotype conversion shifted from variable to stable. The close relationship observed between phenotype and enterotype, revealing a potential pro-growth effect of Bifidobacterium, might be implemented by promoting the use of carbohydrate, activating the synthesis of volatile fatty acids, amino acids and vitamin B6, and inhibiting methane production in the hindgut. The FMT results indicated the beneficial effect of Bifidobacterium on host growth and hindgut development. These results support the notion that the Bifidobacterium-dominated fecal microbiome would be an important driving force for promoting the host growth in the early life. Our findings provide new insights into the potential probiotic mining and application strategies to promote the growth of young animals or improve their growth retardation.
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- 2024
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5. Dataset of the rumen microbiota and epithelial transcriptomics and proteomics in goat affected by solid diets
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Jianmin Chai, Xiaokang Lv, Yimin Zhuang, Qiyu Diao, Kai Cui, Feilong Deng, Ying Li, and Naifeng Zhang
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Science - Abstract
Abstract Although early solid diet supplementation is a common practice to improve the growth and development in goat kids, its biological mechanism how solid diet induces rumen microbiota and epithelial development is still unknow. In this study, rumen fermentation parameters, 16S rRNA sequencing for rumen content and epithelial microbiota, transcriptomics and proteomics of epithelium were determined to classify the effects of solid diet supplementation. Here, we classified the changes of goat phenotypes (i.e., growth performance, rumen fermentation and development) and linked them to the changes of rumen microbiota, transcriptome and expressed proteins. The mechanism of solid diet improving rumen development was elucidated preliminarily. Moreover, different roles between the rumen content and epithelial microbiota were identified. Thess datasets expands our understanding of the association between the early diet intervention and rumen development, providing the useful information how nutrient strategy affects rumen function and subsequently improves the host growth. The generated data provides insights in the importance of rumen niche microbiota and microbe-host interactions, which benefits future studies.
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- 2024
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6. Disorders of acid-base balance promote rumen lipopolysaccharide biosynthesis in dairy cows by modulating the microbiome
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Guobin Hou, Jingtao You, Yimin Zhuang, Duo Gao, Yiming Xu, Wen Jiang, Sumin Li, Xinjie Zhao, Tianyu Chen, Siyuan Zhang, Shuai Liu, Wei Wang, Shengli Li, and Zhijun Cao
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subacute ruminal acidosis ,rumen pH ,lipopolysaccharide ,microbiome ,inflammation ,Microbiology ,QR1-502 - Abstract
IntroductionDisorders of acid-base balance in the rumen of dairy cows have a significant impact on their health and performance. However, the effect of transient differences in pH on susceptibility to subacute ruminal acidosis (SARA) and lipopolysaccharide (LPS) biosynthesis in dairy cows remains unclear.MethodsIn this study, milk, serum, and rumen fluid samples from 40 Holstein dairy cows (on d 56 postpartum) with different rumen pH (2–4 h after morning feeding) were explored to investigate the difference of susceptibility to SARA and the correlation between microbiome, LPS and inflammation. These cows were categorized into low pH (LPH, pH ≤ 6.0, n = 20) and high pH (HPH, pH ≥ 6.5, n = 20) groups.ResultsThe results showed that LPH group increased the concentrations of total volatile fatty acids, acetate, propionate, butyrate and valerate. However, milk yield and milk compositions were unaffected. Compared to the HPH group, the LPH group increased the concentrations of serum BHBA, NEFA, LPS, HIS, IL-2, IL-6, TNF-α, and MDA, and decreased the concentrations of serum IgA, IgM, IgG, SOD, T-AOC, and mTOR. In addition, the LPH group decreased the copies of Ruminococcus flavefaciens and increased the copies of Fibrobacter succinogenes. Microbial community analysis isupplendicated a significant difference in bacterial composition between the two groups. At the phylum level, Bacteroidota and Firmicutes were enriched in the LPH and HPH groups, respectively. At the genus level, the dominant bacteria in the LPH group were Prevotella. Additionally, the LPH group increased the proportions of Gram-negative phenotypes, potentially pathogenic phenotypes and LPS biosynthesis. The close correlation between two key enzymes for LPS synthesis LpxL and LpxM with rumen pH, inflammatory markers, and microorganisms indicates that low pH may increase the risk of inflammation by facilitating the lysis of Gram-negative bacteria and the release of penta-acylated LPS. Penta-acylated and hexa-acylated LPS may be mainly derived from Prevotella and Succinivibrionaceae_UCG-001, respectively.DiscussionOverall, these results support the notion that transient low pH could reflect the risk of cows suffering from SARA and associated inflammation and is strongly associated with penta-acylated LPS. Our findings provide new insights into ruminant health improvement and disease prevention strategies.
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- 2024
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7. Stress-induced hyperglycemia and mortality in patients with traumatic brain injury without preexisting diabetes: A meta-analysis
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Shizhen Cui, Daiqi Xu, Han Xiong, Yimin Zhuang, and Zhaohui He
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Stress-induced hyperglycemia ,traumatic brain injury ,mortality ,meta-analysis ,Biology (General) ,QH301-705.5 - Abstract
Stress-induced hyperglycemia (SIH) is common in patients with traumatic brain injury (TBI) and has been suggested to influence mortality rates. This meta-analysis aims to evaluate the impact of SIH on the mortality of TBI patients without preexisting diabetes mellitus (DM). A comprehensive search was performed in Medline, Web of Science, Embase, Wanfang, and CNKI databases up to May 15, 2024, to retrieve relevant studies. Observational studies reporting the incidence of all-cause mortality among TBI patients without preexisting DM, comparing those with and without SIH, were included. The association between SIH and all-cause mortality was analyzed using risk ratios (RR) and 95% confidence intervals (CI) with a random-effects model. Twelve cohort studies comprising 15 datasets with 16,387 TBI patients were included. The pooled analysis showed that SIH was associated with a higher risk of all-cause mortality (RR: 2.00, 95% CI: 1.72-2.33, p < 0.001), with mild heterogeneity (I² = 25%). Sensitivity analysis confirmed the robustness of these findings. Subgroup analyses indicated no significant differences based on study design, patient age, gender proportion, SIH definition, or follow-up duration. However, the association was slightly weaker but still significant in studies using multivariate analyses (RR: 1.76) compared to univariate analyses (RR: 2.69). In conclusion, SIH was associated with a higher risk of all-cause mortality in TBI patients without preexisting DM. Further research should explore the underlying mechanisms and optimal management strategies for SIH in this population.
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- 2024
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8. Metagenomics reveals the temporal dynamics of the rumen resistome and microbiome in goat kids
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Jianmin Chai, Yimin Zhuang, Kai Cui, Yanliang Bi, and Naifeng Zhang
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Rumen resistome ,Metagenomics ,Microbiome ,Ruminants ,Ages ,Temporal dynamics ,Microbial ecology ,QR100-130 - Abstract
Abstract Background The gut microbiome of domestic animals carries antibiotic resistance genes (ARGs) which can be transmitted to the environment and humans, resulting in challenges of antibiotic resistance. Although it has been reported that the rumen microbiome of ruminants may be a reservoir of ARGs, the factors affecting the temporal dynamics of the rumen resistome are still unclear. Here, we collected rumen content samples of goats at 1, 7, 14, 28, 42, 56, 70, and 84 days of age, analyzed their microbiome and resistome profiles using metagenomics, and assessed the temporal dynamics of the rumen resistome in goats at the early stage of life under a conventional feeding system. Results In our results, the rumen resistome of goat kids contained ARGs to 41 classes, and the richness of ARGs decreased with age. Four antibiotic compound types of ARGs, including drugs, biocides, metals, and multi-compounds, were found during milk feeding, while only drug types of ARGs were observed after supplementation with starter feed. The specific ARGs for each age and their temporal dynamics were characterized, and the network inference model revealed that the interactions among ARGs were related to age. A strong correlation between the profiles of rumen resistome and microbiome was found using Procrustes analysis. Ruminal Escherichia coli within Proteobacteria phylum was the main carrier of ARGs in goats consuming colostrum, while Prevotella ruminicola and Fibrobacter succinogenes associated with cellulose degradation were the carriers of ARGs after starter supplementation. Milk consumption was likely a source of rumen ARGs, and the changes in the rumen resistome with age were correlated with the microbiome modulation by starter supplementation. Conclusions Our data revealed that the temporal dynamics of the rumen resistome are associated with the microbiome, and the reservoir of ARGs in the rumen during early life is likely related to age and diet. It may be a feasible strategy to reduce the rumen and its downstream dissemination of ARGs in ruminants through early-life dietary intervention. Video Abstract
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- 2024
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9. Transcriptomic and metabolomic insights into the roles of exogenous β-hydroxybutyrate acid for the development of rumen epithelium in young goats
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Yimin Zhuang, Jianmin Chai, Mahmoud M. Abdelsattar, Yuze Fu, and Naifeng Zhang
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Rumen ,Beta-hydroxybutyrate acid ,Lipid metabolism ,Transcriptome ,Metabolomics ,Goat ,Animal culture ,SF1-1100 - Abstract
Beta-hydroxybutyric acid (BHBA), as one of the main metabolic ketones in the rumen epithelium, plays critical roles in cellular growth and metabolism. The ketogenic capacity is associated with the maturation of rumen in young ruminants, and the exogenous BHBA in diet may promote the rumen development. However, the effects of exogenous BHBA on rumen remain unknown. This is the first study to investigate the mechanisms of BHBA on gene expression and metabolism of rumen epithelium using young goats as a model through multi-omics techniques. Thirty-two young goats were divided into control, low dose, middle dose, and high dose groups by supplementation of BHBA in starter (0, 3, 6, and 9 g/day, respectively). Results demonstrated the dietary of BHBA promoted the growth performance of young goats and increased width and length of the rumen papilla (P
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- 2023
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10. Dietary β-hydroxybutyric acid improves the growth performance of young ruminants based on rumen microbiota and volatile fatty acid biosynthesis
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Jianmin Chai, Zeyue Liu, Jun Wu, Yuan Kang, Mahmoud M. Abdelsattar, Wei Zhao, Shiqin Wang, Shuli Yang, Feilong Deng, Ying Li, Yimin Zhuang, and Naifeng Zhang
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β-hydroxybutyric acid ,rumen microbiota ,goats ,growth ,volatile fatty acids ,Microbiology ,QR1-502 - Abstract
IntroductionThe ketone body β-hydroxybutyric acid (BHB) plays critical roles in cellular proliferation and metabolic fuel utilization; however, its effects on the rumen microbiota remain unknown.MethodsHere, three doses of BHB (low, medium, and high) were supplemented to early-weaned goat kids.ResultsCompared with controls, the beneficial effects of BHB on growth and rumen development were observed in goats at 90 days of age (d). The low dose of dietary BHB increased the concentration of rumen acetate, propionate, and butyrate on d90. The sequencing results of the rumen microbiota revealed marked shifts in rumen microbial community structure after early-weaned goat kids consumed BHB for 2 months. The signature bacterial ASVs for each treatment were identified and were the main drivers contributing to microbial interactions in the rumen. The bacteria associated with rumen weight were also correlated with body weight. Some classified bacterial signatures, including Prevotella, Olsenella umbonate, and Roseburia faecis, were related to rumen volatile fatty acids and host development.ConclusionOverall, dietary BHB altered rumen microbiota and environments in young goats, which contributed to rumen development and growth.
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- 2024
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11. Altered microbiota, antimicrobial resistance genes, and functional enzyme profiles in the rumen of yak calves fed with milk replacer
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Yimin Zhuang, Wei Guo, Kai Cui, Yan Tu, Qiyu Diao, Naifeng Zhang, Yanliang Bi, and Tao Ma
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rumen ,milk replacer ,yak ,microbiome ,metagenomics ,resistome ,Microbiology ,QR1-502 - Abstract
ABSTRACT The use of milk replacer (MR) is a modern strategy to ensure the health and growth of neonatal ruminants. Some studies have confirmed that dietary factors have significant effects on ruminal antimicrobial resistance genes (ARGs), which, as a potential threat to livestock, have received more attention. However, the effect of different milk sources (milk or MR) on the rumen resistome of yaks is still largely unknown. Here, using metagenome technology, we investigated the occurrence of ruminal ARGs in yaks and their relationship with rumen bacteria in response to different milk sources. The metagenomic result showed that MR feeding significantly increased the abundance of Prevotella members compared to milk feeding. A total of 138 rumen resistome-conveying ARGs to 17 different classes of antimicrobials were detected, of which tetracycline resistance was the predominant. MR feeding also drove the changes in the rumen resistome, and the predicted bacterial origins of ARGs had complex and various manifestations. Moreover, enzymes of butyrate metabolism and carbohydrate-active enzymes encoding carbohydrate and cellulose degradation were increased. This study revealed that MR feeding increased the abundance of beneficial bacteria Prevotella members, changed the microbial resistome, and promoted the metabolic function of volatile fatty acid biosynthesis in the rumen of yaks, which could provide beneficial evidence for the regulation of the rumen microbiome and the intervention of antimicrobial resistance in ruminants by dietary or nutritional methods. IMPORTANCE Yaks, as ruminants inhabiting high-altitude environments, possess a distinct rumen microbiome and are resistant to extreme living conditions. This study investigated the microbiota, resistome, and functional gene profiles in the rumen of yaks fed milk or milk replacer (MR), providing insights into the regulation of the rumen microbiome and the intervention of antimicrobial resistance in yaks through dietary methods. The abundance of Prevotella members increased significantly in response to MR. Tetracycline resistance was the most predominant. The rumen of yaks contained multiple antimicrobial resistance genes (ARGs) originating from different bacteria, which could be driven by MR, and these ARGs displayed intricate and complex interactions. MR also induced changes in functional genes. The enzymes associated with fiber degradation and butyrate metabolism were activated and showed close correlations with Prevotella members and butyrate concentration. This study allows us to deeply understand the ruminal microbiome and ARGs of yaks and their relationship with rumen bacteria in response to different milk sources.
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- 2024
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12. Supplementation with Combined Additive Improved the Production of Dairy Cows and Their Offspring with Maintenance of Antioxidative Stability
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Hongxing Zhang, Yiliyaer Nuermaimaiti, Kebi Hao, Yan Qi, Yiming Xu, Yimin Zhuang, Fei Wang, Guobin Hou, Tianyu Chen, Jianxin Xiao, Gang Guo, Yajing Wang, Shengli Li, Zhijun Cao, and Shuai Liu
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transition cows ,calf ,additives ,blood immunity ,productive performance ,Therapeutics. Pharmacology ,RM1-950 - Abstract
Oxidative stress damage in periparturient cows decreases both production and their health; supplementation with complex additives during the periparturient period has been used as an important strategy to enhance the antioxidant status and production of dairy cows. The periparturient cows not only risk a negative energy balance due to reduced dry matter intake but also represent a sensitive period for oxidative stress. Therefore, we have developed an immunomodulatory and nutritional regulation combined additive (INC) that hopefully can improve the immune status and production of cows during the periparturient period and their offspring health and growth by improving their antioxidant stress status. The INC comprised a diverse array of additives, including water-soluble and fat-soluble vitamins, Selenomethionine, and active dry Saccharomyces cerevisiae. Forty-five multiparous Holstein cows were randomly assigned to three treatments: CON (no INC supplementation, n = 15), INC30 (30 g/d INC supplementation, n = 15), and INC60 (60 g/d INC supplementation, n = 15) based on last lactation milk yield, body condition score, and parity. Newborn calves were administered 4 L of maternal colostrum originating from the corresponding treatment and categorized based on the treatment received by their respective dams. The INC not only served to maintain the antioxidative stress system of dairy cows during the periparturient period but also showed a tendency to improve the immune response (lower tumor necrosis factor and interleukin-6) during the perinatal period. A linear decrease in concentrations of alkaline phosphatase postpartum and β-hydroxybutyrate was observed with INC supplementation. Milk fat yield, milk protein yield, and energy-corrected milk yield were also increased linearly with increasing additive supplementation. Calves in the INC30 group exhibited greater wither height and chest girth but no significant effect on average daily gain or body weight. The diarrhea frequency was linearly decreased with the incremental level of INC. Results indicate that supplementation with INC in peripartum dairy cows could be a major strategy to improve immune response, decrease inflammation, maintain antioxidant stress status in transition dairy cows, and have merit in their calves. In conclusion, this study underlines the benefits of INC supplementation during the transition period, as it improved anti-inflammatory capacity, could positively impact antioxidative stress capacity, and eventually enhanced the production performance of dairy cows and the health and growth of calves.
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- 2024
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13. Editorial: Respiratory microbiome in health and disease
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Yimin Zhuang, Tao Ding, Jiangchao Zhao, and Jianmin Chai
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respiratory microbiome ,health ,respiratory disease ,respiratory tracts ,microbe-microbe interaction ,microbe-host interaction ,Microbiology ,QR1-502 - Published
- 2023
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14. Impact of dietary supplementation of β-hydroxybutyric acid on performance, nutrient digestibility, organ development and serum stress indicators in early-weaned goat kids
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Mahmoud M. Abdelsattar, Einar Vargas-Bello-Pérez, Yimin Zhuang, Yuze Fu, and Naifeng Zhang
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Beta-hydroxybutyric acid ,Goat kid ,Acute-phase protein response ,Weaning stress ,Antioxidant capacity ,Animal culture ,SF1-1100 - Abstract
The objective of this study was to determine the effect of dietary supplementation of β-hydroxybutyric acid (BHBA) on performance, nutrient digestibility, organ development, and serum composition in early-weaned goat kids. Sixty-four goat kids at 30 d of age were assigned to 4 treatments in a completely randomized design: 1) control (basal diet); 2) low (basal diet with 3 g/d per animal BHBA); 3) medium (basal diet with 6 g/d per animal BHBA; and 4) high (basal diet with 9 g/d per animal BHBA). Subsequently, 48 (6 kids per treatment) goat kids were randomly selected and slaughtered at 60 and 90 d of age. Compared with the control group, BHBA at low and high doses increased body weight (P
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- 2022
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15. Early Solid Diet Supplementation Influences the Proteomics of Rumen Epithelium in Goat Kids
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Yimin Zhuang, Xiaokang Lv, Kai Cui, Jianmin Chai, and Naifeng Zhang
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goat ,rumen epithelium ,proteome ,solid feed ,protein expression ,Biology (General) ,QH301-705.5 - Abstract
It is well known that solid diet supplementation in early life can significantly promote rumen development and metabolic function in young ruminants. However, the changes in the expressed proteome and related metabolism in rumen epithelium in response to a supplemented solid diet remain unclear. In this study, rumen epithelial tissue from goats in three diet regimes including milk replacer only (MRO), milk replacer supplemented concentrate (MRC), and milk replacer supplemented concentrate plus alfalfa pellets (MCA) were collected for measurement of the expression of epithelial proteins using proteomic technology (six per group). The results showed that solid diet significantly improved the growth performance of goats, enhanced the ability of rumen fermentation, and promoted the development of epithelial papilla (p < 0.05). Proteome analysis revealed the distinct difference in the expressed protein in the MRC and MCA group compared with the MRO group (42 upregulated proteins and 79 downregulated proteins in MRC; 38 upregulated proteins and 73 downregulated proteins in MCA). Functional analysis showed that solid diet supplementation activated a variety of molecular functions in the epithelium, including protein binding, ATP binding, structural constituent of muscle, etc., in the MRC and MCA groups. Meanwhile, the expression of proteins related to fatty acid metabolism, the PPAR signaling pathway, valine, leucine, and isoleucine degradation, and butanoate metabolism were upregulated, being stimulated by solid feed. In contrast, the proteins associated with carbohydrate digestion and absorption and glycosaminoglycan degradation were downregulated. In addition, the protein expression of enzymes involved in ketone body synthesis in the rumen was generally activated, which was caused by solid feed. In summary, solid feed promoted the development of rumen epithelium by changing the expression of proteins related to fatty acid metabolism, energy synthesis, and signal transduction. The ketone body synthesis pathway might be the most important activated pathway, and provides energy for rumen development.
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- 2023
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16. Effects of Age and Dietary Factors on the Blood Beta-Hydroxybutyric Acid, Metabolites, Immunoglobulins, and Hormones of Goats
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Mahmoud M. Abdelsattar, Einar Vargas-Bello-Pérez, Yimin Zhuang, Yuze Fu, and Naifeng Zhang
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beta-hydroxybutyric acid ,age ,weaning ,blood chemical composition ,immunoglobulins ,Veterinary medicine ,SF600-1100 - Abstract
The study was aimed to examine the effects of age and dietary beta-hydroxybutyric acid (BHBA) on blood BHBA and blood health indicators in goat kids. Thirty male goats of five ages (1, 2, 3, 6, and 12 months old) were selected for blood sampling to determine the influence of age. Another 64 goat kids (half males and half females) were weaned at 1 month old and fed with starter diets with control, low, medium, and high BHBA doses (0, 3, 6, and 9 g/animal/day, respectively). Six goats per treatment were selected for blood analysis at 2 and 3 months of age. There were significant effects (p < 0.01) of ages on the blood parameters of goat kids. The 6- and 12-month-old goats showed significantly lower blood total protein, globulin, BHBA, IgA, and IgM concentrations than did young goats, while they had a higher albumin-to-globulin ratio than young goats. The blood glucose decreased (p < 0.01) and IgG increased over time (p < 0.01). In blood, growth hormone (GH) and insulin-like growth factor I (IGF-I) were lower (p < 0.01) at 1- and 3-month-old goats than 12-month-old goats. The high dietary BHBA improved (p < 0.05) the ratio of albumin to globulin of 2-month-old kids compared with control. The blood GH and IGF-I were lower (p < 0.01) in the medium BHBA dose at 2 months of age than control. These results suggested that age greatly impacted blood composition, especially around weaning, and dietary BHBA showed beneficial regulating effects on blood total protein level in young goats.
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- 2022
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17. Yeast (Saccharomyces cerevisiae) Culture Promotes the Performance of Fattening Sheep by Enhancing Nutrients Digestibility and Rumen Development
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Jie Wang, Guohong Zhao, Yimin Zhuang, Jianmin Chai, and Naifeng Zhang
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yeast culture ,Saccharomyces cerevisiae ,fattening sheep ,growth performance ,nutrient digestibility ,rumen fermentation ,Fermentation industries. Beverages. Alcohol ,TP500-660 - Abstract
Paraprobiotics are potential agents for improving animal health and performance. This experiment investigated the effect of dietary supplementation of yeast (Saccharomyces cerevisiae) culture (YC) on the growth performance, nutrient digestibility, rumen development and microbiome of fattening sheep. Ninety male Hu sheep weighed 38 ± 1.47 kg were randomly assigned to three treatments: CON diet (basal diet), LYC diet (basal diet supplied with 10 and 20 g/d yeast culture at the early and late stages, respectively), and HYC diet (basal diet supplied with 20 and 40 g/d yeast culture at the early and late stages, respectively). Treatments (LYC or HYC) were sprinkled on the feed surface according to the required dosage before feeding the basal diet to each sheep throughout the trial. The trial included early (60 days) and later (30 days) fattening periods. The results showed that average daily gain and feed efficiency were higher (p < 0.05) in the LYC group compared with CON in later and whole stages. Digestibility of DM, OM, CP, NDF and ADF were higher (p < 0.05) in LYC and HYC compared with CON. The retained N, the utilization efficiency of N and the biological value of N were higher (p < 0.05) in LYC compared with CON and HYC. Rumen NH3-N was higher (p < 0.05) in LYC and HYC. The papillary height of the rumen was higher (p < 0.05) in LYC when compared with CON and HYC, whereas rumen wall thickness and muscular layer thickness were higher (p < 0.05) in HYC compared with CON and LYC. The dressing percentage of LYC and HYC was higher (p < 0.05) compared with CON. The diversity, richness and structure of rumen microbiota showed no significant difference (p > 0.05); however, still observed remarkable increases in the relative abundance of several specific genera including Succiniclasticum and Fibrobacter with increasing doses of yeast culture. In addition, at the ASV level, ASV83, ASV123 (Succiniclasticum), and ASV148, ASV250 (Fibrobacter) were increased in YC groups. In conclusion, we confirmed that the supplementation of YC in diet could improve the growth and slaughter performance of fattening Hu sheep through improving nutrient digestion, especially nitrogen utilization, rumen microbial environment and the development of rumen epithelium, which proves the benefits of paraprobiotics in animal production.
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- 2022
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18. Predicting the Digestive Tract Development and Growth Performance of Goat Kids Using Sigmoidal Models
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Mahmoud Abdelsattar, Yimin Zhuang, Kai Cui, Yanliang Bi, and Naifeng Zhang
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goat kids ,rumen development ,growth curve ,inflection point ,area under the curve ,Veterinary medicine ,SF600-1100 ,Zoology ,QL1-991 - Abstract
The transition from monogastric to rumination stage is crucial in ruminants’ growth to avoid stressors—weaning and neonatal mortalities. Poor growth of the digestive tract could adversely affect the performance of the animal. Modeling informative growth curves is of great importance for a better understanding of the effective development pattern, in order to optimize feeding management system, and to achieve more production efficiency. However, little is known about the digestive tract growth curves. For this reason, one big goat farm of Laiwu black breed was chosen as a basis of this study. Forty-eight kids belonging to eight-time points (1, 7, 14, 28, 42, 56, 70, and 84 d; 6 kids for each) were selected and slaughtered. The body weight, body size indices, rumen pH, and stomach parts were determined and fitted to the polynomial and sigmoidal models. In terms of goodness of fit criteria, the Gompertz model was the best model for body weight, body oblique length, tube, and rumen weight. Moreover, the Logistic model was the best model for carcass weight, body height, and chest circumference. In addition, the Quadratic model showed the best fit for dressing percentage, omasum weight, abomasum weight, and rumen volume. Moreover, the cubic model best fitted the ruminal pH and reticulum percentage. The Weibull model was the best model for the reticulum weight and omasum percentage, while the MMF model was the best model describing the growth of chest depth, rumen percentage, and abomasum percentage. The model parameters, R squared, inflection points, area under curve varied among the different dependent variables. The Pearson correlation showed that the digestive tract development was more correlated with age than body weight, but the other variables were more correlated with body weight than age. The study demonstrated the use of empirical sigmoidal and polynomial models to predict growth rates of the digestive tract at relevant age efficiently.
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- 2021
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19. Longitudinal Investigation of the Gut Microbiota in Goat Kids from Birth to Postweaning
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Yimin Zhuang, Jianmin Chai, Kai Cui, Yanliang Bi, Qiyu Diao, Wenqin Huang, Hunter Usdrowski, and Naifeng Zhang
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gut microbiota ,goat ,ruminants ,ages ,biogeography ,temporal dynamics ,Biology (General) ,QH301-705.5 - Abstract
Early microbial colonization in the gut impacts animal performance and lifelong health. However, research on gut microbial colonization and development in young ruminants, especially after weaning, is currently limited. In this study, next-generation sequencing technology was performed to investigate the temporal dynamic changes of the microbial community in the jejunum and colon of goats at 1, 7, 14, 28, 42, 56, 70, and 84 days (d) of age. As age increased, significant increases in microbial diversity, including the number of Observed OTUs and the Shannon Index, were observed in both the jejunum and colon. Regarding beta diversity, significant shifts in community membership and structure from d1 to d84 were observed based on both Bray–Curtis and Jaccard distances. With increasing age, dominant genera in the jejunum shifted from Lactobacillus to unclassified Ruminococcaceae, unclassified Lachnospiraceae and unclassified Clostridiales through starter supplementation, whereas colonic dominant genera changed from Lactobacillus and Butyricicoccus, within d1–d28, to unclassified Ruminococcaceae, unclassified Clostridiales and Campylobacter after solid diet supplementation. The linear discriminant analysis (LDA) effect size (LEfSe) analysis revealed bacterial features that are stage-specific in the jejunum and colon, respectively. In the jejunum and colon, a significantly distinct structure and membership of the microbiota was observed across all ages. The growth stage-associated microbiota in each gut compartment was also identified as a marker for biogeography. Our data indicate the temporal and spatial differences of the gut microbiota in goats are important for their performance and health. Early microbial colonization can influence microbial composition in later life (e.g., post-weaning phase). This study provides insights that the temporal dynamics of gut microbiota development from newborn to post-weaning can aid in developing feeding strategies to improve goat health and production.
- Published
- 2020
- Full Text
- View/download PDF
20. The Signature Microbiota Drive Rumen Function Shifts in Goat Kids Introduced to Solid Diet Regimes
- Author
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Xiaokang Lv, Jianmin Chai, Qiyu Diao, Wenqin Huang, Yimin Zhuang, and Naifeng Zhang
- Subjects
goats ,rumen microbiota ,solid diet ,rumen development ,neutral detergent fibers ,volatile fatty acids ,Biology (General) ,QH301-705.5 - Abstract
The feeding regime of early, supplementary solid diet improved rumen development and production in goat kids. However, the signature microbiota responsible for linking dietary regimes to rumen function shifts are still unclear. This work analyzed the rumen microbiome and functions affected by an early solid diet regime using a combination of machine learning algorithms. Volatile fatty acids (i.e., acetate, propionate and butyrate) fermented by microbes were found to increase significantly in the supplementary solid diet groups. Predominant genera were found to alter significantly from unclassified Sphingobacteriaceae (non-supplementary group) to Prevotella (supplementary solid diet groups). Random Forest classification model revealed signature microbiota for solid diet that positively correlated with macronutrient intake, and linearly increased with volatile fatty acid production. Bacteria associated with carbohydrate and protein metabolism were also identified. Utilization of a Fish Taco analysis portrayed a set of intersecting core species contributed to rumen function shifts by the solid diet regime. The core community structures consisted of the specific, signature microbiota and the manipulation of their symbiotic partners are manipulated by extra nutrients from concentrate and/or forage, and then produce more volatile fatty acids to promote rumen development and functions eventually host development. Our study provides mechanisms of the microbiome governed by a solid diet regime early in life, and highlights the signature microbiota involved in animal health and production.
- Published
- 2019
- Full Text
- View/download PDF
21. DyPipe: A Holistic Approach to Accelerating Dynamic Neural Networks with Dynamic Pipelining.
- Author
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Yimin Zhuang, Xing Hu 0001, Xiaobing Chen, and Tian Zhi
- Published
- 2023
- Full Text
- View/download PDF
22. Tetris: A Heuristic Static Memory Management Framework for Uniform Memory Multicore Neural Network Accelerators.
- Author
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Xiaobing Chen, Hao Qi 0004, Shaohui Peng, Yimin Zhuang, Tian Zhi, and Yunji Chen
- Published
- 2022
- Full Text
- View/download PDF
23. Cambricon-Q: A Hybrid Architecture for Efficient Training.
- Author
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Yongwei Zhao, Chang Liu 0021, Zidong Du, Qi Guo 0001, Xing Hu 0001, Yimin Zhuang, Zhenxing Zhang, Xinkai Song, Wei Li 0008, Xishan Zhang, Ling Li 0001, Zhiwei Xu 0002, and Tianshi Chen 0002
- Published
- 2021
- Full Text
- View/download PDF
24. Deep Fusion: A Software Scheduling Method for Memory Access Optimization.
- Author
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Yimin Zhuang, Shaohui Peng, Xiaobing Chen, Shengyuan Zhou, Tian Zhi, Wei Li 0008, and Shaoli Liu
- Published
- 2019
- Full Text
- View/download PDF
25. Compiling Optimization for Neural Network Accelerators.
- Author
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Jin Song, Yimin Zhuang, Xiaobing Chen, Tian Zhi, and Shaoli Liu
- Published
- 2019
- Full Text
- View/download PDF
26. Partition and Scheduling Algorithms for Neural Network Accelerators.
- Author
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Xiaobing Chen, Shaohui Peng, Luyang Jin, Yimin Zhuang, Jin Song, Weijian Du, Shaoli Liu, and Tian Zhi
- Published
- 2019
- Full Text
- View/download PDF
27. ZhuQue: A Neural Network Programming Model Based on Labeled Data Layout.
- Author
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Weijian Du, Linyang Wu, Xiaobing Chen, Yimin Zhuang, and Tian Zhi
- Published
- 2019
- Full Text
- View/download PDF
28. Obstructive Sleep Apnea-Related Knowledge, Attitude, Experience, and Behaviors Among Orthodontic Professionals: A Survey
- Author
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Lizhuo Lin, Tingting Zhao, Peter Ngan, Yimin Zhuang, Danchen Qin, Fang Hua, and Hong He
- Subjects
knowledge ,Otorhinolaryngology ,attitude ,questionnaire ,Neurology (clinical) ,orthodontics ,obstructive sleep apnea - Abstract
Purpose: To assess obstructive sleep apnea (OSA)-related experience, knowledge, attitude, and behaviors among orthodontic professionals in China and identify factors associated with their knowledge levels, attitude toward referring and self-confidence in the management of patients with OSA.Methods: An online cross-sectional survey was conducted using a 31-item questionnaire developed with a professional online survey tool (www.wjx.cn) and distributed via WeChat (Tencent, Shenzhen, China). Data were collected between January 16-23, 2022, and analyzed using the chi-square test, Fisher’s exact test, and multivariate generalized estimation equations.Results: A total of 1760 professionals responded to the survey and responses to 1611 questionnaires were valid. The average score of correct answers to the 15 OSA knowledge questions was 12.1 ± 2.0. Most of the professionals agreed that it was necessary to identify patients who might have OSA in practice. The top three sources for gaining knowledge of OSA according to the survey were classrooms and textbooks (76.3%), medical lectures (75.7%), and academic conferences (73.2%). The level of knowledge was significantly correlated with self-confidence in treatment (P < 0.001) and willingness to refer patients to otolaryngologists or clinicians of related disciplines (P < 0.001).Conclusions: Most orthodontic professionals agreed that there was a need to identify OSA patients and learn further about related problems. The treatment confidence and willingness of professionals to refer patients were found related to the level of OSA knowledge. Therefore, OSA-related education should be promoted.
- Published
- 2023
- Full Text
- View/download PDF
29. Dietary medium chain fatty acid and Bacillus in combination alleviate weaning stress of piglets by regulating intestinal microbiota and barrier function
- Author
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Shuai Jiao, Zhenhua Zheng, Yimin Zhuang, Chuanlan Tang, and Naifeng Zhang
- Subjects
Genetics ,Animal Science and Zoology ,General Medicine ,Food Science - Abstract
The present study evaluated the effects of dietary medium-chain fatty acid (MCFA) and Bacillus on growth performance, nutrient digestibility, antioxidant capacity, colonic fermentation, and microbiota of weaning piglets. A total of 400 weaned piglets were randomly divided into 4 treatments, with 10 replicates per treatment and 10 pigs per replicate. The treatment included: basal diet (control, CON), basal diet with 0.588 g/kg MCFA (MCF), basal diet with 1.3 × 109 CFU/kg Bacillus (BAC), and basal diet with 0.588 g/kg MCFA and 1.3 × 109 CFU/kg Bacillus (SYN). Compared with CON group, the average daily gain of MCF and SYN in the early (1 to 9 d) and whole stage (1 to 36 d) of trail were improved (P < 0.05), the feed to gain ratio of MCF in later (10 to 36 d) and whole stage of trial were decreased (P < 0.05), and the diarrhea rate of SYN in the early stage (1 to 9 d) of trial decreased (P < 0.05). The digestibility of dry matter, ether extract, acid detergent fiber digestibility of MCF were decreased (P < 0.05) compared with CON. The serum d-lactic acid in MCF, BAC, and SYN were lower (P < 0.05) compared with CON group. Compared with CON group, the contents of total antioxidant capacity, superoxide dismutase, and glutathione peroxidase were greater (P < 0.05), whereas the content of malondialdehyde and the contents of colonic isobutyrate and isovalerate were lower (P < 0.05) in MCF. The microbial Shannon and Simpson diversity was lower in MCF (P < 0.05) than that in BAC and SYN. The relative abundance of Prevotella was greater (P < 0.05), whereas the Treponema and Oscillibacter were lower (P < 0.05) in MCF than that in BAC and SYN. In addition, the metabolic pathways of bacteria such as pentose phosphate pathway, adenosine nucleotides degradation II were enhanced (P < 0.05), whereas the pathways such as incomplete reductive TCA cycle, and TCA cycle IV (2-oxoglutarate decarboxylase) were decreased (P < 0.05) in MCF compared with BAC. The results indicated that dietary MCFA and Bacillus in combination improved the intestinal barrier function of piglets by changing the intestinal microbiota and its metabolic function, and finally alleviated the diarrhea rate in early weaning stage and improved growth performance in whole trial period. In addition, MCFA was effective in improving feed efficiency and antioxidant capacity of piglets.
- Published
- 2022
30. Solid diet manipulates rumen epithelial microbiota and its interactions with host transcriptomic in young ruminants
- Author
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Xiaokang Lv, Chai Jianmin, Hunter Usdrowski, Yimin Zhuang, Qiyu Diao, Kai Cui, Wenqin Huang, and Naifeng Zhang
- Subjects
animal structures ,Rumen ,Host (biology) ,Microbiota ,food and beverages ,Ruminants ,Biology ,biology.organism_classification ,Microbiology ,Animal Feed ,Early life ,Epithelium ,Diet ,Transcriptome ,fluids and secretions ,medicine.anatomical_structure ,Food supplement ,Rumen microbiota ,medicine ,Animals ,Food science ,Ecology, Evolution, Behavior and Systematics ,Bacteria - Abstract
Solid diet supplementation in the early life stages of ruminants could improve rumen microbiota and tissue development. However, most studies focus on bacteria in the rumen content community. The microbiota attached on rumen epithelium are rarely investigated, and their correlations with rumen content bacteria and host transcripts are unknown. In this study, rumen digesta attached in the epithelium from goats in three diet regimes (milk replacer only, milk replacer supplemented concentrate and milk replacer supplemented concentrate plus alfalfa pellets) were collected for measurement of the epithelial microbiota using next generation sequencing. Correspondingly, the rumen tissues of the same animals were measured with the host transcriptome. The distinct microbial structures and compositions between rumen content and epithelial communities were associated with solid diet supplementation. Regarding rumen development in pre-weaning ruminants, a solid diet, especially its accompanying neutral detergent fibre nutrients, was the most significant driver that influenced the rumen microbiota and epithelium gene expression. Compared with content bacteria, rumen epithelial microbiota had a stronger association with the host transcriptome. The host transcriptome correlated with host phenotypes were associated with rumen epithelial microbiota and solid diet. This study reveals that the epithelial microbiota is crucial for proper rumen development, and solid diet could improve rumen development through both the rumen content and epithelial microbiota.
- Published
- 2021
31. Impact of dietary supplementation of β-hydroxybutyric acid on performance, nutrient digestibility, organ development and serum stress indicators in early-weaned goat kids
- Author
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Mahmoud M. Abdelsattar, Einar Vargas-Bello-Pérez, Yimin Zhuang, Yuze Fu, and Naifeng Zhang
- Subjects
Weaning stress ,Food Animals ,Animal Science and Zoology ,Goat kid ,Beta-hydroxybutyric acid ,Acute-phase protein response ,Antioxidant capacity - Abstract
The objective of this study was to determine the effect of dietary supplementation of β-hydroxybutyric acid (BHBA) on performance, nutrient digestibility, organ development, and serum composition in early-weaned goat kids. Sixty-four goat kids at 30 d of age were assigned to 4 treatments in a completely randomized design: 1) control (basal diet); 2) low (basal diet with 3 g/d per head BHBA); 3) medium (basal diet with 6 g/d per head BHBA; and 4) high (basal diet with 9 g/d per head BHBA). Subsequently, 48 (6 kids per treatment) goat kids were randomly selected and slaughtered at 60 and 90 d of age. Compared with the control group, BHBA at low and high doses increased body weight (P < 0.05), average daily gain (P < 0.01), and average daily starter intake (P < 0.01). The BHBA improved organ development, especially at the lowest dose (P < 0.01). The digestibility of dry matter and crude protein increased with age (P < 0.05). However, BHBA did not affect nutrient digestibility. Compared with the control group, serum ceruloplasmin increased (P < 0.05) with high BHBA level at 90 d of age. However, the serum creatinine (P < 0.05) increased over time but was not affected by BHBA. The serum total antioxidant capacity and superoxide dismutase decreased with the high dose of BHBA at 90 d of age (P < 0.01). In contrast, the serum glutathione peroxidase and malondialdehyde increased with the high doses of BHBA (P < 0.01). Overall, low doses of BHBA were positive for growth performance, organ development, and health status against weaning stress. Whereas high doses of BHBA in the long term could negatively affect antioxidant status.
- Published
- 2021
- Full Text
- View/download PDF
32. Longitudinal Investigation of the Gut Microbiota in Goat Kids from Birth to Postweaning
- Author
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Hunter Usdrowski, Chai Jianmin, Qiyu Diao, Kai Cui, Yanliang Bi, Yimin Zhuang, Naifeng Zhang, and Wenqin Huang
- Subjects
Microbiology (medical) ,Beta diversity ,Zoology ,Gut flora ,medicine.disease_cause ,Microbiology ,digestive system ,Article ,Jejunum ,03 medical and health sciences ,Diversity index ,Virology ,Lactobacillus ,medicine ,Weaning ,lcsh:QH301-705.5 ,biogeography ,030304 developmental biology ,0303 health sciences ,ages ,biology ,gut microbiota ,030306 microbiology ,Campylobacter ,temporal dynamics ,goat ,biology.organism_classification ,medicine.anatomical_structure ,lcsh:Biology (General) ,Microbial population biology ,ruminants - Abstract
Early microbial colonization in the gut impacts animal performance and lifelong health. However, research on gut microbial colonization and development in young ruminants, especially after weaning, is currently limited. In this study, next-generation sequencing technology was performed to investigate the temporal dynamic changes of the microbial community in the jejunum and colon of goats at 1, 7, 14, 28, 42, 56, 70, and 84 days (d) of age. As age increased, significant increases in microbial diversity, including the number of Observed OTUs and the Shannon Index, were observed in both the jejunum and colon. Regarding beta diversity, significant shifts in community membership and structure from d1 to d84 were observed based on both Bray&ndash, Curtis and Jaccard distances. With increasing age, dominant genera in the jejunum shifted from Lactobacillus to unclassified Ruminococcaceae, unclassified Lachnospiraceae and unclassified Clostridiales through starter supplementation, whereas colonic dominant genera changed from Lactobacillus and Butyricicoccus, within d1&ndash, d28, to unclassified Ruminococcaceae, unclassified Clostridiales and Campylobacter after solid diet supplementation. The linear discriminant analysis (LDA) effect size (LEfSe) analysis revealed bacterial features that are stage-specific in the jejunum and colon, respectively. In the jejunum and colon, a significantly distinct structure and membership of the microbiota was observed across all ages. The growth stage-associated microbiota in each gut compartment was also identified as a marker for biogeography. Our data indicate the temporal and spatial differences of the gut microbiota in goats are important for their performance and health. Early microbial colonization can influence microbial composition in later life (e.g., post-weaning phase). This study provides insights that the temporal dynamics of gut microbiota development from newborn to post-weaning can aid in developing feeding strategies to improve goat health and production.
- Published
- 2020
- Full Text
- View/download PDF
33. Early solid diet supplementation influences proteomic of rumen epithelium in goat kids
- Author
-
Yimin Zhuang, Kai Cui, Wenqin Huang, Yong Han, Qiyu Diao, and Naifeng Zhang
- Abstract
Background: Rumen is an important organ for nutrient absorption and metabolism in goats, and its constant development is a prerequisite for the healthy growth of goat kids. Previous studies have shown that the intake of solid feed in early life can significantly promote the development of rumen tissue morphology and metabolic function in young ruminants. However, the expressed proteome in rumen epithelium of goats supplemented solid diet is still limited. In this study, 24 pairs of twin goats were randomly divided into milk replacer group (MR) and milk replacer with supplemented solid diets group (SS) using proteomic analysis based on ITRAQ technique, which allow to further analyze potential biological mechanism. Results: Significant increased papilla length and width, epithelium thickness as well as muscle layers thickness were observed in SS group. A total of 6003 differentially expressed proteins were detected in the SS group compared to the MR group by analyzing the rumen protein expression of six biological replicates, of which 251 proteins were up-regulated and 750 proteins were down-regulated. According to Gene Ontology, the differential expressed proteins (DEPs) were significantly enriched in functions related to cell development and biosynthesis. The networks of KEGG pathways demonstrated that most of the 30 significantly enriched pathways involved in cellular metabolism, signal transduction and immunity. Conclusions: The supplementation of solid feed promoted the growth of rumen epithelial cells, improved the rumen's immune function, and activated lipid metabolism. Our findings provided new insights into the molecular mechanisms underlying rumen developmental differences in goat kids caused by solid feed.
- Published
- 2020
- Full Text
- View/download PDF
34. The Signature Microbiota Driving Rumen Function Shifts in Goat Kids Introduced Solid Diet Regimes
- Author
-
Wenqin Huang, Chai Jianmin, Yimin Zhuang, Qiyu Diao, Naifeng Zhang, and Xiaokang Lv
- Subjects
chemistry.chemical_classification ,animal structures ,biology ,Animal health ,biology.organism_classification ,Rumen ,Nutrient ,chemistry ,Ruminant ,Prevotella ,Propionate ,Food science ,Microbiome ,Function (biology) - Abstract
The feeding regime of early supplementary solid diet improved rumen development and ruminant production. However, the signature microbiota linking dietary regimes to rumen function shifts and hosts are still unclear. We analyzed the rumen microbiome and functions affected by supplementation of solid diet using a combination of machine learning algorithms. The volatile fatty acids (i.e., acetate, propionate and butyrate) fermented by microbes increased significantly in the supplementary solid diet groups. The predominant genera altered significantly from unclassified Sphingobacteriaceae (non-supplementary group) to Prevotella (supplementary solid diet groups) RandomForest classification model revealed signature microbiota for solid diet that positively correlated with macronutrient intake, and linearly increased with volatile fatty acids production. The nutrient specific bacteria for carbohydrate and protein were also identified. According to FishTaco analysis, a set of intersecting core species contributed with rumen function shifts by solid diet. The core community structures consisted of specific signature microbiota and their symbiotic partners are manipulated by extra nutrients from concentrate and/or forage, and then produce more volatile fatty acids to promote rumen development and functions eventually host development. Our study provides mechanism of microbiome governing by solid diet and highlights the signatures microbiota for animal health and production.ImportanceSmall ruminants are essential protein sources for human, so keeping them health and increasing their production are important. The microbial communities resided in rumen play key roles to convert fiber resources to human food. Moreover, rumen physiology experience huge changes after birth, and understanding its microbiome roles could provide insights for other species. Recently, our studies and others have shown that diet changed rumen microbial composition and goat performance. In this study, we identified core community structures that were affected by diet and associated to the rumen development and goat production. This outcome could potentially allow us to select specific microbiome to improve rumen physiology and functions, maintain host health and benefit animal production. Therefore, it gives a significant clue that core microbiome manipulation by feeding strategies can increase animal products. To our knowledge, we firstly used FishTaco for determination of link between signatures abundances and rumen function shifts.
- Published
- 2019
- Full Text
- View/download PDF
35. Deep Fusion: A Software Scheduling Method for Memory Access Optimization
- Author
-
Wei Li, Yimin Zhuang, Tian Zhi, Shengyuan Zhou, Liu Shaoli, Shaohui Peng, and Xiaobing Chen
- Subjects
050101 languages & linguistics ,Speedup ,Artificial neural network ,Computer science ,business.industry ,05 social sciences ,02 engineering and technology ,Reuse ,Bottleneck ,Scheduling (computing) ,Software ,Computer engineering ,0202 electrical engineering, electronic engineering, information engineering ,Deep neural networks ,020201 artificial intelligence & image processing ,0501 psychology and cognitive sciences ,Local independence ,business - Abstract
Deep neural networks (DNNs) have been considered to be the state-of-the-art artificial intelligence methods in a very broad range of applications. However, DNNs are compute intensive and memory intensive which are difficult to be employed in practical scenarios. Due to their favorable parallel computing ability, a series of DNN accelerators have been proposed. However, the improvement of on-chip computing capacity and the increasing number of parameters in the neural networks make access to memory a bottleneck. In this paper, we analyze the existing DNN algorithms. We observe that the special structure of neural networks makes it have two useful characteristics, which are unilateral directivity and local independence. Based on these characteristics, we propose a general software scheduling method to reduce memory access cost. Based on the experimental results, our method can reduce 32% memory access cost and achieve a speedup of 1.6x in average on our experiment platform and the best result is in ResNet-50, which is up to 56% and 2.62x.
- Published
- 2019
- Full Text
- View/download PDF
36. Partition and Scheduling Algorithms for Neural Network Accelerators
- Author
-
Liu Shaoli, Yimin Zhuang, Jin Song, Shaohui Peng, Tian Zhi, Weijian Du, Xiaobing Chen, and Luyang Jin
- Subjects
Speedup ,Quantitative Biology::Neurons and Cognition ,Scheduling heuristics ,Artificial neural network ,Computer science ,Computation ,Computer Science::Neural and Evolutionary Computation ,Combination algorithm ,Parallel computing ,Computer Science::Operating Systems ,Partition (database) ,Separable space ,Scheduling (computing) - Abstract
In recent years, Artificial Neural Networks have evolved rapidly and are applied to various fields. Meanwhile, to enhance computation efficiency of neural network applications, more and more neural network accelerators have been developed. Though traditional task scheduling algorithms on heterogeneous systems have been intensively researched, they can’t be applied to neural network accelerators directly. Based on typical characteristics of neural network accelerators, we formalize the problem of tasks scheduling for neural networks, and transplant two listing heuristic scheduling algorithms, Heterogeneous-Earliest-Finish-Time (HEFT) and Critical-Path-on-a-Processor (CPOP). Inspired by the separable features of neural network operations, we propose two partition algorithms, the Iterative Partition Scheduling Algorithm (IPS) and the Partition Scheduling Combination Algorithm (PSC), which can be associated with scheduling algorithms. Further, we conduct experiments on some typical neural networks, and results show that compared to scheduling-only algorithms the partition associated algorithms achieve about 2x to 3x speedup.
- Published
- 2019
- Full Text
- View/download PDF
37. ZhuQue: A Neural Network Programming Model Based on Labeled Data Layout
- Author
-
Linyang Wu, Xiaobing Chen, Yimin Zhuang, Tian Zhi, and Weijian Du
- Subjects
Complex data type ,Artificial neural network ,business.industry ,Computer science ,Deep learning ,Data classification ,computer.software_genre ,Data type ,Software ,Programming paradigm ,Graph (abstract data type) ,Artificial intelligence ,Data mining ,business ,computer - Abstract
In the last five years, the research of neural network accelerators has made remarkable achievements and provided powerful hardware support for many deep learning algorithms. In order to improve the performance of the neural network accelerator, algorithm optimization and data layout in the neural network development kit (NDK) are indispensable. The rich data types in neural network algorithms determine the diversity of data layout information. How to add complex data layout information to the NDK, to guide the work of all aspects of the software, to avoid user perception and to provide a user-friendly API, has become a series of issues worth studying. This paper implements a neural network development kit based on labeled data layout to solve the above problems, and abstracts a neural network programming model. The programming model establishes a neural network computing graph at “creating time”, “compiling time” sets the data label and “runtime” uses the label to control the data transfer. Compared with the existing NDK, the software has an average performance improvement of 4.76×. In addition, this paper also defines dynamic tags and static tags of neural network data, and proposes a neural network data classification method.
- Published
- 2019
- Full Text
- View/download PDF
38. Compiling Optimization for Neural Network Accelerators
- Author
-
Yimin Zhuang, Xiaobing Chen, Tian Zhi, Liu Shaoli, and Jin Song
- Subjects
Loop unrolling ,Computational model ,Speedup ,Artificial neural network ,Computer science ,Process (computing) ,Graph (abstract data type) ,Parallel computing ,Compiler ,Layer (object-oriented design) ,computer.software_genre ,computer - Abstract
Nowadays artificial neural networks are one of the most common computational models among all the intelligent methods. To cope with the ever-growing scales of neural networks and the restrictions of system energy consumption, there comes out a bunch of neural network (NN) accelerators. However, owing to their dedicated architecture, programming on NN accelerators is different from general processors. In order to improve performance, it is necessary to use global structure information of NN model to optimize the compilation. In this paper, we introduce a series of layer-based compile optimizations for NN accelerators. From top to bottom, we define a type of computational graph, carrying necessary information such as relationship between layer nodes and data nodes. Then according to the pattern of a NN layer computation process, we apply an intra layer loop unrolling and pipelining, including fine-grained and coarse-grained two levels. Similarly, we apply layer fusion optimization based on our computational graph and abstract pipelining stage. After expanding pipelining stages of layers, we can reduce some redundant IO operations, which we call it layer elimination optimization. The experiment results show that with our proposed optimizations the inference process can achieve up to 1.34x speedup than not using fusion optimization.
- Published
- 2019
- Full Text
- View/download PDF
39. Predicting the Digestive Tract Development and Growth Performance of Goat Kids Using Sigmoidal Models
- Author
-
Yanliang Bi, Kai Cui, Yimin Zhuang, Naifeng Zhang, and M. M. Abdelsattar
- Subjects
lcsh:Veterinary medicine ,Coefficient of determination ,rumen development ,General Veterinary ,Omasum ,area under the curve ,Monogastric ,Gompertz function ,Growth curve (biology) ,goat kids ,Abomasum ,Article ,Rumen ,Animal science ,inflection point ,lcsh:Zoology ,lcsh:SF600-1100 ,Animal Science and Zoology ,lcsh:QL1-991 ,Reticulum ,growth curve ,Mathematics - Abstract
The transition from monogastric to rumination stage is crucial in ruminants’ growth to avoid stressors—weaning and neonatal mortalities. Poor growth of the digestive tract could adversely affect the performance of the animal. Modeling informative growth curves is of great importance for a better understanding of the effective development pattern, in order to optimize feeding management system, and to achieve more production efficiency. However, little is known about the digestive tract growth curves. For this reason, one big goat farm of Laiwu black breed was chosen as a basis of this study. Forty-eight kids belonging to eight-time points (1, 7, 14, 28, 42, 56, 70, and 84 d, 6 kids for each) were selected and slaughtered. The body weight, body size indices, rumen pH, and stomach parts were determined and fitted to the polynomial and sigmoidal models. In terms of goodness of fit criteria, the Gompertz model was the best model for body weight, body oblique length, tube, and rumen weight. Moreover, the Logistic model was the best model for carcass weight, body height, and chest circumference. In addition, the Quadratic model showed the best fit for dressing percentage, omasum weight, abomasum weight, and rumen volume. Moreover, the cubic model best fitted the ruminal pH and reticulum percentage. The Weibull model was the best model for the reticulum weight and omasum percentage, while the MMF model was the best model describing the growth of chest depth, rumen percentage, and abomasum percentage. The model parameters, R squared, inflection points, area under curve varied among the different dependent variables. The Pearson correlation showed that the digestive tract development was more correlated with age than body weight, but the other variables were more correlated with body weight than age. The study demonstrated the use of empirical sigmoidal and polynomial models to predict growth rates of the digestive tract at relevant age efficiently.
- Published
- 2021
- Full Text
- View/download PDF
40. The Signature Microbiota Drive Rumen Function Shifts in Goat Kids Introduced to Solid Diet Regimes
- Author
-
Naifeng Zhang, Yimin Zhuang, Wenqin Huang, Chai Jianmin, Qiyu Diao, and Xiaokang Lv
- Subjects
Microbiology (medical) ,goats ,Protein metabolism ,Butyrate ,Biology ,Microbiology ,Article ,03 medical and health sciences ,Rumen ,chemistry.chemical_compound ,Nutrient ,Virology ,rumen microbiota ,Prevotella ,Microbiome ,Food science ,lcsh:QH301-705.5 ,030304 developmental biology ,chemistry.chemical_classification ,0303 health sciences ,neutral detergent fibers ,rumen development ,030306 microbiology ,volatile fatty acids ,Fatty acid ,biology.organism_classification ,lcsh:Biology (General) ,chemistry ,Propionate ,solid diet - Abstract
The feeding regime of early, supplementary solid diet improved rumen development and production in goat kids. However, the signature microbiota responsible for linking dietary regimes to rumen function shifts are still unclear. This work analyzed the rumen microbiome and functions affected by an early solid diet regime using a combination of machine learning algorithms. Volatile fatty acids (i.e., acetate, propionate and butyrate) fermented by microbes were found to increase significantly in the supplementary solid diet groups. Predominant genera were found to alter significantly from unclassified Sphingobacteriaceae (non-supplementary group) to Prevotella (supplementary solid diet groups). Random Forest classification model revealed signature microbiota for solid diet that positively correlated with macronutrient intake, and linearly increased with volatile fatty acid production. Bacteria associated with carbohydrate and protein metabolism were also identified. Utilization of a Fish Taco analysis portrayed a set of intersecting core species contributed to rumen function shifts by the solid diet regime. The core community structures consisted of the specific, signature microbiota and the manipulation of their symbiotic partners are manipulated by extra nutrients from concentrate and/or forage, and then produce more volatile fatty acids to promote rumen development and functions eventually host development. Our study provides mechanisms of the microbiome governed by a solid diet regime early in life, and highlights the signature microbiota involved in animal health and production.
- Published
- 2019
- Full Text
- View/download PDF
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