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Ma T. et al. (2019) Altered mucosa-associated microbiota in the ileum and colon of neonatal calves in response to delayed first colostrum feeding. J Dairy Sci. In press.
Li F. et al. (2019) Host genetics influence the rumen microbiota and heritable rumen microbial features associate with feed efficiency in cattle. Microbiome. 7, 92.
Sun H.-Z. et al. (2019) Invited review: Advances and challenges in application of feedomics to improve dairy cow production and health. J Dairy Sci. 102(7), 5853-5870.
Li F. et al. (2019) Comparative metagenomic and metatranscriptomic analyses reveal the breed effect on the rumen microbiome and its associations with feed efficiency in beef cattle. Microbiome.7, 6.
Sun H.-Z. et al. (2019) A collection of rumen bacteriome data from 334 mid-lactation dairy cows. Sci Data. 6, 180301.
Malmuthuge N. et al. (2019) Taxonomic and functional composition of the small intestinal microbiome in neonatal calves provide a framework for understanding early life gut health. Appl Environ Microb. 02534-18.
Song Y. et al. (2018) Colostrum feeding shapes the hindgut microbiota of dairy calves during the first 12 h of life. FEMS Microbiol Ecol. 95, 1.
Xue M. et al. (2018) Assessment of rumen microbiota from a large cattle cohort reveals the pan and core bacteriome contributing to varied phenotypes. Appl Environ Microb. 00970-00918.
Xie X. et al. (2018) Persistence of cellulolytic bacteria Fibrobacter and Treponema after short-term corn stover-based dietary intervention reveals the potential to improve rumen fibrolytic function. Front Microbiol, 9.
Yang B. et al. (2018) Alfalfa Intervention Alters Rumen Microbial Community Development in Hu Lambs During Early Life. Front Microbiol, 9, 574.
Zhou M. et al. (2018) Assessment of microbiome changes after rumen transfaunation: implications on improving feed efficiency in beef cattle. Microbiome, 6(1), 62.
Zhou M. et al. (2018) Air-Dried Brown Seaweed, Ascophyllum nodosum, Alters the Rumen Microbiome in a Manner That Changes Rumen Fermentation Profiles and Lowers the Prevalence of Foodborne Pathogens. mSphere, 3(1), e00017-00018.
Song Y. et al. (2017) Shift of hindgut microbiota and microbial short chain fatty acids profiles in dairy calves from birth to pre-weaning. FEMS Microbiol Ecol, 94(3), fix179.
Neves A.L. et al. (2017) Enhancing the Resolution of Rumen Microbial Classification from Metatranscriptomic Data Using Kraken and Mothur. Front Microbiol, 8, 2445.
Kouritzin et al. (2017) The colonization and establishment of the neonatal mammalian microbiome. Fine Focus, 89.
Jiao J. et al. (2017) Shifts in Host Mucosal Innate Immune Function Are Associated with Ruminal Microbial Succession in Supplemental Feeding and Grazing Goats at Different Ages. Front Microbiol, 8, 1655.
Fouhse J.M. et al. (2017) Host Immune Selection of Rumen Bacteria through Salivary Secretory IgA. Front Microbiol, 8, 848.
Malmuthuge N. (2017) Understanding the gut microbiome of dairy calves: Opportunities to improve early-life gut health. J Dairy Sci, 100(7), 5996-6005.
Li F. (2017) Metatranscriptomic profiling reveals linkages between the active rumen microbiome and feed efficiency in beef cattle. Appl Environ Microb. 00061-00017.
AlZahal O. et al. (2017) Factors influencing ruminal bacterial community diversity and composition and microbial fibrolytic enzyme abundance in lactating dairy cows with a focus on the role of active dry yeast. J Dairy Sci, 100(6), 4377-4393.
Heo J. et al. (2016) Gut microbiota modulated by probiotics and Garcinia cambogia extract correlate with weight gain and adipocyte sizes in high fat-fed mice. Sci Rep-UK, 6, 33566.
Li F. et al. (2016) Taxonomic assessment of rumen microbiota using total RNA and targeted amplicon sequencing approaches. Front Microbiol, 7, 987.
Malmuthuge N.Guan L.L. (2016) Gut microbiome and omics: a new definition to ruminant production and health. Anim Front, 6(2), 8-12.
Malmuthuge N. et al. (2015) Heat-treated colostrum feeding promotes beneficial bacteria colonization in the small intestine of neonatal calves. J Dairy Sci, 98(11), 8044-8053.
Lee S. et al. (2015) The effect of anaerobic fungal inoculation on the fermentation characteristics of rice straw silages. J Appl Microbiol, 118(3), 565-573.
Zhou M. et al. (2014) Methanogen prevalence throughout the gastrointestinal tract of pre-weaned dairy calves. Gut Microbes, 5(5), 628-638.
Malmuthuge N.Griebel P.J. (2014) Taxonomic identification of commensal bacteria associated with the mucosa and digesta throughout the gastrointestinal tract of pre-weaned calves. Appl Environ Microb. 03864-03813.
Sun H.-Z. et al. (2019) MicroRNA expression profiles across blood and different tissues in cattle. Sci Data, 6, 190013.
Zhao K. et al. (2016) Comparative miRNAome analysis revealed different miRNA expression profiles in bovine sera and exosomes. BMC Genomics, 17(1), 630.
Liang G. et al. (2016) Altered microRNA expression and pre-mRNA splicing events reveal new mechanisms associated with early stage Mycobacterium avium subspecies paratuberculosis infection. Sci Rep-UK, 6, 24964.
Wang D. et al. (2016) Systematic microRNAome profiling reveals the roles of microRNAs in milk protein metabolism and quality: insights on low-quality forage utilization. Sci Rep-UK, 6, 21194.
Bao H. et al. (2015) Genome-wide whole blood microRNAome and transcriptome analyses reveal miRNA-mRNA regulated host response to foodborne pathogen Salmonella infection in swine. Sci Rep-UK, 5, 12620.
Guan Y. et al. (2015) Roles of small RNAs in the effects of nutrition on apoptosis and spermatogenesis in the adult testis. Sci Rep-UK, 5, 10372.
Liang G. et al. (2015) Model systems to analyze the role of miRNAs and commensal microflora in bovine mucosal immune system development. Mol Immunol, 66(1), 57-67.
Meale S. et al. (2014) Effect of diet on microRNA expression in ovine subcutaneous and visceral adipose tissues. J Anim Sci, 92(8), 3328-3337.
Bao H. et al. (2014) MicroRNA buffering and altered variance of gene expression in response to Salmonella infection. PLoS One, 9(4), e94352.
Liang G. et al. (2014) Potential regulatory role of microRNAs in the development of bovine gastrointestinal tract during early life. PLoS One, 9(3), e92592.
Jin W. et al. (2014) Transcriptome microRNA profiling of bovine mammary epithelial cells challenged with Escherichia coli or Staphylococcus aureus bacteria reveals pathogen directed microRNA expression profiles. BMC Genomics, 15(1), 181.
Romao J.M. et al. (2014) MicroRNAs in bovine adipogenesis: genomic context, expression and function. BMC Genomics, 15(1), 137.
Sun H.-Z. et al. (2018) Landscape of multi-tissue global gene expression reveals the regulatory signatures of feed efficiency in beef cattle. Bioinformatics, byt883.
He. Z. et al. (2018) Genome wide transcriptome analysis provides bases on colonic mucosal immune system development affected by colostrum feeding strategies in neonatal calves. BMC Genomics, 19, 635.
Zhao K. et al. (2017) Transcriptome analysis of ruminal epithelia revealed potential regulatory mechanisms involved in host adaptation to gradual high fermentable dietary transition in beef cattle. BMC Genomics, 18(1), 976.
Wang O. et al. (2017) Host mechanisms involved in cattle Escherichia coli O157 shedding: a fundamental understanding for reducing foodborne pathogen in food animal production. Sci Rep-UK, 7(1), 7630.
Ye M. et al. (2017) Comparative transcriptomic analysis of porcine peripheral blood reveals differentially expressed genes from the cytokine–cytokine receptor interaction pathway related to health status. Genome, 60(12), 1021-1028.
Wang B. et al. (2017) Effects of dietary physical or nutritional factors on morphology of rumen papillae and transcriptome changes in lactating dairy cows based on three different forage-based diets. BMC Genomics, 18(1), 353.
Kommadath A. et al. (2017) Genetic architecture of gene expression underlying variation in host response to porcine reproductive and respiratory syndrome virus infection. Sci Rep-UK, 7, 46203.
Liang G. et al. (2016) Transcriptome analysis reveals regional and temporal differences in mucosal immune system development in the small intestine of neonatal calves. BMC Genomics, 17(1), 602.
Kong R.S. et al. (2016) Transcriptome profiling of the rumen epithelium of beef cattle differing in residual feed intake. BMC Genomics 17(1), 592.
Wang O. et al. (2016) Comparative transcriptomic analysis of rectal tissue from beef steers revealed reduced host immunity in Escherichia coli O157: H7 super-shedders. PLoS One, 11(3), e0151284.
Choi I. et al. (2014) Increasing gene discovery and coverage using RNA-seq of globin RNA reduced porcine blood samples. BMC Genomics, 15(1), 954.
David J. et al. (2014) Gene-expression profiling of calves 6 and 9 months after inoculation with Mycobacterium avium subspecies paratuberculosis. Vet Res, 45(1), 96.
Kommadath A. et al. (2014) Gene co-expression network analysis identifies porcine genes associated with variation in Salmonella shedding. BMC Genomics, 15(1), 452.
David J. et al. (2014) Gene expression profiling and putative biomarkers of calves 3 months after infection with Mycobacterium avium subspecies paratuberculosis. Vet Immunl Immunop, 160(1-2), 107-117.
Wu X. et al. (2018) Serum metabolome profiling revealed potential biomarkers for milk protein yield in dairy cows. J Proteomics.
Wang B. et al. (2018) Arteriovenous blood metabolomics: An efficient method to determine the key metabolic pathway for milk synthesis in the intra-mammary gland. Sci Rep-UK, 8(1), 5598.
Li Z. et al. (2018) The Development of Microbiota and Metabolome in Small Intestine of Sika Deer (Cervus nippon) from Birth to Weaning. Front Microbiol, 9, 4.
Sun H.-Z. et al. (2015) Metabolomics of four biofluids from dairy cows: potential biomarkers for milk production and quality. J Proteome Res, 14(2), 1287-1298.