Philip Griebel | University of Saskatchewan (original) (raw)

Papers by Philip Griebel

Research paper thumbnail of Bovine Mucosal Vaccines: Challenges and Opportunities

Veterinary Vaccines: Current Innovations and Future Trends, 2020

Research paper thumbnail of Effects of lipopolysaccharide exposure in primary bovine ruminal epithelial cells

Journal of Dairy Science, 2020

Research paper thumbnail of 23 Differential microRNA expression in jejunal tissue and jejunal lymph nodes following naturally occurring Mycobacterium avium subspecies paratuberculosis infection in Holstein cows

Journal of Animal Science, 2019

Mycobacterium avium subsp. Paratuberculosis (MAP) is the causal agent of Johne’s disease (JD), a ... more Mycobacterium avium subsp. Paratuberculosis (MAP) is the causal agent of Johne’s disease (JD), a chronic intestinal disease affecting ruminants worldwide. This study investigated miRNA expression in jejunal intestine (JE) and jejunal lymph nodes (JELN), and the potential regulatory roles of miRNAs during JD progression. JE and JELN tissues were collected from 5 MAP positive (JD subclinical stage) Holstein cows and 5 MAP negative cows. Following miRNA sequencing, bioinformatic processing with a standard pipeline and functional analysis with ClueGo, 272 and 333 miRNAs were identified in JE and JELN, respectively. Compared with MAP negative cows, 13 and 71 miRNAs were differently expressed (DE) (P < 0.05) in MAP infected JE and JELN, respectively. The most up-regulated and down-regulated miRNAs were bta-miR-485 (fold change = 6.18) and bta-miR-451 (fold change = -6.81), and bta-miR-331-5p (fold change = 35.56) and bta-miR-2285bk (fold change = -61.25) in JE and JELN, respectively. I...

Research paper thumbnail of A dendritic cell-targeted chimeric hepatitis B virus immunotherapeutic vaccine induces both cellular and humoral immune responses in vivo

Human Vaccines & Immunotherapeutics, 2019

Research paper thumbnail of Identification of circulating lineage-negative type-I IFN producing plasmacytoid dendritic cell-like cells in the bovine blood

Veterinary Immunology and Immunopathology, 2009

Research paper thumbnail of Phenotype and function of stromal cells cloned from the ileal peyer's patch of sheep

Research paper thumbnail of Ileal and jejunal Peyer’s patches play distinct roles in mucosal immunity of sheep

Immunology, 1999

The majority of pathogens enter the body through mucosal surfaces and it is now evident that muco... more The majority of pathogens enter the body through mucosal surfaces and it is now evident that mucosal immunity can provide effective disease protection. However, the induction of mucosal immunity will require efficient targeting of mucosal vaccines to appropriate mucosa‐associated lymphoid tissue. An animal model, based upon the surgical preparation of sterile intestinal ‘loops’ (blind‐ended segments of intestine), was developed to evaluate mucosal and systemic immune responses to enteric vaccines in ruminants. The effectiveness of end‐to‐end intestinal anastomoses was evaluated and fetal surgery did not disrupt normal intestinal function in lambs up to 6–7 months after birth. The immunological competence of Peyer’s patches (PP) within the intestinal ‘loops’ was evaluated with a human adenovirus 5 vector expressing the gD gene of bovine herpesvirus‐1. This vaccine vector induced both mucosal and systemic immune responses when injected into intestinal ‘loops’ of 5–6‐week‐old lambs. An...

Research paper thumbnail of Induction of interferon and interferon-induced antiviral effector genes following a primary bovine herpesvirus-1 (BHV-1) respiratory infection

Journal of General Virology, Jul 1, 2017

Research paper thumbnail of Tissue- and age-dependent expression of the bovine DEFB103 gene and protein

Cell and Tissue Research, Aug 25, 2015

Beta-defensin 103 (DEFB103) shares little homology with 8 other members of the bovine beta-defens... more Beta-defensin 103 (DEFB103) shares little homology with 8 other members of the bovine beta-defensin family and in other species DEFB103 protein has diverse functions, including antimicrobial activity, a chemoattractant for dendritic cells, enhancing epithelial wound repair and regulating hair colour. Expression of the bovine DEFB103 gene was surveyed in 27 tissues and transcript was most abundant in tissues with stratified squamous epithelium. Oral cavity epithelial tissues and nictitating membrane consistently expressed high levels of DEFB103 gene transcript. An age-dependent decrease (P &amp;amp;lt; 0.05) in DEFB103 gene expression was only observed for buccal epithelium when comparing healthy 10- to 14-day-old and 10- to 12-month-old calves. A bovine herpesvirus-1 respiratory infection did, however, significantly (P &amp;amp;lt; 0.05) up-regulate DEFB103 gene expression in the buccal epithelium of 6- to 8-month-old calves. Finally, DEFB103 transcript was low in lymph nodes draining the skin and at the limit of detection in other internal organs such as lung, intestine and kidney. Affinity-purified rabbit antisera to bovine DEFB103 was used to identify cells expressing DEFB103 protein within tissues with stratified squamous epitheliums. DEFB103 protein was most abundant in basal epithelial cells and was present in these cells prior to birth. Beta-defensins have been identified as regulators of dendritic cell (DC) chemokine responses and we observed a close association between DCs and epithelial cells expressing DEFB103 in both the fetus and newborn calf. In conclusion, bovine DEFB103 gene expression is most abundant in stratified squamous epithelium with DEFB103 protein localised to basal epithelial cells. These observations are consistent with proposed roles for DEFB103 in DC recruitment and repair of stratified squamous epithelium.

Research paper thumbnail of Passively acquired membrane proteins alter the functional capacity of bovine polymorphonuclear cells

Journal of Leukocyte Biology, Jun 22, 2006

Research paper thumbnail of Comparative analysis of innate immune responses following infection of newborn calves with bovine rotavirus and bovine coronavirus

Journal of General Virology, Oct 1, 2007

Research paper thumbnail of Activation and Regulation of Toll-like Receptor 9: CpGs and Beyond

Mini-reviews in Medicinal Chemistry, Jun 1, 2008

Research paper thumbnail of Identification of a new non-coding exon and haplotype variability in the cattle DEFB103 gene

Research paper thumbnail of No association between β-Defensin 103B (DEFB103B) single nucleotide polymorphisms (SNPs) or haplotypes and Staphylococcus aureus mastitis in Holstein cattle

Proceedings of the World Congress on Genetics Applied to Livestock Production, Aug 21, 2014

Research paper thumbnail of Interferon-gamma and B-cell Activating Factor (BAFF) promote bovine B cell activation independent of TLR9 and T-cell signaling

Veterinary Immunology and Immunopathology, 2012

We previously reported that CD21(+) B cells purified from bovine blood do not respond to CpG-ODN ... more We previously reported that CD21(+) B cells purified from bovine blood do not respond to CpG-ODN stimulation unless either CD14(+) monocytes or B-cell Activating Factor (BAFF), a cytokine produced by activated monocytes, are present. In this report, we present evidence that CD14(+) monocytes are critical for CpG-specific lymphocyte proliferation within the peripheral blood mononuclear cell (PBMC) population but that this response is not mediated by soluble factors produced by CpG-activated monocytes. We further determine that bovine monocytes stimulated with IFN-γ induce expression of the BAFF gene and that recombinant IFN-γ and BAFF induced robust B cell activation when cultured in the absence of CpG ODN. These data suggest that CpG-stimulated monocytes may indirectly promote B cell activation by promoting release of cytokines and/or other soluble factors from accessory cells which in turn act on CpG-stimulated B cells to promote antigen-independent and T cell independent B cell activation. Understanding the T cell independent signals that induce B cell activation has important implications for understanding B cell development in locations where T cells are limited and in understanding polyclonal B cell activation that may contribute to autoimmune diseases.

Research paper thumbnail of EPIphany—A Platform for Analysis and Visualization of Peptide Immunoarray Data

Frontiers in Bioinformatics

Antibodies are critical effector molecules of the humoral immune system. Upon infection or vaccin... more Antibodies are critical effector molecules of the humoral immune system. Upon infection or vaccination, populations of antibodies are generated which bind to various regions of the invading pathogen or exogenous agent. Defining the reactivity and breadth of this antibody response provides an understanding of the antigenic determinants and enables the rational development and assessment of vaccine candidates. High-resolution analysis of these populations typically requires advanced techniques such as B cell receptor repertoire sequencing, mass spectrometry of isolated immunoglobulins, or phage display libraries that are dependent upon equipment and expertise which are prohibitive for many labs. High-density peptide microarrays representing diverse populations of putative linear epitopes (immunoarrays) are an effective alternative for high-throughput examination of antibody reactivity and diversity. While a promising technology, widespread adoption of immunoarrays has been limited by ...

Research paper thumbnail of Adrenergic receptor gene expression in bovine leukocytes

Developmental & Comparative Immunology, 2021

The α- and β-adrenergic receptors (ARs) bind the stress hormones epinephrine (E), norepinephrine ... more The α- and β-adrenergic receptors (ARs) bind the stress hormones epinephrine (E), norepinephrine (NE), and dopamine and activate diverse physiological responses. A lack of information on AR gene expression in leukocytes limits our understanding of how stress alters immune function. Quantitative analyses of AR gene expression was completed for bovine leukocytes. Individual leukocyte lineages and subpopulations within lineages were isolated with high-speed cell sorting to facilitate a targeted analysis of AR gene expression. These analyses confirmed all 9 AR genes were expressed in bovine leukocytes with marked differences in AR gene expression when comparing among leukocyte lineages. Furthermore, separation of polymorphonuclear cells into neutrophils and eosinophils revealed these key innate immune cells also differ significantly in AR gene expression. This study provides the first comprehensive survey of AR gene expression in immune cells of any mammalian species and provides insight into conflicting reports that stress can either activate or suppress immune function.

Research paper thumbnail of Kinome profiling of peripheral blood mononuclear cells collected prior to vaccination reveals biomarkers and potential mechanisms of vaccine unresponsiveness in pigs

Scientific Reports, 2020

Inter-individual variance in host immune responses following vaccination can result in failure to... more Inter-individual variance in host immune responses following vaccination can result in failure to develop protective immunity leaving individuals at risk for infection in addition to compromising herd immunity. While developing more efficacious vaccines is one strategy to mitigate this problem, predicting vaccine responsiveness prior to vaccination could inform which individuals require adjunct disease management strategies. To identify biomarkers of vaccine responsiveness, a cohort of pigs (n = 120) were vaccinated and pigs representing the high (n = 6; 90th percentile) and low (n = 6; 10th percentile) responders based on vaccine-specific antibody responses following vaccination were further analyzed. Kinase-mediated phosphorylation events within peripheral blood mononuclear cells collected prior to vaccination identified 53 differentially phosphorylated peptides when comparing low responders with high responders. Functional enrichment analysis revealed pro-inflammatory cytokine si...

Research paper thumbnail of Kinome Analysis of Honeybee (Apis mellifera L.) Dark-Eyed Pupae Identifies Biomarkers and Mechanisms of Tolerance to Varroa Mite Infestation

Scientific Reports, 2020

The mite Varroa destructor is a serious threat to honeybee populations. Selective breeding for Va... more The mite Varroa destructor is a serious threat to honeybee populations. Selective breeding for Varroa mite tolerance could be accelerated by biomarkers within individual bees that could be applied to evaluate a colony phenotype. Previously, we demonstrated differences in kinase-mediated signaling between bees from colonies of extreme phenotypes of mite susceptibility. We expand these findings by defining a panel of 19 phosphorylation events that differ significantly between individual pupae from multiple colonies with distinct Varroa mite tolerant phenotypes. The predictive capacity of these biomarkers was evaluated by analyzing uninfested pupae from eight colonies representing a spectrum of mite tolerance. The pool of biomarkers effectively discriminated individual pupae on the basis of colony susceptibility to mite infestation. Kinome analysis of uninfested pupae from mite tolerant colonies highlighted an increased innate immune response capacity. The implication that differences ...

Research paper thumbnail of Taxonomic and Functional Compositions of the Small Intestinal Microbiome in Neonatal Calves Provide a Framework for Understanding Early Life Gut Health

Applied and Environmental Microbiology, 2019

Dietary interventions to manipulate neonatal gut microbiota have been proposed to generate long-t... more Dietary interventions to manipulate neonatal gut microbiota have been proposed to generate long-term impacts on hosts. Currently, our understanding of the early gut microbiome of neonatal calves is limited to 16S rRNA gene amplicon based microbial profiling, which is a barrier to developing dietary interventions to improve calf gut health. The use of a metagenome sequencing-based approach in the present study revealed high individual animal variation in taxonomic and functional abundance of intestinal microbiome and potential impacts of early microbiome on mucosal immune responses during the preweaning period. During this developmental period, age- and diet-related changes in microbial diversity, richness, density, and the abundance of taxa and functions were observed. A correlation-based approach to further explore the individual animal variation revealed potential enterotypes that can be linked to calf gut health, which may pave the way to developing strategies to manipulate the m...

Research paper thumbnail of Bovine Mucosal Vaccines: Challenges and Opportunities

Veterinary Vaccines: Current Innovations and Future Trends, 2020

Research paper thumbnail of Effects of lipopolysaccharide exposure in primary bovine ruminal epithelial cells

Journal of Dairy Science, 2020

Research paper thumbnail of 23 Differential microRNA expression in jejunal tissue and jejunal lymph nodes following naturally occurring Mycobacterium avium subspecies paratuberculosis infection in Holstein cows

Journal of Animal Science, 2019

Mycobacterium avium subsp. Paratuberculosis (MAP) is the causal agent of Johne’s disease (JD), a ... more Mycobacterium avium subsp. Paratuberculosis (MAP) is the causal agent of Johne’s disease (JD), a chronic intestinal disease affecting ruminants worldwide. This study investigated miRNA expression in jejunal intestine (JE) and jejunal lymph nodes (JELN), and the potential regulatory roles of miRNAs during JD progression. JE and JELN tissues were collected from 5 MAP positive (JD subclinical stage) Holstein cows and 5 MAP negative cows. Following miRNA sequencing, bioinformatic processing with a standard pipeline and functional analysis with ClueGo, 272 and 333 miRNAs were identified in JE and JELN, respectively. Compared with MAP negative cows, 13 and 71 miRNAs were differently expressed (DE) (P < 0.05) in MAP infected JE and JELN, respectively. The most up-regulated and down-regulated miRNAs were bta-miR-485 (fold change = 6.18) and bta-miR-451 (fold change = -6.81), and bta-miR-331-5p (fold change = 35.56) and bta-miR-2285bk (fold change = -61.25) in JE and JELN, respectively. I...

Research paper thumbnail of A dendritic cell-targeted chimeric hepatitis B virus immunotherapeutic vaccine induces both cellular and humoral immune responses in vivo

Human Vaccines & Immunotherapeutics, 2019

Research paper thumbnail of Identification of circulating lineage-negative type-I IFN producing plasmacytoid dendritic cell-like cells in the bovine blood

Veterinary Immunology and Immunopathology, 2009

Research paper thumbnail of Phenotype and function of stromal cells cloned from the ileal peyer's patch of sheep

Research paper thumbnail of Ileal and jejunal Peyer’s patches play distinct roles in mucosal immunity of sheep

Immunology, 1999

The majority of pathogens enter the body through mucosal surfaces and it is now evident that muco... more The majority of pathogens enter the body through mucosal surfaces and it is now evident that mucosal immunity can provide effective disease protection. However, the induction of mucosal immunity will require efficient targeting of mucosal vaccines to appropriate mucosa‐associated lymphoid tissue. An animal model, based upon the surgical preparation of sterile intestinal ‘loops’ (blind‐ended segments of intestine), was developed to evaluate mucosal and systemic immune responses to enteric vaccines in ruminants. The effectiveness of end‐to‐end intestinal anastomoses was evaluated and fetal surgery did not disrupt normal intestinal function in lambs up to 6–7 months after birth. The immunological competence of Peyer’s patches (PP) within the intestinal ‘loops’ was evaluated with a human adenovirus 5 vector expressing the gD gene of bovine herpesvirus‐1. This vaccine vector induced both mucosal and systemic immune responses when injected into intestinal ‘loops’ of 5–6‐week‐old lambs. An...

Research paper thumbnail of Induction of interferon and interferon-induced antiviral effector genes following a primary bovine herpesvirus-1 (BHV-1) respiratory infection

Journal of General Virology, Jul 1, 2017

Research paper thumbnail of Tissue- and age-dependent expression of the bovine DEFB103 gene and protein

Cell and Tissue Research, Aug 25, 2015

Beta-defensin 103 (DEFB103) shares little homology with 8 other members of the bovine beta-defens... more Beta-defensin 103 (DEFB103) shares little homology with 8 other members of the bovine beta-defensin family and in other species DEFB103 protein has diverse functions, including antimicrobial activity, a chemoattractant for dendritic cells, enhancing epithelial wound repair and regulating hair colour. Expression of the bovine DEFB103 gene was surveyed in 27 tissues and transcript was most abundant in tissues with stratified squamous epithelium. Oral cavity epithelial tissues and nictitating membrane consistently expressed high levels of DEFB103 gene transcript. An age-dependent decrease (P &amp;amp;lt; 0.05) in DEFB103 gene expression was only observed for buccal epithelium when comparing healthy 10- to 14-day-old and 10- to 12-month-old calves. A bovine herpesvirus-1 respiratory infection did, however, significantly (P &amp;amp;lt; 0.05) up-regulate DEFB103 gene expression in the buccal epithelium of 6- to 8-month-old calves. Finally, DEFB103 transcript was low in lymph nodes draining the skin and at the limit of detection in other internal organs such as lung, intestine and kidney. Affinity-purified rabbit antisera to bovine DEFB103 was used to identify cells expressing DEFB103 protein within tissues with stratified squamous epitheliums. DEFB103 protein was most abundant in basal epithelial cells and was present in these cells prior to birth. Beta-defensins have been identified as regulators of dendritic cell (DC) chemokine responses and we observed a close association between DCs and epithelial cells expressing DEFB103 in both the fetus and newborn calf. In conclusion, bovine DEFB103 gene expression is most abundant in stratified squamous epithelium with DEFB103 protein localised to basal epithelial cells. These observations are consistent with proposed roles for DEFB103 in DC recruitment and repair of stratified squamous epithelium.

Research paper thumbnail of Passively acquired membrane proteins alter the functional capacity of bovine polymorphonuclear cells

Journal of Leukocyte Biology, Jun 22, 2006

Research paper thumbnail of Comparative analysis of innate immune responses following infection of newborn calves with bovine rotavirus and bovine coronavirus

Journal of General Virology, Oct 1, 2007

Research paper thumbnail of Activation and Regulation of Toll-like Receptor 9: CpGs and Beyond

Mini-reviews in Medicinal Chemistry, Jun 1, 2008

Research paper thumbnail of Identification of a new non-coding exon and haplotype variability in the cattle DEFB103 gene

Research paper thumbnail of No association between β-Defensin 103B (DEFB103B) single nucleotide polymorphisms (SNPs) or haplotypes and Staphylococcus aureus mastitis in Holstein cattle

Proceedings of the World Congress on Genetics Applied to Livestock Production, Aug 21, 2014

Research paper thumbnail of Interferon-gamma and B-cell Activating Factor (BAFF) promote bovine B cell activation independent of TLR9 and T-cell signaling

Veterinary Immunology and Immunopathology, 2012

We previously reported that CD21(+) B cells purified from bovine blood do not respond to CpG-ODN ... more We previously reported that CD21(+) B cells purified from bovine blood do not respond to CpG-ODN stimulation unless either CD14(+) monocytes or B-cell Activating Factor (BAFF), a cytokine produced by activated monocytes, are present. In this report, we present evidence that CD14(+) monocytes are critical for CpG-specific lymphocyte proliferation within the peripheral blood mononuclear cell (PBMC) population but that this response is not mediated by soluble factors produced by CpG-activated monocytes. We further determine that bovine monocytes stimulated with IFN-γ induce expression of the BAFF gene and that recombinant IFN-γ and BAFF induced robust B cell activation when cultured in the absence of CpG ODN. These data suggest that CpG-stimulated monocytes may indirectly promote B cell activation by promoting release of cytokines and/or other soluble factors from accessory cells which in turn act on CpG-stimulated B cells to promote antigen-independent and T cell independent B cell activation. Understanding the T cell independent signals that induce B cell activation has important implications for understanding B cell development in locations where T cells are limited and in understanding polyclonal B cell activation that may contribute to autoimmune diseases.

Research paper thumbnail of EPIphany—A Platform for Analysis and Visualization of Peptide Immunoarray Data

Frontiers in Bioinformatics

Antibodies are critical effector molecules of the humoral immune system. Upon infection or vaccin... more Antibodies are critical effector molecules of the humoral immune system. Upon infection or vaccination, populations of antibodies are generated which bind to various regions of the invading pathogen or exogenous agent. Defining the reactivity and breadth of this antibody response provides an understanding of the antigenic determinants and enables the rational development and assessment of vaccine candidates. High-resolution analysis of these populations typically requires advanced techniques such as B cell receptor repertoire sequencing, mass spectrometry of isolated immunoglobulins, or phage display libraries that are dependent upon equipment and expertise which are prohibitive for many labs. High-density peptide microarrays representing diverse populations of putative linear epitopes (immunoarrays) are an effective alternative for high-throughput examination of antibody reactivity and diversity. While a promising technology, widespread adoption of immunoarrays has been limited by ...

Research paper thumbnail of Adrenergic receptor gene expression in bovine leukocytes

Developmental & Comparative Immunology, 2021

The α- and β-adrenergic receptors (ARs) bind the stress hormones epinephrine (E), norepinephrine ... more The α- and β-adrenergic receptors (ARs) bind the stress hormones epinephrine (E), norepinephrine (NE), and dopamine and activate diverse physiological responses. A lack of information on AR gene expression in leukocytes limits our understanding of how stress alters immune function. Quantitative analyses of AR gene expression was completed for bovine leukocytes. Individual leukocyte lineages and subpopulations within lineages were isolated with high-speed cell sorting to facilitate a targeted analysis of AR gene expression. These analyses confirmed all 9 AR genes were expressed in bovine leukocytes with marked differences in AR gene expression when comparing among leukocyte lineages. Furthermore, separation of polymorphonuclear cells into neutrophils and eosinophils revealed these key innate immune cells also differ significantly in AR gene expression. This study provides the first comprehensive survey of AR gene expression in immune cells of any mammalian species and provides insight into conflicting reports that stress can either activate or suppress immune function.

Research paper thumbnail of Kinome profiling of peripheral blood mononuclear cells collected prior to vaccination reveals biomarkers and potential mechanisms of vaccine unresponsiveness in pigs

Scientific Reports, 2020

Inter-individual variance in host immune responses following vaccination can result in failure to... more Inter-individual variance in host immune responses following vaccination can result in failure to develop protective immunity leaving individuals at risk for infection in addition to compromising herd immunity. While developing more efficacious vaccines is one strategy to mitigate this problem, predicting vaccine responsiveness prior to vaccination could inform which individuals require adjunct disease management strategies. To identify biomarkers of vaccine responsiveness, a cohort of pigs (n = 120) were vaccinated and pigs representing the high (n = 6; 90th percentile) and low (n = 6; 10th percentile) responders based on vaccine-specific antibody responses following vaccination were further analyzed. Kinase-mediated phosphorylation events within peripheral blood mononuclear cells collected prior to vaccination identified 53 differentially phosphorylated peptides when comparing low responders with high responders. Functional enrichment analysis revealed pro-inflammatory cytokine si...

Research paper thumbnail of Kinome Analysis of Honeybee (Apis mellifera L.) Dark-Eyed Pupae Identifies Biomarkers and Mechanisms of Tolerance to Varroa Mite Infestation

Scientific Reports, 2020

The mite Varroa destructor is a serious threat to honeybee populations. Selective breeding for Va... more The mite Varroa destructor is a serious threat to honeybee populations. Selective breeding for Varroa mite tolerance could be accelerated by biomarkers within individual bees that could be applied to evaluate a colony phenotype. Previously, we demonstrated differences in kinase-mediated signaling between bees from colonies of extreme phenotypes of mite susceptibility. We expand these findings by defining a panel of 19 phosphorylation events that differ significantly between individual pupae from multiple colonies with distinct Varroa mite tolerant phenotypes. The predictive capacity of these biomarkers was evaluated by analyzing uninfested pupae from eight colonies representing a spectrum of mite tolerance. The pool of biomarkers effectively discriminated individual pupae on the basis of colony susceptibility to mite infestation. Kinome analysis of uninfested pupae from mite tolerant colonies highlighted an increased innate immune response capacity. The implication that differences ...

Research paper thumbnail of Taxonomic and Functional Compositions of the Small Intestinal Microbiome in Neonatal Calves Provide a Framework for Understanding Early Life Gut Health

Applied and Environmental Microbiology, 2019

Dietary interventions to manipulate neonatal gut microbiota have been proposed to generate long-t... more Dietary interventions to manipulate neonatal gut microbiota have been proposed to generate long-term impacts on hosts. Currently, our understanding of the early gut microbiome of neonatal calves is limited to 16S rRNA gene amplicon based microbial profiling, which is a barrier to developing dietary interventions to improve calf gut health. The use of a metagenome sequencing-based approach in the present study revealed high individual animal variation in taxonomic and functional abundance of intestinal microbiome and potential impacts of early microbiome on mucosal immune responses during the preweaning period. During this developmental period, age- and diet-related changes in microbial diversity, richness, density, and the abundance of taxa and functions were observed. A correlation-based approach to further explore the individual animal variation revealed potential enterotypes that can be linked to calf gut health, which may pave the way to developing strategies to manipulate the m...