A computational approach to understanding maternal influences on the development of ruminant neonates

Donia, Mohamed

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https://hdl.handle.net/2142/132778 Copy

Description

Title

A computational approach to understanding maternal influences on the development of ruminant neonates

Author(s)

Donia, Mohamed

Issue Date

2025-11-25

Director of Research (if dissertation) or Advisor (if thesis)

Lowe, James F

Doctoral Committee Chair(s)

Lowe, James F

Committee Member(s)

• Aldridge , Brian M
• Zuckermann, Federico A
• Gaulke, Christopher A
• Laouar, Amale
• Jarosinski, Keith

Department of Study

Pathobiology

Discipline

VMS - Pathobiology

Degree Granting Institution

University of Illinois Urbana-Champaign

Degree Name

Ph.D.

Degree Level

Dissertation

Keyword(s)

• Maternal cells
• Colosturm
• Neonatal immune development
• snRNA-seq (single-nucleus RNA sequencing)
• Gut-associated lymphoid tissue (GALT)
• Fecal Microbiome
• Antimicrobial resistance
• Jejunal and ileal Peyer’s patches
• Immune programming
• immune tolerance
• Calves
• and Lambs.

Abstract

Ruminant neonates are inherently vulnerable to diseases because they are born immunologically naïve and agammaglobulinemic due to the synepitheliochorial placenta, which precludes the prenatal transfer of maternal immunoglobulins (IgGs) and immune cells. This vulnerability is further exacerbated by overlapping early-life health challenges, including metabolic, microbial, mucosal, and mental stress. Additionally, ruminant newborns possess limited energy and nutrient reserves within their bodies. Therefore, they rely on maternal support through the ingestion of colostrum to fulfill their immunological and nutritional needs. Colostrum is a late-gestation mammary gland secretion rich in immunoglobulins, growth factors, cytokines, and viable maternal cells, which help the newborns to bypass this critical developmental period. While the detrimental effects associated with the failure of passive transfer of colostral immunoglobulins on neonatal immunity and disease susceptibility are well established, the influence of colostral cells on neonatal immune development is often overlooked. Emerging evidence indicates that viable transcolostral maternal cell transfer provides sustained, active immunological support to developing neonates, rather than the transient passive antibody supply. Studies have also reported the pivotal role of colostral cells in early immune programming and the induction of immune tolerance. The absence or loss of this cellular transfer may have long-term consequences, including increased neonatal morbidity and mortality due to impaired immune competence against infectious diseases. Despite these critical functional roles, common colostrum management practices in livestock production systems, such as refrigeration, freezing, and pasteurization, often have an adverse impact on maternal cell viability, thereby diminishing their long-term immune benefits. In this dissertation, a refined ewe-twin lamb model was established to investigate the impact of maternal colostral cells on commercially relevant outcomes, including neonatal lamb growth and immune responses to routine husbandry-related health challenges. In this model, twin lambs born to the same ewe were randomly assigned to receive either cell-rich colostrum (CRC) or cell-free colostrum (CFC) derived from the same maternal source, ensuring identical exposure to soluble immune and nutritional factors while differing only in viable cell content. The research further employed a computational single-nucleus RNA sequencing (snRNA-seq) approach to investigate the impact of these maternal colostral cells on mucosal immune development at the cellular level. As a first step, the snRNA-seq framework was standardized and validated by characterizing regional differences in gut-associated lymphoid tissues (GALT) using a neonatal calf model. It was subsequently applied to the developed ewe-twin lamb model to characterize the complex cellular landscape of maternal cells in ovine colostrum and to elucidate their functional contributions to the mucosal health resilience in neonatal lambs. In particular, comparing the transcriptional profile and signaling networks of Peyer’s patches cells from the twin lambs that received either cell-rich or cell-free colostrum. Further research investigated another critical management factor influencing neonatal development, specifically, the impact of parenteral Ceftiofur administration on the developmental dynamics of the early-life fecal microbiota and antibiotic resistome in neonatal lambs. During our initial study, the ewe-twin lamb model was employed across two lambing seasons (n = 78) to evaluate the impact of maternal colostral cells on neonatal performance and commercially relevant outcomes. Twin lambs born to the same dam were randomly assigned to receive either CRC or CFC within 12 hours of birth. They were monitored for growth, post-castration wound healing, and fecal parasitic shedding during the early postnatal period. CRC-fed lambs demonstrated significantly improved post-castration healing scores at days 7, 35, and 42, along with lower swelling scores at days 7 and 35 compared to CFC-fed lambs. They also exhibited markedly reduced intestinal shedding of coccidia oocysts between days 63 and 70, which may reflect enhanced mucosal immune defense. Moreover, CRC-fed lambs displayed a favorable growth trajectory over the first 60 days of life, collectively indicating that the presence of viable maternal colostral cells contributes to improved tissue repair and mucosal protection in neonatal lambs. In the second study, the effects of a common management intervention, parenteral administration of Ceftiofur Crystalline Free Acid (CCFA), on early-life development were investigated. Shotgun metagenomic sequencing of fecal swabs collected from neonatal lambs at days 0, 7, 14, 28, and 56 of age revealed that a single CCFA injection induced a transient reduction in both alpha and beta microbial diversity and decreased the relative abundance of specific bacterial taxa, including Salmonella and Clostridiales, during the nursing period. Although the microbial community exhibited resilience and largely recovered by day 56, core taxa in CCFA-treated lambs harbored multiple antibiotic resistance genes (ARGs), most notably those conferring beta-lactam resistance, underscoring a persistent ecological consequence of early-life antibiotic exposure. The third study standardized the workflow and bioinformatic pipelines of high-resolution snRNA-seq, which were used to investigate its capability of identifying regional structural and functional specialization of the gut-associated lymphoid tissue (GALT) in a 3-day-old calf at two different anatomic locations: ileum and jejunum. Comparative analysis of the ileal (PPi) and jejunal (PPj) Peyer’s patches, along with their associated mesenteric (MLNi, MLNj) and pre-femoral (PF) lymph nodes as a non-mucosal lymphoid tissue, revealed distinct cellular and molecular features across intestinal regions. The ileal Peyer’s patches contained the highest proportion of B cells and exhibited elevated proliferative activity, particularly among B cell populations. Each anatomical site displayed a unique transcriptional and immune pathway signature, as well as specific, distinct intercellular communication networks, confirming strong regional specialization within the neonatal intestinal immune system. In the fourth study, snRNA-seq farmwork was employed to comprehensively characterize the cellular composition and functional landscape of ovine colostrum. The analysis revealed a highly heterogeneous population of cells, including multiple epithelial subtypes (secretory alveolar, specialized, and basal luminal), macrophages, dendritic cells (DCs), T cells, progenitor-like cells, and neuron-like cells. Specialized epithelial cells exhibited transcriptional enrichment in pathways related to tight junctions, cell adhesion, and barrier integrity, suggesting a key role in maintaining epithelial cohesion and selective permeability. In contrast, immune cell populations displayed activation of MAPK signaling, lysosomal activity, and antigen presentation pathways, consistent with functional readiness for immune defense. Notably, while most maternal colostral cells were in a non-proliferative state, T cells exhibited distinct mitotic activity. This active proliferative state suggests a functional relevance to neonatal immunity after ingestion by newborns. Together, the findings of this study provided a high-resolution identification of maternal colostral cells and highlighted their potential role as a biologically active component in colostrum, which may transfer functional maternal cellular signals to the neonatal tissues. Subsequently, in our final study, Peyer’s patches from neonatal twin lambs born to the same dam used in the fourth study were subjected to snRNA-seq workflow at Day 7 of age to investigate the influence of the maternally derived colostral cells in lambs fed either CRC or CFC. In addition, maternal colostral cells were computationally traced within the neonatal Peyer’s patches cell populations. The study showed that maternally derived T cells were trafficking exclusively to the jejunal Peyer’s patches (PPj) of the CRC lamb. These maternal T cells exhibited a distinct transcriptional profile associated with effector/memory-like states, strongly enriched for pathways linked to T cell receptor signaling and immune activation. CRC feeding orchestrates region-specific transcriptional programs: B cells, T cells, and enterocytes in CRC lambs, particularly in the jejunum, display robust transcriptional activation in pathways critical for adaptive immunity, including Th17 differentiation, B cell receptor signaling, and PD-1/PD-L1 signaling. Furthermore, CRC lambs showed a more extensive intercellular communication network, particularly in the jejunum, with signaling pathways that suggest enhanced epithelial-immune coordination, tolerance, and homeostasis. Collectively, the computational and high-resolution transcriptomic approach confirms that maternal colostral cells are active modulators that integrate into the neonatal mucosa, accelerate adaptive immune priming, and enhance epithelial integrity, thereby providing critical resilience against early-life health challenges. These findings provide empirical evidence supporting the adoption of colostrum management practices that preserve cell viability, thereby enhancing neonatal health, promoting optimal development, and potentially reducing neonatal mortality, ultimately improving animal welfare.

Graduation Semester

2025-12

Type of Resource

Thesis

Handle URL

https://hdl.handle.net/2142/132778

Copyright and License Information

Copyright 2025 Mohamed Donia

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