About

Morgan Farnell is a Professor, Associate Department Head, and Extension Program Leader in the Department of Poultry Science at Texas A&M University. He specializes in Avian Microbiology and Immunology, contributing to research and extension efforts within the field of poultry science. Farnell is a member of Texas A&M AgriLife, which encompasses the Texas A&M AgriLife Extension Service, Texas A&M AgriLife Research, and other related entities. His role involves leadership in poultry science education, research, and extension activities, supporting the development of knowledge and practices in poultry health and production.

Research topics

• Biology
• Medicine
• Immunology
• Computer Science
• Internal medicine
• Microbiology
• Biochemistry
• Chemistry
• Molecular biology
• Food science
• Environmental science
• Cell biology

Selected publications

• Evaluation of a prebiotic mannan-oligosaccharide on Salmonella Enteritidis cecal colonization and immune response of broiler chickens

  Poultry Science · 2025-10-01 · 1 citations

  articleOpen accessSenior authorCorresponding

  Salmonella causes 1.35 million cases of foodborne illness in the United States annually. We hypothesized that the administration of ActiveMOS®, a prebiotic mannan-oligosaccharide (MOS) product, would reduce Salmonella Enteritidis (SE) cecal colonization and improve immune function in young broilers. The objectives of this study were to assess the effects of MOS on SE cecal colonization, serum cytokines, lipopolysaccharide (LPS), and immunoglobulin M (IgM). This study consisted of two independent 14 d trials. Day-of-hatch broilers (n = 240/trial) were evenly distributed across eight floor pens and randomly assigned to four treatments. Treatments were as follows: control (0.0), 1.0, 1.5, and 2.0 kg of MOS/metric ton (MT) of feed. Broilers were orally gavaged with PBS for unchallenged treatments or SE for challenged treatments at 7 d of age. Birds were euthanized one week post gavage. Salmonella Enteritidis cecal colonization, serum pro-inflammatory cytokines- interferon gamma (IFNγ), interleukin-2 (IL-2), IL-6, IL-16, IL-21; anti-inflammatory/regulatory cytokines- IFNα, IL-10; chemokines- regulated on activation, normal T-cell expressed and secreted (RANTES), macrophage inflammatory protein-1β (MIP-1β), MIP-3α; colony-stimulating factors- macrophage colony-stimulating factor (M-CSF); and growth factors- vascular endothelial growth factor (VEGF), IgM titers, and LPS concentrations were evaluated. Data were analyzed via a two-way ANOVA with an α = 0.05. In the first trial, Salmonella was significantly reduced by 1.07 and 0.84 log in the 1.5 kg/MT and 2.0 kg/MT MOS inclusions, respectively. In trial two, a significant 1.14 log reduction of SE in the 1.5 kg/MT MOS diet was observed. For unchallenged birds, all MOS treatments decreased IFNα levels. However, in the control basal diet, levels of IFNα were significantly diminished in SE challenged chicks. Decreased expression of IL-16 and MIP-1β was detected (p < 0.05) in SE challenged broilers compared to unchallenged birds. Levels of RANTES were significantly increased in 1.0 kg/MT and 2.0 kg/MT MOS inclusions compared to all other diets. No significant differences were observed with any other cytokines or LPS. The isotype IgM was reduced in all treatments compared to the control diet in both unchallenged and SE challenged birds, suggesting depressed humoral immunity when MOS was fed. Although a mechanism of action was not determined, these data suggest that MOS at the 1.5 kg/MT inclusion was efficacious in reducing SE.

  PublisherDOI

• Evaluation of powdered disinfectants to reduce bacterial contamination of footwear

  The Journal of Applied Poultry Research · 2025-12-03

  articleOpen accessSenior authorCorresponding

  Footwear is a known route for spreading microorganisms to farms and between poultry houses. While disinfectant foot pans are commonly used, liquid products lose efficacy when organic matter such as feces or litter is present. This study evaluated powdered peracetic acid, sodium percarbonate, quaternary ammonium compound, and bleach disinfectants for their ability to reduce bacteria on contaminated boot molds under heavy organic loads. Each product was evaluated individually by inoculating concrete boot molds in plastic boot covers with layer manure and tested a short versus long contact time. Microbial loads of total aerobes, Staphylococci , and coliforms were enumerated after treatment. Results indicated that all four products reduced microbial loads compared to rinsing only, suggesting successful use even with short contact times. Efficacy of the sodium percarbonate and quaternary ammonium compounds were more time dependent, while the peracetic acid and bleach products were less so. Powdered disinfectants offer a viable alternative to liquid foot pans, but product selection may need to be tailored to meet individual farm needs.

  PublisherDOI

• Socio-Psychological and External Factors Influencing Biosecurity Compliance in U.S. Poultry Farming

  Veterinary Sciences · 2025-09-24 · 1 citations

  articleOpen access

  Understanding why poultry farmers follow or neglect biosecurity practices is key to improving communication about the control of infectious and notifiable diseases like avian influenza. This study explored how socio-psychological, demographic, and contextual factors influence biosecurity compliance among U.S. poultry farmers. A questionnaire distributed at a poultry industry event yielded 67 responses from farmers, which were analyzed using a multivariable logistic regression with backward elimination. The predictors of high biosecurity tested included perceived outbreak impact, farming experience, and reliance on different information sources to form opinions on disease control. The final model showed that farmers who perceived that a disease outbreak would have a low impact were significantly less likely to follow strict biosecurity measures than those perceiving a higher impact (OR = 0.19, 95% CI [0.036, 0.925]). While compliance with biosecurity was high for most participants, certain practices, such as limiting flock outdoor access or contact with wild birds, were less commonly applied. Further research is needed to identify neglected biosecurity practices and the barriers to their implementation. Notable variations in farmers' engagement with information sources suggest that communication strategies should involve trusted intermediaries to enhance risk awareness and biosecurity implementation support.

  PublisherOA PDFDOI

• Serum cytokine profile of neonatal broiler chickens infected with Salmonella Typhimurium

  Frontiers in Physiology · 2024-02-23 · 8 citations

  articleOpen accessSenior authorCorresponding

  The avian immune system responds to Salmonella infection by expressing cytokines and chemokines. We hypothesized that the immune status of Salmonella Typhimurium (ST) challenged neonatal broilers would differ from the uninfected treatment. The objective of this experiment was to evaluate 12 cytokines. Day of hatch male chicks were randomly allocated into a control or ST challenged group. At day three of age, sterile diluent or 5.0 × 10 8 CFU of ST was given orally to each chick. Blood was obtained 24 h post challenge and serum separated for later analysis (n = 30 chicks/treatment). Significant ( p ≤ 0.05) increases in pro-inflammatory cytokines -interleukin-6 (IL-6), IL-16, and IL-21; anti-inflammatory cytokines - IL-10; chemokines -regulated on activation, normal T cell expressed and secreted (RANTES), macrophage inflammatory protein-1β (MIP-1β), and MIP-3α; colony stimulating factors -macrophage colony-stimulating factor (M-CSF); and growth factors -vascular endothelial growth factor (VEGF) were observed in the serum of the challenged chicks when compared to the control. No significant differences were observed in IL-2, interferon gamma (IFNγ), and IFNα. These data indicate the detection of mucosal immune responses in broiler chickens following ST infection. The heightened levels of pro-inflammatory cytokines, chemokines, and colony stimulating factors align with known inflammatory mechanisms, like the influx of immune cells. However, the elevation of IL-10 was unexpected, due to its immunoregulatory properties. Notably, the rise in VEGF levels is compelling, as it suggests the possibility of tissue repair and angiogenesis in ST infected birds.

  PublisherOA PDFDOI

• Microbial assessment of poultry farm biosecurity. Proceeding of The First International Avian Influenza Summit, University of Arkansas- October 16-17, 2023”

  GMPC Thesis & Opinions Platform · 2023-10-01 · 1 citations

  articleOpen access1st authorCorresponding

  Biosecurity may be defined as protection from pathogens or disease. This may include the separation of the flock from living vectors or inanimate objects called fomites. While prevention of host-specific and zoonotic diseases is important, the commercial poultry industry is already preoccupied with the challenges of day-to-day operations. The purpose of this project was to illustrate how surfaces that may seem clean are heavily contaminated with microorganisms that may be responsible for human and avian diseases. We also evaluated three common intervention strategies, including disposable boot covers, foot baths, and tire disinfection. Poultry environmental samples were collected at the Texas A\&amp;M University Poultry Science Research Center, including fan shrouds, side air inlets, cool cell reservoirs, truck tires, truck floor mats, doorknobs, controller panels, a bioaerosol air sampler, and an impactor air sampler. A total of 30 samples were collected per sample type, which was homogenized, serially diluted, and spread plated onto agar media to culture total aerobes, Staphylococci, and coliform bacteria. 6.6 log10 colony-forming units cfu/cm2 of aerobic bacteria were found at the greatest concentration, followed by Staphylococci (5.6 log10 colony-forming units cfu/cm2) and coliforms (2 log10 colony-forming units cfu/cm2). This pattern was observed in most of the samples. Boot covers, foot baths, and tire disinfection were tested for efficacy. While disposable boot covers significantly reduced the number of aerobes, Staphylococci, and coliforms, as many as 300 microorganisms per cm2 still made it through to the inner boot cover. Disinfectants are commonly misused due to not properly clearing the surface prior to application or allowing the proper contact time. We found that while disinfection significantly reduced these indicator organisms, that reductions were only 10 to 100-fold, leaving many viable bacteria behind. Increased contact time from 3 seconds to 10 minutes resulted in significant reductions of aerobes and Staphylococcus. The tire wash data mirrored our foot bath data. Data was shared from previous laboratory and field trials. Less than 1% sterile poultry litter significantly reduced disinfectant efficacy across four product categories. Extended storage time of 30 weeks reduced product efficacy as well. We shared electron micrographs to illustrate how visually clean and smooth surfaces provide many hiding places for microbes, reducing disinfectant efficacy. While risk can never be reduced to zero, it may be reduced and controlled with good management practices. Cleaning and disinfection should follow a five-step process of dry cleaning, soap wash, rinse, drying, and finally disinfection. Labels should be read closely so that the product is used safely and effectively. While there are many viable products on the market, disinfecting a clean surface and following recommendations for contact time are very important to get the best results. Following best management practices such as reducing pest (insect/rodent) harborage and following your integrated pest management program will help reduce risk significantly.

  PublisherOA PDFDOI

• From crypts to enteroids: establishment and characterization of avian intestinal organoids

  Poultry Science · 2021 · 41 citations

  • Biology
  • Cell biology
  • Molecular biology

  Intestinal organoids (IO), known as "mini-guts", derived from intestinal crypts, are self-organizing three-dimensional (3D) multicellular ex vivo models that recapitulate intestine epithelial structure and function and have been widely used for studying intestinal physiology, pathophysiology, molecular mechanisms of host-pathogen interactions, and intestinal disease in mammals. However, studies on avian IO are limited and the development of long-term cultures of IO model for poultry research is lacking. Therefore, the objectives of this study were to generate crypt-derived organoids from chicken intestines and to optimize conditions for cell growth and enrichments, passages, and cryopreservation. Crypts were collected from the small intestines of birds at embryonic d-19 and ceca from layer and broiler chickens with ages ranging from d 1 to 20 wk, embedded in a basement membrane matrix, and cultured with organoid growth media (OGM) prepared in house. The crypt-derived organoids were successfully grown and propagated to form 3D spheres like structures that were cultured for up to 3 wk. Organoids were formed on d one, budding appeared on d 3, and robust budding was observed on d 7 and beyond. For cryopreservation, dissociated organoids were resuspended in a freezing medium. The characteristics of IO upon extended passages and freeze-thaw cycles were analyzed using reverse transcription (RT)-PCR, immunoblotting, and live cell imaging. Immunoblotting and RT-PCR using E-cadherin (the marker for epithelial cells), leucine-rich repeat-containing G protein-coupled receptor 5 (LGR5, the marker for stem cells), chromogranin A (the marker for enteroendocrine cells), lysozyme (the marker for Paneth cells), and mucin (the biomarker for goblet cells) confirmed that IO were composed of heterogeneous cell populations, including epithelial cells, stem cells, enteroendocrine cells, Paneth cells, and goblet cells. Furthermore, OGM supplemented with both valproic acid and CHIR99021, a glycogen synthase kinase 3β inhibitor and a histone deacetylase inhibitor, increased the size of the avian IO (P < 0.001). To the best of our knowledge, this is the first comprehensive report for establishing long-term, organoid culture models from small intestines and ceca of layer and broiler chickens. This model will facilitate elucidation of the mechanisms impacting host-pathogen interactions, eventually leading to the discovery of pathogen intervention strategies in poultry.

  PublisherDOI

• Determination of Antimicrobial Resistance Patterns in Salmonella from Commercial Poultry as Influenced by Microbiological Culture and Antimicrobial Susceptibility Testing Methods

  Microorganisms · 2021 · 1 citations

  Senior authorCorresponding
  • Microbiology
  • Biology
  • Medicine

  isolates from poultry samples and could affect the accuracy of population or industry surveillance insights and intervention strategies.

  PublisherOA PDFDOI

• Impact of feeding bigheaded carp fish meal on meat quality and sensory attributes in organic broiler chickens

  The Journal of Applied Poultry Research · 2021-11-19 · 3 citations

  articleOpen access

  Novel protein feeds are needed in ecological and organic poultry production to supply natural sources of amino acids, particularly methionine. Synthetic amino acids are increasingly banned in certified organic production. Carp is an invasive fish in the United States and its harvest can help provide natural source of methionine, while reducing an undesirable population. In our previous study, we formulated a diet using extruded carp-based meal (CBM) to replace synthetic methionine in broiler diets and conducted a feeding trial to test its effect on broiler performance. For this study, birds were processed at the end of the feeding trial and evaluated for quality and sensory attributes of meat from birds fed with CBM diet. Controls were normal diet that contained methionine and the carp meal was used to replace methionine and a portion of soybean meal. Results suggest that birds fed with CBM diet did not differ from the Control in live weight, carcass weight, breast weight, ready-to-cook yield, wing yield, tenders, and thigh yields (P > 0.05). Breast meat was more light (L*) for birds from the CBM treatment compared to the Control and the pH was lower (P < 0.05). For the thigh meat, birds fed CBM diets resulted in higher protein and less fat compared to the Control (P < 0.05). In the consumer analysis, overall impression, flavor, and mouthfeel were lower for the CBM breast meat than the Control and scored lower in terms of tenderness and juiciness (P < 0.05). Interestingly, thigh meat from CBM had more omega-3 fatty acids, which has a human health benefit. The results indicate that carp-based meal hold potential as a novel protein to replace synthetic methionine in organic broiler diets.

  PublisherDOI

• Evaluation of Euthanasia Methods on Behavioral and Physiological Responses of Newly Hatched Male Layer Chicks

  Animals · 2021-06-17 · 9 citations

  articleOpen accessSenior authorCorresponding

  Newly hatched male layer chicks are considered as “by-products” in the egg industry and must be humanely euthanized at the hatchery. Instantaneous mechanical destruction (maceration) is the predominant euthanasia method applied in poultry hatcheries and is approved by the American Veterinary Medical Association (AVMA). However, maceration is not perceived by the public to be a humane means of euthanasia. The effects of alternative euthanasia methods, including carbon dioxide (CO2) or nitrogen (N2) inhalation, and a commercial negative pressure stunning system on behavioral and physiological responses of day-of-hatch male layer chicks, were evaluated in a field trial. Chick behaviors, including ataxia, loss of posture, convulsions, cessation of vocalization, and cessation of movement, were monitored. Serum hormones were assessed at the end of each of the alternative euthanasia treatments, including a control group allowed to breathe normal atmospheric air. The N2 method induced unconsciousness and death later than the CO2 and negative pressure methods, and increased serum corticosterone concentrations of neonatal chicks. Carbon dioxide inhalation increased serotonin concentrations as compared to controls, as well as the N2 and the negative pressure methods. The behavioral and physical responses observed in this study suggest that both CO2 inhalation and negative pressure stunning can be employed to humanely euthanize neonatal male layer chicks.

  PublisherOA PDFDOI

• Effect of Feeding a High Calcium: Phosphorus Ratio, Phosphorous Deficient Diet on Hypophosphatemic Rickets Onset in Broilers

  Agriculture · 2021-10-01 · 17 citations

  articleOpen accessSenior authorCorresponding

  Recently, a P-deficient diet caused rickets in commercial chicks within three days. This study aimed to investigate the duration of onset of rickets in chicks. Data were collected from 3–11 day old chicks raised on 88 commercial farms. Male day-old Arbor Acres Plus broilers (n = 450) were studied in three trials, with three to four treatments each. Each treatment used one of the following crumbled feeds: control feed (calcium (Ca): phosphorus (P)-1.41), slightly high Ca:P feed (SHCa:P, Ca:P-2.69), high Ca:P ratio, P deficient feed (HCa:P, Ca:P-3.08), and HCa:P feed plus 1.5% dicalcium phosphate (HCa:P + DP). Each treatment had three replicates with 15 birds each. Rickets was induced by HCa:P, and cured by HCa:P + DP, confirmed by gross anatomy, gait score, serum P concentration and growth performance. Lameness was not found in control groups, whereas, observed in the HCa:P groups as early as day 2.7 on commercial farms and day 3 in experimental farm. Serum P was reduced in HCa:P (p &lt; 0.01). Bodyweight and feed intake started decreasing at day 3 on commercial farms and in all trials (p &lt; 0.01). The duration of onset of hypophosphatemic rickets in broiler chicks fed HCa:P crumbled feed is approximately three days.

  PublisherOA PDFDOI

Frequent coauthors

• J.A. Byrd

  Southern Plains Agricultural Research Center

  25 shared

• Michael H. Kogut

  Southern Plains Agricultural Research Center

  17 shared

• Yuhua Z. Farnell

  Texas A&M University

  14 shared

• F. Solís de los Santos

  12 shared

• David M. Nagorney

  WinnMed

  11 shared

• A.M. Donoghue

  Agricultural Research Service

  10 shared

• Dan Zhao

  Henan University

  10 shared

• Kenneth J. Genovese

  Southern Plains Agricultural Research Center

  9 shared

Education

• Ph.D., Poultry Science

  Texas A&M University

  2000

• M.S., Poultry Science

  Texas A&M University

  1996

• B.S., Poultry Science

  Texas A&M University

  1994