Biology subjects

Ricke, S. C.

Publications and source records attributed to Ricke, S. C..

6 recordsLinked to original sources

bioRxiv2026

Alternative management strategy reshapes litter microbiome dynamics in a commercial broiler rearing system

Pre-harvest litter management is a key determinant of broiler production conditions, influencing NH generation, pathogen exposure, nutrient retention, and microbial reservoirs that accumulate across production cycles. Conventional chemical and physical management strategies can support flock health, but their effects on pathogen-associated bacterial populations are often transient and may not account for the microbial interactions that govern persistence, exclusion, and community succession. Here, we evaluated an alternative litter management strategy combining IndigoLT(R) pre-/postbiotic with reduced-rate NaHSO across two broiler growouts, with litter sampled at the end of each flock to determine impact on prokaryotic microbiome structure, physicochemistry, and Enterococcus abundance. Alternative management influenced observed richness, phylogenetic diversity, community composition, and co-occurrence network structure while reducing the relative abundance of Enterococcus, including E. cecorum and E. hirae. Digital PCR corroborated sequencing-based Enterococcus abundance patterns, although 16S-based treatment effects were not always reflected as lower absolute copy number at terminal sampling, consistent with reduced proportional dominance rather than sustained absolute suppression. Complementary biofilm- and growth-inhibition assays performed with IndigoLT(R) demonstrated context-dependent antibiofilm and bacteriostatic activity against reference and poultry-derived Enterococcus isolates, with stronger responses for E. cecorum than E. hirae and bactericidal-level reductions in viable recovery at higher exposure levels. These findings demonstrate that biologic-based litter management can alter microbiome structure and pathogen-associated taxa under commercial production conditions, providing a basis for microbiome-informed amendment strategies aimed at reducing pathogen load and supporting broiler health.

microbiology↗

bioRxiv2025

Poultry Litter Microbiome Shifts in Commercial Broiler Houses Following a Biotic-Based Litter Treatment

Litter management plays a critical role in broiler production, affecting bird health, performance, and environmental impact. This preliminary study evaluated the effects of IndigoLT, a biological amendment, in combination with a 40% sodium bisulfate (NaHSO) regimen on litter microbiome composition, compared to a standard NaHSO-only treatment. Litter samples (n = 18) were collected from three commercial broiler houses following flock removal: one control (NaHSO-only), one treated with IndigoLT for a single flock, and one treated for two consecutive flocks. The V4 region of the 16S rRNA gene was sequenced to assess prokaryotic community composition. Alpha diversity metrics (Faiths phylogenetic diversity, observed ASVs, Pielous evenness, Shannon diversity) did not differ significantly across treatments (ANOVA, p > 0.05). In contrast, PERMANOVA analyses of Bray-Curtis, Jaccard, Weighted and Unweighted UniFrac distances revealed significant shifts in {beta} diversity between IndigoLT-amended and control groups (q < 0.05), with no significant differences between the one- and two-flock IndigoLT treatments. Core microbiome and differential abundance analyses suggested that IndigoLT, when paired with reduced NaHSO input, may accelerate organic matter decomposition, promote nitrogen retention, and suppress potentially pathogenic taxa. Although limited by the absence of baseline sampling and biological replication, these findings suggest that IndigoLT influences litter microbial succession. Future work should aim to optimize inclusion rates most complementary between NaHSO and IndigoLT to enhance litter quality, reduce NH volatilization, and support bird health.

microbiology↗

bioRxiv2025

Lifetime exposure to known and emerging groundwater contaminants significantly alters poultry microbiome and metabolome

The exposome encompasses all lifetime environmental exposures affecting health. Its complexity and high data dimensionality make it challenging to link specific exposure combinations to adverse health outcomes. Establishing relevant exposome criteria is key to addressing current knowledge gaps. This study evaluated contaminant levels in Wisconsin groundwater and their effects on host health. We focused on three co-occurring chemicals that were detected at concentrations exceeding groundwater standards, nitrate, atrazine and imidacloprid, and the emerging contaminant, microplastics. In this study, broilers were exposed to a low dose chemical mixture (35,000 ppb nitrate + 1.7 ppb atrazine + 0.58 ppb imidacloprid) and high dose chemical mixture (100,000 ppb nitrate + 3,000 ppb atrazine + 3,000 ppb imidacloprid) or polyethylene microplastics (PE MPs) for 49 days. We observed that both ternary mixtures and PE fiber MPs significantly altered the cecal microbiomes as determined by the enrichment of genera, Fournierella, Ruminococcus and an unclassified genus in the family Coriobacteriaceae. In addition, +PE fiber presence dysregulated metabolic pathways associated with bile acid biosynthesis and lipid metabolism. Similarly, perturbations to cecal microbial activity for both ternary chemical mixtures were confirmed via modulation of six metabolites including methylisopelletierine which had a higher total ion intensity than the control group. Interestingly, there were no detectable pathological effects to either the +PE fiber or ternary mixture treatment groups. Overall, the data presented here demonstrates that low doses of environmental contaminants are sufficient to dysregulate cecal taxonomic composition and microbial activity without inducing detectable pathological effects. ImportanceWe found that exposure to mixtures of environmental toxins caused gut dysbiosis observed by changes to the chicken cecal microbiome and metabolome. This highlights the importance of conducting such studies with environmentally relevant mixtures of contaminants at detected concentrations to understand the actual risks associated with exposures like drinking contaminated groundwater over a long period of time. Our findings demonstrate that gut microbial metabolites, now known to be key regulators and signaling molecules in a wide range of host health issues, are the source of the negative health outcomes; superseding cell death or pathological damage that are caused by acute exposures. These changes have implications for predicting negative long-term chronic health outcomes.

systems biology↗

bioRxiv2025

Viability Differentiation Improves the Diagnostic Potential of 16S rRNA Gene Sequencing in Ready-to-Eat Meat Manufacturing

Molecular-based microbiological approaches have become valuable tools for the food industry. However, even the most advanced molecular techniques are limited in their ability to differentiate based on viability creating the potential for biased results when applied to the food industry. The objective of this study was to generate a viable microbial bio-map of a commercial ready-to-eat (RTE) meat manufacturing process and assess its utility as a diagnostic tool. Product samples were collected from a commercial RTE meat manufacturing facility at various locations throughout processing. Samples were homogenized and aliquoted for culture-based microbial isolation and 16S rRNA gene sequencing. Homogenates were split into pairs and subject to either no treatment (Control) or treated with 25 M PMAxx (PMA) to remove free and non-viable cellular DNA. Overall, PMA treatment resulted in a less rich microbial community compared to Control samples. Paired analysis revealed that the impact of PMA varied by location with the greatest effects being observed at the beginning and end of manufacturing. Both Control and PMA treated samples identified a shift in the microbial population after thermal processing; however, only PMA treated samples identified a secondary shift in the microbial population occurring after slicing. Taxonomic analysis identified Lactobacillus as a predominant genera in sliced and packaged products. These results were further confirmed by the identification of Lactobacillus sakei on packaged product using a culture-based approach. These results suggest PMA treatment provides a higher level of sequencing resolution by removing background DNA. ImportanceMicrobial bio-mapping is a valuable tool for the meat and poultry industry to assess process control and evaluate the efficacy of intervention systems. In recent years it has become more common to incorporate the use of molecular techniques, such as qPCR and 16S rRNA, to quantitatively track target pathogens and gain a more holistic understanding of the microbial community throughout processing. One major limitation we face when applying these DNA-based techniques to the food industry is their inability to differentiate between DNA from viable versus non-viable cells, which may result in the false identification of pathogenic or spoilage microorganisms and bias microbiota results. To practically apply this technology in a ready-to-eat meat manufacturing setting, it is crucial to develop and validate strategies that are capable of differentiating between viable and non-viable cellular DNA.

microbiology↗

bioRxiv2025

Characterization of the Gastrointestinal Tract Holstein x Angus Cross Cattle Microbiome During Harvest after Feed Withdrawal

Stress during the beef pre-harvest period can induce an inflammatory response and acidotic conditions in the gastrointestinal tract (GIT), which affects the gastrointestinal tract microbiome. The objective of this study was to characterize the status of the GIT microbiome at harvest in beef cattle entering a small USDA processing facility. Nine beef cattle were shipped from a producer in Columbia County, WI to the USDA processing facility at University of Wisconsin-Madison and were harvested across four dates. Digesta samples were collected from eight GIT locations: rumen solids, rumen liquids, abomasum, duodenum, jejunum, ileum, cecum, and large intestines. After DNA extraction with the DNeasy Blood & Tissue Kit, the V4 region of the 16S rRNA gene was amplified and sequenced on the Illumina MiSeq platform. Sequences were analyzed for alpha and beta diversity metrics (ANOVA and ADONOS), core microbiome, ANCOM, and co-occurrence network analyses. Harvest date and GIT location had a significant impact on microbial diversity and community composition (P<0.05), and there was an interaction between GIT location and harvest date (P<0.05). Taxonomic composition shifted throughout the GIT, though Prevotella and Treponema were core members in several different GIT locations. The co-occurrence analysis revealed microorganisms potentially associated with clinical infections, such as Moryella in the rumen and Acinetobacter in the hindgut, were considered keystone species. These results suggest that the pre-harvest period may negatively impact the beef cattle GIT microbiome. Modulating the GIT microbiome during the pre-harvest period may offer an opportunity to improve food safety.

molecular biology↗

bioRxiv2023

Co-exposure to Polyethylene Fiber and Salmonella enterica Typhimurium Alters Microbiome and Metabolome of in vitro Chicken Cecal Mesocosms

Humans and animals encounter a summation of exposures during their lifetime (the exposome). In recent years, the scope of the exposome has begun to include microplastics. Microplastics (MPs) have increasingly been found in locations where there could be an interaction with Salmonella enterica Typhimurium, one of the commonly isolated serovars from processed chicken. In this study, the microbiota response to a 24-hour co-exposure to Salmonella enterica Typhimurium and/or low-density polyethylene (PE) microplastics in an in vitro broiler cecal model was determined using 16S rRNA amplicon sequencing (Illumina) and untargeted metabolomics. Community sequencing results indicated that PE fiber with and without S. Typhimurium yielded a lower Firmicutes/Bacteroides ratio compared to other treatment groups, which is associated with poor gut health, and overall had greater changes to the cecal microbial community composition. However, changes in the total metabolome were primarily driven by the presence of S. Typhimurium. Additionally, the co-exposure to PE Fiber and S. Typhimurium caused greater cecal microbial community and metabolome changes than either exposure alone. Our results indicate that polymer shape is an important factor in effects resulting from exposure. It also demonstrates that microplastic-pathogen interactions cause metabolic alterations to the chicken cecal microbiome in an in vitro chicken cecal model. IMPORTANCEResearching the exposome, a summation of exposure of ones lifespan, will aid in determining the environmental factors that contribute to disease states. There is an emerging concern that microplastic-pathogen interactions in the gastrointestinal tract of broiler chickens may lead to an increase in Salmonella infection across flocks and eventually increased incidence of human salmonellosis cases. In this research article, we elucidated the effects of co-exposure to polyethylene microplastics and Salmonella enterica serovar Typhimurium on the ceca microbial community. Salmonella presence caused strong shifts in the cecal metabolome but not the microbiome. The inverse was true for polyethylene fiber. Polyethylene powder had almost no effect. The co-exposure had worse effects than either alone. This demonstrates that exposure effects to the gut microbial community are contaminant specific. When combined, the interactions between exposures exacerbate changes to the gut environment. The results herein support current Salmonella mitigation efforts and understanding microplastics-pathogen interactions.

systems biology↗