Introduction
Conversion of farm-raised livestock into safe, high-quality meat for commercial distribution is complex. Meat processing plants are dynamic systems that receive a continuous input of diverse animals, workers, organic material/soil, water, and air. Each of these inputs can act as a source of bacteria and other microorganisms that can influence the microbial ecology of the meat processing plant and the meat itself (Cobo-Díaz et al., 2021; Yang et al., 2023).
In-plant processes used to convert living muscle tissue into meat can also contribute to the microbial ecology of the plant, and also directly shape the microbiota on the pork carcass, raw meat primal and subprimal cuts, and further processed pork products (Yang et al., 2023). Many of these processing steps are specifically designed to reduce microbial load, and in particular pathogens whose presence often depends on factors such as the animal host species, environmental conditions within the meat processing plant, and effective implementation of Good Manufacturing Practices and Work Instructions that limit contamination and the formation of biofilms (Bai et al., 2021; Bridier et al., 2019; Giaouris et al., 2014). Although most bacteria in the microbiota are not pathogenic to humans or animals, their presence and proliferation under favorable conditions can negatively impact meat quality and shelf life, which makes the meat microbiota during processing a prime target for reducing losses due to meat quality issues (De Filippis et al., 2013; Hultman et al., 2015; Pothakos et al., 2015).
A schematic depicting the fresh pork supply chain (not including market sows and boars) is presented in Figure 1. The process begins as live pigs are transported via truck and trailer to a pork slaughter facility, where the pigs are unloaded and held in lairage pens before entering the packing facility. From there, a series of processes is initiated to efficiently convert the living pig muscle to pork meat. This involves a combination of process engineering, automation, and human interaction, with each step having potential impact on the microbial ecology of final pork products. It also involves a delicate balance between processing times, exposure temperatures, and muscle biochemistry to produce a high-quality meat product that is desired by consumers and optimal for processing yields and functionality. The purpose of this review paper is to provide an overview of current scientific knowledge about each processing step and its contribution to the fresh pork microbiota.
Schematic of the fresh pork supply chain.
Establishment of the microbiome in a processing plant
Use of 16S rRNA gene amplicon sequencing has allowed for a broader understanding of how the microbiome of the built environment becomes established in new buildings, and how it may differ depending on location and exposure to building inhabitants (Lax et al., 2017; Lax and Gilbert, 2015; Wood et al., 2015). Within food service preparation facilities, microbiome establishment and potential cross contamination routes within the facility have been observed, and microbiome differences have been associated with the food type being prepared in each respective area (Stellato et al., 2015), variation in sanitation (Stellato et al., 2015), and seasonality as it relates to the use of fans in preparation areas (Lim et al., 2021).
Most scientific literature related to the microbiome of the built environment to date has been conducted in human-inhabited environments such as hospitals and gyms. In contrast, the modern commercial pork processing plant is a complex network of machinery and human-facilitated processes designed to convert a living, farm-raised animal into safe, high-quality food. Due to the dynamic nature of the microorganisms being brought into the facility by the pigs, meat, workers, or variation in daily sanitation practices, establishment of the microbiome within a processing plant is often dynamic as well (Asmus et al., 2025a; Barcenilla et al., 2024; Campos Calero et al., 2020).
A 16S rRNA gene amplicon-based study conducted by Cobo-Díaz et al. (2021) described microbial colonization patterns across multiple locations within a newly operating pork cutting plant in Spain. During the first 2 months of operation, the core microbiota was dominated primarily by Pseudomonas, and alpha diversity increased as the plant moved from the initial sanitation phase with no processing (T1), to the start of carcass processing over the first 2 months of operation (T2), and then over the next 14 months of operation (T3) (Cobo-Díaz et al., 2021). As the microbiome became increasingly diverse across the 3 time points, the genera Acinetobacter, Psychrobacter, Brevundimonas, and Acidovorax all increased from T2 to T3, perhaps reflecting the establishment of the overall biofilm microbiome in the facility. Floor drains had the highest microbial alpha diversity of all sampling locations across all 3 timepoints (Cobo-Díaz et al., 2021). Sampling time (22.8%), surface type (14.5%), and location of the processing room (5.3%) each influenced taxonomic composition of the microbiome (Cobo-Díaz et al., 2021). Although the microbiome composition of T1 and T2 did not differ, their composition differed from samples collected in T3, suggesting that the microbiota composition and diversity increase as the environment is exposed to more variation inherent to the pork harvest process (Cobo-Díaz et al., 2021).
Belk et al. (2022) also found similar microbiome composition and alpha diversity trends when using 16S rRNA gene amplicon sequencing to assess changes in the microbiome in a newly opened multi-species processing pilot facility over the first 18 months of operation. Additionally, this study found that the temperature of the room was an important factor in the compositional establishment of the microbial communities. Rooms with low temperatures were dominated by psychrotrophs such as Pseudomonas, but warmer rooms such as the harvest floor and live animal holding areas contained a more diverse microbiome, with greater evenness of taxa (Belk et al., 2022).
Immobilization, exsanguination, carcass wash/dehair
Conversion of living muscle to meat involves several distinct biochemical changes that occur as the body is unable to maintain metabolic activity through the harvest process. Optimal processes employed by the processing plant are necessary to facilitate these biochemical changes and ultimately create a high-quality and functional meat product with minimal risk of spoilage and pathogen presence (Aberle et al., 2001).
The first step of harvest is to immobilize (or stun) the live pig to render the animal unconscious. Although different stunning techniques are allowed in pork, a majority of large processors in the United States use CO2 stunning over electrical stunning because of improvements in humane animal handling and an improvement in overall meat quality (Channon et al., 2003; Marcon et al., 2019; Shackelford et al., 2012; Velarde et al., 2000).
The first exposure of the interior of the unconscious hog carcass to the outside environment occurs during exsanguination as the hog is shackled by one hind leg, suspended upside down, and both the carotid artery and jugular vein are severed via a cut through the exposed neck. The hide typically remains on the hog carcass during processing (in most large pork plants), and is a distinguishing factor from the harvest of other livestock, such as beef or lamb, where the hide/pelt is removed immediately post-exsanguination. Thus, the hog carcass skin surface needs to be washed and dehaired before evisceration for food safety reasons.
The pig-associated microbial community observed during lairage, stun, and exsanguination has been recently described. In one study, the microbial composition and diversity of the pig skin did not differ significantly between the live pig in lairage and when the same animals were shackled post-stun (Gaire et al., 2024). However, in a different study, compositional differences were observed between the skin surface microbiota of the live pig and post-stun, with the former dominated by Firmicutes (91%) and the latter being dominated by both Firmicutes (46%) and Proteobacteria (21%) (Campos Calero et al., 2020). Mesophilic aerobic plate counts (APC) from skin surface samples of the post-stun carcass varied from 6.0 to 7.72 log colony-forming units (CFU)/cm2 and did not change significantly through exsanguination (Campos Calero et al., 2018; Wheatley et al., 2014). Additionally, the presence of Enterobacteriaceae (EB) is a notable feature of the post-stun microbial skin surface community, with EB counts of 3.55 +/− 0.77 log CFU/mL observed from swabs obtained immediately after exsanguination (Bueno López et al., 2022). Although not the case for APC, EB counts differed by anatomical location on the carcass, with the belly reflecting lower EB counts than hams or jowls (Wheatley et al., 2014). The microbiota of the post-stun carcass skin is dominated by Gram-positive organisms, primarily of the Firmicutes and Bacteroidetes phyla (Campos Calero et al., 2020; Gaire et al., 2024; Gill and Bryant, 1992). Genera such as Clostridium sensu stricto 1, Streptococcus, Curvibacter, Helicobacter, Lactobacillus, and Anaerococcus were found to dominate the post-stun carcass (Campos Calero et al., 2020; Gaire et al., 2024; Zwirzitz et al., 2020).
After exsanguination, the carcass is exposed to a scald process that facilitates the removal of hair and loosens organic matter from the skin surface. Scalding is typically accomplished by either vertical steam scalding or by a communal tub scalder. Communal tub scalding involves a large tank of water heated to 60°C to 70°C, with each carcass immersed in the tank and exposed to the scald water treatment for approximately 8 to 10 min. As a result, a large number of pigs are usually scalded in the same batch of water, with the same scald water used across multiple processing shifts. Scald tank water is typically discarded at the end of the processing day and the tank refilled and heated during the sanitation shift. Although vertical steam scalding units are becoming more common in new plant construction and have advantages in terms of energy efficiency, temperature control, and carcass-to-carcass contamination exposure (Frontmatec, 2025), communal tub scalding units are still commonly used throughout the pork industry.
Since the scald water medium involves a high level of organic matter, thermal lethality kinetics of scalding have been investigated. Two studies assessed thermal kinetics of Salmonella and Yersinia enterocolitica in scald water sampled from a commercial pork processing facility. For a Salmonella cocktail derived from isolates from pig carcasses, the D60°C was 1.5 min, z = 5.7 min (Bolton et al., 2003), suggesting that an 8-min exposure of the carcass to a 60°C scald process would deliver a 5.3 log reduction of Salmonella. However, the thermal resistance of Y. enterocolitica was found to be higher, with a D60°C of 2.7 min, z = 7.8 (Bolton et al., 2013). Thus, an 8-min scald process would deliver a 2.96 log reduction of Y. enterocolitica, much smaller than the reduction for Salmonella. These differential results highlight potential variation in thermal resistance of non-spore-forming bacteria present within the carcass microbiota when exposed to a high organic matter, communal tub scald treatment.
After scalding, a majority of the carcass hair is removed by a series of high-speed, mechanical paddles that physically release the hair from the carcass. The remainder of the dehairing process consists of 2 key steps, both of which can influence the presence of bacteria on the surface of the postmortem carcass: singeing and polishing. Singeing involves exposing the entire surface of a pork carcass to a series of high-temperature flames to help remove residual hair not removed during scalding and the initial hair removal. This is followed by polishing, which uses mechanical brushes, whips, or paddles to wash the carcass and eliminate any remaining hair or organic matter left on the pork carcass.
Scalding/dehairing, singeing, and polishing are the first steps in the harvest process during which the microbial community undergoes a shift from what was present on the surface of the live animal to what remains after the surface of the carcass is cleaned and prepared for evisceration and further processing. Notable changes in the overall microbial load have been observed as the carcass is cleaned and dehaired. These processing steps resulted in a reduction of skin surface APC, with microbial counts decreasing by 1.0 to 3.46 log CFU/mL. (Bueno López et al., 2022; Campos Calero et al., 2018; Gill and Bryant, 1992; Wheatley et al., 2014; Zwirzitz et al., 2020). Similar reductions were also observed for EB counts (Bueno López et al., 2022; Corbellini et al., 2016; Wheatley et al., 2014).
In addition to microbial load reductions, the composition and diversity of the skin surface microbiota have also been observed to shift post-cleaning/dehairing. Beta diversity of carcass skin swabs collected post-singe and post-polishing differed from post-stun carcass skin samples (Gaire et al., 2024; Zwirzitz et al., 2020). Zwirzitz et al. (2020) observed that the genera Anoxybacillus, Chryseobacterium, and Moraxella dominated the post-singe pork carcass surface, accounting for up to 50% relative abundance of the total microbiota. Environmental samples taken from equipment present in the dehairing and polishing zones were also dominated by the class Gammaproteobacteria (75.8% relative abundance), whereas the genera Moraxella and Acinetobacter together accounted for greater than 50% relative abundance of the Gammaproteobacteria observed (Bridier et al., 2019).
Using the Bayesian SourceTracker predictor, Zwirzitz et al. (2020) observed that the rectal swab of the pig and the stun environment were not major sources of contamination in the meat. In agreement, Gaire et al. (2024) also observed that the microbial community present in lairage contributed a minor proportion of the post-scald/dehairing microbiota (<5%), suggesting the effectiveness of the singeing intervention in eliminating bacteria present on the skin surface at lairage (Gaire et al., 2024).
Together, these results suggest that although microbial load decreases, a more diverse microbiome is present on the carcass after skin cleaning and dehairing. A possible explanation for increased alpha diversity could be the mechanical nature of the polisher, which could spread bacteria that survive singeing as it cleans the carcass surface before evisceration. This may also result in the polisher developing its own microbiome biofilm throughout the processing day as it is exposed to more carcasses post-singeing. This may be why carcass surface counts of both APC (Wheatley et al., 2014) and EB (Corbellini et al., 2016) increased between singeing and polishing. Additionally, a decrease in both Richness and Shannon’s index occurred post-singeing, but both metrics increased after polishing (Gaire et al., 2024; Zwirzitz et al., 2020). Furthermore, polishing contributed substantially to the chilled pork carcass microbiota, accounting for more than 40% of the overall composition (Zwirzitz et al., 2020).
Evisceration
Evisceration is a complex process that involves removing the head and internal organs from the carcass. As a result, evisceration also exposes the exterior surfaces of the carcass to potential contamination from GI tract organisms. Although automation can be applied to some parts of the evisceration process, most steps require some level of human involvement. Due to its complexity and the interaction of the carcass surface with equipment, workers, and internal viscera, evisceration poses a risk of cross-contamination, both between carcasses and within an individual carcass (Warriner et al., 2002).
In general, carcass surface microbial loads remain consistent throughout the evisceration process. Although carcass surface APC did not differ from postpolishing through evisceration (Bueno López et al., 2022; Gill and Bryant, 1992; Wheatley et al., 2014; Zwirzitz et al., 2020), carcass surface EB counts did increase from polishing through evisceration (Bueno López et al., 2022; Zwirzitz et al., 2020). A decrease in both Richness and Shannon’s index was observed from polishing through evisceration, indicating that the microbiota became less diverse after polishing, even though the overall microbial load did not increase (Zwirzitz et al., 2020). Gaire et al (2024) observed minimal variation in the microbiome diversity or composition from pre-evisceration to post-evisceration carcasses. A limited number of genera were found to be differentially abundant following the evisceration process, with 13 out of 208 genera having lower abundance and 10 out of 208 genera having greater abundance post- versus pre-evisceration (Gaire et al., 2024).
Changes in the microbial population that occur during evisceration may be carcass and process-specific. Wheatley et al (2014) observed site-specific increases in surface EB counts from polishing through evisceration, with EB counts increasing in both the belly and the jowl after evisceration, but remaining consistent on the ham. Additionally, Bridier et al (2019) analyzed the microbiota of equipment at multiple points in the evisceration process. The 4 most abundant genera at the neck clipper (an early step in the evisceration process) were Enhydrobacter (52.8%–77.7% relative abundance), Acinetobacter, Moraxella, and Psychrobacter. The carcass opener (a later step in the evisceration process) was dominated by Moraxella (up to 91.8% relative abundance), with Acinetobacter, Enhydrobacter, and Psychrobacter being observed at much lower relative abundance. These findings suggest that contamination from evisceration equipment may contribute to variations in microbiota composition.
Evisceration is the first step in the conversion of muscle to meat that involves a high degree of human interaction. A risk for carcass cross-contamination exists every time the carcass is touched by a worker’s glove or with each individual cut (Kim et al., 2024). As a result, practices to sanitize cutting equipment have been evaluated. A one-second dip of cutting equipment in 82.2°C hot water (Goulter et al., 2008), 48.9°C warm water with 400 ppm quaternary ammonium compound (Taormina and Dorsa, 2007), or a 5 s dip in 40°C warm water with 2% lactic acid (Leps et al., 2013) reduced APC, Salmonella, and E. coli by approximately 1–2 log CFU/cm2.
Additionally, antimicrobial interventions can be employed by pork processors at the end of evisceration and before the carcass enters the chiller, as this is the last opportunity to provide a surface treatment to the warm, pre-chilled carcass. Common interventions employed as a post-evisceration final carcass wash include high velocity spray solutions of 71°C hot water, 2% to 4% lactic acid, 400 ppm peroxyacetic acid, and 400 to 600 ppm hypobromous acid. Although these interventions are commonly used, their impact on pathogen load can vary with factors such as microbial load, spray velocity, and surface temperature. Skin surface inoculated Salmonella, E. coli, and Campylobacter jejuni count reductions ranged from 0.2 log CFU/cm2 to 3.3 log CFU/cm2 after exposure to the preceding antimicrobial interventions (Eastwood et al., 2021; Pozuelo et al., 2021; Wheeler et al., 2014). Although carcass surface interventions have been shown to reduce pathogen load in inoculated studies, their impact on the composition and diversity of the carcass microbiota is not well understood.
Carcass chilling
After exsanguination, the depletion of oxygen and disruption of the electron transport chain cause muscle tissue to shift from aerobic metabolism to anaerobic glycolysis, leading to lactate accumulation and a drop in muscle pH. As adenosine triphosphate (ATP) becomes fully depleted, mostly permanent cross-bridges form between actin and myosin, causing irreversible muscle contraction. This unresolved muscle contraction, known as rigor mortis, marks the conversion of muscle to meat. The rate of pH decline is affected by carcass temperature and plays a critical role in meat quality (Pearson, 1987). Higher carcass temperature accelerates pH decline and leads to increased protein denaturation, paler meat color, and reduced water-holding capacity (Lonergan et al., 2001; Pearson, 1987). However, chilling the carcass too quickly before the onset of rigor can lead to cold shortening or thaw rigor, both of which result in undesirable toughness (Aberle et al., 2001; Dransfield and Lockyer, 1985). To balance this, pork carcasses must be chilled rapidly enough to preserve quality but not so quickly as to trigger quality defects such as cold shortening. Conventional chilling achieves a gradual temperature drop to 4°C within 18–24 h, whereas modern blast chill systems briefly expose carcasses to −32°C air before transitioning them to 2°C storage, allowing faster cooling without inducing cold shortening and thereby enhancing pork quality and functionality (Springer et al., 2003).
In addition to its effect on muscle/meat temperature, chilling also influences the composition of the microbiota present on the surface of the carcass. Aerobic plate count on the carcass surface has been observed to remain constant (Gill and Bryant, 1992; Wheatley et al., 2014) or slightly decrease (Zwirzitz et al., 2020) in a conventional chill system. In blast chill systems, scientists have reported reduced recovery of viable cells measured by both APC (4.52 log CFU/mL vs. 2.92 log CFU/mL) and EB (2.03 log CFU/mL vs. 0.97 log CFU/mL) (Bueno López et al., 2022).
Differences in both composition and diversity of the pork carcass surface microbiome have also been demonstrated as the carcass transitions from evisceration to chilling. Gaire et al. (2024) observed that the composition of the carcass microbiome differed between post-evisceration and post-chilling cooler samples. Additionally, the microbiome profile of the cooler samples was highly diverse, with significant beta dispersion observed in pork carcass samples (Gaire et al., 2024). This indicated substantial variation in microbiome composition between individual carcasses within the cooler. Despite the high intrasample variability, 52 genera were differentially abundant between post-evisceration and the cooler (Gaire et al., 2024). Although the genera Aeromonas, Moraxella, and Neisseria were less abundant in pork carcass cooler samples as compared to post-evisceration carcass samples, Pseudomonas was notably more abundant (Gaire et al., 2024).
SourceTracker analysis revealed that a majority of bacterial taxa in pork carcass cooler samples were derived from either an unknown source (53%) or from the post-evisceration carcass (45%) (Gaire et al., 2024). This was in contrast to post-evisceration samples, in which 90% of the bacterial taxa also were present in pre-evisceration samples from the same carcasses (Gaire et al., 2024). In agreement, another recent study observed that a majority of the post-chilled carcass microbiota was derived from an unknown source (31%), but the gloves of workers handling the carcass (8.3%) and the environment of the chiller (4.4%) also contributed to the microbiota present on the carcass surface (Zwirzitz et al., 2020). Therefore, carcass chilling could either be a potential source of microbial contamination of the carcass surface or possibly a fitness effect associated with the environmental selection and viable recovery of some cells vs. others.
Primal and subprimal fabrication
Primal fabrication is the process of partitioning pork carcasses into 4 anatomically distinct primal cuts. The 4 pork primal cuts are the Pork Leg or Ham (Instituational Meat Purchase Specification [IMPS] #401A, USDA-AMS, 2020), Pork Loin (IMPS #410), Pork Belly (IMPS #408), and Pork Shoulder (IMPS #403). To maximize process efficiency in large, commercial pork plants and to account for the anatomical uniqueness of each primal cut relative to its end use, individual fabrication processing lines are devoted to each primal cut for further processing into subprimal pork cuts.
The microbiota of fresh meat is likely derived from 2 main sources: first, from the microbiota specific to the animal, and second, from the environment (Chaillou et al., 2015), which includes environmental interactions of the market pig, carcass, and meat throughout the entirety of the fresh pork supply chain (Figure 1). Across multiple species (fish, shrimp, poultry, pork, beef), a core environmental microbiome is believed to exist that is driven specifically by environmental factors outside of the processing plant, such as water and soil (Chaillou et al., 2015). Additionally, a distinct core microbiota unique to either seafood or meat was observed, likely influenced by their respective environmental exposures. Seafood microbiota was associated with the aquatic environment and fish-specific gut microbiota, whereas meat microbiota was associated with the skin and gastrointestinal tract of terrestrial animals (Chaillou et al., 2015).
Specific to meat, several studies have reported the contribution of the processing line environment to the composition of the carcass surface microbiota before fabrication. Braley et al. (2022) reported site-specific microbiota on post-chill pork carcasses, noting higher EB counts on the shoulder than on the ham (Braley et al., 2022). However, the composition of the surface microbiota at each sampling location on carcasses was observed to be similar. Kang et al (2020) also observed that microbiota present on beef carcasses were similar to what was observed on both contact surfaces and beef trim, but were compositionally dissimilar between different processing plants (Kang et al., 2020). Similarly, Peruzy et al. (2021) reported that, although the microbiota of different anatomical regions of pork carcasses were typically dominated by the same genera, compositional variation and differences in alpha diversity were observed between pork carcasses sampled from 2 different processing facilities (Peruzy et al., 2021). Although the processing layouts of the 2 facilities were similar, differences in the singeing process were noted: one facility employed a mechanical singeing method, whereas the other used a manual approach that may have resulted in a non-uniform or incorrect singeing procedure.
Although differences in pork carcass microbiota can be influenced by environmental exposures that occur pre-fabrication, it has also been shown that subsequent primal and subprimal meat cuts can harbor unique microbiomes, suggesting that fabrication itself can differentially influence the resulting fresh pork microbiome. Shedleur-Bourguignon et al. (2023) characterized the environmental microbiome of multiple subprimal fabrication lines in a pork processing facility and observed differences in both alpha and beta diversity of contact surface samples from the main production line, loin, shoulder, belly, and ham fabrication lines (Shedleur-Bourguignon et al., 2023), suggesting that the diversity and composition of the contact surface environment of each fabrication line is unique within the same processing plant. Similarly, differences in both alpha and beta diversity were observed between pork tenderloin and belly meat samples, although no difference in APC was detected between the 2 meat types (Asmus et al., 2025a). Genera such as Campylobacter, Clostridium sensu stricto 1, Yersinia, and Moraxella were more abundant in the belly, whereas Bacillus, Pseudomonas, and Enhydrobacter were more abundant in the tenderloin (Asmus et al., 2025a).
Characterization of the microbiota from meat and food contact surfaces during pork carcass fabrication revealed compositional differences between fabrication lines. Differences in beta diversity were observed between both meat and environmental contact surface samples from the belly and Boston butt fabrication lines (Asmus et al., 2025b). Within each fabrication line, the microbiota composition was also different between the meat and its associated contact surface. These compositional differences were driven at the amplicon sequence variant (ASV) level, with a substantial portion of ASVs (range 47.3%–51.2%) uniquely associated with either the meat or the contact surface from either the belly or Boston butt fabrication lines (Asmus et al., 2025b). Additionally, the composition of the microbiota was strongly associated with processing date across the meat (R2 = 0.24–0.25) and contact surfaces (R2 = 0.23–0.34) from both fabrication lines, suggesting that unique daily factors before fabrication influence the microbiota present on raw pork processed on individual processing dates (Asmus et al., 2025b).
The processing environment can influence the composition of fresh meat microbiota. Spoilage organisms and pathogens, including L. monocytogenes, can transfer from inert surfaces like stainless steel and plastic to meat surfaces (Midelet and Carpentier, 2002). Across multiple processing facilities of both small and large scale, microbiota of meat and cutting surfaces were found to be very complex (Barcenilla et al., 2024; De Filippis et al., 2013; Stellato et al., 2016). The core microbiota observed in both the environment and meat included the genera Pseudomonas, Streptococcus, Brochothrix, Psychrobacter, and Acinetobacter (Barcenilla et al., 2024; De Filippis et al., 2013; Stellato et al., 2016). However, specific clustering of the microbiota composition was observed between meat and environmental samples. Meat samples were comprised of higher levels of Pseudomonas and several Enterobacteriaceae, whereas environmental samples were comprised of higher levels of Staphylococcus, Streptococcus, Leuconostoc, Brochothrix, and Psychrobacter (Stellato et al., 2016). However, a recent study by Xu et al. (2025) observed that spoilage bacteria persisted over a 6-mo period in various plant locations (floor drains, processing lines, coolers, packaging, storage), and that these same strains of spoilage bacteria were also observed in packaged fresh pork from the same processing plant (Xu et al., 2025). These findings highlight the potential influence that persistent, biofilm-forming spoilage strains throughout the processing environment may have on the microbial composition of fresh pork.
In addition to the influence of the plant environment, human interaction on each individual fabrication line can also influence fresh meat microbiota. A compositional association was demonstrated between the surface of meat and meat handlers in the processing plant (Li et al., 2022). Using SourceTracker analysis, a high proportion of microbes observed on the post-chilled pork carcass were associated with the microbiota of workers’ gloves in both evisceration and also from workers associated with handling of the post-chilled pork carcass (Zwirzitz et al., 2020). Kim et al (2024) determined that the primary source of contamination of the chilled pork carcass was predominantly microbiota inherent to the initial unwashed pork carcass (77.5%), but that a small proportion (5.7%) was sourced from the worker’s gloves.
Further processing
Similar to the fabrication line, the further processing environment can influence the overall microbial community present on finished food items. A study by Barcenilla et al (2024) across 3 different processing facilities assessed the microbiota of fresh pork meat through multiple points in processing, including fabrication, the food contact surfaces associated with fabrication, and at the end of shelf life. Each of these surfaces was found to harbor a complex microbiota, and compositional differences in the microbiota were observed between the fresh meat, food contact surfaces, and the final product at the end of shelf life (Barcenilla et al., 2024). Pseudomonas fragi was the dominant species in raw pork meat from all 3 processing facilities. However, the dominant taxa at the end of shelf life were either Brochothrix thermosphacta (plant 1) or Lactobacillus sakei (plant 2). Raw pork at the end of shelf life from plant 3 contained a more even compositional distribution, with Pseudomonas fragi, Brochothrix thermosphacta, and Acinetobacter harbinensis having the highest relative abundance. Although Brochothrix thermosphacta and Lactobacillus sakei were present in the raw pork meat and food contact surfaces of each of the processing plants, all were in low relative abundance, suggesting that refrigerated storage conditions over time (<7 d) may have provided growth conditions that favored the proliferation of these particular taxa throughout the shelf life of the product (Barcenilla et al., 2024).
The influence of the raw processing environment can sometimes be overlooked in the production of ready-to-eat (RTE) food items that often involve a thermal pasteurization step (Hultman et al., 2015; Pothakos et al., 2015). In an investigation of high-spoilage, cooked RTE sausage, abundant mesophilic spoilage bacteria such as Leuconostoc, Brochthrix, and Yersinia were found throughout the processing environment in low relative abundance (4% on contact surfaces, 2 to 5% in meat). However, the same Leuconostoc operational taxonomic units found in the pre-processed meat and processing environment were also observed in high abundance (>98%) in the subsequent spoiled cooked sausages (Hultman et al., 2015). Similarly, the presence of Leuconostoc gelidum was found in low relative abundance, but high prevalence throughout the plant environment and also in ingredients used to make cooked RTE meals (Pothakos et al., 2015). However, L. gelidum became the most dominant microbe at the end of the product shelf life, outgrowing common spoilage bacterial taxa such as Pseudomonas, Brochothrix, and Lactobacillus (Pothakos et al., 2015). Similarly, Barcenilla et al (2024) observed the dominance of taxa such as Lactobacillus sakei, L. gelidum, and Brochothrix thermosphacta at the end of shelf life in fermented sausage and cured meat. Each of these taxa was present at low relative abundance throughout the processing environment and on raw materials before further processing (Barcenilla et al., 2024).
Cleaning and sanitation
Effective cleaning and sanitation of the processing plant environment alters the microbiota of the plant environment and applies a selection impact on various microbes, causing a shift in the composition of the microbiome that can ultimately impact the shelf life and quality of the final product. In a large-scale commercial pork processing plant, the production day typically consists of three 8-h shifts. Two of these shifts are dedicated to production, and the last 8-h shift is dedicated to cleaning and sanitation. Visual inspection of processing lines after cleaning and sanitation is often used to determine the acceptability of the cleaning/sanitation process before start-up of the processing line in the next shift. Rapid surface measurements, such as the detection of ATP, can also be used to determine the presence of non-visible soil that may remain after sanitation. Verification via the use of environmental swabbing and testing for various organisms, usually as a quantitative metric, is also implemented to meet regulatory requirements.
The impact of effective cleaning and sanitation on processing plant microbial ecology has been demonstrated. Across the dehair, whip, neck clipper, and carcass opener steps in the harvest process, effective cleaning and sanitation reduced bacterial diversity and evenness at each of these steps (Bridier et al., 2019). Cleaning coupled with the use of either a 20 or 40 ppm gaseous ozone sanitizer reduced contamination levels in each of the processing rooms of a pork processing facility (Botta et al., 2020). However, not all bacterial taxa responded to the gaseous ozone treatment in the same manner. Although psychrotrophic spoilage bacteria such as Pseudomonas and Brochothrix were reduced in plate count numbers, Staphylococci were found to be resistant to the gaseous ozone sanitation treatment (Botta et al., 2020).
Intense, multi-component sanitation such as Decon7 (Decon7 Systems, Inc., Coppell, TX, USA) is a practice that some processors employ on an annual, semi-annual, or “as needed” basis. This treatment is designed to eliminate persistent biofilms that may exist in a processing plant and has been shown to effectively reduce biofilms present in plant drains, at least in the short term. However, in the weeks after treatment, researchers observed increased diversity and a shift in the composition of biofilm microbiota (Wang et al., 2024). Additionally, drain samples had enhanced ability to form biofilms after intense sanitation treatment compared to before the treatment, which was also linked to increased Salmonella survival within the biofilm (Wang et al., 2024). The authors speculated that weaker environmental bacteria may have been eliminated by the intense sanitation treatment, whereas highly tolerant species survived and then thrived after the removal of bacterial competitors (Wang et al., 2024). Studies such as these highlight the dynamic nature of the microbial ecosystem within a plant, and the delicate balance that exists between the plant environment, process management practices, and the microbiota of the meat.
Conclusion
The fresh pork supply chain is a complex system in which the market pig, carcass, and meat encounter diverse indirect exposures and direct contacts that shape microbiota quantity and composition. These microbial interactions play a crucial role in determining the safety and quality of fresh pork. This review also highlights the utility of both traditional culture-based analyses and advanced genomic techniques, such as 16S rRNA amplicon sequencing and shotgun metagenomics, in providing a deeper understanding of microbial dynamics throughout the supply chain. By examining how the composition of the fresh pork microbiota evolves at different processing stages, pork processors can better assess the impact of each step on food safety and quality. This knowledge can help support the development of targeted intervention strategies throughout the fresh pork supply chain to reduce variation in quality and enhance the safety of fresh pork.
Conflict of Interest
The authors declare the following financial interests/personal relationships which may be considered as potential competing interests: Aaron E. Asmus is an employee of Hormel Foods Corporation.
Acknowledgments
This work was funded by Hormel Foods Corporation.
Author Contribution
Aaron Asmus: Conceptualization, Writing - Original Draft, Writing - Review & Editing, Funding acquisition. Keith Belk: Writing - Review & Editing. Noelle Noyes: Writing - Review & Editing, Supervision.
Literature Cited
Aberle, E. D., J. C. Forrest, D. E. Gerrard, and E. W. Mills. 2001. Conversion of muscle to meat and development of meat quality. In: Principles of meat science, 4th ed. Kendall/Hunt, Dubuque, IA. p. 83–109.
Asmus, A. E., T. N. Gaire, K. J. Schweisthal, S. M. Staben, and N. R. Noyes. 2025a. Microbiome characterization of two fresh pork cuts during production in a pork fabrication facility. Microbiology Spectrum 13:e02209–24. doi: https://doi.org/10.1128/spectrum.02209-24
Asmus, A. E., T. N. Gaire, K. M. Heimer, K. E. Belk, R. S. Singer, T. J. Johnson, and N. R. Noyes.2025b. Fresh pork microbiota is temporally dynamic and compositionally diverse across meat, contact surfaces, and processing lines in a pork processing facility. Appl. Environ. Microbiol. 91:e00044–25. doi: https://doi.org/10.1128/aem.00044-25
Bai, X., C. H. Nakatsu, and A. K. Bhunia. 2021. Bacterial biofilms and their implications in pathogenesis and food safety. Foods (Basel, Switzerland) 10:2117. doi: https://doi.org/10.3390/foods10092117
Barcenilla, C., J. F. Cobo-Díaz, A. Puente, V. Valentino, F. De Filippis, D. Ercolini, N. Carlino, F. Pinto, N. Segata, M. Prieto, M. López, and A. Alvarez-Ordóñez. 2024. In-depth characterization of food and environmental microbiomes across different meat processing plants. Microbiome 12:199. doi: https://doi.org/10.1186/s40168-024-01856-3
Belk, A. D., A. N. Frazier, L. K. Fuerniss, R. Delmore, K. Belk, B. Borlee, I. Geornaras, J. N. Martin, and J. L. Metcalf. 2022. A pilot study: The development of a facility-associated microbiome and its association with the presence of Listeria spp. in one small meat processing facility. Microbiology Spectrum 10:e0204522. doi: https://doi.org/10.1128/spectrum.02045-22
Bolton, D. J., C. Ivory, and D. McDowell. 2013. Thermal inactivation of Yersinia enterocolitica in pork slaughter plant scald tank water. Meat Sci. 95:668–671. doi: https://doi.org/10.1016/j.meatsci.2012.11.034
Bolton, D. J., R. Pearce, J. J. Sheridan, D. A. McDowell, and I. S. Blair. 2003. Decontamination of pork carcasses during scalding and the prevention of Salmonella cross-contamination. J. Appl. Microbiol. 94:1036–1042. doi: https://doi.org/10.1046/j.1365-2672.2003.01938.x
Botta, C., I. Ferrocino, A. Pessione, L. Cocolin, and K. Rantsiou. 2020. Spatiotemporal distribution of the environmental microbiota in food processing plants as impacted by cleaning and sanitizing procedures: the case of slaughterhouses and gaseous ozone. Appl. Environ. Microbiol. 86:e01861–20. doi: https://doi.org/10.1128/AEM.01861-20
Braley, C., P. Fravalo, M.-L. Gaucher, G. Larivière-Gauthier, F. Shedleur-Bourguignon, J. Longpré, and A. Thibodeau. 2022. Similar carcass surface microbiota observed following primary processing of different pig batches. Front. Microbiol. 13:849883. doi: https://doi.org/10.3389/fmicb.2022.849883
Bridier, A., P. Le Grandois, M.-H. Moreau, C. Prénom, A. Le Roux, C. Feurer, and C. Soumet. 2019. Impact of cleaning and disinfection procedures on microbial ecology and Salmonella antimicrobial resistance in a pig slaughterhouse. Sci. Rep. 9:12947. doi: https://doi.org/10.1038/s41598-019-49464-8
Bueno López, R., D. A. Vargas, R. L. Jimenez, D. E. Casas, M. F. Miller, M. M. Brashears, and X. M. Sanchez-Plata. 2022. Quantitative bio-mapping of salmonella and indicator organisms at different stages in a commercial pork processing facility. Foods (Basel, Switzerland) 11:2580. doi: https://doi.org/10.3390/foods11172580
Campos Calero, G., N. Caballero Gómez, N. Benomar, B. Pérez Montoro, C. W. Knapp, A. Gálvez, and H. Abriouel.2018. Deciphering resistome and virulome diversity in a porcine slaughterhouse and pork products through its production chain. Front. Microbiol. 9:2099. doi: https://doi.org/10.3389/fmicb.2018.02099
Campos Calero, G., N. Caballero Gómez, L. Lavilla Lerma, N. Benomar, C. W. Knapp, and H. Abriouel. 2020. In silico mapping of microbial communities and stress responses in a porcine slaughterhouse and pork products through its production chain, and the efficacy of HLE disinfectant. Food Res. Int. (Ottawa, Ont.), 136:109486. doi: https://doi.org/10.1016/j.foodres.2020.109486
Chaillou, S., A. Chaulot-Talmon, H. Caekebeke, M. Cardinal, S. Christieans, C. Denis, M. Hélène Desmonts, X. Dousset, C. Feurer, E. Hamon, J.-J. Joffraud, S. La Carbona, F. Leroi, S. Leroy, S. Lorre, S. Macé, M.-F. Pilet, H. Prévost, M. Rivollier, D. Roux, R. Talon, M. Zagorec, and M.-C. Champomier-Vergès. 2015. Origin and ecological selection of core and food-specific bacterial communities associated with meat and seafood spoilage. ISME J. 9:1105–1118. doi: https://doi.org/10.1038/ismej.2014.202
Channon, H. A., A. Payne, and R. D. Warner. 2003. Effect of stun duration and current level applied during head to back and head only electrical stunning of pigs on pork quality compared with pigs stunned with CO(2). Meat Sci. 65:1325–1333. doi: https://doi.org/10.1016/S0309-1740(03)00053-6
Cobo-Díaz, J. F., A. Alvarez-Molina, A. Alexa, C. J. Walsh, O. Mencía-Ares, P. Puente-Gómez, E. Likotrafiti, P. Fernández-Gómez, B. Prieto, F. Crispie, L. Ruiz, M. González-Raurich, M. López, M. Prieto, P. Cotter, and A. Alvarez-Ordóñez. 2021. Microbial colonization and resistome dynamics in food processing environments of a newly opened pork cutting industry during 1.5 years of activity. Microbiome 9:204. doi: https://doi.org/10.1186/s40168-021-01131-9
Corbellini, L. G., A. B. Júnior, E. de Freitas Costa, A. S. R. Duarte, E. R. Albuquerque, J. D. Kich, M. Cardoso, and M. Nauta. 2016. Effect of slaughterhouse and day of sample on the probability of a pig carcass being Salmonella-positive according to the Enterobacteriaceae count in the largest Brazilian pork production region. Int. J. Food Microbiol. 228:58–66. doi: https://doi.org/10.1016/j.ijfoodmicro.2016.03.030
De Filippis, F., A. La Storia, F. Villani, and D. Ercolini. 2013. Exploring the sources of bacterial spoilers in beefsteaks by culture-independent high-throughput sequencing. PloS One 8:e70222. doi: https://doi.org/10.1371/journal.pone.0070222
Dransfield, E., and D. K. Lockyer. 1985. Cold-shortening toughness in excised pork M. Longissimus dorsi. Meat Sci. 13:19–32. doi: https://doi.org/10.1016/S0309-1740(85)80002-4
Eastwood, L. C., T. M. Taylor, J. W. Savell, K. B. Gehring, and A. N. Arnold. 2021. Efficacy of antimicrobial interventions in reducing Salmonella enterica, Shiga toxin-producing Escherichia coli, Campylobacter, and Escherichia coli biotype I surrogates on non-chilled and chilled, skin-on and skinless pork. Meat Sci. 172:108309. doi: https://doi.org/10.1016/j.meatsci.2020.108309
Frontmatec. 2025. Pig scalding system—Optimal temperature of carcasses. Vertical Steam Scalding. https://www.frontmatec.com/en/pork-solutions/unclean-line/scalding-dehairing/vertical-steam-scalding (Accessed 16 March 2025.)https://www.frontmatec.com/en/pork-solutions/unclean-line/scalding-dehairing/vertical-steam-scalding
Gaire, T. N., C. Odland, B. Zhang, I. Slizovskiy, B. Jorgenson, T. Wehri, M. Meneguzzi, B. Wass, J. Schuld, D. Hanson, E. Doster, J. Singer, J. Cannon, A. Asmus, T. Ray, S. Dee, J. Nerem, P. Davies, and N. R. Noyes. 2024. Slaughtering processes impact microbial communities and antimicrobial resistance genes of pig carcasses. Sci. Total Environ. 946:174394. doi: https://doi.org/10.1016/j.scitotenv.2024.174394
Giaouris, E., E. Heir, M. Hébraud, N. Chorianopoulos, S. Langsrud, T. Møretrø, O. Habimana, M. Desvaux, S. Renier, and G.-J. Nychas. 2014. Attachment and biofilm formation by foodborne bacteria in meat processing environments: Causes, implications, role of bacterial interactions and control by alternative novel methods. Meat Sci. 97:298–309. doi: https://doi.org/10.1016/j.meatsci.2013.05.023
Gill, C. O., and J. Bryant. 1992. The contamination of pork with spoilage bacteria during commercial dressing, chilling and cutting of pig carcasses. Int. J. Food Microbiol. 16:51–62. doi: https://doi.org/10.1016/0168-1605(92)90125-m
Goulter, R. M., G. A. Dykes, and A. Small. 2008. Decontamination of knives used in the meat industry: Effect of different water temperature and treatment time combinations on the reduction of bacterial numbers on knife surfaces. J. Food Protect. 71:1338–1342. doi: https://doi.org/10.4315/0362-028x-71.7.1338
Hultman, J., R. Rahkila, J. Ali, J. Rousu, and K. J. Björkroth. 2015. Meat processing plant microbiome and contamination patterns of cold-tolerant bacteria causing food safety and spoilage risks in the manufacture of vacuum-packaged cooked sausages. Appl. Environ. Microbiol. 81:7088–7097. doi: https://doi.org/10.1128/AEM.02228-15
Kang, S., J. T. Ravensdale, R. Coorey, G. A. Dykes, R. S. Barlow. 2020. Bacterial community analysis using 16S rRNA amplicon sequencing in the boning room of Australian beef export abattoirs. Int. J. Food Microbiol. 332:108779. doi: https://doi.org/10.1016/j.ijfoodmicro.2020.108779
Kim, M., C. Barnett-Neefs, R. A. Chavez, E. Kealey, M. Wiedmann, M. J. Stasiewicz. 2024. Risk assessment predicts most of the salmonellosis risk in raw chicken parts is concentrated in those few products with high levels of high-virulence serotypes of salmonella. J. Food Protect. 87:100304. doi: https://doi.org/10.1016/j.jfp.2024.100304
Lax, S., and J. A. Gilbert. 2015. Hospital-associated microbiota and implications for nosocomial infections. Trends Mol. Med. 21:427–432. doi: https://doi.org/10.1016/j.molmed.2015.03.005
Lax, S., N. Sangwan, D. Smith, P. Larsen, K. M. Handley, M. Richardson, K. Guyton, M. Krezalek, B. D. Shogan, J. Defazio, I. Flemming, B. Shakhsheer, S. Weber, E. Landon, S. Garcia-Houchins, J. Siegel, J. Alverdy, R. Knight, B. Stephens, and J. A. Gilbert. 2017. Bacterial colonization and succession in a newly opened hospital. Sci. Transl. Med. 9:eaah6500. doi: https://doi.org/10.1126/scitranslmed.aah6500
Leps, J., K. Einschütz, N. Langkabel, and R. Fries. 2013. Efficacy of knife disinfection techniques in meat processing. Meat Sci. 95:185–189. doi: https://doi.org/10.1016/j.meatsci.2013.04.035
Li, L., Y. Xiao, C. Wang, R. H. Olsen, H. Meng, L. Shi. 2022. Exploring the resistome, virulome, mobilome and microbiome along pork production chain using metagenomics. Int. J. Food Microbiol. 371:109674. doi: https://doi.org/10.1016/j.ijfoodmicro.2022.109674
Lim, E. S., J. J. Kim, W. J. Sul, J. S. Kim, B. Kim, H. Kim, and O. K. Koo. 2021. Metagenomic analysis of microbial composition revealed cross-contamination pathway of bacteria at a foodservice facility. Front. Microbiol. 12:636329. doi: https://doi.org/10.3389/fmicb.2021.636329
Lonergan, S. M., E. Huff-Lonergan, L. J. Rowe, D. L. Kuhlers, and S. B. Jungst. 2001. Selection for lean growth efficiency in Duroc pigs influences pork quality. J. Anim. Sci. 79:2075–2085. doi: https://doi.org/10.2527/2001.7982075x
Marcon, A. V., F. R. Caldara, G. F. de Oliveira, L. M. P. Gonçalves, R. G. Garcia, I. C. L. A. Paz, C. Crone, and A. Marcon. 2019. Pork quality after electrical or carbon dioxide stunning at slaughter. Meat Sci. 156:93–97. doi: https://doi.org/10.1016/j.meatsci.2019.04.022
Midelet, G., and B. Carpentier. 2002. Transfer of microorganisms, including Listeria monocytogenes, from various materials to beef. Appl. Environ. Microbiol. 68:4015–4024. doi: https://doi.org/10.1128/AEM.68.8.4015-4024.2002
Pearson, A. M. 1987. Muscle function and postmortem changes. In: J. F. Price and B. S. Schwigert (Eds.) The Science of Meat and Meat Products. 3rd ed. Food and Nutrition Press, Inc., Westport, CT. p 155–191.
Peruzy, M. F., K. Houf, M. Joossens, Z. Yu, Y. T. R. Proroga, and N. Murru. 2021. Evaluation of microbial contamination of different pork carcass areas through culture-dependent and independent methods in small-scale slaughterhouses. Int. J. Food Microbiol. 336:108902. doi: https://doi.org/10.1016/j.ijfoodmicro.2020.108902
Pothakos, V., G. Stellato, D. Ercolini, and F. Devlieghere. 2015. Processing environment and ingredients are both sources of leuconostoc gelidum, which emerges as a major spoiler in ready-to-eat meals. Appl. Environ. Microbiol. 81:3529–3541. doi: https://doi.org/10.1128/AEM.03941-14
Pozuelo, K. C., D. Vega, K. Habib, F. Najar-Villarreal, Q. Kang, V. Trinetta, T. G. O’Quinn, R. K. Phebus, and S. E. Gragg. 2021. Validation of post-harvest antimicrobial interventions to control Shiga toxin-producing Escherichia coli (STEC) on market hog carcass surfaces. Int. J. Food Microbiol. 358:109421. doi: https://doi.org/10.1016/j.ijfoodmicro.2021.109421
Shackelford, S. D., D. A. King, and T. L. Wheeler. 2012. Chilling rate effects on pork loin tenderness in commercial processing plants. J. Anim. Sci. 90:2842–2849. doi: https://doi.org/10.2527/jas.2011-4855
Shedleur-Bourguignon, F., T. Duchemin, W. P. Thériault, J. Longpré, A. Thibodeau, M. N. Hocine, and P. Fravalo. 2023. Distinct microbiotas are associated with different production lines in the cutting room of a swine slaughterhouse. Microorganisms, 11:133. doi: https://doi.org/10.3390/microorganisms11010133
Springer, M. P., M. A. Carr, C. B. Ramsey, and M. F. Miller. 2003. Accelerated chilling of carcasses to improve pork quality. J. Anim. Sci. 81:1464–1472. doi: https://doi.org/10.2527/2003.8161464x
Stellato, G., A. La Storia, T. Cirillo, and D. Ercolini. 2015. Bacterial biogeographical patterns in a cooking center for hospital foodservice. Int. J. Food Microbiol. 193:99–108. doi: https://doi.org/10.1016/j.ijfoodmicro.2014.10.018
Stellato, G., A. La Storia, F. De Filippis, G. Borriello, F. Villani, and D. Ercolini. 2016. Overlap of spoilage-associated microbiota between meat and the meat processing environment in small-scale and large-scale retail distributions. Appl. Environ. Microbiol. 82:4045–4054. doi: https://doi.org/10.1128/AEM.00793-16
Taormina, P. J., and W. J. Dorsa. 2007. Evaluation of hot-water and sanitizer dip treatments of knives contaminated with bacteria and meat residue. J. Food Protect. 70:648–654. doi: https://doi.org/10.4315/0362-028x-70.3.648
United States Department of Agriculture Agricultural Marketing Service (USDA-AMS). 2020. Institutional Meat Purchase Specifications | Agricultural Marketing Service. https://www.ams.usda.gov/grades-standards/imps (Accessed 16 March 2025.)https://www.ams.usda.gov/grades-standards/imps
Velarde, A., M. Gispert, L. Faucitano, X. Manteca, and A. Diestre. 2000. The effect of stunning method on the incidence of PSE meat and haemorrhages in pork carcasses. Meat Sci. 55:309–314. doi: https://doi.org/10.1016/s0309-1740(99)00158-8
Wang, R., M. Guragain, S. Chitlapilly Dass, V. Palanisamy, and J. M. Bosilevac. 2024. Impact of intense sanitization on environmental biofilm communities and the survival of Salmonella enterica at a beef processing plant. Front Microbiol. 15. doi: https://doi.org/10.3389/fmicb.2024.1338600
Warriner, K., T. G. Aldsworth, S. Kaur, and C. E. R. Dodd. 2002. Cross-contamination of carcasses and equipment during pork processing. J. Appl. Microbiol. 93:169–177. doi: https://doi.org/10.1046/j.1365-2672.2002.01678.x
Wheatley, P., E. S. Giotis, and A. I. McKevitt. 2014. Effects of slaughtering operations on carcass contamination in an Irish pork production plant. Irish Vet. J. 67:1. doi: https://doi.org/10.1186/2046-0481-67-1
Wheeler, T. L., N. Kalchayanand, and J. M. Bosilevac. 2014. Pre- and post-harvest interventions to reduce pathogen contamination in the U.S. beef industry. Meat Sci. 98:372–382. doi: https://doi.org/10.1016/j.meatsci.2014.06.026
Wood, M., S. M. Gibbons, S. Lax, T. W. Eshoo-Anton, S. M. Owens, S. Kennedy, J. A. Gilbert, and J. T. Hampton-Marcell. 2015. Athletic equipment microbiota are shaped by interactions with human skin. Microbiome 3:25. doi: https://doi.org/10.1186/s40168-015-0088-3
Xu, Z. S., V. D. Pham, X. Yang, M. G. Gänzle. 2025. High-throughput analysis of microbiomes in a meat processing facility: Are food processing facilities an establishment niche for persisting bacterial communities? Microbiome 13:25. doi: https://doi.org/10.1186/s40168-024-02026-1
Yang, X., C. Narvaez-Bravo, and P. Zhang. 2023. Driving forces shaping the microbial ecology in meat packing plants. Front. Microbiol. 14:1333696. doi: https://doi.org/10.3389/fmicb.2023.1333696
Zwirzitz, B., S. U. Wetzels, E. D. Dixon, B. Stessl, A. Zaiser, I. Rabanser, S. Thalguter, B. Pinior, F.-F. Roch, C. Strachan, J. Zanghellini, M. Dzieciol, M. Wagner, and E. Selberherr. 2020. The sources and transmission routes of microbial populations throughout a meat processing facility. NPJ Biofilms and Microbiomes, 6:Article 1. doi: https://doi.org/10.1038/s41522-020-0136-z