More than 150 species of microorganisms were identified in animal feces that can cause infectious diseases in humans including E. coli, Salmonella, Giardia, Campylobacter, and Cryptosporidium parvum. Some viruses in animal feces can also cause health problems to both livestock and humans. Researchers have found that E. coli O157: H7 can infect the edible part of lettuce through its roots. Natvig and colleagues found that cleaning cannot effectively remove pathogens off the surface of vegetables. Cow manure is frequently used as fertilizer that is spread onto the land for crop production. Because of the presence of zoonotic pathogens in untreated manure, using such manure as fertilizer for crops may serve as a vehicle for pathogen transmission in the food supply chain. In our study, the main phyla among the bacterial communities detected in the dairy farm matrix were Proteobacteria, Firmicutes, Bacteroidetes, and Actinobacteria, which have been reported to be common phyla of bacteria in both cow manure and soil. In addition to these common phyla, 16S rDNA sequence analysis also indicated that a large number of bacteria in the phylum TM7 were present in the samples analyzed in our study; in fact, drying room it was the ninth most common phylum detected. TM7 has no known pure-culture representatives and is only characterized by 16S ribosomal DNA sequence data.
The phylum TM7 is widely distributed in the environment , and recent studies reported the existence of TM7 in the cattle gut. Although it remains to be confirmed whether TM7 in the cattle gut is part of the microbiota or an environmental contaminant, studies have demonstrated that TM7 is associated with human inflammatory mucosal diseases and oral disease. The function of TM7 in the environment is still poorly understood due to the absence of pure cultures. The existence of TM7 in dairy fecal samples and manure samples in our study suggested that if this type of manure is used as fertilizer in farms, then caution should be taken since TM7 has been shown to be pathogenic. The bacterial population in fresh feces is a mixture of the intestinal microorganisms, bacteria from the air, and digested foraged bacteria. Because fresh feces were collected immediately after defecation, the bacterial population in the fresh feces might be more similar to that in the intestinal environment. When compared with fresh feces, manure contained a less diverse bacterial community composition. This is probably due to the bacterial die-off that occurs naturally after fecal shedding and the accumulation of environmental pressures. In addition, the bacterial community structure changed during the process of manure accumulation due to bacterial interactions in this environment. Therefore, the bacterial population in manure consists of a mixture of soil bacteria and the newly established community.
As reported by other researchers, the methods of manure treatment could alter the bacterial community in the manure, which was con- firmed by analysis of the microbial population using sequencing methods. Stacking of manure can result in alteration of the bacterial populations due to the exposure to oxygen that may typically promote the growth of facultative anaerobic organisms. Facultative anaerobes, which initially inhabited the intestines in relatively low numbers, may undergo anabiosis during the subsequent excretion process. We found that during feces accumulation, the types of microbial communities present declined, but the number of some of bacteria rose, which may be related to the proliferation of interstitial anaerobic bacteria. Our results demonstrated that the accumulation of manure leads to shifts in the bacterial community composition. Our results indicated that approximately 50% of the bacterial population in feces comprised Firmicutes, which was consistent with previous reports. Most bacteria in the mammalian gut microflora are specific to the environmental niche of the gastrointestinal tract and are barely able to survive outside this environment. This explains the decrease in gut bacteria in accumulated manure and the increase in other bacteria. Another cause for concern in manure is the presence of antibiotic resistance genes carried by certain pathogenic bacteria, such as those belonging to the family Clostridiaceae, including C. tetani, C. botulinum, and C. perfringens. These bacteria were also detected in the manure in our study. Moreover, the application of manure to soil impacts on the soil microbial community by introducing some bacterial taxa as well as new nutrients.
The persistence of these bacteria in soil may enhance the likelihood of these bacteria entering the food chain through contaminated crops and becoming active antibiotic resistance gene donors when transferred back to anaerobic conditions in an animal or human gut. Acinetobacter, Pseudomonas, and Lysinibacillus species are strictly aerobic bacteria and are not usual members of the gut microflora. Although these species of bacteria may not be able to survive in the gut when facing different growth conditions and changed environments, they can potentially share and transmit antibiotic resistance genes or virulence genes to other bacteria. Other studies have corroborated the role of the Acinetobacter and Pseudomonas taxa in the persistence of antibiotic resistance genes in manure treated soils. In our study, we also found that three genera of bacteria appeared in all types of samples, with Acinetobacter and Streptococcus being more abundant in fresh feces and manure than in soil and Pseudomonas being more abundant in soil and manure than in fresh feces. The abundance of Staphylococcus in manure was higher than that in fresh feces and soil, the most important member of this genus being S. aureus. S. aureus is still described as one of the most frequently isolated etiological agents associated with bovine intramammary infections, and some studies have shown a high incidence of S. aureus with genomic variation in resistance genes, which may pose a threat to public and animal health in Ningxia Province, China. These pathogens displayed differences in antimicrobial resistance and could serve as carriers introducing antibiotic resistance genes into the food chain. Our results suggested that the application of poorly treated dairy manure as a soil amendment or organic fertilizer poses a potential risk for food safety and public health due to the potential transmission of antibiotic resistance genes or virulence genes and the possibility of introducing zoonotic pathogens into the environment. Therefore, accumulation of manure without any further treatment poses a direct hazard to the farm environment and the surroundings, which is a security risk for dairy farming and human public health. Livestock manure is a source of pollution, but it is also a huge organic resource that can been used in many areas after proper treatment. There are many ways for treatment of livestock manure. Decomposing components of livestock manure is a relatively common method. It is generally believed that composting at the temperature above 50° C for 5-10 days can meet the standard of harmlessness of manure [57, 58], but pathogenic microorganisms cannot be guaranteed during the accumulation process. The lower animals such as maggots and cockroaches can be used to decompose the manure of the livestock. This method can not only process livestock manure but also provide animal protein for feed. Maggots of the fly are very good animal protein feeds. Biological fermentation is another way for treatment of livestock manure. After biological fermentation, vertical farming units harmful microorganisms such as pathogenic bacteria and parasitic eggs can be eliminated. Livestock manure has a high calorific value and can be used as a fuel to obtain heat. Livestock manure is rich in cellulose, which can also be used as a raw material to produce ethanol. All of the above methods can eliminate pathogens to varying degrees; however, more research is needed to explain whether antibiotic residues in manure can be eliminated. In summary, this study revealed the microbial community composition and diversity in the dairy farm matrix, as well as the abundance and distribution of pathogens. Our results demonstrated that accumulated manure that has not been subjected to further treatment may lead to a shift in the bacterial community composition and the enrichment of zoonoses. \
Dairy manure that has not undergone proper treatment therefore poses a threat to the environment and to public health. Therefore, developing and updating manure treatment practices should be considered a priority in dairy farm management. Our findings provide a theoretical basis for the necessity to treat dairy manure to prevent the spread of human pathogenic bacteria and other pathogens, thereby laying the foundation for sustainable local food-producing animal agriculture and protection of public health in the Ningxia region.Accurate detection of physical interference between two or more bodies is crucial in the design of many engineering systems. Modeling interference between physical bodies is, therefore, an important problem in computational design. Non-interference constraints appear in numerical optimization problems that manipulate an object within an environment containing other objects such that there is no collision. Efficient and accurate modeling of the non-interference constraints is critical for fast and reliable solutions in the overarching optimization problem. Prior literature on these problems describe these constraints using inconsistent terminology, e.g., anatomical constraints, spatial integration constraints, boundary constraints, and interference checks . We observe that these terms represent the same underlying constraint. We propose to call these constraints geometric non-interference constraints since they are employed in design optimization to ensure a design where there exists no interference between two or more geometric shapes or paths of motion. In our study, a geometric shape is associated with the design configuration of an engineering system at a particular instance of time. The geometric shapes of interest in this paper are curves in two dimensions, or orientable surfaces in three dimensions. We assume that the geometric shapes are non-self-intersecting but make no assumptions on whether they are open or closed. A path of motion or trajectory is the set of points that traces the motion of a point on the engineering system as the system changes configuration over time. The paths considered in this paper are simply curves in two or three dimensions. We use the term layout to refer to a set of geometric shapes. Based on the definitions above, we identify three major classes of optimization problems with geometric non-interference constraints: layout optimization, shape optimization, and optimal path planning. All three classes are parts of the scope of problems we address in this paper. Layout optimization optimizes the positions of geometric shapes via translation subject to geometric non-interference, with or without additional boundary constraints. For example, the wind farm layout optimization problem consists in positioning the wind turbines within a wind farm in an optimal way such that interference between turbines and the boundary of the farm is avoided. Another example of a layout optimization problem is the packing problem. Packing problems consist of positioning objects within a space to ensure the minimum space is occupied or the maximum number of objects are placed without geometric interference. Shape optimization seeks to optimize geometric shapes subject to geometric noninterference, with or without additional boundary constraints. For example, shape optimization of an aircraft fuselage optimizes the shape of a fuselage with constraints ensuring that the passengers, crew, payload, and all the subsystems fit inside the fuselage. Optimal path planning optimizes the trajectory of a point or a set of points subject to geometric non-interference, with or without additional boundary constraints. Robot motion planning is a class of problems that falls under optimal path planning and is widely researched. The design optimization of surgical robots is an example of a problem involving robot motion planning that has had recent attention. In the design optimization of surgical robots, non-interference constraints are imposed such that the robot does not collide with the anatomy of a patient during operation. Additionally, it is desirable for the robot to maintain a safe distance from the anatomy, motivating the use of a distance-based non-interference constraint formulation in such problems. Historically, gradient-free algorithms have been more commonly used to solve such problems, e.g., in layout optimization and in robot motion planning. A major reason behind this was the difficulty in efficiently computing the derivatives for a complex model. As models become more complex, that is, with more disciplines and design variables, solutions become impracticable with gradient-free algorithms since these algorithms scale poorly with the number of design variables. However, the recent emergence of modeling frameworks such as OpenMDAO has enabled efficient design of large-scale and multidisciplinary systems using gradient-based optimization, including some of the aforementioned problems with geometric non-interference constraints.