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Introduction to the microbiome: Impacts, benefits, and challenges in healthy and diseased animals. K. Leistikow
The microbiome is all the genetic material of agents living inside the living being (bacteria, viruses, fungi, protozoa, archaea). They are essential for our genome (>100 trillion microbes), our metabolism, and essential physiological functions, they are even related to pathologies such as cancer, the modulation of our behavior, and antimicrobial resistances. They are involved in the pathology of infectious agents, emotions, cognition, the intestinal barrier, and immunity. The microbiome is transmitted vertically,also by the diet and the environment, conditioned by numerous factors. The microbiota of healthy and diseased animals in different locations are different (intestine, lung, reproductive system). Interpreting the microbiome is complex and numerous research studies and clinical trials have shown this to be the case. The big question is "What is the ideal microbiome?" Research avenues focus on understanding and evaluating microbiota in pigs at different stages of production. The antibiotic treatments along with adaptation and horizontal and vertical evolution of the different microbes have an important impact.
There are many causes of antibiotic resistance, and we must also consider the impact of antibiotics on the microbiome depending on their spectrum of action, causing dysbiosis (biotic expansion, reduction of diversity) and triggering resistance to certain infectious agents that can be transmitted from dams to piglets.
More than 90% of bacteria live and grow primarily in biofilm form. More than 80% of all bacterial infections are caused by biofilm formation, making it difficult in some cases for the antibiotic to penetrate the biofilm that forms in water pipes, floors, walls, and facilities where organic matter is present. It is estimated that eliminating all dry matter during sanitary downtime procedures in piglet housing can improve piglet growth by 3.5%. Microbes can adapt by both vertical and horizontal gene transfer (conjugation-plasmids, transduction-phages, and transformation). More than 78% of all E. coli isolates at ISU, USA, have genes for more than three toxicity factors. Microbiomes from different sections of the intestine have different composition and interact with each other in a competitive, coexisting, or priority manner, which explains, in part, the increased risk of enteric pathologies when multiple pathogens are present (E. coli + Lawsonia x1.51 – E. coli + Lawsonia + Clostridium x1.78 and E. coli + Salmonella + Lawsonia + Clostridium x2.44), and it plays an important effect on the immune response.
Not all microorganisms can grow in the laboratory, so studying their interactions in vivo is complex. We have sequencing as a weapon. The central dogma of biology focuses on differentiating genes - mRNA, microbiome, and metabolome. The methods used are numerous and complex: culturome, amplicon, metagenome, virome, and metactransriptome from microbes, DNA, or mRNA. In analyzing the results, alpha diversity must be assessed against beta diversity both in the number of organisms per sample and their comparative abundance between samples. Greater diversity is better because it can better adapt to changes and it prevents the ecosystem from collapsing, which would facilitate the invasion of infectious agents. Can the microbiome of animals positively regulate the environment and improve human health by improving soil and water quality?
Modulating the microbiome with feed interventions: Strategies and challenges in swine and livestock production. N. Noyes
The microbiome is incredibly dynamic, especially in young animals (Luo, 2022). The distribution of enterotypes is 85%, 8%, and 7% for E1, E2, and E3 respectively in suckling piglets, varying to 16/50/34% in weaned piglets and 0/60/40% in growing pigs. In pigs, as in humans and other species, there are three phases in the evolution of the microbiome: developmental phase, transitional phase, and stable phase. There are also large differences in microbiome composition in different tissues and organs (Holman DB, 2017). For example, in the gastric mucosa, Firmicutes abounds with fewer Bacteroidetes and Proteobacteria in equal parts. In the duodenum there are no Bacteroidetes as in the jejunum. Proteobacteria predominates in the duodenal mucosa and Firmicutes in the jejunal mucosa. In addition, to complicate the interpretation, there are considerable differences between groups of animals and farms. It is therefore important to look at the associations between the most relevant phenotypes associated with the best production results (changes in average daily gain, health status). Is it possible to ignore all the variations in microorganisms and just keep the most relevant ones (those that account for 90% of the total)? Many of the published studies give hypotheses that sometimes cause confusion.
Nutritional interventions and technologies for productivity in healthy and challenged animals. D. Rosero. Iowa State University
Numerous risk factors cause post-weaning mortality in piglets. The age at weaning is essential. At weaning, we separate them from their mother, we change the presentation of the diet, we change the environment, we mix the piglets, and they come into contact with new pathogens and antigens. Digestive barrier functions are compromised in early weaning (mannitol flux decreases with age). Mortality (%) = Exp (3.73 + (-0.092 x Age at weaning)). Logically, mortality at weaning increases when there are epidemic cases of PRRSV compared to piglets with endemic or negative PRRS. In the case of E. coli, mortality is higher the younger the piglets are (16>18>21 days old). We must consider that many pathogens are waiting to find the opportunity to present themselves and cause disease, and can cause both subclinical and clinical problems. Maternal health has a major impact on the early health of piglets ("It all starts at the sow farm"). PRRSV impacts the average daily gain through its effect on feed intake, reducing these parameters by 58% and 51% respectively.
We have different action measures to minimize the negative effects. In terms of production techniques, we should improve colostrum intake and increase the age at weaning to over 23 days, as well as facilitate early feed intake (first three days post-weaning), which defines the average daily gain during the post-weaning phase. Piglets should be provided with solid feed in the farrowing pen as soon as possible. A greater number of piglets don't eat in the three days post-weaning when they haven't eaten early compared to when they have (28% and 15% non-eaters respectively).
Functional amino acids such as tryptophan, threonine, and methionine play an important role in increased intake. Certain raw materials that improve piglets' immune capacity also help us to get them to eat earlier and more, as is the case with milk protein and plasma, as well as milk immunoglobulins. The IgA present in milk mitigates the effect of certain pathogens (E. coli). The 1-3 beta-glucans from yeast activate innate immunity, having a clear dose-response effect. Numerous nutritional additives impact digestive health such as Cu and Zn improving feed intake in the days after weaning and reducing intestinal villus atrophy. Reducing protein levels to lower proteolytic fermentation reduces the incidence of diarrhea by minimizing the metabolites produced (amines, ammonia, S2H). In numerous studies, although high protein levels increase the incidence of diarrhea, they do not necessarily hinder productive parameters. Including high levels of soybean meal with or without phytases affects the quality of the feces, with the use of super doses (>2000 FTU) being positive.
Bone mineralization is related to the incidence of locomotor disorders. One way to analyze this is to determine the ash levels, density, and histopathology of certain bones, such as the metacarpals and 2nd and 10th ribs. Ash levels vary depending on whether complete or defatted fragments are analyzed. Scientific studies have observed a reduction in standard deviations when bones are analyzed after having had their fat removed, which is greater in finishing pigs than in piglets since the former can have up to 10% fat. This means that the ash levels in finishing pigs (when we analyze defatted bones) have between 14-15% more content, while in piglets it is usually 11-12% higher.
Deficient phosphorus levels in pigs over prolonged periods can result in low serum phosphorus levels, which is being observed in some of the studies presented, where healthier pigs have 16% more serum phosphorus compared to delayed pigs. The same is true for calcium and vitamin D levels. Serum phosphorus ranges from 4.5 to 18 mg/dL.
Work on precision nutrition has increased in the last ten years, as has research on micronutrient requirements (vitamins and trace elements). Already in 1960, vitamin E and selenium deficiency were related to sudden death and reproductive failure, and today we know that piglets weaned too young have low serum vitamin E levels after weaning and that colostrum and milk are deficient in vitamin D, an essential nutrient not only for optimizing bone development, but also for improving immune functions. They estimate that pigs' vitamin requirements today are higher than the NRC recommendations. Thus, precision nutrition is a concept that tends to improve efficiency and sustainability as it considers genetic progress, and changes in facilities and management while understanding its association with changes in nutritional requirements to optimize pig productivity, health, and welfare.
Swine health through nutrition: Cooperative strategies to maximize productivity and potential. E. Toohill y C. Neill. Carthage Veterinary Service
Health and nutrition are two of the essential pillars of swine production so interaction between the two teams is important, although we know that sometimes the two departments are not aligned, causing frustration between the two and throughout the company. When veterinarians and nutritionists work together we can expect great things. It is critical to define the problem by establishing consistent and clear communication between the people involved, for which on-farm visits are essential. This allows us to see the problem while minimizing subjective or conditioned judgments, determining where, how many, when, and how.
From a nutritional perspective, we must review the formulation, feed quality (color, flavor, foreign materials, particle size), and determine the appropriate feed for the production phase.
From a sanitary perspective, we must assess pathogens, pig resistance to pathologies, stress factors, presence of clinical signs (prevalence per day and week), mortality per day and week related to diet changes, piglet weights, farrowing room sanitation, sanitary down times, and farrowing pen management (colostrum).
Once the problem has been determined, we must take measures and evaluate the results over time. We must jointly evaluate the productive parameters: entry and exit weights, average daily gain, average daily consumption in the first week and the rest of the time, days to market and mortality. How much they grow in the first week after weaning determines their growth for the rest of their lives, which, logically, is directly related to feed consumption in that week. Mortality is one of the main parameters for assessing the interaction between health and nutrition.
Antonio Palomo Yagüe
