Abstract:Treatment of common pathogens, such as Salmonella species, Escherichia coli, Staphylococcus aureus, etc., is a big challenge for a practitioner. Antibiotics’ side effects during their application for the treatment of infectious diseases should not be underestimated as they have many issues, such as the transfer of antibiotics-resistant genes, dysbiosis, and antibiotic-resistant strains, which is the main hurdle in the eradication of diseases. To avoid these antibiotics complications, in modern countries, the i… Show more
“…Factors such as soil composition and microbial diversity can either facilitate or limit the survival of Listeria [42], indicating that microbial competition, potentially including competition from Rummeliibacillus, could influence the prevalence of Listeria. Lactic acid bacteria (LAB) [43], including Lactococcus [44] and Lactobacillus species, are known for their role in producing fermented foods and for their ability to inhibit the growth of pathogenic bacteria through the production of lactic acid, bacteriocins, and AMPs. Acidification of the environment due to lactic acid generation by LAB inhibits the growth of [45,46] Listeria and Salmonella.…”
In this study, we explore how transformer models, which are known for their attention mechanisms, can improve pathogen prediction in pastured poultry farming. By combining farm management practices with microbiome data, our model outperforms traditional prediction methods in terms of the F1 score—an evaluation metric for model performance—thus fulfilling an essential need in predictive microbiology. Additionally, the emphasis is on making our model’s predictions explainable. We introduce a novel approach for identifying feature importance using the model’s attention matrix and the PageRank algorithm, offering insights that enhance our comprehension of established techniques such as DeepLIFT. Our results showcase the efficacy of transformer models in pathogen prediction for food safety and mark a noteworthy contribution to the progress of explainable AI within the biomedical sciences. This study sheds light on the impact of effective farm management practices and highlights the importance of technological advancements in ensuring food safety.
“…Factors such as soil composition and microbial diversity can either facilitate or limit the survival of Listeria [42], indicating that microbial competition, potentially including competition from Rummeliibacillus, could influence the prevalence of Listeria. Lactic acid bacteria (LAB) [43], including Lactococcus [44] and Lactobacillus species, are known for their role in producing fermented foods and for their ability to inhibit the growth of pathogenic bacteria through the production of lactic acid, bacteriocins, and AMPs. Acidification of the environment due to lactic acid generation by LAB inhibits the growth of [45,46] Listeria and Salmonella.…”
In this study, we explore how transformer models, which are known for their attention mechanisms, can improve pathogen prediction in pastured poultry farming. By combining farm management practices with microbiome data, our model outperforms traditional prediction methods in terms of the F1 score—an evaluation metric for model performance—thus fulfilling an essential need in predictive microbiology. Additionally, the emphasis is on making our model’s predictions explainable. We introduce a novel approach for identifying feature importance using the model’s attention matrix and the PageRank algorithm, offering insights that enhance our comprehension of established techniques such as DeepLIFT. Our results showcase the efficacy of transformer models in pathogen prediction for food safety and mark a noteworthy contribution to the progress of explainable AI within the biomedical sciences. This study sheds light on the impact of effective farm management practices and highlights the importance of technological advancements in ensuring food safety.
Coccidia of the genus
Eimeria
are specialized intracellular parasitic protozoa that cause severe coccidiosis when they infect their hosts. Animals infected with
Eimeria
develop clinical symptoms, such as anorexia, diarrhea, and hematochezia, which can even cause death. Although the current preferred regimen for the treatment of coccidiosis is antibiotics, this treatment strategy is limited by the ban on antibiotics and the growing problem of drug resistance. Therefore, the exploration of alternative methods for controlling coccidiosis has attracted much attention.
Lactobacillus plantarum
has been shown to have many beneficial effects. In this study,
L. plantarum
M2 was used as a research object to investigate the effect of
L. plantarum
on intestinal inflammation induced by infection with
Eimeria falciformis
in mice by detecting indicators, such as oocyst output, serum cytokines, and the intestinal microbiota. Compared with that in the infection group, the percent weight loss of the mice that were administered with
L. plantarum
M2 was significantly reduced (
P
< 0.05). Supplemented
L. plantarum
M2 and probiotics combined with diclazuril can reduce the total oocyst output significantly (
P
< 0.05,
P
< 0.001).
L. plantarum
M2 had outstanding performance in maintaining intestinal barrier function, and the levels of the mucin MUC1 and the tight junction protein E-cadherin were significantly elevated (
P
< 0.01,
P
< 0.05). Studies have shown that probiotic supplementation can alleviate adverse reactions after infection and significantly improve intestinal barrier function. In addition, probiotics combined with diclazuril could optimize the partial efficacy of diclazuril, which not only enhanced the effect of antibiotics but also alleviated their adverse effects. This study expands the application of probiotics, provides new ideas for alternative strategies for coccidia control, and suggests a basis for related research on lactobacilli antagonizing intracellular pathogen infection.
IMPORTANCE
Coccidia of the genus
Eimeria
are specialized intracellular parasitic protozoa, and the current preferred regimen for the treatment of coccidiosis is antibiotics. However, due to antibiotic bans and drug resistance, the exploration of alternative methods for controlling coccidiosis has attracted much attention. In this work, we focused on
Lactobacillus plantarum
M2 and found that probiotic supplementation can alleviate adverse reactions after infection and improve intestinal barrier function. This study proposes the possibility of using lactic acid bacteria to control coccidiosis, and its potential mechanism needs further exploration.
In recent years, lactic acid bacteria, widely used in food fermentation, have been recognized as beneficial components of the human microbiome in which they play an important role [...]
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