Improved MeSH analysis software tools for farm animals.
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ABSTRACT:
SUBMITTER: Amorim ST
PROVIDER: S-EPMC9300174 | biostudies-literature | 2022 Feb
REPOSITORIES: biostudies-literature
Publications
Improved MeSH analysis software tools for farm animals.
Amorim Sabrina T ST Tsuyuzaki Koki K Nikaido Itoshi I Morota Gota G
Animal genetics 20211202 1
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Project description:Limited and judicious antimicrobial usage (AMU) is considered the key to saving the success of human and veterinary medicine in treating infections. With the limited alternatives for antimicrobials, farm biosecurity (and herd management) is considered a promising tool to mitigate the non-judicious AMU and to maintain animal health, production, and welfare. The present scoping review aims to analyse the effect of farm biosecurity on AMU in livestock systems and formulate recommendations. Peer-reviewed manuscripts published between 2001-2022 were analyzed using the PRISMA framework using PubMed, Scopus, and Science Direct databases. After applying the inclusion criteria, 27 studies were found to assess the effect of farm biosecurity (or management practices) on AMU at the herd/farm level in quantitative/semi-quantitative terms. These studies were carried out in 16 countries, of which 74.1% (20/27) were from 11 European countries. The highest number of studies were from pig farms [51.8% (14/27)], followed by poultry (chicken) farms [25.9% (7/27)], cattle farms [11.1% (3/27)], and a single study from a turkey farm. Two studies include both pig and poultry farms. Most of the studies were cross-sectional [70.4% (19/27)], seven were longitudinal, and one was a case-control study. Complex interactions were observed among factors influencing AMU, such as biosecurity measures, farm characteristics, farmers' attitudes, availability of animal health services, stewardship, etc. A positive association between farm biosecurity and reduction in AMU was observed in 51.8% (14/27) of the studies, and 18.5% (5/27) showed that improvement in farm management practices was associated with a reduction in AMU. Two studies highlighted that coaching and awareness among farmers might lead to a decrease in AMU. A single study on economic assessment concluded biosecurity practices as a cost-effective way to reduce AMU. On the other hand, five studies showed an uncertain or spurious association between farm biosecurity and AMU. We recommend the reinforcement of the concept of farm biosecurity, especially in lower- and middle-income countries (LMICs). Further, there is a need to strengthen the evidence on the association between farm biosecurity and AMU in region- and species-specific farm settings.
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Project description:In livestock species, the monolayer of epithelial cells covering the digestive mucosa plays an essential role for nutrition and gut barrier function. However, research on farm animal intestinal epithelium has been hampered by the lack of appropriate in vitro models. Over the past decade, methods to culture livestock intestinal organoids have been developed in pig, bovine, rabbit, horse, sheep and chicken. Gut organoids from farm animals are obtained by seeding tissue-derived intestinal epithelial stem cells in a 3-dimensional culture environment reproducing in vitro the stem cell niche. These organoids can be generated rapidly within days and are formed by a monolayer of polarized epithelial cells containing the diverse differentiated epithelial progeny, recapitulating the original structure and function of the native epithelium. The phenotype of intestinal organoids is stable in long-term culture and reflects characteristics of the digestive segment of origin. Farm animal intestinal organoids can be amplified in vitro, cryopreserved and used for multiple experiments, allowing an efficient reduction of the use of live animals for experimentation. Most of the studies using livestock intestinal organoids were used to investigate host-microbe interactions at the epithelial surface, mainly focused on enteric infections with viruses, bacteria or parasites. Numerous other applications of farm animal intestinal organoids include studies on nutrient absorption, genome editing and bioactive compounds screening relevant for agricultural, veterinary and biomedical sciences. Further improvements of the methods used to culture intestinal organoids from farm animals are required to replicate more closely the intestinal tissue complexity, including the presence of non-epithelial cell types and of the gut microbiota. Harmonization of the methods used to culture livestock intestinal organoids will also be required to increase the reproducibility of the results obtained in these models. In this review, we summarize the methods used to generate and cryopreserve intestinal organoids in farm animals, present their phenotypes and discuss current and future applications of this innovative culture system of the digestive epithelium.
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Project description:IntroductionThe field of metabolomics has expanded greatly over the past two decades, both as an experimental science with applications in many areas, as well as in regards to data standards and bioinformatics software tools. The diversity of experimental designs and instrumental technologies used for metabolomics has led to the need for distinct data analysis methods and the development of many software tools.ObjectivesTo compile a comprehensive list of the most widely used freely available software and tools that are used primarily in metabolomics.MethodsThe most widely used tools were selected for inclusion in the review by either ≥ 50 citations on Web of Science (as of 08/09/16) or the use of the tool being reported in the recent Metabolomics Society survey. Tools were then categorised by the type of instrumental data (i.e. LC-MS, GC-MS or NMR) and the functionality (i.e. pre- and post-processing, statistical analysis, workflow and other functions) they are designed for.ResultsA comprehensive list of the most used tools was compiled. Each tool is discussed within the context of its application domain and in relation to comparable tools of the same domain. An extended list including additional tools is available at https://github.com/RASpicer/MetabolomicsTools which is classified and searchable via a simple controlled vocabulary.ConclusionThis review presents the most widely used tools for metabolomics analysis, categorised based on their main functionality. As future work, we suggest a direct comparison of tools' abilities to perform specific data analysis tasks e.g. peak picking.
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