Raw Cow Milk Bacterial Consortium as Bioindicator of Circulating Anti-Microbial Resistance (AMR).
TL;DR: (meta)proteomics analysis of bacterial compartment of raw milk is applied to obtain a method that provides a measurement of circulating AMR involved proteins and gathers information about the whole bacterial composition.
Abstract: The environment, including animals and animal products, is colonized by bacterial species that are typical and specific of every different ecological niche. Natural and human-related ecological pressure promotes the selection and expression of genes related to antimicrobial resistance (AMR). These genes might be present in a bacterial consortium but might not necessarily be expressed. Their expression could be induced by the presence of antimicrobial compounds that could originate from a given ecological niche or from human activity. In this work, we applied (meta)proteomics analysis of bacterial compartment of raw milk in order to obtain a method that provides a measurement of circulating AMR involved proteins and gathers information about the whole bacterial composition. Results from milk analysis revealed the presence of 29 proteins/proteoforms linked to AMR. The detection of mainly β-lactamases suggests the possibility of using the milk microbiome as a bioindicator for the investigation of AMR. Moreover, it was possible to achieve a culture-free qualitative and functional analysis of raw milk bacterial consortia.
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TL;DR: It is shown that the use of such a ‘mini-experiment’ design improved the reproducibility and accurate detection of exemplary treatment effects in about half of all investigated strain comparisons.
Abstract: In light of the hotly discussed ‘reproducibility crisis’, a rethinking of current methodologies appears essential. Implementing multi-laboratory designs has been shown to enhance the external validity and hence the reproducibility of findings from animal research. We here aimed at proposing a new experimental strategy that transfers this logic into a single-laboratory setting. We systematically introduced heterogeneity into our study population by splitting an experiment into several ‘mini-experiments’ spread over different time points a few weeks apart. We hypothesised to observe improved reproducibility in such a ‘mini-experiment’ design in comparison to a conventionally standardised design, according to which all animals are tested at one specific point in time. By comparing both designs across independent replicates, we could indeed show that the use of such a ‘mini-experiment’ design improved the reproducibility and accurate detection of exemplary treatment effects (behavioural and physiological differences between four mouse strains) in about half of all investigated strain comparisons. Thus, we successfully implemented and empirically validated an easy-to-handle strategy to tackle poor reproducibility in single-laboratory studies. Since other experiments within different life science disciplines share the main characteristics with the investigation reported here, these studies are likely to also benefit from this approach.
78 citations
TL;DR: The results of this study emphasise the importance of the training panel design in relation to the genetic material to which the resulting prediction model is to be applied, and the design of training sets is in turn central to achieving sufficient levels of accuracy.
Abstract: Genomic selection offers several routes for increasing the genetic gain or efficiency of plant breeding programmes. In various species of livestock, there is empirical evidence of increased rates of genetic gain from the use of genomic selection to target different aspects of the breeder’s equation. Accurate predictions of genomic breeding value are central to this, and the design of training sets is in turn central to achieving sufficient levels of accuracy. In summary, small numbers of close relatives and very large numbers of distant relatives are expected to enable predictions with higher accuracy. To quantify the effect of some of the properties of training sets on the accuracy of genomic selection in crops, we performed an extensive field-based winter wheat trial. In summary, this trial involved the construction of 44 F2:4 bi- and tri-parental populations, from which 2992 lines were grown on four field locations and yield was measured. For each line, genotype data were generated for 25 K segregating SNP markers. The overall heritability of yield was estimated to 0.65, and estimates within individual families ranged between 0.10 and 0.85. Genomic prediction accuracies of yield BLUEs were 0.125–0.127 using two different cross-validation approaches and generally increased with training set size. Using related crosses in training and validation sets generally resulted in higher prediction accuracies than using unrelated crosses. The results of this study emphasise the importance of the training panel design in relation to the genetic material to which the resulting prediction model is to be applied.
64 citations
TL;DR: A review of the main existing models of doxorubicin-induced cardiomyopathy using small laboratory animals is presented in this article, where the authors discuss the most significant challenges to the development of new methods of prevention and treatment, as well as to the unambiguous choice of a specific treatment regimen using the existing pharmacological tools.
Abstract: Today the pharmacological possibilities of treating cancer are expanding and as a result, life expectancy is increasing against the background of chemotherapy and supportive treatment. In the conditions of successful antitumor treatment, complications associated with its toxic effect on healthy tissues and organs began to come to the fore. Anthracycline cardiomyopathy was the first serious cardiovascular complication to draw the attention of oncologists and cardiologists around the world. Anthracycline drugs such as doxorubicin, epirubicin, idarubicin are still widely used in oncological practice to treat a wide range of solid and hematological malignancies. Doxorubicin-induced cardiomyopathy is closely associated with an increase in oxidative stress, as evidenced by reactive oxygen species (ROS) nduced damage such as lipid peroxidation, and decreased levels of antioxidants. Myofibrillar destruction and dysregulation of intracellular calcium are also important mechanisms, usually associated with doxorubicin-induced cardiotoxicity. Despite the abundance of data on various mechanisms involved in the implementation of doxorubicin-induced cardiotoxicity, a final understanding of the mechanism of the development of doxorubicin cardiomyopathy has not yet been formed. It poses the most significant challenges to the development of new methods of prevention and treatment, as well as to the unambiguous choice of a specific treatment regimen using the existing pharmacological tools. In order to resolve these issues new models that could reflect the development of the chemotherapy drugs effects are needed. In this review we have summarized and analyzed information on the main existing models of doxorubicin cardiomyopathy using small laboratory animals. In addition, this paper discusses further areas of research devoted to the development and validation of new improved models of doxorubicin cardiomyopathy suitable both for studying the mechanisms of its implementation and for the preclinical drugs effectiveness assessment.
42 citations
TL;DR: In this paper, the authors defined microalgae as a potential feedstock for domestic animals due to their abundance of proteins, carbohydrates, lipids, minerals, vitamins, and other high-value products.
Abstract: There is an immediate need to identify alternative sources of high-nutrient feedstocks for domestic livestock production and poultry, not only to support growing food demands but also to produce microalgae-source functional foods with multiple health benefits. Various species of microalgae and cyanobacteria are used to supplement existing feedstocks. In this review, microalgae have been defined as a potential feedstock for domestic animals due to their abundance of proteins, carbohydrates, lipids, minerals, vitamins, and other high-value products. Additionally, the positive physiological effects on products of animals fed with microalgal biomass have been compiled and recommendations are listed to enhance the assimilation of biomolecules in ruminant and nonruminant animals, which possess differing digestive systems. Furthermore, the role of microalgae as prebiotics is also discussed. With regards to large scale cultivation of microalgae for use as feed, many economic trade-offs must be considered such as the selection of strains with desired nutritional properties, cultivation systems, and steps for downstream processing. These factors are highlighted with further investigations needed to reduce the overall costs of cultivation. Finally, this review outlines the pros and cons of utilizing microalgae as a supplementary feedstock for poultry and cattle, existing cultivation strategies, and the economics of large-scale microalgal production.
42 citations
TL;DR: In this article, the role of functional feed additives in enhancing the growth and health of nursery pigs during the post-weaning period is discussed. But, the authors did not consider the nutritional intervention using a single feed additive or a combination of different additives that can enhance feed intake, increase weight gain and reduce mortality and morbidity.
Abstract: The primary goal of nursery pig management is making a smooth weaning transition to minimize weaning associated depressed growth and diseases. Weaning causes morphological and functional changes of the small intestine of pigs, where most of the nutrients are being digested and absorbed. While various stressors induce post-weaning growth depression, the abrupt change from milk to solid feed is one of the most apparent challenges to pigs. Feeding functional feed additives may be viable solutions to promote the growth of nursery pigs by enhancing nutrient digestion, intestinal morphology, immune status, and by restoring intestinal balance. The aim of this review was to provide available scientific information on the roles of functional feed additives in enhancing intestinal health and growth during nursery phase. Among many potential functional feed additives, the palatability of the ingredient and the optimum supplemental level are varied, and these should be considered when applying into nursery pig diets. Considering different stressors pigs deal with in the post-weaning period, research on nutritional intervention using a single feed additive or a combination of different additives that can enhance feed intake, increase weight gain, and reduce mortality and morbidity are needed to provide viable solutions for pig producers. Further research in relation to the feed palatability, supplemental level, as well as interactions between different ingredients are needed.
34 citations
References
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TL;DR: A method is described, filter-aided sample preparation (FASP), which combines the advantages of in-gel and in-solution digestion for mass spectrometry–based proteomics and allows single-run analyses of organelles and an unprecedented depth of proteome coverage.
Abstract: A method, filter-aided sample preparation (FASP) combines the advantages of in-gel and in-solution digestion for mass spectrometry–based proteomics, allowing deeper proteomic coverage in a shorter analysis time, using small sample amounts. We describe a method, filter-aided sample preparation (FASP), which combines the advantages of in-gel and in-solution digestion for mass spectrometry–based proteomics. We completely solubilized the proteome in sodium dodecyl sulfate, which we then exchanged by urea on a standard filtration device. Peptides eluted after digestion on the filter were pure, allowing single-run analyses of organelles and an unprecedented depth of proteome coverage.
6,096 citations
"Raw Cow Milk Bacterial Consortium a..." refers methods in this paper
...Bead beating for bacterial lysis, the FASP method [10,30] for the purification of the protein digestion and DIA IMS mass spectrometry analysis allowed enough dataset depth to study the composition of the bacterial consortia....
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TL;DR: The Comprehensive Antibiotic Resistance Database (CARD) is a manually curated resource containing high quality reference data on the molecular basis of antimicrobial resistance (AMR), with an emphasis on the genes, proteins and mutations involved in AMR.
Abstract: The Comprehensive Antibiotic Resistance Database (CARD; http://arpcardmcmasterca) is a manually curated resource containing high quality reference data on the molecular basis of antimicrobial resistance (AMR), with an emphasis on the genes, proteins and mutations involved in AMR CARD is ontologically structured, model centric, and spans the breadth of AMR drug classes and resistance mechanisms, including intrinsic, mutation-driven and acquired resistance It is built upon the Antibiotic Resistance Ontology (ARO), a custom built, interconnected and hierarchical controlled vocabulary allowing advanced data sharing and organization Its design allows the development of novel genome analysis tools, such as the Resistance Gene Identifier (RGI) for resistome prediction from raw genome sequence Recent improvements include extensive curation of additional reference sequences and mutations, development of a unique Model Ontology and accompanying AMR detection models to power sequence analysis, new visualization tools, and expansion of the RGI for detection of emergent AMR threats CARD curation is updated monthly based on an interplay of manual literature curation, computational text mining, and genome analysis
1,726 citations
TL;DR: A new Resistomes & Variants module provides analysis and statistical summary of in silico predicted resistance variants from 82 pathogens and over 100 000 genomes, able to summarize predicted resistance using the information included in CARD, identify trends in AMR mobility and determine previously undescribed and novel resistance variants.
Abstract: The Comprehensive Antibiotic Resistance Database (CARD; https://card.mcmaster.ca) is a curated resource providing reference DNA and protein sequences, detection models and bioinformatics tools on the molecular basis of bacterial antimicrobial resistance (AMR). CARD focuses on providing high-quality reference data and molecular sequences within a controlled vocabulary, the Antibiotic Resistance Ontology (ARO), designed by the CARD biocuration team to integrate with software development efforts for resistome analysis and prediction, such as CARD's Resistance Gene Identifier (RGI) software. Since 2017, CARD has expanded through extensive curation of reference sequences, revision of the ontological structure, curation of over 500 new AMR detection models, development of a new classification paradigm and expansion of analytical tools. Most notably, a new Resistomes & Variants module provides analysis and statistical summary of in silico predicted resistance variants from 82 pathogens and over 100 000 genomes. By adding these resistance variants to CARD, we are able to summarize predicted resistance using the information included in CARD, identify trends in AMR mobility and determine previously undescribed and novel resistance variants. Here, we describe updates and recent expansions to CARD and its biocuration process, including new resources for community biocuration of AMR molecular reference data.
1,526 citations
"Raw Cow Milk Bacterial Consortium a..." refers methods in this paper
...Among other proteins with AMR potential identified using the CARD15 database there is an isoform of the Aminoglycoside N(6’)-acetyltransferase of Enterococcus hirae....
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...In order to identify the whole bacterial proteome, the obtained MS datasets were analyzed using different databases: UniProt KB/Swiss-Prot restricted to all reviewed Bacteria protein sequences (UniProt KB) and the Comprehensive Antibiotic Resistance Database (CARD) [14]....
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...Figure 3 shows the Venn diagram of the proteins identified in the two extractions using the CARD 15 database....
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...The same raw MS dataset was then searched against the CARD 15 database....
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...The qualitative identification of proteins was obtained by searching two different databases: (i) bacteria (UniProt KB/Swiss-Prot Protein Knowledgebase restricted to all Bacteria taxonomy) and (ii) The Comprehensive AMR Database (CARD, https://card.mcmaster.ca/) as FASTA files [13,14]....
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TL;DR: A screen of a sample of the culturable microbiome of Lechuguilla Cave, New Mexico, in a region of the cave that has been isolated for over 4 million years reported that, like surface microbes, these bacteria were highly resistant to antibiotics; some strains were resistant to 14 different commercially available antibiotics.
Abstract: Antibiotic resistance is a global challenge that impacts all pharmaceutically used antibiotics. The origin of the genes associated with this resistance is of significant importance to our understanding of the evolution and dissemination of antibiotic resistance in pathogens. A growing body of evidence implicates environmental organisms as reservoirs of these resistance genes; however, the role of anthropogenic use of antibiotics in the emergence of these genes is controversial. We report a screen of a sample of the culturable microbiome of Lechuguilla Cave, New Mexico, in a region of the cave that has been isolated for over 4 million years. We report that, like surface microbes, these bacteria were highly resistant to antibiotics; some strains were resistant to 14 different commercially available antibiotics. Resistance was detected to a wide range of structurally different antibiotics including daptomycin, an antibiotic of last resort in the treatment of drug resistant Gram-positive pathogens. Enzyme-mediated mechanisms of resistance were also discovered for natural and semi-synthetic macrolide antibiotics via glycosylation and through a kinase-mediated phosphorylation mechanism. Sequencing of the genome of one of the resistant bacteria identified a macrolide kinase encoding gene and characterization of its product revealed it to be related to a known family of kinases circulating in modern drug resistant pathogens. The implications of this study are significant to our understanding of the prevalence of resistance, even in microbiomes isolated from human use of antibiotics. This supports a growing understanding that antibiotic resistance is natural, ancient, and hard wired in the microbial pangenome.
587 citations
"Raw Cow Milk Bacterial Consortium a..." refers background in this paper
...The intrinsic resistome predates the clinical use of antibiotics posing the question whether AMR occurred earlier than the human antibiotics production and spread [3]....
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TL;DR: The possibility of inhibiting elements comprising the intrinsic resistome in bacterial pathogens offers the promise for repurposing existing antibiotics against intrinsically resistant bacteria.
435 citations
"Raw Cow Milk Bacterial Consortium a..." refers background in this paper
...Antimicrobial resistance (AMR) is a trait that can be horizontally transferred by previously resistant bacteria or can be generated by the occurrence of new mutations [1]....
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