The occurrence of antibiotic resistance genes in the microbiota of yak, beef and dairy cattle characterized by a metagenomic approach.
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ABSTRACT:
SUBMITTER: Wang W
PROVIDER: S-EPMC8313426 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:It is well-established that antimicrobial use is a major factor for the development of antimicrobial resistance. To analyze the associations between antimicrobial resistance and usage of antimicrobial agents, data from monitoring and surveillance systems are crucial. Within the project VetCAb (Veterinary Consumption of Antibiotics), antibiotic usage data in German livestock is regularly collected and evaluated. Based on a cross-sectional study in 2011, the project was continued as the longitudinal study VetCAb-Sentinel with ongoing participant recruitment and data collection from 2013. The data collection is based on official German application and delivery forms (ADF), voluntarily provided by veterinarians and farmers. In this study the results of antibiotic usage data of dairy cows, dairy calves and beef cattle were described, using a semi-annual treatment frequency, and 95,944 ADF issued between 2011 and 2015 were analyzed. Results show that the median of the treatment frequency in dairy calf and beef cattle holdings slightly decreased from 0.4 to 0.3 and from 0.2 to 0 days, respectively, whereas the median in dairy cow holdings ranged between 1.9 and 2.3 during the observed period. Temporal changes and the effect of the factors "farm size" and "region" on the treatment frequency were investigated, using multiple linear mixed and logistic regression models. Generally, the factor "time" has a statistically significant impact on the treatment frequency in all production types. In addition, a temporal trend test over the first six half-years shows that an increasing linear trend can be stated in dairy cows and dairy calves (p = 0.017; p = 0.004, respectively). If the time-period is extended to all eight half-years under study, this turns into a quadratic effect (dairy cows: p = 0.006; dairy calves: p < 0.001). In dairy calves and beef cattle the factor "farm size" also has a statistically significant impact. The factor "region," in contrast, shows no statistically significant impact at all. Compared to other livestock populations in Germany, the use of antimicrobials in dairy cows, dairy calves, and beef cattle appears to be low, but varies across several associated factors. Considering these effects, it is recommended that the size of dairy calf and beef cattle holdings is regularly considered in the evaluation of antimicrobial usage data over time.
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Project description:The overuse of antibiotics in livestock contributes to the antibiotic resistance pandemic. The assessment of the actual antibiotic consumption is crucial in limiting the expansion of the problem effectively. The aim of this study was to provide the first qualitative and quantitative analysis of antimicrobial usage using data from paper-based registers on dairy and beef farms located in the Umbria region, Italy. Antimicrobial therapies of a one-year period were collected from 101 farms with at least 50 cattle each. Defined daily doses (DDDvet) and defined course doses (DCDvet) were calculated per administration route and antimicrobial class. The total courses administered were fewer in beef (330.7 × 10-3 DCDvet/year) than in dairy farms (1034.1 × 10-3 DCDvet/year). The use of the highest priority critically important antimicrobials (HPCIAs) was higher (p = 0.0033) in dairy than in beef herds. In terms of DDDvet, the parenteral fluoroquinolone administration ranked second and fourth on dairy and beef farms, respectively; the consumption of beta-lactams was ten times higher on dairy than on beef farms. Our results confirm that intensive dairy management practices are associated with increased antibiotic consumption and highlight the necessity to strengthen the existing stewardship programs by involving all stakeholders in effective antimicrobial resistance reduction plans.
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Project description:Animal temperament can be defined as a response to environmental or social stimuli. There are a number of temperament traits in cattle that contribute to their welfare, including their response to handling or milking, response to challenge such as human approach or intervention at calving, and response to conspecifics. In a number of these areas, the genetic basis of the trait has been studied. Heritabilities have been estimated and in some cases quantitative trait loci (QTL) have been identified. The variation is sometimes considerable and moderate heritabilities have been found for the major handling temperament traits, making them amenable to selection. Studies have also investigated the correlations between temperament and other traits, such as productivity and meat quality. Despite this, there are relatively few examples of temperament traits being used in selection programmes. Most often, animals are screened for aggression or excessive fear during handling or milking, with extreme animals being culled, or EBVs for temperament are estimated, but these traits are not commonly included routinely in selection indices, despite there being economic, welfare and human safety drivers for their. There may be a number of constraints and barriers. For some traits and breeds, there may be difficulties in collecting behavioral data on sufficiently large populations of animals to estimate genetic parameters. Most selection indices require estimates of economic values, and it is often difficult to assign an economic value to a temperament trait. The effects of selection primarily for productivity traits on temperament and welfare are discussed. Future opportunities include automated data collection methods and the wider use of genomic information in selection.
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Project description:Analyzing the associations between genotypic changes and phenotypic traits on a genome-wide scale can contribute to understanding the functional roles of distinct genetic variations during breed development. We performed a whole-genome analysis of Angus and Jersey cattle breeds using conditional mutual information, which is an information-theoretic method estimating the conditional independency among multiple factor variables. The proposed conditional mutual information-based approach allows breed-discriminative genetic variations to be explicitly identified from tens of millions of SNP (single nucleotide polymorphism) positions on a genome-wide scale while minimizing the usage of prior knowledge. Using this data-driven approach, we identified biologically relevant functional genes, including breed-specific variants for cattle traits such as beef and dairy production. The identified lipid-related genes were shown to be significantly associated with lipid and triglyceride metabolism, fat cell differentiation, and muscle development. In addition, we confirmed that milk-related genes are involved in mammary gland development, lactation, and mastitis-associated processes. Our results provide the distinct properties of Angus and Jersey cattle at a genome-wide level. Moreover, this study offers important insights into discovering unrevealed genetic variants for breed-specific traits and the identification of genetic signatures of diverse cattle breeds with respect to target breed-specific properties.
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Project description:The gut microbiota is closely associated with the health and production performance of livestock. Partial studies on ruminant microbiota are already in progress in the Qinghai-Tibetan Plateau Area (QTPA) in China, but large-scale and representative profiles for the QTPA are still lacking. Here, 16S rRNA sequencing was used to analyze 340 samples from yak, cattle, yak-cattle hybrids, and Tibetan sheep, which lived in a shared environment from 4 eco-regions of the QTPA during the same season, and aimed to investigate the fecal microbiota community composition, diversity, and potential function. All samples were clustered into 2 enterotypes, which were derived from the genera Ruminococcaceae UCG-005 and Acinetobacter, respectively. Environment, human activity, species, and parasitization all affected the fecal microbiota. By assessing the relationship between the fecal microbiota and the above variables, we identified a scattered pattern of fecal microbiota dissimilarity based more significantly on diet over other factors. Additionally, gastrointestinal nematode infection could reduce the capacity of the bacterial community for biosynthesis of other secondary metabolites, carbohydrate metabolism, and nucleotide metabolism. Ultimately, this study provided a fecal microbiota profile for ruminants living in 4 eco-regions of the QTPA and its potential future applications in developing animal husbandry regimes. IMPORTANCE Cattle, yak, and sheep reside as the main ruminants distributed throughout most regions of Qinghai-Tibetan Plateau Area (QTPA) in China. However, there is a lack of large-scale research in the QTPA on their fecal microbiota, which can regulate and reflect host health as an internalized "microbial organ." Our study depicted the fecal microbiota community composition and diversity of yak, cattle, yak-cattle hybrids, and Tibetan sheep from 4 eco-regions of the QTPA. Additionally, our results demonstrated here that the ruminant samples could be clustered into 2 enterotypes and that diet outweighed other factors in shaping fecal microbiota in the QTPA. This study provided a basis for understanding the microbiota characteristic of ruminants and its possible applications for livestock production in the QTPA.
| S-EPMC9430443 | biostudies-literature
Project description:The sales amount of antimicrobials intended for use in dairy cattle, beef cattle and broilers from 2008 to 2019 was evaluated for each antimicrobial class and administration route using dosage-based indicators. Our results revealed that the antimicrobial sales amount sold for use in dairy cattle in 2019 in terms of total weight of active ingredient, the number of defined daily doses (DDDs) (theoretical amount of biomass subjected to antimicrobial treatment in a year) and the number of treatment days (TDs) (theoretical number of days of treatment that an animal is subjected to in a year) calculated using Japanese DDD values (DDDjp values) was 36,751 kg, 8,261,848,000 kg·days and 15.5 days, respectively. Likewise, the antimicrobial sales amount sold for use in beef cattle and broilers in 2019 in terms of these metrics was 33,403 kg, 3,928,248,000 kg·days and 3.61 days, and 69,773 kg, 2,947,848,000 kg·days and 10.66 days, respectively. There was a considerable difference between the number of DDDs calculated using DDDjp values and that calculated using European DDD values (DDDvet values) for antimicrobial products sold for use in dairy and beef cattle. Our results also revealed that the sales amount of some antimicrobials, such as cephalosporins and quinolones represented larger proportions when calculated using dosage-based indicators than when calculated using the weight of active ingredient. Considering that Japanese veterinarians and farmers are more likely to conform to the Japanese dosage recommendations rather than the European ones, these results indicate the need for using dosage-based metrics, in particular metrics based on Japanese dosages rather than European dosages.
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Project description:Yak (Bos grunniens) is an unique ruminant species in the Qinghai-Tibetan Plateau (QTP). The ruminant gastrointestinal tract (GIT) microbiota is not only associated with the nutrients metabolism, but also contributes to the host's local adaptation. Examining the microbiota between cattle and yak in different geography could improve our understanding about the role of microbiota in metabolism and adaptation. To this end, we compared the microbiota in rumen, reticulum, omasum, and abomasum of dairy cattle, yellow cattle, and three yak herds (WQ yak, SZ yak, and ZB yak) lived in different altitude, based on sequencing the bacterial 16S rRNA gene on Illumina Miseq. The bacterial diversity was significantly different among five breeds, whereas the difference among four stomach regions is limited. The phyla Bacteroidetes and Firmicutes were the dominated bacteria regardless of breeds and regions. The nonmetric multidimensional scaling (NMDS) results showed that the microbiota in dairy cattle, yellow cattle and WQ yak significantly differed from that in SZ yak and ZB yak for all four stomach compartments. Canonical correlation analysis revealed that Prevotella and Succiniclasticum spp. were abundant in dairy cattle, yellow cattle and WQ yak, whereas the Christensenellaceae R7 group and the Lachnospiraceae UCG 008 group were prevalent in SZ yak and ZB yak. Moreover, the microbiota in WQ yak was significantly different from that in SZ yak and ZB yak, which were characterized by the higher relative abundance Romboutsia spp., Eubacterium coprostanoligenes, Acetobacter spp., Mycoplasma spp., and Rikenellaceae RC9 group. Overall, these results improves our knowledge about the GIT microbiota composition of QTP ruminant.
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| PRJNA948924 | ENA
Project description:Antibiotic resistance is a global threat to public health, with antibiotic resistance genes (ARGs) being one of the emerging contaminants; furthermore, animal manure is an important reservoir of biocide resistance genes (BRGs) and metal resistance genes (MRGs). However, few studies have reported differences in the abundance and diversity of BRGs and MRGs between different types of animal manure and the changes in BRGs and MRGs before and after composting. This study employed a metagenomics-based approach to investigate ARGs, BRGs, MRGs, and mobile genetic elements (MGEs) of yak and cattle manure before and after composting under grazing and intensive feeding patterns. The total abundances of ARGs, clinical ARGs, BRGs, MRGs, and MGEs were lower in the manure of grazing livestock than in the manure of the intensively fed group. After composting, the total abundances of ARGs, clinical ARGs, and MGEs in intensively fed livestock manure decreased, whereas those of ARGs, clinical ARGs, MRGs, and MGEs increased in grazing livestock manure. The synergy between MGEs mediated horizontal gene transfer and vertical gene transmission via host bacteria proliferation, which was the main driver that altered the abundance and diversity of ARGs, BRGs, and MRGs in livestock manure and compost. Additionally, tetQ, IS91, mdtF, and fabK were potential indicators for estimating the total abundance of clinical ARGs, BRGs, MRGs, and MGEs in livestock manure and compost. These findings suggest that grazing livestock manure can be directly discharged into the fields, whereas intensively fed livestock manure should be composted before returning to the field. IMPORTANCE The recent increase in the prevalence of antibiotic resistance genes (ARGs), biocide resistance genes (BRGs), and metal resistance genes (MRGs) in livestock manure poses risks to human health. Composting is known to be a promising technology for reducing the abundance of resistance genes. This study investigated the differences and changes in the abundances of ARGs, BRGs, and MRGs between yak and cattle manure under grazing and intensive feeding patterns before and after composting. The results indicate that the feeding pattern significantly affected the abundances of resistance genes in livestock manure. Manure in intensive farming should be composted before being discharged into the field, while grazing livestock manure is not suitable for composting due to an increased number of resistance genes.
| S-EPMC10370317 | biostudies-literature
Project description:Domestication is a key factor of genetic variation; however, the mechanism by which domestication alters gut microbiota is poorly understood. Here, to explore the variation in the structure, function, rapidly evolved genes (REGs), and enzyme profiles of cellulase and hemicellulose in fecal microbiota, we studied the fecal microbiota in wild, half-blood, and domestic yaks based on 16S rDNA sequencing, shotgun-metagenomic sequencing, and the measurement of short-chain-fatty-acids (SCFAs) concentration. Results indicated that wild and half-blood yaks harbored an increased abundance of the phylum Firmicutes and reduced abundance of the genus Akkermansia, which are both associated with efficient energy harvesting. The gut microbial diversity decreased in domestic yaks. The results of the shotgun-metagenomic sequencing showed that the wild yak harbored an increased abundance of microbial pathways that play crucial roles in digestion and growth of the host, whereas the domestic yak harbored an increased abundance of methane-metabolism-related pathways. Wild yaks had enriched amounts of REGs in energy and carbohydrate metabolism pathways, and possessed a significantly increased abundance of cellulases and endohemicellulases in the glycoside hydrolase family compared to domestic yaks. The concentrations of acetic, propionic, n-butyric, i-butyric, n-valeric, and i-valeric acid were highest in wild yaks. Our study displayed the domestic effect on the phenotype of composition, function in gut microbiota, and SCFAs associated with gut microbiota, which had a closely association with the growth performance of the livestock. These findings may enlighten the researchers to construct more links between economic characteristics and gut microbiota, and develop new commercial strains in livestock based on the biotechnology of gut microbiota.
| S-EPMC8059439 | biostudies-literature