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remains of value to further establish overall trends in AMR prevalence. Surveillance and Metagenomics There is an overall need for improved surveillance of AMR in wildlife. Furthermore, the influence of various ecological and biogeographic factors

Open access
in American Journal of Veterinary Research

gastrointestinal tract microbes have not been or cannot be cultured, molecular approaches such as metagenomics, which involves genomic analysis of assemblages of organisms, are needed to study the true diversity and distribution of antimicrobial resistance genes

Full access
in American Journal of Veterinary Research

microbiome analyses could be performed by means of shotgun sequencing, that method is generally limited to metagenomic sequencing of bacteria. Moreover, traditional methods, such as microbiological culture, serology, or targeted DNA- or RNA-based testing

Full access
in American Journal of Veterinary Research

removal of contaminant sequences in marker-gene and metagenomics data . Microbiome . 2018 ; 6 ( 1 ): 226 . doi: 10.1186/s40168-018-0605-2 25. Dixon P . VEGAN, a package of R functions for community ecology . J Veg Sci . 2003 ; 14 : 927 – 930

Open access
in American Journal of Veterinary Research

Abstract

OBJECTIVE

The purpose of this study was to characterize the relationship of diet and management factors with the glandular gastric mucosal microbiome. We hypothesize that the gastric mucosal microbial community is influenced by diet and management factors. Our specific objective is to characterize the gastric mucosal microbiome in relation to these factors.

ANIMALS

57 client-owned horses in the southern Louisiana region with and without equine glandular gastric disease.

PROCEDURES

Diet and management data were collected via a questionnaire. Gastroscopy was used for evaluation of equine gastric ulcer syndrome and collection of glandular mucosal pinch biopsies. 16S rRNA amplicon sequencing was used for microbiome analysis. Similarity and diversity indices and sequence read counts of individual taxa were compared between diet and management factors.

RESULTS

Differences were detected in association with offering hay, type of hay, sweet feed, turnout, and stalling. Offering hay and stalling showed differences in similarity indices, whereas hay type, sweet feed, and turnout showed differences in similarity and diversity indices. Offering hay, hay type, and sweet feed were also associated with differences in individual sequence read counts.

CLINICAL RELEVANCE

This study provides preliminary characterization of the complex relationship between the glandular gastric microbiome and diet/management factors. The ideal microbiome to promote a healthy glandular gastric environment remains unknown.

Full access
in Journal of the American Veterinary Medical Association

veterinary bacterial pathogens, including Clostridium perfringens and E coli , in which there are strong associations between gene presence and pathogenicity. 15 , 16 Figure 2 Comparison of the use of PCR, whole genome sequencing, and metagenomic

Open access

because the protocol had not yet been completed at the time of the second fecal collection. However, some clarifications are imperative. A recent study 4 in dogs demonstrated robust correlations between untargeted metagenomic sequencing, such as the one

Open access
in American Journal of Veterinary Research

, epigenomics, proteomics, transcriptomics, metabolomics, metagenomics, big data, artificial intelligence , machine learning, and precision medicine to explore and conquer these devastating diseases. In addition, Dr. Kanthasamy has initiated a translational

Open access
in American Journal of Veterinary Research

are now used for taxonomic assignment and referred to as metagenomics. In metagenomics, all nucleic acids are extracted from a clinical sample, sequenced, and compared to a microbial database for exact genotypic classification, identification, and

Open access
in Journal of the American Veterinary Medical Association

with clinically predictive information on the likelihood of successful treatment of the patient’s infection with a particular antimicrobial. Genotypic test methods, such as whole genome sequencing (WGS), targeted sequencing, and metagenomic sequencing

Open access