24 September 2025

2 minute read

By: Chris Wright

North America

Editor's note: The following is an edited version of a presentation by Emmalise M. Meyer and colleagues at the University of Nebraska, USA, delivered at the 2024 North American PRRS Symposium.

Recent disease outbreaks emphasize the continued economic threat of infectious diseases to the global swine industry. These challenges highlight the need for efficient approaches to identify and characterize novel pathogens while furthering development of modern surveillance and management technologies that capture relevant disease phenotypes.

Natural infections can be efficiently used to capture a multitude of relationships between host genetics and different viral and bacterial pathogens. The objective of this study is to evaluate relationships between full-spectrum microbial profiling, host genetics, animal growth and health status in a typical swine farm.

Growth data and multiple tissue samples were collected from four batches of terminal crossbred pigs (4 x 250 pigs). During the grow/finish phase (~100 days), the pigs were allocated into a room with 25 pens, with 10 pigs/pen. Body weight was obtained at birth, weaning and three times during grow/finish phase. Individual blood samples, fecal and nasal swabs were collected at weaning, and three times during the grow/finish phase. During this phase, weekly pen-based oral fluids were collected using ropes (~ 15 time points/pen). Initial oral metagenomic data, based on Oxford Nanopore sequencing, reflected common nursery microbial profile including specific oral or upper-respiratory microbiota.

There were 455 microbial species detected with a presence larger than 0.01%. Atypical porcine pestivirus (APPV), with 51 sequencing reads obtained, was the most abundant viral species observed. Other viruses included porcine astrovirus 4, porcine sapelovirus or porcine bocavirus 5.

The bacterial profile included opportunistic pathogens (e.g., Streptococcus suis), oral- (e.g., Prevotella dentalis, Rothia mucilaginosa) or fecal-specific (e.g., Clostridium sp.) and known pathogenic species (e.g., Glaesserella parasuis).

Tail clips or ear notches were collected and used for DNA isolation. High-quality genotypes were obtained by filtering the raw data. This genomic information will be integrated with microbial profiling and used in genome-wide associations to discover genetic markers associated with resilience to specific pathogens and improved health status. The long-term goal of this project is to develop molecular surveillance tools and management solutions that improve genetic resilience to infectious diseases, increase fitness, and reduce economic losses to swine producers.