High throughput genomic sequencing of bioaerosols in broiler chicken production facilities

Abstract

Chronic inhalation exposure to agricultural dust promotes the development of chronic respiratory diseases among poultry workers. Poultry dust is composed of dander, chicken feed, litter bedding and microbes. However, the microbial composition and abundance has not been fully elucidated. Genomic DNA was extracted from settled dust and personal inhalable dust collected while performing litter sampling or mortality collection tasks. DNA libraries were sequenced using a paired-end sequencing-by-synthesis approach on an Illumina HiSeq 2500. Sequencing data showed that poultry dust is predominantly composed of bacteria (64-67%) with a small quantity of avian, human and feed DNA (< 2% of total reads). Staphylococcus sp. AL1, Salinicoccus carnicancri and Lactobacillus crispatus were the most abundant bacterial species in personal exposure samples of inhalable dust. Settled dust had a moderate relative abundance of these species as well as Staphylococcus lentus and Lactobacillus salivarius. There was a statistical difference between the microbial composition of aerosolized and settled dust. Unlike settled dust composition, aerosolized dust composition had little variance between samples. These data provide an extensive analysis of the microbial composition and relative abundance in personal inhalable poultry dust and settled poultry dust.

Figure 1

The primary sources of genomic DNA in poultry dust. FastQ Screen was used to determine the percentage of total sequencing reads from microbes, chickens, humans, feed particulates (Zea mays and Glycine max) and ligated adapters in genomic DNA extracted from poultry dust collected during litter sampling (black), settled (grey) and mortality collection (white).

Figure 2

Microbial taxonomic profile of aerosolized or settled poultry dust. Relative abundance of (A) domain and (B) phylum taxonomic profiles in inhalable and settled poultry dust was determined by analysis with the MetaPhlAn2 package. Personal inhalable dust samples were collected during litter sampling (black) or mortality collection (white). Settled dust (grey) samples were obtained from the side‐walls and curtains of the poultry house.

Figure 3

Microbial relative abundance in aerosolized or settled poultry dust. Heat map was generated using MetaPhlAn2 and illustrates the 25 most abundant species in inhalable litter sampling dust (LS1‐15) (white), settled dust (SD1‐3) (grey), inhalable mortality collection dust (MC1‐3) (white) collected on broiler chicken farms. Columns represent the relationship between dust samples, and rows represent the relative abundance of species in the poultry dust.

Figure 4

Indicators of either aerosolized or settled dust based on bacterial taxonomical profile. Linear discriminant analysis Effect Size (LEfSe) greater than 3 (P < 0.05) was used to illustrate the statistical differences in relative abundances between inhalable litter sampling dust (black), settled dust (grey) and inhalable mortality collection dust (white). The analysis can discriminate based on ‘features’ of the abundance profile including phyla (p), class (c), order (o), family (f), genus (g), species (s) and strain (t).

Figure 5

Relationship between the sources of poultry dust. Ordination graph was derived from the Bray‐Curtis dissimilarity matrix calculated in Python. Principal component analysis shows the distances between microbial compositions in inhalable litter sampling dust (black), settled dust (grey) and inhalable mortality collection dust (white). The distance between samples is proportional to their similarity of microbial composition.