Nanopore versus Illumina to study the gut bacterial diversity of sows and piglets between farms with high and low health status

Abstract

Background: Antibiotics are used in animal husbandry to control infectious diseases. Different stressors can compromise animal health, leaving piglets vulnerable to pathogens, especially enterotoxigenic Escherichia coli (ETEC), which causes post-weaning diarrhoea (PWD), the major source of mortality and morbidity in swine production. Furthermore, PWD is a recurrent disease for certain farms, suggesting a link between gut microbial composition and animal health. The aim of this study was to identify the intestinal microbiota of pigs on farms with high health status (HHS) and low health status (LHS) to determine the relationships between sanitary status and gut health. Therefore, three pig farms with LHS presenting recurrent problems of PWD and three farms with HHS were selected to characterise the intestinal microbiome of sows and their piglets. 16 S rRNA gene sequencing technology was used to determine the associations of the gut microbiome with health. With the aim of bringing the MinION Nanopore device to the field for its portability and taxonomic resolution, the results obtained with Illumina were compared to those obtained with Nanopore.

Results: Overall, the results indicated remarkable differences in intestinal microbial communities between animals from LHS farms and those from HHS farms, suggesting that the microbiomes of LHS animals were enriched with potential pathogenic microorganisms, mainly from the Pseudomonadota phylum, such as the genus Escherichia-Shigella, and their associated related species. Moreover, animals from HHS were enriched with beneficial microorganisms, such as Lactobacillus spp., Christensenellaceae R7 group, Treponema, Acetitomaculum and Oscillospiraceae UCG-005.

Conclusions: This study identifies potential microorganisms that may contribute to health and disease in pig farms with HHS and LHS, suggesting that tracking their occurrence might provide insight into sanitary conditions. Moreover, this research highlights the compatibility between Illumina and Nanopore sequencing platforms, justifying the use of MinION Nanopore device in field applications for in situ studies of PWD. This application has the potential to enhance sustainable economic growth in swine farms by enabling more effective monitoring and management of animal health.

Keywords: Antimicrobial resistance; Illumina sequencing; Intestinal microbiome; Nanopore sequencing; Pigs; Post-weaning diarrhoea; Swine.

Fig. 1

Comparison of alpha diversity. Alpha diversity at genus taxonomic level in swine gut microbiome community richness (Observed features index) and evenness (Shannon index) between mothers and piglet samples from HHS (purple) and LHS (yellow) sanitary status for (A) Illumina and (B) Nanopore sequencing method. Means with “*”, “**” and “***” are significantly different in 0.05, 0.01, and 0.001 (Pairwise Wilcoxon test)

Fig. 2

Comparison of beta diversity. PCoA of beta diversity plot at genus taxonomic level in faecal samples of (A) mothers and (B) piglets between HHS (round) and LHS (triangle) sanitary status in different Illumina (brown) and Nanopore (blue) sequencing methods. Significant differences between sequencing method (Illumina vs. Nanopore) in mothers (PERMANOVA, P = 0.0001) and piglets (PERMANOVA, P = 0.0001) and piglets in HHS vs. LHS for Illumina (PERMANOVA, P = 0.0226) and Nanopore (PERMANOVA, P = 0.0201) sequencing method

Fig. 3

Correlation study between sequencing platforms. Correlations between the relative abundances of the most abundant taxa from the Illumina and Nanopore datasets. (A) Phylum level (Pearson’s r: 0.96, P 3.2 × 10⁻¹⁰) and (B) genus level (Pearson’s r: 0.66, P 2.2 × 10^− 16). Legend with Phylum taxonomic rang. Black line corresponds to a 1:1 ratio, and the grey line shows the confidence interval between the two sequencing methods

Fig. 4

Venn diagram analysis. Representation of shared and unique genera in mothers and piglets under different sanitary status conditions (HHS vs. LHS) (https://www.interactivenn.net/) for (A) Illumina sequencing platform (brown) and (B) Nanopore sequencing platform (blue)

Fig. 5

Bar chart of species abundance. Relative abundance (%) of the remarkable species identified in mothers and piglets from HHS and LHS farms from the Nanopore dataset. Each colour represents a specific species

Fig. 6

Histogram of linear discriminant analysis (LDA) effect size (LEfSe) computed for bacterial taxa at genus level. Differentially abundant among HHS (purple) and LHS (yellow) groups for mothers (A) and piglets (B) from Nanopore dataset. Kw cutoff = 0.05 and LDA cutoff = 2