Identification of the core bacteria in rectums of diarrheic and non-diarrheic piglets

Jing Sun,Liangpeng Ge,Hang Zhong,Zuohua Liu,Lei Du,Xiaolei Li,Yuchun Ding

doi:10.1038/s41598-019-55328-y

Jing Sun, Liangpeng Ge + Show 5 more

Open Access

https://doi.org/10.1038/s41598-019-55328-y

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Abstract

Porcine diarrhea is a global problem that leads to large economic losses of the porcine industry. There are numerous factors related to piglet diarrhea, and compelling evidence suggests that gut microbiota is vital to host health. However, the key bacterial differences between non-diarrheic and diarrheic piglets are not well understood. In the present study, a total of 85 commercial piglets at three pig farms in Sichuan Province and Chongqing Municipality, China were investigated. To accomplish this, anal swab samples were collected from piglets during the lactation (0–19 days old in this study), weaning (20–21 days old), and post-weaning periods (22–40 days), and fecal microbiota were assessed by 16S rRNA gene V4 region sequencing using the Illumina Miseq platform. We found age-related biomarker microbes in the fecal microbiota of diarrheic piglets. Specifically, the family Enterobacteriaceae was a biomarker of diarrheic piglets during lactation (cluster A, 7–12 days old), whereas the Bacteroidales family S24–7 group was found to be a biomarker of diarrheic pigs during weaning (cluster B, 20–21 days old). Co-correlation network analysis revealed that the genus Escherichia-Shigella was the core component of diarrheic microbiota, while the genus Prevotellacea UCG-003 was the key bacterium in non-diarrheic microbiota of piglets in Southwest China. Furthermore, changes in bacterial metabolic function between diarrheic piglets and non-diarrheic piglets were estimated by PICRUSt analysis, which revealed that the dominant functions of fecal microbes were membrane transport, carbohydrate metabolism, amino acid metabolism, and energy metabolism. Remarkably, genes related to transporters, DNA repair and recombination proteins, purine metabolism, ribosome, secretion systems, transcription factors, and pyrimidine metabolism were decreased in diarrheic piglets, but no significant biomarkers were found between groups using LEfSe analysis.

Highlights

Porcine diarrhea is a global problem that leads to large economic losses of the porcine industry
Genus Veillonella (Firmicutes) was the dominant bacteria in fecal microbiota in porcine epidemic diarrhea virus (PEDV)-infected piglets during the suckling transition stage[15], while higher Escherichia-Shigella (Proteobacteria) in the feces was in Enterotoxigenic Escherichia coli-induced diarrhea in piglets[16]
We found that members of the phylum Proteobacteria were reduced from four genera (Escherichia-Shigella, Actinobacillus, Pasteurella, and Sutterella) in the diarrheic group to only one genus (Pasteurella) in the non-diarrheic group, suggesting that an increase in the abundance and diversity of the phylum Proteobacteria played a pivotal role in piglet diarrhea

Summary

Introduction

Porcine diarrhea is a global problem that leads to large economic losses of the porcine industry. Changes in bacterial metabolic function between diarrheic piglets and non-diarrheic piglets were estimated by PICRUSt analysis, which revealed that the dominant functions of fecal microbes were membrane transport, carbohydrate metabolism, amino acid metabolism, and energy metabolism. The cause of diarrhea was not considered when sampling, and a total of 52 and 33 swab samples were collected from diarrheic piglets and non-diarrheic piglets, respectively, of the same or similar age in the same hog house for 16S ribosomal RNA gene V4 region sequencing using the Illumina Miseq platform. We compared and analyzed bacterial changes in the composition and function of the feces of piglets that were suffering from diarrhea and those that did not develop diarrhea to identify key differences in the fecal microbiota of piglets to reveal diarrhea-related bacteria

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