Relationships among Fecal, Air, Oral, and Tracheal Microbial Communities in Pigs in a Respiratory Infection Disease Model

Abstract

The association of the lower respiratory tract microbiome in pigs with that of other tissues and environment is still unclear. This study aimed to describe the microbiome of tracheal and oral fluids, air, and feces in the late stage of Mycoplasma hyopneumoniae infection in pigs, and assess the association between the tracheal microbiome and those from air, feces, and oral fluids. Tracheal fluids (n = 73), feces (n = 71), oropharyngeal fluids (n = 8), and air (n = 12) were collected in seeder pigs (inoculated with M. hyopneumoniae) and contact pigs (113 days post exposure to seeder pigs). After DNA extraction, the V4 region from 16S rRNA gene was sequenced and reads were processed using Divisive Amplicon Denoising Algorithm (DADA2). Clostridium and Streptococcus were among the top five genera identified in all sample types. Mycoplasma hyopneumoniae in tracheal fluids was associated with a reduction of diversity and increment of M. hyorhinis, Glaesserella parasuis, and Pasteurella multocida in tracheal fluids, as well as a reduction of Ruminiclostridium, Barnesiella, and Lactobacillus in feces. Air contributed in a greater proportion to bacteria in the trachea compared with feces and oral fluids. In conclusion, evidence suggests the existence of complex interactions between bacterial communities from distant and distinct niches.

Oral Vaccination Reduces the Effects of Lawsonia intracellularis Challenge on the Swine Small and Large Intestine Microbiome

“…In ileal digesta and cecal digesta, bacteria of the Ruminiclostridium genus were also less abundant in the challenged pigs. Interestingly, Ruminiclostridium abundance in fecal samples has recently been shown to be significantly and inversely correlated to Mycoplasma hyopneumoniae abundance in infected swine and are known to produce butyrate (29). Both L. intracellularis and M. hyopneumoniae are prevalent bacterial pathogens known to cause significant production losses, including during co-infection even when pigs are not exhibiting clinical signs (30).…”

Insights into the Oral Bacterial Microbiota of Sows

“…Being suitable for nucleic acid detection, oral fluids can also be used more extensively to characterize the oral bacterial microbiota of individuals or groups of animals. As they are also suitable for the detection of nucleic acids, oral fluids have recently been shown to be useful to study the oral bacterial microbiota [52]. Indeed, Valeris-Chacin and co-authors used oral fluids to study the oral bacterial microbiota of pigs, relying on the quantification of M. hyopneumoniae and its correlation with community diversity and composition.…”

“…Conversely, M. hyopneumoniae has so far been encountered most frequently in tracheal fluid, while its concentration in oral fluid was generally undetectable. The reason for such a distribution could be ascribed to its tropism for tracheal cilia [52]. On the other hand, according to Murase and co-authors, saliva is the major habitat of S. suis [5].…”

Altered Nasal Microbiota Composition Associated with Development of Polyserositis by Mycoplasma hyorhinis

“…Similarly, differences in the oropharyngeal microbiota have been associated with the development of respiratory diseases in pigs [ 13 ]. Higher relative abundance of the Moraxella genus was associated with respiratory pathology and Lactobacillus was associated with healthy animals [ 13 , 14 ].…”