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. 2021 Jan 27;9(2):252.
doi: 10.3390/microorganisms9020252.

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

Robert Valeris-Chacin  1 , Amanda Sponheim  2   3 , Eduardo Fano  3 , Richard Isaacson  1 , Randall S Singer  1 , Joel Nerem  4 , Fernando L Leite  3 , Maria Pieters  2
Affiliations

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

Robert Valeris-Chacin et al. Microorganisms. .

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.

Keywords: Mycoplasma hyopneumoniae; environment; fecal; microbiome; swine; tracheal.

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Conflict of interest statement

A.S., E.F., and F.L.L. are employed by Boehringer Ingelheim Animal Health USA Inc. However, the evaluation of commercial products was not part of this investigation.

Figures

Figure 1
Figure 1
Amplicon sequence variants (ASVs) shared among sample types. Intersection size: number of ASVs comprising a specific nonoverlapping set. Dark circles indicate the sample types that are part of the set. Dark circles connected by a line indicate that two or more sample types are part of the set. The plot was made using UpSetR package in R [47] with the layout described by Lex and Gehlenborg [48].
Figure 2
Figure 2
Association of alpha diversity (inverse Simpson index) with sample type and Mycoplasma hyopneumoniae real-time PCR Ct values in tracheal fluids. 95% CI: 95% confidence interval.
Figure 3
Figure 3
Microbial communities clustering analysis. Each dot represents an individual sample. Five different dissimilarity indices were performed and are shown in the following order (left to right, top to bottom): Aitchison, Bray–Curtis, Jaccard, Unifrac, and weighted Unifrac. Samples are color-coded by type. Orange: air; green: feces; teal: oral fluids; purple: tracheal fluids.
Figure 4
Figure 4
Amplicon sequence variants differentially abundant in fecal samples according to Mycoplasma hyopneumoniae status of paired tracheal fluid samples. Real-time PCR in tracheal samples was used to establish M. hyopneumoniae status.
Figure 5
Figure 5
Proportions of the tracheal fluid microbial community potentially originating from fecal, air, or oral fluid sources. Each pie represents the tracheal fluid of one individual pig (n = 73). Sources are color-coded. Orange: air; green: feces; teal: oral fluids; light gray: unknown.
See this image and copyright information in PMC

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