Relationships among Microbial Communities in Pigs

Today, we are sharing a recent article published in the journal Microorganisms by Dr. Valeris-Chacin and the MycoLab. The publication, available in open access, focuses on the relationships among fecal, air, oral, and tracheal microbial communities in pigs.

the objectives of this study were to describe the microbiome associated with tracheal and oral fluids, air, and feces during late stages of M. hyopneumoniae infection in pigs, to assess their potential association with infection status, and to infer to what extent the tracheal microbiome is related to microbial communities from air, feces, and oral fluids.


Seventy-three commercial pigs split into two groups (seeders which were experimentally inoculated with M. hyopneumoniae and contact pigs which became naturally infected) were housed in pens of 28 animals with a 6:1 contact-to-seeder ratio. Samples were collected 113 days after experimental inoculation. Tracheal fluids, oral fluids, and air samples were then tested by PCR for Mycoplasma hyopneumoniae. Additionally, tracheal fluids, oral fluids, air and fecal samples were processed to amplify the V4 region of the 16S rRNA gene, which was subsequently sequenced.


Fifty-nine of the 73 tracheal fluids tested positive for Mycoplasma hyopneumoniae whereas only one oral fluids sample (out of 8) and no air sample tested positive.

The Clostridium genus was the most abundant one in fecal, oral and air samples whereas Actinobacillus was the preponderant one in the tracheal fluids that tested negative for M. hyopneumoniae. The Mycoplasma genus was the most abundant found in the positive tracheal samples.

When looking at the bacterial diversity found in tracheal fluids, a statistically significant reduction was shown when the estimated concentration of M. hyopneumoniae in tracheal fluids was high (low Ct-value).

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.

The overall analysis of the dissimilarities among the microbial communities showed consistently three distinct cluster: fecal samples, air samples, and oral and tracheal fluids. There was a significant association between sample type and the diversity observed.

Additionally, the M. hyopneumoniae status modified the diversity observed in tracheal fluids and the association between diversity and sample types. Indeed, M. hyopneumoniae infection status was associated with an increase of the relative abundance of the following swine pathogens: M. hyorhinisG. parasuis, and P. multocida.

Read the entire article


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.