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.
Highlights
The collection of microorganisms and their genetic elements, persistently or transiently present in a certain ecological niche, is known as its microbiome
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
Rarefaction curves showed that the asymptote of the number of amplicon sequence variants (ASV) was reached in all sample types (Figure S1)
Summary
The collection of microorganisms and their genetic elements, persistently or transiently present in a certain ecological niche, is known as its microbiome. The microbiome can be decomposed in different dimensions depending on the type of microorganisms of interest, e.g., the viral microbiome (virome), the fungal microbiome (mycobiome), or the bacterial microbiome. The latter is the most commonly studied and is associated with a plethora of effects in animal hosts, such as breakdown of otherwise indigestible feedstuff (influencing feed efficiency [1]), competitive exclusion of pathogens [2], priming and regulation of the mucosal immune system [3,4], and disease [5]. The fecal microbiome is more related to the large intestine microbiome [9] and some of the genera commonly present in high abundance include
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