Table 1 Summary of studies on the porcine respiratory microbiota
From: The porcine respiratory microbiome: recent insights and future challenges
Study population | Sampling | Positive and negative sequencing controls | Sequencing platform (16S rRNA gene region) | Data processing software (reference database) | Main finding | Reference | ||
|---|---|---|---|---|---|---|---|---|
No. of animals | Age of animals | Respiratory tract | Sample type | |||||
Microbiome development | ||||||||
 10 Yorkshire-Landrace pigs | 0–7 weeks | URT | Nasal swab | Absent | Illumina MiSeq (V4) | mothur (RDP) | The nasal microbiota of pigs undergoes a remarkable evolution during the first 7 weeks of life | 21 |
 34 piglets | 0–4 weeks | URT | Tonsil swab | Extraction control, Escherichia coli DH5α genomic control and mock community DNA | Illumina MiSeq (V4) | mothur (SILVA) | The tonsillar microbiome of piglets does not show composition stability until 3 weeks, and shared similarities with the sow vaginal and teat skin microbiome | 18 |
 16 piglets | 0–19 weeks | URT | Tonsil swab | Extraction control | Illumina MiSeq (V4) | mothur (SILVA) | Significant community shifts during the development of the tonsillar microbiome are correlated with disruption events, including weaning, changes in feed, antibiotic treatment, and movement to new housing | 23 |
Bacterial topography in healthy animals | ||||||||
 8 pigs from a herd with health status and 4 pigs from a healthy herd with a history of chronic respiratory problems | 18–20 weeks | URT | Tonsil swab and tissue | Absent | GS 454 FLX-Titanium (full-length 16S rRNA gene) | RDP pyrosequencing pipeline (RDP) | Actinobacillus, Pasteurella and Haemophilus form the tonsillar core microbiome | 38 |
 5 MRSA-positive and 8 MRSA-negative pigs from a farm that used a liquid feeding system and 7 MRSA-negative pigs from a farm that used conventional feeding practices | 1–2 weeks prior to slaughter | URT | Nasal swab | Absent | Illumina MiSeq (V4) | mothur (Silva) | The nasal cavity of slaughter-age pigs harbours a rich and diverse microbial community that can be influenced by diet and farm management practices | 24 |
 100 pigs classified as S. aureus carriers (n = 44) and non-carriers (n = 56) | Last 3 week of production cycle | URT | Nasal swab | Absent | GS 454 FLX Titanium (V3-V5) | BION-meta (RDP) | The nasal microbiota may play a role in the individual predisposition to S. aureus nasal carriage in pigs | 36 |
 6 pigs | Not specified | URT | Swabs and biopsies of true and false vocal folds of larynges | Extraction and PCR controls | GS 454 FLX-Titanium (V3-V5) | mothur (SILVA) | There is no difference in laryngeal microbial communities when sampled via swab or biopsy from either the true or false vocal fold | 42 |
 Two lavage pools from 20 lungs presenting enzootic pneumonia signs and 20 lungs without macroscopic pneumonia signs | Not specified | LRT | BAL | Absent | GS 454 FLX Titanium (shotgun metagenomics) | MG-RAST (M5NR) | In farms with a history of chronic respiratory problems, Mycoplasma hyopneumoniae is present in lungs with or without enzootic pneumonia signs | 46 |
 20 lungs from the six-generation offspring of a population crossed by eight pig breeds (seven healthy, six and seven with moderate or severe lesion, respectively) | 240 ± 3 days | LRT | BAL | Extraction and PCR controls | Illumina MiSeq (V3-V4) | QIIME (Greengenes) | Reduced microbial diversity but more biomass was observed in severe-lesion lungs compared to healthy lungs | 43 |
 20 Duroc–Landrace–Yorkshire piglets (10 PRRSV-challenged and 10 controls) | 8–10 weeks | LRT | BAL | Absent | Illumina MiSeq (V3-V4) | mothur (SILVA) | Challenging pigs with the PRRSV increase the presence in the lungs of opportunistic pathogens, including Haemophilus parasuis and Mycoplasma hyorhinis | 45 |
Microbiome relationship with disease and productivity | ||||||||
 100 piglets from 4 farms with Glässer’s disease outbreaks and from 6 control farms (10 piglets/farms) | 3–4 weeks before weaning | URT | Nasal swab | Absent | Illumina MiSeq (V3-V4) | QIIME (Greengenes) | The nasal microbiota of piglets is associated to the clinical status of the farm, leading to different susceptibilities to invasive infection by opportunistic pathogens | 35 |
 30 pigs | Not specified | URT | Nasal swab | Extraction control, PCR control and Staphylococcus mock community | Illumina MiSeq (V1-V2) | BION-meta (RDP) | The MRSA nasal colonization is negatively correlated with the level of Streptococcus | 37 |
 33 piglets (23 diseased and 10 healthy) | 2–3 weeks | URT | Oropharyngeal swab | Extraction control | Illumina MiSeq (V3-V4) | RDP Classifier (SILVA) | Moraxella, Veillonella, and Porphyromonas may play a potential role in PRDC and Lactobacillus may have a protective role against respiratory diseases | 41 |
 0 piglets | 8 weeks | URT | Nasal swab | Absent | Illumina MiSeq (V1-V3) | QIIME (Greengenes) | The impact of parenteral antibiotics on the pig nasal microbiota is variable and modulates the nasal microbiota structure | 29 |
 31 piglets (based on the BioSample number in NCBI Sequence Read Archive) | 3/4-weeks | URT | Nasal swab | Absent | Illumina MiSeq (V3-V4) | QIIME (RDP) | Removal of perinatal antimicrobials at weaning increases the bacterial diversity in nasal microbiota and the relative abundance of beneficial genera | 31 |
 44 piglets | 6 weeks | URT | Tonsil surface | Extraction control and mock community | Illumina MiSeq (V4) | DADA2 (SILVA) | Chlortetracycline administration enhances the shedding and colonization of multidrug resistant S. Typhimurium in pigs | 39 |
 65 piglets | 2–3 weeks | URT | Nasal swab and tonsils tissue | Absent | Illumina MiSeq (V4) | mothur (SILVA) | Short-term exposure to broad-spectrum antibiotics (oxytetracycline) can disturb the URT microbiota | 30 |
 120 Duroc–Landrace–Yorkshire pigs (the nasal microbiota of 72 pigs was analysed) | Not specified | URT | Nasal swab | Absent | Illumina MiSeq (V3-V4) | QIIME (Greengenes) | Concentrations of ammonia higher than 25 ppm may cause respiratory damage and even pneumonia by affecting the colonization rates of harmful bacteria and beneficial bacteria | 26 |
 175 piglets | 19–22 days | LRT | Bronchial mucosa | Absent | Illumina MiSeq (V3-V4) | QIIME (SILVA) | Increasing the physical complexity of rearing environment provides suboptimal conditions for establishing a healthy microbial community in the growing pigs | 25 |
 8 piglets | 1–7 weeks | URT | Oropharyngeal swab | Extraction control, PCR control and mock community | Illumina iSeq (V4) | QIIME (Greengenes) | The rate of average daily gain of piglets is associated with a characteristic oropharyngeal microbial signature | 56 |
 28 Duroc–Landrace–Yorkshire pigs (eight healthy and 20 PRDC-affected) | 270 ± 3 days | LRT | BAL | Absent | Illumina MiSeq (V3-V4) | QIIME (RDP) | In PRDC-affected pigs, the proportion of harmful genera increased, and the richness of beneficial genera decreased | 44 |