Influence of Pig Farming on the Human Nasal Microbiota: Key Role of Airborne Microbial Communities

Bioaerosols Play a Major Role in the Nasopharyngeal Microbiota Content in Agricultural Environment

Background: Bioaerosols are a major concern for public health and sampling for exposure assessment purposes is challenging. The nasopharyngeal region could be a potent carrier of long-term bioaerosol exposure agents. This study aimed to evaluate the correlation between nasopharyngeal bacterial flora of swine workers and the swine barns bioaerosol biodiversity. Methods: Air samples from eight swine barns as well as nasopharyngeal swabs from pig workers (n = 25) and from a non-exposed control group (n = 29) were sequenced using 16S rRNA gene high-throughput sequencing. Wastewater treatment plants were used as the industrial, low-dust, non-agricultural environment control to validate the microbial link between the bioaerosol content (air) and the nasopharynxes of workers. Results: A multivariate analysis showed air samples and nasopharyngeal flora of pig workers cluster together, compared to the non-exposed control group. The significance was confirmed with the PERMANOVA statistical test (p-value of 0.0001). Unlike the farm environment, nasopharynx samples from wastewater workers did not cluster with air samples from wastewater treatment plants. The difference in the microbial community of nasopharynx of swine workers and a control group suggest that swine workers are carriers of germs found in bioaerosols. Conclusion: Nasopharynx sampling and microbiota could be used as a proxy of air sampling for exposure assessment studies or for the determination of exposure markers in highly contaminated agricultural environments.

Microbial species and biodiversity in settling dust within and between pig farms

The airborne fungal and bacterial species present in pig farm dust have not been well characterised even though these bioaerosols are known to cause inflammation and other airway maladies. In this study, the microbial species and composition in airborne dust within and between pig farms were investigated. Passively sedimenting dust from six pig farms were collected using electrostatic dust collectors. The bacterial and fungal species were identified using matrix-assisted laser desorption-ionisation time-of-flight mass spectrometry (MALDI-TOF MS) and next generation sequencing (NGS). Dust samples taken within the same stable section revealed high resemblance and stability. Constrained statistical analysis of the microbial community compositions indicated that the types of stable did not appear to have a great effect on the bacterial and fungal β-diversity. In contrast to this, the farm from which samples were taken appeared to have the greatest effect on the bacterial β-diversity, but this trend was not observed for the fungal β-diversity. The most common bacteria and fungi according to NGS data were anaerobes typically associated with the pig intestinal tract and yeasts respectively. Bacterial sedimentation varied at a rate between 10³ and 10⁹ CFU/m²/day, with the most common species after aerobic incubation being Aerococcus viridans and Staphylococcus equorum, while Clostridium perfringens and Staphylococcus simulans were the most common species after anaerobic incubation. A total of 28 different species of bacteria and fungi were classifiable as pathogens. In conclusion, the biodiversity in pig farm dust shows a high diversity of bacterial species. However, samples from the same stable section resembled each other, but also different sections within the same farm also resembled each other, thus indicating a high degree of community stability in the dust source. In regards to fungal identification, the biodiversity was observed to be similar between samples from different stable sections and farms, indicating a higher degree of similarities in the mycobiomes found across pig farms studied.

Gut Microbiota Profiling of Aflatoxin B1-Induced Rats Treated with Lactobacillus casei Shirota

Aflatoxin B1 (AFB1) is a ubiquitous carcinogenic food contaminant. Gut microbiota is of vital importance for the host's health, regrettably, limited studies have reported the effects of xenobiotic toxins towards gut microbiota. Thus, the present study aims to investigate the interactions between AFB1 and the gut microbiota. Besides, an AFB1-binding microorganism, Lactobacillus casei Shirota (Lcs) was tested on its ability to ameliorate the changes on gut microbiota induced by AFB1. The fecal contents of three groups of rats included an untreated control group, an AFB1 group, as well as an Lcs + AFB1 group, were analyzed. Using the MiSeq platform, the PCR products of 16S rDNA gene extracted from the feces were subjected to next-generation sequencing. The alpha diversity index (Shannon) showed that the richness of communities increased significantly in the Lcs + AFB1 group compared to the control and AFB1 groups. Meanwhile, beta diversity indices demonstrated that AFB1 group significantly deviated from the control and Lcs + AFB1 groups. AFB1-exposed rats were especially high in Alloprevotella spp. abundance. Such alteration in the bacterial composition might give an insight on the interactions of AFB1 towards gut microbiota and how Lcs plays its role in detoxification of AFB1.

Gut microbiota dynamics in travelers returning from India colonized with extended-spectrum cephalosporin-resistant Enterobacteriaceae: A longitudinal study

BACKGROUND

Intestinal colonization by extended-spectrum cephalosporin-resistant Enterobacteriaceae (ESC-R-Ent) has been attributed to travel to high prevalence countries. However, the dynamics of the microbiota changes during ESC-R-Ent colonization and whether there is a particular bacterial composition which is associated with subsequent colonization is unknown.

METHODS

Forty healthy volunteers living in Switzerland underwent screening before and after a trip to India, and also 3, 6 and 12 months after traveling. Culture-based ESC-R-Ent screening and microbiota analysis based on 16S rRNA amplicon sequencing were performed at all time points.

RESULTS

Prevalence of ESC-R-Ent colonization before traveling was 10% (n = 4), whereas it increased to 76% (n = 31) after the trip. Based on bacterial diversity analyses of the gut microbiota, there were few but significant differences for colonized versus non-colonized individuals. However, an alternative, cluster based analysis revealed that individuals remained in the same cluster over time indicating that neither traveling nor ESC-R-Ent colonization significantly influences bacterial composition. Moreover, none of the found microbiota clusters were significantly associated with subsequent risk of ESC-R-Ent colonization.

CONCLUSION

Based on their microbiota patterns, every volunteer was at the same risk of ESC-R-Ent colonization while traveling to India. Therefore, other risk factors for ESC-R-Ent colonization are responsible for this phenomenon.

Airborne MRSA and Total Staphylococcus aureus as Associated With Particles of Different Sizes on Pig Farms

Airborne methicillin-resistant Staphylococcus aureus (MRSA) have previously been found on pig farms, which may lead to nasal deposition of MRSA in humans via inhalation. The anterior nares are the main niche for S. aureus, and S. aureus can cause, e.g. wound infection and pneumonia. The aim of this study was to acquire knowledge about the potential deposition of airborne MRSA, specifically, and of total S. aureus (including both methicillin-sensitive S. aureus and MRSA, in the following called S. aureus) in the different parts of the airways during occupancy on pig farms. Measurements of airborne MRSA and S. aureus were performed on four pig farms using a six and a three-stage sampler during different work tasks, such as high-pressure cleaning and everyday inspection. MRSA were quantified using MRSA-selective agar, and S. aureus were quantified using Staphylococcus selective agar. The identity of the bacteria were confirmed using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. The geometric mean (GM) concentrations of MRSA and S. aureus were 447 cfu/m3 air and 1.8 × 103 cfu/m3 air, respectively. The highest concentrations of MRSA and S. aureus were found among pigs in a weaner stable and during high-pressure cleaning of an empty stable, respectively. The lowest concentrations of MRSA and S. aureus were found in a stable with sick pigs and in feed-storages, respectively. Most MRSA and S. aureus were associated with particles between 7 and 12 µm. On average, the particle size fractions potentially depositing in the upper airways constituted 70%, in the primary and secondary bronchi 22%, and in the terminal bronchi and alveoli 8% of the inhalable MRSA and S. aureus concentration. Across the sampled areas, the geometric mean diameter (Dg) of particles with MRSA and S. aureus were 7.2 and 6.4 µm, respectively, and no significant difference was found between these Dgs. The Dg of the airborne particles with the studied bacterium was significantly associated with the different locations on the farms. The largest Dgs were found in the air samples from the aisles and on the fence to the pens, while the smallest Dgs were found in samples from the pens among the pigs and in samples taken at greater distances from the pigs: in the hallway, feed-storage, and entry room. In conclusion, airborne MRSA and S. aureus were found in sample fractions potentially depositing in all six parts of the airways. However, the majority was found to potentially deposit in the upper airways. The concentration of airborne MRSA and S. aureus and MRSA, as well as the fraction potentially depositing in the different parts of the airways, depended on the specific work task being performed and the location on the farm.

How Can We Define "Optimal Microbiota?": A Comparative Review of Structure and Functions of Microbiota of Animals, Fish, and Plants in Agriculture

All multicellular organisms benefit from their own microbiota, which play important roles in maintaining the host nutritional health and immunity. Recently, the number of studies on the microbiota of animals, fish, and plants of economic importance is rapidly expanding and there are increasing expectations that productivity and sustainability in agricultural management can be improved by microbiota manipulation. However, optimizing microbiota is still a challenging task because of the lack of knowledge on the dominant microorganisms or significant variations between microbiota, reflecting sampling biases, different agricultural management as well as breeding backgrounds. To offer a more generalized view on microbiota in agriculture, which can be used for defining criteria of “optimal microbiota” as the goal of manipulation, we summarize here current knowledge on microbiota on animals, fish, and plants with emphasis on bacterial community structure and metabolic functions, and how microbiota can be affected by domestication, conventional agricultural practices, and use of antimicrobial agents. Finally, we discuss future tasks for defining “optimal microbiota,” which can improve host growth, nutrition, and immunity and reduce the use of antimicrobial agents in agriculture.

One Health Relationships Between Human, Animal, and Environmental Microbiomes: A Mini-Review

The One Health concept stresses the ecological relationships between human, animal, and environmental health. Much of the One Health literature to date has examined the transfer of pathogens from animals (e.g., emerging zoonoses) and the environment to humans. The recent rapid development of technology to perform high throughput DNA sequencing has expanded this view to include the study of entire microbial communities. Applying the One Health approach to the microbiome allows for consideration of both pathogenic and non-pathogenic microbial transfer between humans, animals, and the environment. We review recent research studies of such transmission, the molecular and statistical methods being used, and the implications of such microbiome relationships for human health. Our review identified evidence that the environmental microbiome as well as the microbiome of animals in close contact can affect both the human microbiome and human health outcomes. Such microbiome transfer can take place in the household as well as the workplace setting. Urbanization of built environments leads to changes in the environmental microbiome which could be a factor in human health. While affected by environmental exposures, the human microbiome also can modulate the response to environmental factors through effects on metabolic and immune function. Better understanding of these microbiome interactions between humans, animals, and the shared environment will require continued development of improved statistical and ecological modeling approaches. Such enhanced understanding could lead to innovative interventions to prevent and manage a variety of human health and disease states.