High throughput genomic sequencing of bioaerosols in broiler chicken production facilities

The Association between Broiler Litter Microbiota and the Supplementation of Bacillus Probiotics in a Leaky Gut Model

Probiotics provided from hatch have a major influence on microbiota development, and together with environmental and bedding microbiota, shape the microbial community of the litter. We investigated the influence of probiotic supplementation and a leaky gut challenge induced using dexamethasone (DEX) on the litter microbial community and litter parameters. The probiotic product was a mix of three Bacillus amyloliquefaciens strains. The litter microbiota were compared to the microbial communities from other gut sections. The litter samples had higher microbial diversity compared to the caecum, gizzard, jejunum, and jejunal mucosa. The high similarity between the litter phylum-level microbiota and gizzard microbiota detected in our study could be a consequence of ingested feed and litter passing through the gizzard. Moreover, the litter microbial community is fundamentally distinct from the intestinal microbiota, as evidenced by the number of genera present in the litter but absent from all the intestinal sections and vice versa. Furthermore, LEfSe analysis identified distinct microbial taxa across different groups, with specific genera associated with different treatments. In terms of litter quality, the birds in the DEX groups had a significantly higher moisture content, indicating successful leaky gut challenge, while probiotic supplementation did not significantly affect the moisture levels. These findings provide comprehensive insights into the distinct microbiota characteristics of litter.

Dietary strategies can increase cloacal endotoxin levels and modulate the resident microbiota in broiler chickens

Endotoxins released from poultry feces have been associated with impaired human health. Because endotoxins are released from gram-negative intestinal bacteria, it was hypothesized that dietary strategies may influence endotoxin excretion via modulation of gut microbiota. We therefore tested dietary strategies that could potentially reduce cloacal endotoxin levels in broiler chickens. One-day-old male Ross 308 (N = 1,344) broilers were housed in 48 pens (N = 8 pens/treatment, 28 chickens per pen) and fed 1 of 6 diets for 35 days (d) in a 3-phase feeding program: a basic diet (CON) that served as the reference diet, or basic diet supplemented with butyrate (BUT), inulin (INU), medium-chain fatty acids (MCFA) or Original XPC™LS (XPC), or a high-fiber-low-protein (HF-LP) diet. A significant (P < 0.05) increase in cloacal endotoxin concentration at d 35 was observed in BUT as compared to CON. Analysis of cloacal microbiota showed a trend (P < 0.07) for a higher gram-negative/gram-positive ratio and for a higher relative abundance of gram-negative bacteria at d 35 (P ≤ 0.08) in BUT and HF-LP as compared to CON. A significant (P < 0.05) increase in average daily gain (ADG) and improved feed conversion ratio (P < 0.05) were observed in MCFA during the grower phase (d 14-28), and a significant (P < 0.05) increase in average daily feed intake (ADFI) was observed in MCFA during d 0 to 28. Broilers fed HF-LP had a significantly (P < 0.05) higher FCR and lower ADG throughout the rearing period. No treatment effects were found on footpad dermatitis, but BUT had worst hock burn scores at d 35 (P < 0.01) and MCFA had worst cleanliness scores at d 21 but not at d 35 (treatment*age P < 0.05), while INU had better cleanliness as compared to CON at d 35 (P < 0.05). In conclusion, especially BUT and HF-LP were able to modulate resident microbiota and BUT also increased cloacal endotoxin levels, which was opposite to our hypothesis. The present study indicates that cloacal endotoxin release can be affected by the diet but further study is needed to find dietary treatments that can reduce cloacal endotoxin release.

Relationship of the Poultry Microbiome to Pathogen Colonization, Farm Management, Poultry Production, and Foodborne Illness Risk Assessment

Despite the continuous progress in food science and technology, the global burden of foodborne illnesses remains substantial, with pathogens in food causing millions of infections each year. Traditional microbiological culture methods are inadequate in detecting the full spectrum of these microorganisms, highlighting the need for more comprehensive detection strategies. This review paper aims to elucidate the relationship between foodborne pathogen colonization and the composition of the poultry microbiome, and how this knowledge can be used for improved food safety. Our review highlights that the relationship between pathogen colonization varies across different sections of the poultry microbiome. Further, our review suggests that the microbiome profile of poultry litter, farm soil, and farm dust may serve as potential indicators of the farm environment's food safety issues. We also agree that the microbiome of processed chicken samples may reveal potential pathogen contamination and food quality issues. In addition, utilizing predictive modeling techniques on the collected microbiome data, we suggest establishing correlations between particular taxonomic groups and the colonization of pathogens, thus providing insights into food safety, and offering a comprehensive overview of the microbial community. In conclusion, this review underscores the potential of microbiome analysis as a powerful tool in food safety, pathogen detection, and risk assessment.

Microbial contamination in grocery stores from Portugal and Spain - The neglected indoor environment to be tackled in the scope of the One Health approach

Microbial contamination in grocery shops (GS) should be evaluated since food commodities are commonly handled by workers and customers increasing the risk of food contamination and disease transmission. The aim of this study was to evaluate the microbial contamination in Portuguese and Spanish GS with a multi-approach protocol using passive (electrostatic dust cloths and surface swabs) sampling methods. The molecular detection of Aspergillus sections, mycotoxin analysis, screening of azole resistance as well as cytotoxicity measurement were conducted to better estimate the potential health risks of exposure and to identify possible relations between the risk factors studied. Fruits/vegetables sampling location was the one identified has being the most contaminated (bacteria and fungi) area in GS from both countries. Aspergillus section Fumigati and Fusarium species were observed in samples from Portuguese groceries with reduced susceptibilities to azoles commonly used in the clinical treatment of fungal infections. Fumonisin B2 was detected in Portuguese GS possible unveiling this emergent threat concerning occupational exposure and food safety. Overall, the results obtained raise concerns regarding human health and food safety and must be surveilled applying a One Health approach.

Bacterial Community Characteristics Shaped by Artificial Environmental PM2.5 Control in Intensive Broiler Houses

Multilayer cage-houses for broiler rearing have been widely used in intensive Chinese farming in the last decade. This study investigated the characteristics and influencing factors of bacterial communities in the PM2.5 of broiler cage-houses. The PM2.5 samples and environmental variables were collected inside and outside of three parallel broiler houses at the early, middle, and late rearing stages; broiler manure was also gathered simultaneously. The bacterial 16S rRNA sequencing results indicated that indoor bacterial communities were different from the outdoor atmosphere and manure. Furthermore, the variations in airborne bacterial composition and structure were highly influenced by the environmental control variables at different growth stages. The db-RDA results showed that temperature and wind speed, which were artificially modified according to managing the needs for broiler growth, were the main factors affecting the diversity of dominant taxa. Indoor airborne and manurial samples shared numerous common genera, which contained high abundances of manure-origin bacteria. Additionally, the airborne bacterial community tended to stabilize in the middle and late stages, but the population of potentially pathogenic bacteria grew gradually. Overall, this study enhances the understanding of airborne bacteria variations and highlighted the potential role of environmental control measures in intensive farming.

Exploring the effect of the microbiota on the production of duck striped eggs

The microbiota has received plenty of attention in recent years due to its influence on host health and productivity. The striped eggs have reduced hatching performance and resulted in economic loss. The reasons are still unknown. Microbiota is one of the potentially important factors contributing to striped egg formation. This study investigates the relationship between the microbiota and striped eggs. The litter samples, feed samples, and cloacal swab samples of female ducks that produce striped eggs and normal eggs were performed for microbial diversity and composition using 16S rRNA sequencing. The results showed that there was no significant difference between feed microbiota and cloacal swab microbiota by alpha diversity, whereas, the number of microorganisms in the litter samples of female ducks that produced striped eggs was less than those of female ducks with normal eggs. There were compositional differences in litter microbiota of female ducks between the striped egg and the normal eggs. Among them, the abundance of Staphylococcus, Corynebacterium, and Brevibacterium in the litter of female ducks that produced striped eggs was significantly higher than that produced normal eggs. And these differential bacteria maybe affect the health of female ducks and cause abnormalities in the formation process of duck eggs. Therefore, the reduction of harmful bacteria may protect the reproductive health of female ducks and decrease the proportion of striped eggs. It provides an important reference to explore why female ducks produce striped eggs.

Poultry exposure and environmental protection against asthma in rural children

BACKGROUND

Asthma is one of the most common chronic diseases in childhood, and the prevalence has been increasing over the past few decades. One of the most consistent epidemiological findings is that children living in a farming or rural environment are protected from development of asthma and allergies, but the protective factors in rural China are not clear.

METHODS

A community-based, cross-sectional epidemiological study was performed in a total of 17,587 children aged 5-8 years, 3435 from Hong Kong (urban) and 14,152 from Conghua (rural county in southern China). Asthma and allergic symptoms as well as environmental exposures were ascertained by using a standardized and validated questionnaire.

RESULTS

The prevalence of current wheeze was significantly lower in rural Conghua than that of urban Hong Kong (1.7% vs. 7.7%, p < 0.001). A lower rate of asthma ever was also reported in rural children compared with their urban counterparts (2.5% vs. 5.3%, p < 0.001). After adjusting for confounding factors, exposure to agricultural farming (adjusted odds ratio 0.74, 95% confidence interval: 0.56-0.97) and poultry (0.75, 0.59-0.96) were the most important factors associated with the asthma-protective effect in the rural area. Further propensity score-adjusted analysis indicated that such protection conferred by living in the rural environment was mainly attributable to poultry exposure.

CONCLUSIONS

We confirmed that the prevalence of asthma and atopic disorders was significantly lower in rural children when compared with their urban peers. Exposure to poultry and agricultural farming are the most important factors associated with asthma protection in the rural area.

Occupational risk factors in health of broiler-farm workers: A systematic review

The present study aimed to identify gaps in literature regarding occupational risks to broiler farming workers. A systematic review was performed in which inclusion criteria were workers in poultry farms. The search was done between May and June 2019 with online papers. Keywords were "poultry farmer," "poultry worker," and "poultry workers" as terms of an axis of a theoretical framework. Results indicated as predominant topics lung diseases, nasal mucosa or paranasal sinus contamination, and aflatoxicosis. The identified gaps in scientific publications are related to mitigation of occupational risks. Prevalent described risks are associated to exposure to chemicals gases, vapors and aerosols, biological hazards (micro-organisms), ergonomic risks, wrong working posture, excessive body movement and inadequate behaviors. Preventive policies about poultry farmer's health and safety needs to be adopted to reduce potentially dangerous risk factors and increase productivity.

Bacterial extracellular vesicles isolated from organic dust induce neutrophilic inflammation in the lung

Inhalation of organic dust is an occupational hazard leading to the development of respiratory symptoms and respiratory diseases. Bioaerosols from concentrated animal feeding operations are rich in bacteria and could carry bacterial extracellular vesicles (EVs) that could induce lung inflammation. It is not known if organic dust contains bacterial EVs and whether they modulate lung inflammation. Herein, we show that poultry organic dust contains bacterial EVs (dust EVs) that induce lung inflammation. Treatment of airway epithelial cells, THP-1-monocytes and -macrophages with dust EVs rapidly induced IL-8, IL-6, ICAM-1, proIL-1β, and TNF-α levels. In airway epithelial cells, induction of inflammatory mediators was due to increased mRNA levels and NF-κB activation. Induction of inflammatory mediators by dust EVs was not inhibited by polymyxin B. Single and repeated treatments of mice with dust EVs increased lung KC, IL-6, and TNF-α levels without significantly altering IL-17A levels. Increases in cytokines were associated with enhanced neutrophil infiltration into the lung. Repeated treatments of mice with dust EVs increased lung mean linear intercept and increased collagen deposition around airways indicating lung remodeling. Peribronchial cell infiltrates and airway epithelial thickening were also observed in treated mice. Because bacterial EVs are nanometer-sized particles, they can reach and accumulate in the bronchiolar and alveolar regions causing lung injury leading to the development of respiratory diseases. Our studies have provided new evidence for the presence of bacterial EVs in organic dust and for their role as one of the causative agents of organic dust-induced lung inflammation and lung injury.

Recent Advances in Monitoring, Sampling, and Sensing Techniques for Bioaerosols in the Atmosphere

Bioaerosols in the form of microscopic airborne particles pose pervasive risks to humans and livestock. As either fully active components (e.g., viruses, bacteria, and fungi) or as whole or part of inactive fragments, they are among the least investigated pollutants in nature. Their identification and quantification are essential to addressing related dangers and to establishing proper exposure thresholds. However, difficulties in the development (and selection) of detection techniques and an associated lack of standardized procedures make the sensing of bioaerosols challenging. Through a comprehensive literature search, this review examines the mechanisms of conventional and advanced bioaerosol detection methods. It also provides a roadmap for future research and development in the selection of suitable methodologies for bioaerosol detection. The development of sample collection and sensing technology make it possible for continuous and automated operation. However, intensive efforts should be put to overcome the limitations of current technology as most of the currently available options tend to suffer from lengthy sample acquisition times and/or nonspecificity of probe material.

Contribution of the Broiler Breeders' Fecal Microbiota to the Establishment of the Eggshell Microbiota

In broiler chicken production, microbial populations on the eggshell surface following oviposition are still poorly characterized, though they may significantly impact both poultry and public health. The aim of this study was to describe the microbiota of both broiler breeder hens’ feces and the surface of their eggs to assess the contribution of the parental fecal microbiota to the eggshell microbiota. A total of twelve breeder flocks in Quebec, Canada, were sampled at two different times, and a total of 940 feces and 16,400 egg surface samples were recovered. Using 16S rRNA gene sequencing, we showed that even if the microbiota of both feces and eggshells were mainly composed of the phyla Firmicutes, Actinobacteria, Proteobacteria, and Bacteroidetes, the bacterial community compositions and structures differed between both types of samples. Our results also showed that both the sampling time and the flock identity significantly influenced the alpha- and the beta-diversities of the studied microbiomes. Using a Venn diagram, we showed that 1790 operational taxonomic units (OTUs) were shared between feces and eggshell samples. Sequences associated with genera of potentially pathogenic and spoilage bacteria, Acinetobacter, Campylobacter, Escherichia/Shigella, Helicobacter, Listeria, Proteus, Pseudomonas, Salmonella, and Staphylococcus, were shared between sample types. Some OTUs highly represented in the fecal microbiota and associated with Lactobacillus and Streptococcus genera, were absent from eggshells, suggesting a selection during the microbiota transfer and/or the potential role of environmental contamination. To the best of our knowledge, this is the first study using 16S rRNA sequencing to describe the contribution of the transfer from the fecal microbial ecosystem of laying breeder hens to the establishment of the microbiota on the surface of laid eggs, as well as the bacterial communities at both the broiler breeder feces and the eggshell levels.

Composition and Function of Chicken Gut Microbiota

Simple Summary

Chickens evolved for millions of years to be hatched in a nest in contact with an adult hen. However, current commercial production of chickens is based on hatching chicks in a clean hatchery environment in the absence of adult hens. The ancestors of domestic chickens inhabited a living environment different from that used for current commercial production. Currently, the lifespan of broilers is around 5 weeks, the lifespan of egg layers is around one year while chickens can live for 15–20 years. This means that studies on chicken–microbiota interactions are of specific importance. The intestinal tract of commercially hatched chicks is gradually colonised from environmental sources only, however, if the chicks are provided experimentally with microbiota from a hen they can be colonised by adult-type microbiota from the very first days of life and become resistant to infections with pathogenic Escherichia coli, Clostridium perfringens, or Salmonella. Because of such specificities in the interactions of chickens with their gut microbiota, current knowledge in this area is critically presented in this review.

Abstract

Studies analyzing the composition of gut microbiota are quite common at present, mainly due to the rapid development of DNA sequencing technologies within the last decade. This is valid also for chickens and their gut microbiota. However, chickens represent a specific model for host–microbiota interactions since contact between parents and offspring has been completely interrupted in domesticated chickens. Nearly all studies describe microbiota of chicks from hatcheries and these chickens are considered as references and controls. In reality, such chickens represent an extreme experimental group since control chicks should be, by nature, hatched in nests in contact with the parent hen. Not properly realising this fact and utilising only 16S rRNA sequencing results means that many conclusions are of questionable biological relevance. The specifics of chicken-related gut microbiota are therefore stressed in this review together with current knowledge of the biological role of selected microbiota members. These microbiota members are then evaluated for their intended use as a form of next-generation probiotics.

PM2.5 from a broiler breeding production system: The characteristics and microbial community analysis

Particulate matter (PM) released from the processes of livestock production has a negative impact on the health of animals and workers. Herein, the concentration, major chemical components, morphology and microbiological compositions of particulate matter 2.5 (PM_2.5, particles with aerodynamic diameter less than 2.5 μm) in a broiler breeding house were investigated. The results showed that the PM_2.5 distribution in the chicken house was affected by the illumination, draught fans, chicken frame structure and activity of the chickens in the broiler breeding house. Component analysis showed that organic carbon (OC) accounted for the largest proportion, and followed by element carbon (EC), SO₄^2-, NO₃^-, NH₄⁺, Na⁺, K⁺ and Ca²⁺. Ultrastructural observations revealed that the shape of PM_2.5 had a round, rectangular, chain-like and irregular shape. The concentration of endotoxin was approximately 0.3 EU/m³. Microbiological analysis showed that at the genus level, the pathogenic bacteria included Staphylococcus, Corynebacterium, Enterococcus, Parabacteroides, Escherichia and Megamonas. The abundant harmful fungi were Aspergillus, Scopulariopsis, Wallemia, and Fusarium. Through redundancy analysis (RDA) analysis, we determined that OC, EC, Na⁺, K⁺, and NH₄⁺ had strong correlations with Brachybacterium, Brevibacterium, Corynebacterium, Escherichia, Scopulariopsis and Microascus. SO₄^2- was closely related to Scopulariopsis and Salinicoccus. Salinicoccus was also strongly correlated with NO₃^-. Our results indicated that feed, faeces, and outside soot are contributed to the increase in PM_2.5 concentration in the chicken house, while the sources of the dominant bacterial and fungi might be feed, faeces, suspended outside soil and cereal crops.

Recovery of Fungal Cells from Air Samples: a Tale of Loss and Gain

There are limitations in establishing a direct link between fungal exposure and health effects due to the methodology used, among other reasons. Culture methods ignore the nonviable/uncultivable fraction of airborne fungi. Molecular methods allow for a better understanding of the environmental health impacts of microbial communities. However, there are challenges when applying these techniques to bioaerosols, particularly to fungal cells. This study reveals that there is a loss of fungal cells when samples are recovered from air using wet samplers and aimed to create and test an improved protocol for concentrating mold spores via filtration prior to DNA extraction. Results obtained using the new technique showed that up to 3 orders of magnitude more fungal DNA was retrieved from the samples using quantitative PCR. A sequencing approach with MiSeq revealed a different diversity profile depending on the methodology used. Specifically, 8 fungal families out of 19 families tested were highlighted to be differentially abundant in centrifuged and filtered samples. An experiment using laboratory settings showed the same spore loss during centrifugation for Aspergillus niger and Penicillium roquefortii strains. We believe that this work helped identify and address fungal cell loss during processing of air samples, including centrifugation steps, and propose an alternative method for a more accurate evaluation of fungal exposure and diversity.IMPORTANCE This work shed light on a significant issue regarding the loss of fungal spores when recovered from air samples using liquid medium and centrifugation to concentrate air particles before DNA extraction. We provide proof that the loss affects the overall fungal diversity of aerosols and that some taxa are differentially more affected than others. Furthermore, a laboratory experiment confirmed the environmental results obtained during field sampling. The filtration protocol described in this work offers a better description of the fungal diversity of aerosols and should be used in fungal aerosol studies.

Bioaerosol concentrations generated from toilet flushing in a hospital-based patient care setting

Background

In the United States, 1.7 million immunocompromised patients contract a healthcare-associated infection, annually. These infections increase morbidity, mortality and costs of care. A relatively unexplored route of transmission is the generation of bioaerosols during patient care. Transmission of pathogenic microorganisms may result from inhalation or surface contamination of bioaerosols. The toilet flushing of patient fecal waste may be a source of bioaerosols. To date, no study has investigated bioaerosol concentrations from flushing fecal wastes during patient care.

Methods

Particle and bioaerosol concentrations were measured in hospital bathrooms across three sampling conditions; no waste no flush, no waste with flush, and fecal waste with flush. Particle and bioaerosol concentrations were measured with a particle counter bioaerosol sampler both before after a toilet flushing event at distances of 0.15, 0.5, and 1 m from the toilet for 5, 10, 15 min.

Results

Particle concentrations measured before and after the flush were found to be significantly different (0.3-10 μm). Bioaerosol concentrations when flushing fecal waste were found to be significantly greater than background concentrations (p-value = 0.005). However, the bioaerosol concentrations were not different across time (p-value = 0.977) or distance (p-value = 0.911) from the toilet, suggesting that aerosols generated may remain for longer than 30 min post flush. Toilets produce aerosol particles when flushed, with the majority of the particles being 0.3 μm in diameter. The particles aerosolized include microorganisms remaining from previous use or from fecal wastes. Differences in bioaerosol concentrations across conditions also suggest that toilet flushing is a source of bioaerosols that may result in transmission of pathogenic microorganisms.

Conclusions

This study is the first to quantify particles and bioaerosols produced from flushing a hospital toilet during routine patient care. Future studies are needed targeting pathogens associated with gastrointestinal illness and evaluating aerosol exposure reduction interventions.

Evaluation of a sprinkler cooling system on inhalable dust and ammonia concentrations in broiler chicken production

Workers are exposed to dust in broiler chicken production during daily work activities. Poultry dust may contain inflammatory agents (e.g., endotoxin) and inhalation exposure has been associated with pulmonary symptoms. Current practice to reduce worker exposure to poultry dust is the use of respiratory protection (e.g., elastomeric face-piece respirator with a P100 and ammonia chemical cartridge). Limited research has been conducted to evaluate engineering controls to reduce dust and ammonia concentrations in broiler chicken production; therefore, the purpose of this research was to evaluate the effectiveness of a water sprinkling system to reduce inhalable dust and ammonia concentrations in a broiler chicken house. Inhalable dust and ammonia concentrations were measured daily for the production cycle of a flock of broiler chickens (63 days). Inhalable dust was measured gravimetrically using an inhalable sampler and ammonia was measured by a direct reading sensor. Sampling was performed on a stationary mannequin inside two broiler chicken houses. One house used a sprinkler cooling system to deliver a water mist throughout the house and the second house was an untreated control. The sprinkler system activated after day 5 of chicken placement, releasing water periodically from 6 am to 10 pm. The amount of sprinkling increased at day 10 and day 15 as recommended by the manufacturer. Geometric mean (GM) inhalable dust concentrations measured in the treatment house (5.5 mg/m³) were not different (p = 0.33) than those found in the control house (6.0 mg/m³). The GM ammonia concentrations were also not different (p = 0.34) across the treatment and control house [10.6 ppm (GSD: 1.80); GM 9.51 ppm (GSD: 1.77)], respectively. The use of cost effective engineering, administrative and personal exposure controls are needed in the poultry industry to effectively reduce worker's exposure to hazardous concentrations of dust and ammonia.

High throughput genomic sequencing of bioaerosols in broiler chicken production facilities

Chronic inhalation exposure to agricultural dust promotes the development of chronic respiratory diseases among poultry workers. Poultry dust is composed of dander, chicken feed, litter bedding and microbes. However, the microbial composition and abundance has not been fully elucidated. Genomic DNA was extracted from settled dust and personal inhalable dust collected while performing litter sampling or mortality collection tasks. DNA libraries were sequenced using a paired-end sequencing-by-synthesis approach on an Illumina HiSeq 2500. Sequencing data showed that poultry dust is predominantly composed of bacteria (64-67%) with a small quantity of avian, human and feed DNA (< 2% of total reads). Staphylococcus sp. AL1, Salinicoccus carnicancri and Lactobacillus crispatus were the most abundant bacterial species in personal exposure samples of inhalable dust. Settled dust had a moderate relative abundance of these species as well as Staphylococcus lentus and Lactobacillus salivarius. There was a statistical difference between the microbial composition of aerosolized and settled dust. Unlike settled dust composition, aerosolized dust composition had little variance between samples. These data provide an extensive analysis of the microbial composition and relative abundance in personal inhalable poultry dust and settled poultry dust.