Bacterial communities in aerosols and manure samples from two different dairies in central and Sonoma valleys of California

Aggregative Swab Sampling Method for Romaine Lettuce Show Similar Quality and Safety Indicators and Microbial Profiles Compared to Composite Produce Leaf Samples in a Pilot Study

Composite produce leaf samples from commercial production rarely test positive for pathogens, potentially due to low pathogen prevalence or the relatively small number of plants sampled. Aggregative sampling may offer a more representative alternative. This pilot study investigated whether aggregative swab samples performed similarly to produce leaf samples in their ability to recover quality indicators (APCs and coliforms), detect Escherichia coli, and recover representative microbial profiles. Aggregative swabs of the outer leaves of romaine plants (n = 12) and composite samples consisting of various grabs of produce leaves (n = 14) were collected from 60 by 28 ft sections of a one-acre commercial romaine lettuce field. Aerobic plate counts were 9.17 ± 0.43 and 9.21 ± 0.42 log(CFU/g) for produce leaf samples and swabs, respectively. Means and variance were not significantly different (p = 0.38 and p = 0.92, respectively). Coliform recoveries were 3.80 ± 0.76 and 4.19 ± 1.15 log(CFU/g) for produce leaf and swabs, respectively. Means and variances were not significantly different (p = 0.30 and p = 0.16, respectively). Swabs detected generic E. coli in 8 of 12 samples, more often than produce leaf samples (3 of 14 positive, Fisher's p = 0.045). Full-length 16S rRNA microbial profiling revealed that swab and produce leaf samples did not show significantly different alpha diversities (p = 0.75) and had many of the most prevalent bacterial taxa in common and in similar abundances. These data suggest that aggregative swabs perform similarly to, if not better than, produce leaf samples in recovering indicators of quality (aerobic and coliform bacteria) and food safety (E. coli), justifying further method development and validation.

Comparison of Three Air Sampling Methods for the Quantification of Salmonella, Shiga-toxigenic Escherichia coli (STEC), Coliforms, and Generic E. coli from Bioaerosols of Cattle and Poultry Farms

Recent fresh produce outbreaks potentially associated with bioaerosol contamination from animal operations in adjacent land highlighted the need for further study to better understand the associated risk. The purpose of this research was to evaluate three sampling methods for quantifying target bacterial bioaerosols from animal operations. A dairy cattle and poultry farm located in Georgia, U.S. were visited six times each. Air was collected for 10 min using: 2-stage Andersen impactor with and without mineral oil overlay and impingement samplers. Sampling devices were run concurrently at 0.1, 1, and 2 m heights (n = 36). Andersen samplers were loaded with CHROMagar™ Salmonella, CHROMagar™ STEC, or Brilliance™ coliforms/E. coli. The impingement sampler contained buffered peptone water (20 mL) which was vacuum filtered through a 0.45 µm filter and placed onto the respective media. Plates were incubated at 37 ℃ for 48 h. PCR confirmation followed targeting ttr for Salmonella and stx1, stx2, and eae genes for STEC. No significant differences were found among methods to quantify coliforms and E. coli. Salmonella and STEC bioaerosols were not detected by any of the methods (Limit of detection: 0.55 log CFU/m3). E. coli bioaerosols were significantly greater in the poultry (2.76-5.00 log CFU/m3) than in the cattle farm (0.55-2.82 log CFU/m3) (p < 0.05), and similarly distributed at both stages in the Andersen sampler (stage 1:>7 μm; stage 2: 0.65-7 μm particle size). Sampling day did not have a significant effect on the recovery of coliforms/E. coli bioaerosols in the poultry farm when samples were taken at the broiler house exhaust fan (p > 0.05). A greater and constant emission of coliforms and E. coli bioaerosols from the poultry farm warrants further investigation. These data will help inform bioaerosol sampling techniques which can be used for the quantification of bacterial foodborne pathogens and indicator organisms for future research.

Size-resolved ambient bioaerosols concentration, antibiotic resistance, and community composition during autumn and winter seasons in Qatar

This study investigates the size distribution, microbial composition, and antibiotic resistance (ABR) of airborne bioaerosols at a suburban location in Doha, Qatar between October 2021 and January 2022. Samples were collected using an Andersen six-stage viable cascade impactor and a liquid impinger. Findings showed that the mean bacteria concentration (464 CFU/m3) was significantly higher than that of fungi (242 CFU/m3) during the study period. Both bacteria and fungi were most abundant in the aerodynamic size fractions of 1.10-2.21 μm, with peak concentrations observed in the mornings and lowest concentrations in the afternoons across all size fractions. A total of 24 different culturable species were identified, with the most abundant ones being Pasteurella pneumotropica (9.71%), Pantoea spp. 1 (8.73%), and Proteus penneri (7.77%) spp. At the phylum level, the bacterial community configurations during the autumn and winter seasons were nearly identical as revealed by molecular genomics, with Proteobacteria being the most predominant, followed by Firmicutes, Bacteroidetes, Acidobacteriota, and Planctomycetota. However, there was a significant variation in dominant genera between autumn and winter. The most abundant genera included Sphingomonas, Paraburkholderia, Comamonas, Bacillus, and Lysinibacillus. Several bacterial genera identified in this study have important public health and ecological implications, including the risk of respiratory tract infections. Furthermore, the study found that ABR was highest in December, with bioaerosols exhibiting resistance to at least 5 out of 10 antibiotics, and 100% resistance to Metronidazole in all samples. Metagenomics analysis revealed the presence of various airborne bacteria that were not detected through culture-dependent methods. This study provides valuable insights into the airborne microbial composition, temporal variability and ABR in the Arabian Gulf region.

Exploration of phyllosphere microbiomes in wheat varieties with differing aphid resistance

BACKGROUND

Leaf-associated microbes play an important role in plant development and response to exogenous stress. Insect herbivores are known to alter the phyllosphere microbiome. However, whether the host plant's defense against insects is related to the phyllosphere microbiome remains mostly elusive. Here, we investigated bacterial communities in the phyllosphere and endosphere of eight wheat cultivars with differing aphid resistance, grown in the same farmland.

RESULTS

The bacterial community in both the phyllosphere and endosphere showed significant differences among most wheat cultivars. The phyllosphere was connected to more complex and stable microbial networks than the endosphere in most wheat cultivars. Moreover, the genera Pantoea, Massilia, and Pseudomonas were found to play a major role in shaping the microbial community in the wheat phyllosphere. Additionally, wheat plants showed phenotype-specific associations with the genera Massilia and Pseudomonas. The abundance of the genus Exiguobacterium in the phyllosphere exhibited a significant negative correlation with the aphid hazard grade in the wheat plants.

CONCLUSION

Communities of leaf-associated microbes in wheat plants were mainly driven by the host genotype. Members of the genus Exiguobacterium may have adverse effects on wheat aphids. Our findings provide new clues supporting the development of aphid control strategies based on phyllosphere microbiome engineering.

Oral seeding and niche-adaptation of middle ear biofilms in health

The entrenched dogma of a sterile middle ear mucosa in health is incongruent with its periodic aeration and seeding with saliva aerosols. To test this, we sequenced 16S rRNA-V4 amplicons from otic secretions collected at the nasopharyngeal orifice of the tympanic tube and, as controls, oropharyngeal and buccal samples. The otic samples harbored a rich diversity of oral keystone genera and similar functional traits but were enriched in anaerobic genera in the Bacteroidetes (Prevotella and Alloprevotella), Fusobacteria (Fusobacterium and Leptotrichia) and Firmicutes (Veillonella) phyla. Facultative anaerobes in the Streptococcus genus were also abundant in the otic and oral samples but corresponded to distinct, and sometimes novel, cultivars, consistent with the ecological diversification of the oral migrants once in the middle ear microenvironment. Neutral community models also predicted a large contribution of oral dispersal to the otic communities and the positive selection of taxa better adapted to growth and reproduction under limited aeration. These results challenge the traditional view of a sterile middle ear in health and highlight hitherto unknown roles for oral dispersal and episodic ventilation in seeding and diversifying otic biofilms.

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The middle ear mucosa harbors a rich bacterial community in health.

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Oral migration is the primary mechanism for seeding otic biofilms.

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Periodic aeration of the middle ear enriches for anaerobic taxa and promotes the ecological diversification of oral migrants.

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Our study challenges the entrenched dogma of a sterile middle ear in health.

Removal of bovine digital dermatitis-associated treponemes from hoof knives after foot-trimming: a disinfection field study

Background

Bovine digital dermatitis (BDD) is an infectious foot disease found commonly in dairy herds. Foot-trimming is an important husbandry procedure for reducing the ensuing lameness; however, epidemiological, and microbiological studies have identified this as a risk activity for transmitting BDD.

Three disinfectants have previously been identified in laboratory work as effective for removing viable BDD-associated Treponema spp., from hoof knife blades. The present study enrolled 133 dairy cattle with BDD lesions, and swabbed hoof knife blades before and after foot-trimming, and after knife disinfection with one of three disinfectants (1:100 FAM30®, 2% Virkon® and 2% sodium hypochlorite) to assess their efficacy under field conditions.

Results

Detection of BDD treponeme phylogroup DNA was undertaken by direct PCR of swabs, and viable treponemes were detected by PCR of swab cultures after 6 weeks’ incubation.

Where hoof knives did not contact the lesion, BDD-associated treponemes were detected after foot-trimming in 12/22 (54.5%) cases by direct PCR and 1/22 (4.5%) cases by PCR of cultured organisms. Where contact was made with the lesion, 111/111 (100%) samples taken after trimming were positive by direct PCR and 47/118 (39.8%) were positive by culture PCR. Viable organisms were identified in cultures from lesion stages M2, M3, M4 and M4.1. No viable organisms were detected after disinfection of hoof knives.

Conclusions

Hoof knives post-trimming were frequently contaminated with BDD-associated treponeme DNA. Viable organisms were identified in cultures whether contact had been made between hoof knife and lesion or not, although contact clearly increased the frequency of detection of viable organisms. The three disinfectants tested were effective for removing viable organisms. The disinfection protocol used in this study should therefore be considered reliable for adoption as standard industry practice.

Bedding and bedding management practices are associated with mesophilic and thermophilic spore levels in bulk tank raw milk

Mesophilic and thermophilic spore-forming bacteria represent a challenge to the dairy industry, as these bacteria are capable of surviving adverse conditions associated with processing and sanitation and eventually spoil dairy products. The dairy farm environment, including soil, manure, silage, and bedding, has been implicated as a source for spores in raw milk. High levels of spores have previously been isolated from bedding, and different bedding materials have been associated with spore levels in bulk tank (BT) raw milk; however, the effect of different bedding types, bedding management practices, and bedding spore levels on the variance of spore levels in BT raw milk has not been investigated. To this end, farm and bedding management surveys were administered and unused bedding, used bedding, and BT raw milk samples were collected from dairy farms (1 or 2 times per farm) across the United States over 1 yr; the final data set included 182 dairy farms in 18 states. Bedding suspensions and BT raw milk were spore pasteurized (80°C for 12 min), and mesophilic and thermophilic spores were enumerated. Piecewise structural equation modeling analysis was used to determine direct and indirect pathways of association among farm and bedding practices, levels of spores in unused and used bedding, and levels of spores in BT raw milk. Separate models were constructed for mesophilic and thermophilic spore levels. The analyses showed that bedding material had a direct influence on levels of spores in unused and used bedding as well as an indirect association with spore levels in BT raw milk through used bedding spore levels. Specific bedding and farm management practices as well as cow hygiene in the housing area were associated with mesophilic and thermophilic spore levels in unused bedding, used bedding, and BT raw milk. Notably, levels of spores in used bedding were positively related to those in unused bedding, and used bedding spore levels were positively related to those in BT raw milk. The results of this study increase the understanding of the levels and ecology of mesophilic and thermophilic spores in raw milk, emphasize the possible role of bedding as a source of spores on-farm, and present opportunities for dairy producers to reduce spore levels in BT raw milk.

Comparison between random forest and gradient boosting machine methods for predicting Listeria spp. prevalence in the environment of pastured poultry farms

Foodborne pathogens such as Listeria spp. contain the ability to survive and multiply in poultry farming environments, which provides a route of contamination for poultry processing environments and final poultry products. An understanding of the effect of meteorological variables on the prevalence of Listeria spp. in the farming environment is lacking. Soil and feces samples were collected from 11 pastured poultry farms from 2014 to 2017. Random forest (RF) and gradient boosting machine (GBM) predictive models were generated to describe and predict Listeria spp. prevalence in feces and soil samples based on meteorological factors at the farming location. This study attempted to demonstrate the use of GBM models in a food safety context and compare their use to RF models. Both feces models performed very well, with area under the curve (AUC) values of 0.905 and 0.855 for the RF and GBM models, respectively. The soil GBM model outperformed the RF model with AUCs of 0.873 and 0.700, respectively. The developed models can be used to predict the prevalence of Listeria spp. in pastured poultry farm environments and should be of great use to poultry farmers, producers, and risk managers.

Temporal Stability of Escherichia coli Concentrations in Waters of Two Irrigation Ponds in Maryland

Fecal contamination of water sources is an important water quality issue for agricultural irrigation ponds. Escherichia coli concentrations are commonly used to evaluate recreational and irrigation water quality. We hypothesized that there may exist temporally stable spatial patterns of E. coli concentrations across ponds, meaning that some areas mostly have higher and other areas mostly lower than average concentrations of E. coli To test this hypothesis, we sampled two irrigation ponds in Maryland at nodes of spatial grids biweekly during the summer of 2016. Environmental covariates-temperature, turbidity, conductivity, pH, dissolved oxygen, chlorophyll a, and nutrients-were measured in conjunction with E. coli concentrations. Temporal stability was assessed using mean relative differences between measurements in each location and averaged measurements across ponds. Temporally stable spatial patterns of E. coli concentrations and the majority of environmental covariates were expressed for both ponds. In the pond interior, larger relative mean differences in chlorophyll a corresponded to smaller mean relative differences in E. coli concentrations, with a Spearman's rank correlation coefficient of 0.819. Turbidity and ammonium concentrations were the two other environmental covariates with the largest positive correlations between their location ranks and the E. coli concentration location ranks. Tenfold differences were found between geometric mean E. coli concentrations in locations that were consistently high or consistently low. The existence of temporally stable patterns of E. coli concentrations can affect the results of microbial water quality assessment in ponds and should be accounted for in microbial water quality monitoring design.IMPORTANCE The microbial quality of water in irrigation water sources must be assessed to prevent the spread of microbes that can cause disease in humans because of produce consumption. The microbial quality of irrigation water is evaluated based on concentrations of Escherichia coli as the indicator organism. Given the high spatial and temporal variability of E. coli concentrations in irrigation water sources, recommendations are needed on where and when samples of water have to be taken for microbial analysis. This work demonstrates the presence of a temporally stable spatial pattern in the distributions of E. coli concentrations across irrigation ponds. The ponds studied had zones where E. coli concentrations were mostly higher than average and zones where the concentrations were mostly lower than average over the entire observation period, covering the season when water was used for irrigation. Accounting for the existence of such zones will improve the design and implementation of microbial water quality monitoring.

Identifying and modeling meteorological risk factors associated with pre-harvest contamination of Listeria species in a mixed produce and dairy farm

This study sought to investigate the prevalence of Listeria species (including L. monocytogenes) in a mixed produce and dairy farm and to identify specific meteorological factors affecting Listeria spp. presence. Environmental samples were collected monthly from locations within the mixed farm over 14months and were analyzed for Listeria spp. Meteorological factors were evaluated for their association with the presence of Listeria spp. by using logistic regression (LR) and random forest (RF). The developed LR model identified wind speed and precipitation as significant risk factors (P<0.05), indicating higher wind speed at day 2 prior to sampling and higher average precipitation over the previous 25days before sampling increased the probability of isolation of Listeria spp. from the mixed farm. Results from RF revealed that average wind speed at day 2 prior to sampling and average precipitation in the previous 25days before sampling were the most important factors influencing the presence of Listeria spp., which supported the findings from LR. These findings indicate that the occurrence of Listeria spp. was influenced by wind speed and precipitation, suggesting run-off and wind-driven dust might be possible routes of pathogen transmission in mixed farms. The developed LR and RF models, with robust predictive performances as measured by the area under the receiver operating characteristic curves, can be used to predict Listeria spp. contamination risk in a mixed farm under different weather conditions and can help with the evaluation of farm management practices and the development of control strategies aimed at reducing pre-harvest microbial contamination in a mixed farming system.

Effect of proximity to a cattle feedlot on Escherichia coli O157:H7 contamination of leafy greens and evaluation of the potential for airborne transmission

The impact of proximity to a beef cattle feedlot on Escherichia coli O157:H7 contamination of leafy greens was examined. In each of 2 years, leafy greens were planted in nine plots located 60, 120, and 180 m from a cattle feedlot (3 plots at each distance). Leafy greens (270) and feedlot manure samples (100) were collected six different times from June to September in each year. Both E. coli O157:H7 and total E. coli bacteria were recovered from leafy greens at all plot distances. E. coli O157:H7 was recovered from 3.5% of leafy green samples per plot at 60 m, which was higher (P < 0.05) than the 1.8% of positive samples per plot at 180 m, indicating a decrease in contamination as distance from the feedlot was increased. Although E. coli O157:H7 was not recovered from air samples at any distance, total E. coli was recovered from air samples at the feedlot edge and all plot distances, indicating that airborne transport of the pathogen can occur. Results suggest that risk for airborne transport of E. coli O157:H7 from cattle production is increased when cattle pen surfaces are very dry and when this situation is combined with cattle management or cattle behaviors that generate airborne dust. Current leafy green field distance guidelines of 120 m (400 feet) may not be adequate to limit the transmission of E. coli O157:H7 to produce crops planted near concentrated animal feeding operations. Additional research is needed to determine safe set-back distances between cattle feedlots and crop production that will reduce fresh produce contamination.

The growing season, but not the farming system, is a food safety risk determinant for leafy greens in the mid-Atlantic region of the United States

Small- and medium-size farms in the mid-Atlantic region of the United States use varied agricultural practices to produce leafy greens during spring and fall, but the impact of preharvest practices on food safety risk remains unclear. To assess farm-level risk factors, bacterial indicators, Salmonella enterica, and Shiga toxin-producing Escherichia coli (STEC) from 32 organic and conventional farms were analyzed. A total of 577 leafy greens, irrigation water, compost, field soil, and pond sediment samples were collected. Salmonella was recovered from 2.2% of leafy greens (n = 369) and 7.7% of sediment (n = 13) samples. There was an association between Salmonella recovery and growing season (fall versus spring) (P = 0.006) but not farming system (organic or conventional) (P = 0.920) or region (P = 0.991). No STEC was isolated. In all, 10% of samples were positive for E. coli: 6% of leafy greens, 18% of irrigation water, 10% of soil, 38% of sediment, and 27% of compost samples. Farming system was not a significant factor for levels of E. coli or aerobic mesophiles on leafy greens but was a significant factor for total coliforms (TC) (P < 0.001), with higher counts from organic farm samples. Growing season was a factor for aerobic mesophiles on leafy greens (P = 0.004), with higher levels in fall than in spring. Water source was a factor for all indicator bacteria (P < 0.001), and end-of-line groundwater had marginally higher TC counts than source samples (P = 0.059). Overall, the data suggest that seasonal events, weather conditions, and proximity of compost piles might be important factors contributing to microbial contamination on farms growing leafy greens.

Pathogen reduction in minimally managed composting of bovine manure

Spread of manure pathogens is of considerable concern due to use of manure for land application. In this study, the effects of four static pile treatment options for bovine manure on die-off of a generic Escherichia coli, E. coli O157:H7 surrogate, Salmonella Senftenberg, Salm. Typhimurium, and Listeria monocytogenes were evaluated. Bovine manure spiked with these bacteria were placed in cassettes at the top, middle, and bottom sections of four static pile treatments that reflect minimal changes in pile construction with and without straw. Temperatures were monitored continuously during the 28 day self-heating period. E. coli and salmonellae were reduced from 8 to 9 log10 CFU g(-1) to undetectable levels (<1.77 log10 MPN g(-1)) at 25-30 cm depths within 7 days in all pile sections except for the manure-only pile in which 3-4 logs of reduction were obtained. No L. monocytogenes initially present at 6.62 log10 CFU g(-1) were recovered from straw-amended piles after 14 days, in contrast with manure-only treatment in which this pathogen was recovered even at 28 days. Decline of target bacterial populations corresponded to exposure to temperatures above 45°C for more than 3 days and amendments of manure with straw to increase thermophilic zones. Use of straw to increase aeration, self-heating capacity, and heat retention in manure piles provides producers a minimal management option for composting that enhances pathogen die-off and thereby reduces risk of environmental spread when manure is applied to land.

Systematic review of respiratory health among dairy workers

The dairy industry is changing on a global scale with larger, more efficient operations. The impact of this change on worker health and safety, specifically, associations between occupational lung disease and inhalation exposures, has yet to be reported in a comprehensive review of the scientific literature. Therefore, a three-tier process was used to identify information using a keyword search of online databases of scientific literature. Of the 147 citations reviewed, 52 met initial screening criteria, and 30 were included in this review. Dairy workers experience lung conditions such as asthma, chronic obstructive pulmonary disease, hypersensitivity pneumonitis, chronic bronchitis, and cancer. Recent pulmonary function studies have identified obstructive lung changes among dairy farm workers. The increased scale of dairy production with significant changes in technology and work practices has altered inhalation exposure patterns among dairy workers. The inhalation exposure in the dairy work environment may elicit differing inflammatory responses in relation to timing of initial exposure as well as to repeated exposures. Few studies have measured inhalation exposure while simultaneously assessing the impact of the exposure on lung function of dairy farm workers. Even fewer studies have been implemented to assess the impact of aerosol control technology to reduce inhalation exposure. Future research should evaluate worker exposure to aerosols through a task-based approach while utilizing novel methods to assess inhalation exposure and associated inflammatory responses. Finally, potential solutions should be developed and tested to reduce inhalation exposure to inflammatory agents and respiratory diseases in the dairy farm work environment.

Comparison of DNA extraction kits and modification of DNA elution procedure for the quantitation of subdominant bacteria from piggery effluents with real-time PCR

Four commercial DNA extraction kits and a minor modification in the DNA elution procedure were evaluated for the quantitation of bacteria in pig manure samples. The PowerSoil®, PowerFecal®, NucleoSpin® Soil kits and QIAamp® DNA Stool Mini kit were tested on raw manure samples and on lagoon effluents for their ability to quantify total bacteria and a subdominant bacteria specific of pig manure contamination: Lactobacillus amylovorus. The NucleoSpin® Soil kit (NS kit), and to a lesser extent the PowerFecal® kit were the most efficient methods. Regardless of the kit utilized, the modified elution procedure increased DNA yield in the lagoon effluent by a factor of 1.4 to 1.8. When tested on 10 piggery effluent samples, compared to the QIAamp kit, the NS kit combined with the modified elution step, increased by a factor up to 1.7 log₁₀ the values of the concentration of L. amylovorus. Regardless of the type of manure, the best DNA quality and the highest concentrations of bacteria were obtained using the NS kit combined with the modification of the elution procedure. The method recommended here significantly improved quantitation of subdominant bacteria in manure.

Estimation of infectious risks in residential populations exposed to airborne pathogens during center pivot irrigation of dairy wastewaters

In the western United States where dairy wastewaters are commonly land applied, there are concerns over individuals being exposed to airborne pathogens. In response, a quantitative microbial risk assessment (QMRA) was performed to estimate infectious risks after inhalation exposure of pathogens aerosolized during center pivot irrigation of diluted dairy wastewaters. The dispersion of pathogens (Campylobacter jejuni, Escherichia coli O157:H7, non-O157 E. coli, Listeria monocytogenes, and Salmonella spp.) was modeled using the atmospheric dispersion model, AERMOD. Pathogen concentrations at downwind receptors were used to calculate infectious risks during one-time (1, 8, and 24 h) and multiday (7 d at 1 h d(-1)) exposure events using a β-Poisson dose-response model. This assessment considered risk of infection in residential populations that were 1 to 10 km from a center pivot operation. In the simulations, infectious risks were estimated to be the greatest in individuals closest to the center pivot, as a result of a higher pathogen dose. On the basis of the results from this QMRA, it is recommended that wastewaters only be applied during daylight hours when inactivation and dilution of airborne pathogens is highest. Further refinement of the dispersion and dose-response models should be considered to increase the utility of this QMRA.

Traditional cheeses: rich and diverse microbiota with associated benefits

The risks and benefits of traditional cheeses, mainly raw milk cheeses, are rarely set out objectively, whence the recurrent confused debate over their pros and cons. This review starts by emphasizing the particularities of the microbiota in traditional cheeses. It then describes the sensory, hygiene, and possible health benefits associated with traditional cheeses. The microbial diversity underlying the benefits of raw milk cheese depends on both the milk microbiota and on traditional practices, including inoculation practices. Traditional know-how from farming to cheese processing helps to maintain both the richness of the microbiota in individual cheeses and the diversity between cheeses throughout processing. All in all more than 400 species of lactic acid bacteria, Gram and catalase-positive bacteria, Gram-negative bacteria, yeasts and moulds have been detected in raw milk. This biodiversity decreases in cheese cores, where a small number of lactic acid bacteria species are numerically dominant, but persists on the cheese surfaces, which harbour numerous species of bacteria, yeasts and moulds. Diversity between cheeses is due particularly to wide variations in the dynamics of the same species in different cheeses. Flavour is more intense and rich in raw milk cheeses than in processed ones. This is mainly because an abundant native microbiota can express in raw milk cheeses, which is not the case in cheeses made from pasteurized or microfiltered milk. Compared to commercial strains, indigenous lactic acid bacteria isolated from milk/cheese, and surface bacteria and yeasts isolated from traditional brines, were associated with more complex volatile profiles and higher scores for some sensorial attributes. The ability of traditional cheeses to combat pathogens is related more to native antipathogenic strains or microbial consortia than to natural non-microbial inhibitor(s) from milk. Quite different native microbiota can protect against Listeria monocytogenes in cheeses (in both core and surface) and on the wooden surfaces of traditional equipment. The inhibition seems to be associated with their qualitative and quantitative composition rather than with their degree of diversity. The inhibitory mechanisms are not well elucidated. Both cross-sectional and cohort studies have evidenced a strong association of raw-milk consumption with protection against allergic/atopic diseases; further studies are needed to determine whether such association extends to traditional raw-milk cheese consumption. In the future, the use of meta-omics methods should help to decipher how traditional cheese ecosystems form and function, opening the way to new methods of risk-benefit management from farm to ripened cheese.

The characterization of microorganisms in dairy wastewater storage ponds

Dairy wastewaters from storage ponds are commonly land applied to irrigate forage crops. Given that diverse microbial populations are associated with cattle feces, the objective of this study was to use a culture-independent approach to characterize bacteria and archaea in dairy wastewaters. Using domain-specific primers, a region of the 16S rRNA gene was amplified from pooled DNA extracts from 30 dairy wastewaters and subsequently used to create a clone library. A total of 152 bacterial clones were examined and sequence matches were affiliated with the following groups: Actinobacteria, Bacteroidetes, Firmicutes, Proteobacteria, and Synergistetes. Firmicutes was identified as the largest phylum, representing up to 69% of the clone sequences. Of 167 clones representing Archaea, seven genera were found to be closely related (91-100% sequence similarity) to isolates obtained from sediments and feces. Most of the putative sequence matches (98%) represented members from the class Methanomicrobia. With respect to the archaeal clones, only one of the putative sequence matches was affiliated with a methanogenic bacterium known to inhabit the rumen.

Altered protozoan and bacterial communities and survival of Escherichia coli O157:H7 in monensin-treated wastewater from a dairy lagoon

Surviving predation is a fitness trait of Escherichia coli O157:H7 (EcO157) that provides ample time for the pathogen to be transported from reservoirs (e.g. dairies and feedlots) to farm produce grown in proximity. Ionophore dietary supplements that inhibit rumen protozoa may provide such a selective advantage for EcO157 to proliferate in lagoons as the pathogen is released along with the undigested supplement as manure washings. This study evaluated the fate of an outbreak strain of EcO157, protozoan and bacterial communities in wastewater treated with monensin. Although total protozoa and native bacteria were unaffected by monensin, the time for 90% decrease in EcO157 increased from 0.8 to 5.1 days. 18S and 16S rRNA gene sequencing of wastewater samples revealed that monensin eliminated almost all colpodean and oligohymenophorean ciliates, probably facilitating the extended survival of EcO157. Total protozoan numbers remained high in treated wastewater as monensin enriched 94% of protozoan sequences undetected with untreated wastewater. Monensin stimulated 30-fold increases in Cyrtohymena citrina, a spirotrichean ciliate, and also biflagellate bicosoecids and cercozoans. Sequences of gram-negative Proteobacteria increased from 1% to 46% with monensin, but gram-positive Firmicutes decreased from 93% to 46%. It is noteworthy that EcO157 numbers increased significantly (P<0.01) in Sonneborn medium containing monensin, probably due to monensin-inhibited growth of Vorticella microstoma (P<0.05), a ciliate isolated from wastewater. We conclude that dietary monensin inhibits ciliate protozoa that feed on EcO157. Feed supplements or other methods that enrich these protozoa in cattle manure could be a novel strategy to control the environmental dissemination of EcO157 from dairies to produce production environments.

Leaf microbiota in an agroecosystem: spatiotemporal variation in bacterial community composition on field-grown lettuce

The presence, size and importance of bacterial communities on plant leaf surfaces are widely appreciated. However, information is scarce regarding their composition and how it changes along geographical and seasonal scales. We collected 106 samples of field-grown Romaine lettuce from commercial production regions in California and Arizona during the 2009-2010 crop cycle. Total bacterial populations averaged between 10(5) and 10(6) per gram of tissue, whereas counts of culturable bacteria were on average one (summer season) or two (winter season) orders of magnitude lower. Pyrosequencing of 16S rRNA gene amplicons from 88 samples revealed that Proteobacteria, Firmicutes, Bacteroidetes and Actinobacteria were the most abundantly represented phyla. At the genus level, Pseudomonas, Bacillus, Massilia, Arthrobacter and Pantoea were the most consistently found across samples, suggesting that they form the bacterial 'core' phyllosphere microbiota on lettuce. The foliar presence of Xanthomonas campestris pv. vitians, which is the causal agent of bacterial leaf spot of lettuce, correlated positively with the relative representation of bacteria from the genus Alkanindiges, but negatively with Bacillus, Erwinia and Pantoea. Summer samples showed an overrepresentation of Enterobacteriaceae sequences and culturable coliforms compared with winter samples. The distance between fields or the timing of a dust storm, but not Romaine cultivar, explained differences in bacterial community composition between several of the fields sampled. As one of the largest surveys of leaf surface microbiology, this study offers new insights into the extent and underlying causes of variability in bacterial community composition on plant leaves as a function of time, space and environment.

Use of a culture-independent approach to characterize aerosolized bacteria near an open-freestall dairy operation

Animal manures are known to harbor a variety of zoonotic pathogens, which are suspected of being transported off-site as aerosols from confined feeding operations. In this study, aerosols were collected using a high-volume sampler downwind from a 10,000 cow open-freestall dairy and nearby fields being sprinkler irrigated with wastewater. DNA extracts were prepared from the aerosol samples, then a region of the 16S ribosomal RNA gene was sequenced for bacterial identification and phylogenetic classification. At the dairy and irrigation sites, Proteobacteria (α-, β-, and γ-subdivisions) was the most abundant phylum, representing 78% and 69% of all sequences, respectively, while Actinobacteria, Bacteroidetes and Firmicutes represented only 10% or less of the sequences. Of the 191 clones sequenced from the dairy aerosol samples, 6 sequences were found to be homologous with uncultured bacteria from cow milk, rumen, and fecal samples. However, none of the sequence matches was affiliated with bacteria known to be pathogenic to otherwise healthy humans. Although our results do suggest a high diversity among the aerosolized bacteria, the sampling strategy employed in this study may not account for the variable nature of bioaerosol emissions.