Microbiota formed on attached stainless steel coupons correlates with the natural biofilm of the sink surface in domestic kitchens

Longitudinal bacterial community dynamics and sodium hypochlorite intervention in a newly built university building

Urbanisation and building advancements have increased microbial growth in indoor environments, altering human interactions with these microorganisms. Restrooms and their sinks harbour diverse bacterial communities, that differ from those found in natural environments, that could have negative implications for human health. Over two and a half years, this study examined the diversity, temporal dynamics, and resilience of bacterial communities in restroom sink P-traps in a newly built university building. Structured into two phases, the first phase consisted of continuous monitoring of bacterial community dynamics for two years (n = 352), while the second phase involved an intervention with sodium hypochlorite (bleach) and subsequent sampling (n = 132). In the first phase, we show that sink communities converge, becoming more compositionally similar to other sinks within the building. Bacterial families such as Rhodocyclaceae and Flavobacteriaceae dominated across the sinks, and others such as Comamonadaceae, Moraxellaceae and Enterbacteriaceae were highly prevalent. When comparing bacterial structure and composition to other sinks located on the university campus, the mean bacterial dissimilarity decreased over time, indicating compositional similarity, particularly with the newer buildings on campus. The second phase demonstrated resilience by the bacterial sink communities. Following bleach treatments, a distinct increase in Acinetobacter was observed. However, by the fourth week after bleach invention, bacterial communities had re-established to levels observed prior to treatment. This study had the unique opportunity to sample a newly built building before occupancy and for the subsequent two and a half years. The findings provide crucial insights into the development and resilience of sink P-trap bacterial communities in restrooms, laying the groundwork for more targeted approaches to disinfection strategies.

Bacterial microbiome diversity along poultry slaughtering lines: insights from chicken carcasses and environmental sources

Introduction

This study aimed to determine the bacterial diversity of chicken carcasses and their surrounding environment at various stages along a poultry slaughter line.

Material and Methods

Amplicon sequencing of the 16S rRNA gene was employed to assess the shifts in bacterial community diversity at both phylum and genus levels. Samples were collected from September to November 2021, targeting carcass surfaces at various operational stages (post-defeathering, post-evisceration, post-water chilling, and post-cooling), as well as from the internal environments and air of these units. The study took place in a vertically integrated poultry slaughterhouse in Konya, Turkey.

Results

Microbial diversity increased after the chilling and storage stages as a result of redistribution of the microorganisms after the physical effect of the slaughtering stages. The final product sample taken after storage had the highest bacterial abundance. The abundance at this stage was found to be strongly correlated with that at other slaughtering stages, as well as with the abundance in chilling water and on the personnel's hands. The common genera in chicken carcasses during slaughter stages were Macrococcus, Acinetobacter, Enterococcus, Escherichia-Shigella, Psychrobacter, Streptococcus, Lactococcus and Ligilactobacillus. Microbiome data in environmental samples indicated that the genera in highest relative abundance were Bacillus, Anoxybacillus, Acinetobacter and Psychrobacter. In air samples, the storage room had the highest diversity and in this place Bacillus spp. and Staphylococcus spp. were in the majority.

Conclusion

This study may provide some useful information to pinpoint the critical contamination sources in the poultry slaughtering process.

Bacterial levels and diversity in kitchen sponges and dishwashing brushes used by consumers

AIMS

The purpose of the work was to investigate bacterial levels and diversity as well as survival of Salmonella in used dish washing sponges and brushes and identify consumer practices that can potentially explain bacterial status of these items.

METHODS AND RESULTS

Used washing up utensils were collected from consumers. The bacterial numbers (TVC) were very variable with an extremely high median level (10.3 log cfu/item) in Portuguese sponges and lower levels in Norwegian items (7.3 and 7.0 cfu/item for sponges and brushes). No self-reported practices or household composition could explain differences found in TVC levels among the collected sponges. Lower mean TVC levels were found in unworn brushes and brushes regularly cleaned with soap, but the differences were modest (1.5 log or less). A common set of bacteria was found in brushes and sponges, dominated by Acinetobacter, Chryseobacterium, Enhydrobacter, Enterobacteriaceae and Pseudomonas. There was no difference in TVC or bacterial diversity between conventional and antimicrobial sponges containing silver after four weeks of use. For used brushes inoculated with Salmonella and allowed to dry overnight, a significant reduction in Salmonella numbers was observed. No reduction was observed for brushes stored humid (in a plastic bag) or for sponges regardless of storing conditions.

CONCLUSIONS

Overall, lower bacterial levels were observed in used brushes than in sponges, and Salmonella died more rapidly in brushes. A common set of non-pathogenic bacteria dominated in brushes and sponges.

SIGNIFICANCE AND IMPACT OF STUDY

The study demonstrates that the use of brushes may be more hygienic than the use of sponges.

Capture and Ex-Situ Analysis of Environmental Biofilms in Livestock Buildings

Little information about biofilm microbial communities on the surface of livestock buildings is available yet. While these spatially organized communities proliferate in close contact with animals and can harbor undesirable microorganisms, no standardized methods have been described to sample them non-destructively. We propose a reproducible coupon-based capture method associated with a set of complementary ex-situ analysis tools to describe the major features of those communities. To demonstrate the biofilm dynamics in a pig farm building, we analyzed the coupons on polymeric and metallic materials, as representative of these environments, over 4 weeks. Confocal laser scanning microscopy (CLSM) revealed a rapid coverage of the coupons with a thick layer of biological material and the existence of dispersed clusters of active metabolic microorganisms. After detaching the cells from the coupons, counts to quantify the CFU/cm² were done with high reproducibility. High-throughput sequencing of the 16S rRNA V3-V4 region shows bacterial diversity profiles in accordance with reported bacteria diversity in pig intestinal ecosystems and reveals differences between materials. The coupon-based methodology allows us to deepen our knowledge on biofilm structure and composition on the surface of a pig farm and opens the door for application in different types of livestock buildings.

Analysing microbiome intervention design studies: Comparison of alternative multivariate statistical methods

The diet plays a major role in shaping gut microbiome composition and function in both humans and animals, and dietary intervention trials are often used to investigate and understand these effects. A plethora of statistical methods for analysing the differential abundance of microbial taxa exists, and new methods are constantly being developed, but there is a lack of benchmarking studies and clear consensus on the best multivariate statistical practices. This makes it hard for a biologist to decide which method to use. We compared the outcomes of generic multivariate ANOVA (ASCA and FFMANOVA) against statistical methods commonly used for community analyses (PERMANOVA and SIMPER) and methods designed for analysis of count data from high-throughput sequencing experiments (ALDEx2, ANCOM and DESeq2). The comparison is based on both simulated data and five published dietary intervention trials representing different subjects and study designs. We found that the methods testing differences at the community level were in agreement regarding both effect size and statistical significance. However, the methods that provided ranking and identification of differentially abundant operational taxonomic units (OTUs) gave incongruent results, implying that the choice of method is likely to influence the biological interpretations. The generic multivariate ANOVA tools have the flexibility needed for analysing multifactorial experiments and provide outputs at both the community and OTU levels; good performance in the simulation studies suggests that these statistical tools are also suitable for microbiome data sets.

Biofilms Enhance the Adsorption of Toxic Contaminants on Plastic Microfibers under Environmentally Relevant Conditions

Microplastics (MPs) exposed to the natural environment provide an ideal surface for biofilm formation, which potentially acts as a reactive phase facilitating the sorption of hazardous contaminants. Until now, changes in the contaminant sorption capacity of MPs due to biofilm formation have not been quantified. This is the first study that compared the capacity of naturally aged, biofilm-covered microplastic fibers (BMFs) to adsorb perfluorooctane sulfonate (PFOS) and lead (Pb) at environmentally relevant concentrations. Changes in the surface properties and morphology of aged microplastic fibers (MF) were studied by surface area analysis, infrared spectroscopy, and scanning electron microscopy. Results revealed that aged MFs exhibited higher surface areas because of biomass accumulation compared to virgin samples and followed the order polypropylene>polyethylene>nylon>polyester. The concentrations of adsorbed Pb and PFOS were 4-25% and 20-85% higher in aged MFs and varied among the polymer types. The increased contaminant adsorption was linked with the altered surface area and the hydrophobic/hydrophilic characteristics of the samples. Overall, the present study demonstrates that biofilms play a decisive role in contaminant-plastic interactions and significantly enhance the vector potential of MFs for toxic environmental contaminants. We anticipate that knowledge generated from this study will help refine the planetary risk assessment of MPs.

Microbial, environmental and anthropogenic factors influencing the indoor microbiome of the built environment

A built environment is a human-made environment providing surroundings for human occupancy, activities, and settlement. It is supposed to safeguard humans from all undesirable and harmful pollutants; however, indoor concentrations of some pollutants are much greater than that of the outdoors. Bioaerosols infiltrate from the outdoors in addition to many indoor sources of bioaerosols including the use of various chemicals as well as activities like cooking, smoking, cleaning, or even normal movement. They are also associated with a number of serious health concerns. Various ecological factors associated with the generation, the persistence as well as the dispersal of these microbial components of indoor bioaerosols, are discussed in this review, that have not been considered all together till now. The factors like microbial taxa, environmental factors, and anthropogenic activities (human occupancy, activities, and impact of urbanization) are addressed in the review. Effects of both indoor environmental factors like architectural design, lighting, ventilation, temperature, humidity, indoor/outdoor ratio, particulate matter, indoor chemistry as well as outdoor environmental factors like geography, seasons, and meteorology on the microbial concentrations have been discussed. Efforts are underway to design selective pressures for microbes to create a healthy symbiotic built microbiome as the "right" indoor microbiome is a "healthy" indoor microbiome.

Wastewater treatment alters microbial colonization of microplastics

Microplastics are ubiquitous contaminants in aquatic habitats globally, and wastewater treatment plants (WWTPs) are point sources of microplastics. Within aquatic habitats microplastics are colonized by microbial biofilms, which can include pathogenic taxa and taxa associated with plastic breakdown. Microplastics enter WWTPs in sewage and exit in sludge or effluent, but the role that WWTPs play in establishing or modifying microplastic bacterial assemblages is unknown. We analyzed microplastics and associated biofilms in raw sewage, effluent water, and sludge from two WWTPs. Both plants retained >99% of influent microplastics in sludge, and sludge microplastics showed higher bacterial species richness and higher abundance of taxa associated with bioflocculation (e.g. Xanthomonas) than influent microplastics, suggesting that colonization of microplastics within the WWTP may play a role in retention. Microplastics in WWTP effluent included significantly lower abundances of some potentially pathogenic bacterial taxa (e.g. Campylobacteraceae) compared to influent microplastics; however, other potentially pathogenic taxa (e.g. Acinetobacter) remained abundant on effluent microplastics, and several taxa linked to plastic breakdown (e.g. Klebsiella, Pseudomonas, and Sphingomonas) were significantly more abundant on effluent compared to influent microplastics. These results indicate that diverse bacterial assemblages colonize microplastics within sewage and that WWTPs can play a significant role in modifying the microplastic-associated assemblages, which may affect the fate of microplastics within the WWTPs and the environment.

Serovar-dependent differences in Hfq-regulated phenotypes inActinobacillus pleuropneumoniae

The RNA chaperone Hfq regulates diverse processes in numerous bacteria. In this study, we compared phenotypes (growth rate, adherence, response to different stress conditions and virulence in Galleria mellonella) of wild-type (WT) and isogenic hfq mutants of three serovars (1, 8 and 15) of the porcine pathogen Actinobacillus pleuropneumoniae. Similar growth in rich broth was seen for all strains except Ap1∆hfq, which showed slightly reduced growth throughout the 24 h time course, and the complemented Ap8∆hfqC mutant had a prolonged lag phase. Differences were seen between the three serovar WT strains regarding adherence, stress response and virulence in G. mellonella, and deletion of hfq affected some, but not all of these phenotypes, depending on serovar. Complementation by expression of cloned hfq from an endogenous promoter only restored some WT phenotypes, indicating that complex regulatory networks may be involved, and that levels of Hfq may be as important as presence/absence of the protein regarding its contribution to gene regulation. Our results support that Hfq is a pleiotropic global regulator in A. pleuropneumoniae, but serovar-related differences exist. These results highlight the importance of testing multiple strains/serovars within a given species when determining contributions of global regulators, such as Hfq, to expression of complex phenotypes.

Tracking bacteriome variation over time in Listeria monocytogenes-positive foci in food industry

The variation in microbial composition over time was assessed in biofilms formed in situ on selected non-food and food contact surfaces of meat and fish industries, previously identified as Listeria monocytogenes-positive foci. First, all samples were analysed for the detection and quantification of L. monocytogenes using ISO 11290-1 and ISO 11290-2 norms, respectively. Although the pathogen was initially detected in all samples, direct quantification was not possible. Psychrotrophic bacteria counts were among resident microbiota in meat industry samples (Mean_max = 6.14 log CFU/cm²) compared to those form fish industry (Mean_max = 5.85 log CFU/cm²). Visual analysis of the biofilms using epifluorescence microscopy revealed a trend to form microcolonies in which damaged/dead cells would act as anchoring structures. 16S rRNA gene metagenetic analysis demonstrated that, although Proteobacteria (71.37%) initially dominated the bacterial communities at one meat industry location, there was a dramatic shift in composition as the biofilms matured, where Actinobacteria (79.72%) became the major phylum present in later samples. This change was largely due to an increase of Nocardiaceae, Micrococcaceae and Microbacteriaceae. Nevertheless, for the other sampling location, the relative abundance of the dominating phylum (Firmicutes) remained consistent over the entire sampling period (Mean = 63.02%). In fish industry samples, Proteobacteria also initially dominated early on (90.69%) but subsequent sampling showed a higher diversity in which Bacteroidetes and Proteobacteria were the most abundant phyla accounting for the 48.04 and 37.98%, respectively by the last sampling period. Regardless of the location, the community profiles of the endpoint samples were similar to those reported previously. This demonstrated that in a given industrial setting there is a trend to establish a determinate biofilm structure due to the environmental factors and the constant incoming microbiota. This information could be used to improve the existing sanitisation protocols or for the design of novel strategies.

Antibiofilm Efficacy of Peptide 1018 against Listeria monocytogenes and Shiga Toxigenic Escherichia coli on Equipment Surfaces

Listeria monocytogenes and Shiga toxigenic Escherichia coli (STEC) are important foodborne bacterial pathogens that can form biofilms on equipment surfaces at food processing facilities. Pathogens in biofilms are resistant to conventional antimicrobials and require higher antimicrobial concentrations to be inactivated. In this study, the efficacy of a synthetic innate defense regulator peptide 1018 (peptide 1018) for inactivating L. monocytogenes and STEC (O26, O111, O145, O157) biofilms on stainless steel and polycarbonate surfaces was investigated. Stainless steel and polycarbonate coupons (12 mm in diameter) were used in a Centers for Disease Control and Prevention biofilm reactor containing 400 mL of 10% tryptic soy broth (TSB) that had been inoculated with an individual strain of L. monocytogenes or STEC to obtain 6 log CFU/mL populations. The reactor was set with a constant flow rate at 50 mL/h of 10% TSB for 48 h. After 48 h, coupons were treated with peptide 1018 at 0, 10, 20, or 50 μg/mL in phosphate buffer saline (PBS) for 24 h. Surviving bacterial populations were determined by scraping off the coupons and spiral plating on selective media. Significantly higher levels of pathogens in biofilms formed by certain bacterial strains, including L. monocytogenes F6854, E. coli O157:H7 RM4407 and NADC5713, and non-O157 E. coli NADC3629, were recovered on polycarbonate surfaces than on stainless steel. Antibiofilm efficacy of peptide 1018 against pathogens was concentration-dependent and varied with the type of pathogen and material surfaces. Peptide 1018 at 50 μg/mL significantly inactivated all tested bacterial biofilms on both surfaces compared with the PBS control (P < 0.05). L. monocytogenes was the bacterium most sensitive to peptide 1018; on stainless steel surfaces treated with 50 μg/mL peptide 1018, there was a 3.7- to 4.6-log CFU/cm² reduction in Listeria populations compared with a 1.0- to 3.5-log CFU/cm² reduction of STEC. Results suggest that peptide 1018 may be used to inactivate L. monocytogenes and STEC biofilms on equipment surfaces.

Microbial Ecology Evaluation of an Iberian Pig Processing Plant through Implementing SCH Sensors and the Influence of the Resident Microbiota on Listeria monocytogenes

There is a whole community of microorganisms capable of surviving the cleaning and disinfection processes in the food industry. These persistent microorganisms can enhance or inhibit biofilm formation and the proliferation of foodborne pathogens. Cleaning and disinfection protocols will never reduce the contamination load to 0; however, it is crucial to know which resident species are present and the risk they represent to pathogens, such as Listeria monocytogenes, as they can be further used as a complementary control strategy. The aim of this study was to evaluate the resident surface microbiota in an Iberian pig processing plant after carrying out the cleaning and disinfection processes. To do so, surface sensors were implemented, sampled, and evaluated by culture plate count. Further, isolated microorganisms were identified through biochemical tests. The results show that the surfaces are dominated by Bacillus spp., Pseudomonas spp., different enterobacteria, Mannheimia haemolytica, Rhizobium radiobacter, Staphylococcus spp., Aeromonas spp., lactic acid bacteria, and yeasts and molds. Moreover, their probable relationship with the presence of L. monocytogenes in three areas of the plant is also explained. Further studies of the resident microbiota and their interaction with pathogens such as L. monocytogenes are required. New control strategies that promote the most advantageous profile of microorganisms in the resident microbiota could be a possible alternative for pathogen control in the food industry. To this end, the understanding of the resident microbiota on the surfaces of the food industry and its relation with pathogen presence is crucial.

Bacterial diversity on stainless steel surfaces of egg processing companies and potential of selected isolates to spoil liquid whole egg products

AIMS

To assess the bacterial diversity in the French egg processing industry and to explore the adhesion and spoilage potential of selected bacteria.

METHODS AND RESULTS

Sterile stainless steel chips were suspended for 2 months inside the pipelines of seven egg processing companies, before and after the pasteurizer, at warm and cold seasons. After exposure, the bacterial diversity was assessed by 16S rDNA sequencing. The 231 collected isolates were mainly facultative anaerobic Gram positive bacteria, such as Streptococcus, Staphylococcus, Bacillus and Kocuria. Sixty-five representative isolates were further characterized in vitro regarding the potential for adhesion and egg product spoilage. A high diversity was observed from one genus to another. Kocuria and Rothia isolates showed significantly higher adhesion than the isolates of the other genera. Only the isolates belonging to the genera Bacillus and Lysinibacillus, associated with high enzymatic activities on a solid egg-based medium, were able to induce spoilage of liquid whole egg.

CONCLUSIONS

Bacteria collected on stainless steel surfaces placed in egg processing industries could be associated to liquid egg product spoilage.

SIGNIFICANCE AND IMPACT OF THE STUDY

This study provides new insights on the bacterial contamination in egg processing companies and represents a first step for the effective control of undesirable bacteria in liquid egg products.

A Brief Recap of Microbial Adhesion and Biofilms

Food and beverage industries operate their production units under stringent hygiene standards to verify high-quality products. However, the presence of biofilms can cause hygienic problems in the industries in the case of pathogenic organisms. Microorganisms can form biofilms, which are resistant to cleaning and disinfection. Microorganisms in biofilms are closely packed in a matrix that acts as a barrier to cleaning and disinfection. Biofilms are observed in processing equipment and open surfaces, resulting in food safety problems or weakening of production efficiency. This review provides a recap of the biofouling process, including the production mechanisms and control techniques of microbial adhesion. Microbial adhesion and colonization are the sine qua non of the establishment of bacterial pathogenesis and this report focuses on their prevention.

Salmonella and Campylobacter biofilm formation: a comparative assessment from farm to fork

It takes several steps to bring food from the farm to the fork (dining table), and contamination with food-borne pathogens can occur at any point in the process. Campylobacter spp. and Salmonella spp. are the main microorganisms responsible for foodborne disease in the EU. These two pathogens are able to persist throughout the food supply chain thanks to their ability to form biofilms. Owing to the high prevalence of Salmonella and especially of Campylobacter in the food supply chain and the huge efforts of food authorities to reduce these levels, it is of great importance to fully understand their mechanisms of persistence. Diverse studies have evaluated the biofilm-forming capacity of foodborne pathogens isolated at different steps of food production. Nonetheless, the principal obstacle of these studies is to reproduce the real conditions that microorganisms encounter in the food supply chain. While there are a wide number of Salmonella biofilm studies, information on Campylobacter biofilms is still limited. A comparison between the two microorganisms could help to develop new research in the field of Campylobacter biofilms. Therefore, this review evaluates relevant work in the field of Salmonella and Campylobacter biofilms and the applicability of the data obtained from these studies to real working conditions. © 2018 Society of Chemical Industry.

Microbes and associated soluble and volatile chemicals on periodically wet household surfaces

BACKGROUND

Microorganisms influence the chemical milieu of their environment, and chemical metabolites can affect ecological processes. In built environments, where people spend the majority of their time, very little is known about how surface-borne microorganisms influence the chemistry of the indoor spaces. Here, we applied multidisciplinary approaches to investigate aspects of chemical microbiology in a house.

METHODS

We characterized the microbial and chemical composition of two common and frequently wet surfaces in a residential setting: kitchen sink and bathroom shower. Microbial communities were studied using culture-dependent and independent techniques, including targeting RNA for amplicon sequencing. Volatile and soluble chemicals from paired samples were analyzed using state-of-the-art techniques to explore the links between the observed microbiota and chemical exudates.

RESULTS

Microbial analysis revealed a rich biological presence on the surfaces exposed in kitchen sinks and bathroom shower stalls. Microbial composition, matched for DNA and RNA targets, varied by surface type and sampling period. Bacteria were found to have an average of 25× more gene copies than fungi. Biomass estimates based on qPCR were well correlated with measured total volatile organic compound (VOC) emissions. Abundant VOCs included products associated with fatty acid production. Molecular networking revealed a diversity of surface-borne compounds that likely originate from microbes and from household products.

CONCLUSIONS

Microbes played a role in structuring the chemical profiles on and emitted from kitchen sinks and shower stalls. Microbial VOCs (mVOCs) were predominately associated with the processing of fatty acids. The mVOC composition may be more stable than that of microbial communities, which can show temporal and spatial variation in their responses to changing environmental conditions. The mVOC output from microbial metabolism on kitchen sinks and bathroom showers should be apparent through careful measurement, even against a broader background of VOCs in homes, some of which may originate from microbes in other locations within the home. A deeper understanding of the chemical interactions between microbes on household surfaces will require experimentation under relevant environmental conditions, with a finer temporal resolution, to build on the observational study results presented here.