Propensity for biofilm formation by aerobic mesophilic and thermophilic spore forming bacteria isolated from Chinese milk powders

Invited review: Role of Bacillus licheniformis in the dairy industry- friends or foes?

Bacillus licheniformis is one of the major spore-forming bacteria with great genotypic diversity in raw milk, dairy ingredients, final dairy products, and is found throughout the dairy processing continuum. Though being widely used as a probiotic strain, this species also serves as a potential risk in the dairy industry based on its roles in foodborne illness and dairy spoilage. Biofilm formation of B. licheniformis in combined with the heat resistance of its spores, make it impossible to prevent the presence of B. licheniformis in final dairy products by traditional cleaning and disinfection procedures. Despite the extensive efforts on the identification of B. licheniformis from various dairy samples, no reviews have been reported on both hazard and benefits of this spore-former. This review discusses the prevalence of B. licheniformis from raw milk to commercial dairy products, biofilm formation and spoilage potential of B. licheniformis, and its potential prevention methods. In addition, the potential benefits of B. licheniformis in the dairy industry were also summarized.

Interspecies interactions in dairy biofilms drive community structure and response against cleaning and disinfection

Interspecies interactions within a biofilm community influence population dynamics and community structure, which in turn may affect the bacterial stress response to antimicrobials. This study was conducted to assess the impact of interactions between Kocuria salsicia and a three-species biofilm community (comprising Stenotrophomonas rhizophila, Bacillus licheniformis, and Microbacterium lacticum) on biofilm mass, the abundance of individual species, and their survival under a laboratory-scale cleaning and disinfection (C&D) regime. The presence of K. salsicia enhanced the cell numbers of all three species in pairwise interactions. The outcomes derived from summing up pairwise interactions did not accurately predict the bacterial population dynamics within communities of more than two species. In four-species biofilms, we observed the dominance of S. rhizophila and B. licheniformis, alongside a concurrent reduction in the cell counts of K. salsicia and M. lacticum. This pattern suggests that the underlying interactions are not purely non-transitive; instead, a more complex interplay results in the dominance of specific species. We observed that bacterial spatial organization and matrix production in different mixed-species combinations affected survival in response to C&D. Confocal microscopy analysis of spatial organization showed that S. rhizophila localized on the biofilm formed by B. licheniformis and M. lacticum, and S. rhizophila was more susceptible to C&D. Matrix production in B. licheniformis, evidenced by alterations in biofilm mass and by scanning electron microscopy, demonstrated its protective role against C&D, not only for this species itself, but also for neighbouring species. Our findings emphasise that various social interactions within a biofilm community not only affect bacterial population dynamics but also influence the biofilm community's response to C&D stress.

Genotype-phenotype evaluation of the heterogeneity in biofilm formation by diverse Bacillus licheniformis strains isolated from dairy products

The spoilage bacterium Bacillus licheniformis has been identified as a quick and strong biofilm former in the dairy industry. In our previous study, intra-species variation in bacterial biofilms has been observed in diverse B. licheniformis strains from different genetic backgrounds; however, the mechanisms driving the observed heterogeneity of biofilms remain to be determined. In this study, the genotype-phenotype evaluation of the heterogeneity in biofilm formation of four B. licheniformis strains were examined. The heterogeneity in biofilm phenotype was accessed in aspects of bacterial growth and motility, cell viability, biofilm matrix production, and biofilm architectures. The underlying mechanisms of the intra-species variability in biofilms were also explored by whole genome resequencing (WGR). Results from bacterial motility tests showed a diverse motility among the strains, but there was no clear correlation between bacterial motility and biofilm formation. The cell viability results showed a different number of live cells in biofilms at the intra-species level. Analysis of chemical components in biofilm matrix demonstrated the great intra-species differences regarding extracellular matrix composition, and a negative correlation between biofilm formation on stainless steel and the protein: carbohydrate ratio in biofilm matrix was observed. Confocal laser scanning microscopy analysis also revealed the intra-species variability by showing great differences in general properties of B. licheniformis biofilms. WGR results identified important pathways involved in biofilm formation, such as two-component systems, quorum sensing, starch and sucrose metabolism, ABC transporters, glyoxylate and dicarboxylate metabolism, purine metabolism, and a phosphotransferase system. Overall, the above results emphasize the necessity of exploring the intra-species variation in biofilms, and would provide in-depth knowledge for designing efficient biofilm control strategies in the dairy industry.

Unraveling the significance of calcium as a biofilm promotion signal for Bacillus licheniformis strains isolated from dairy products

Bacillus licheniformis, a quick and strong biofilm former, is served as a persistent microbial contamination in the dairy industry. Its biofilm formation process is usually regulated by environmental factors including the divalent cation Ca2+. This work aims to investigate how different concentrations of Ca2+ change biofilm-related phenotypes (bacterial motility, biofilm-forming capacity, biofilm structures, and EPS production) of dairy B. licheniformis strains. The Ca2+ ions dependent regulation mechanism for B. licheniformis biofilm formation was further investigated by RNA-sequencing analysis. Results revealed that supplementation of Ca2+ increased B. licheniformis biofilm formation in a dose-dependent way, and enhanced average coverage and thickness of biofilms with complex structures were observed by confocal laser scanning microscopy. Bacterial mobility of B. licheniformis was increased by the supplementation of Ca2+ except the swarming ability at 20 mM of Ca2+. The addition of Ca2+ decreased the contents of polysaccharides but promoted proteins production in EPS, and the ratio of proteins/polysaccharides content was significantly enhanced with increasing Ca2+ concentrations. RNA-sequencing results clearly indicated the variation in regulating biofilm formation under different Ca2+ concentrations, as 939 (671 upregulated and 268 downregulated) and 951 genes (581 upregulated and 370 downregulated) in B. licheniformis BL2-11 were induced by 10 and 20 mM of Ca2+, respectively. Differential genes were annotated in various KEGG pathways, including flagellar assembly, two-component system, quorum sensing, ABC transporters, and related carbohydrate and amino acid metabolism pathways. Collectively, the results unravel the significance of Ca2+ as a biofilm-promoting signal for B. licheniformis in the dairy industry.

Multi-omics reveals the increased biofilm formation of Salmonella Typhimurium M3 by the induction of tetracycline at sub-inhibitory concentrations

Exposure to sub-inhibitory concentrations (sub-MICs) of antibiotics could induce the biofilm formation of microorganisms, but its underlying mechanisms still remain elusive. In the present work, biofilm formation by Salmonella Typhimurium M3 was increased when in the presence of tetracycline at sub-MIC, and the highest induction was observed with tetracycline at 1/8 MIC. The integration of RNA-sequencing and untargeted metabolomics was applied in order to further decipher the potential mechanisms for this observation. In total, 439 genes and 144 metabolites of S. Typhimurium M3 were significantly expressed after its exposure to 1/8 MIC of tetracycline. In addition, the co-expression analysis revealed that 6 genes and 8 metabolites play a key role in response to 1/8 MIC of tetracycline. The differential genes and metabolites were represented in 12 KEGG pathways, including five pathways of amino acid metabolism (beta-alanine metabolism, tryptophan metabolism, arginine and proline metabolism, phenylalanine, tyrosine and tryptophan biosynthesis, and glutathione metabolism), three lipid metabolism pathways (biosynthesis of unsaturated fatty acids, fatty acid degradation, and fatty acid biosynthesis), two nucleotide metabolism pathways (purine metabolism, and pyrimidine metabolism), pantothenate and CoA biosynthesis, and ABC transporters. Metabolites (anthranilate, indole, and putrescine) from amino acid metabolism may act as signaling molecules to promote the biofilm formation of S. Typhimurium M3. The results of this work highlight the importance of low antimicrobial concentrations on foodborne pathogens of environmental origin.

Geobacillus Bacteriophages from Compost Heaps: Representatives of Three New Genera within Thermophilic Siphoviruses

We report a detailed characterization of five thermophilic bacteriophages (phages) that were isolated from compost heaps in Vilnius, Lithuania using Geobacillus thermodenitrificans strains as the hosts for phage propagation. The efficiency of plating experiments revealed that phages formed plaques from 45 to 80 °C. Furthermore, most of the phages formed plaques surrounded by halo zones, indicating the presence of phage-encoded bacterial exopolysaccharide (EPS)-degrading depolymerases. Transmission Electron Microscopy (TEM) analysis revealed that all phages were siphoviruses characterized by an isometric head (from ~63 nm to ~67 nm in diameter) and a non-contractile flexible tail (from ~137 nm to ~150 nm in length). The genome sequencing resulted in genomes ranging from 38,161 to 39,016 bp. Comparative genomic and phylogenetic analysis revealed that all the isolated phages had no close relatives to date, and potentially represent three new genera within siphoviruses. The results of this study not only improve our knowledge about poorly explored thermophilic bacteriophages but also give new insights for further investigation of thermophilic and/or thermostable enzymes of bacterial viruses.

Correlation Analysis of Microbial Contamination and Alkaline Phosphatase Activity in Raw Milk and Dairy Products

Microbial contamination in raw milk and dairy products can detrimentally affect product quality and human health. In this study, the aerobic plate count, aerobic Bacillus abundance, thermophilic aerobic Bacillus abundance, and alkaline phosphatase activity were determined in 435 raw milk, 451 pasteurized milk, and 617 sterilized milk samples collected from 13 Chinese provinces (or municipalities). Approximately 9.89% and 2.22% of raw milk and pasteurized milk samples exceeded the threshold values for the aerobic plate count, respectively. The proportions of aerobic Bacillus in raw milk, pasteurized milk, and sterilized milk were 54.02%, 14.41%, and 1.30%, respectively. The proportions of thermophilic aerobic Bacillus species were 7.36% in raw milk and 4.88% in pasteurized milk samples, and no bacteria were counted in sterilized milk. Approximately 36.18% of raw milk samples contained >500,000 mU/L of alkaline phosphatase activity, while 9.71% of pasteurized milk samples contained >350 mU/L. For raw milk, there was a positive correlation between the aerobic plate count, the aerobic Bacillus abundance, and the alkaline phosphatase activity, and there was a positive correlation between the aerobic Bacillus abundance, the thermophilic aerobic Bacillus count, and the alkaline phosphatase activity. For pasteurized milk, there was a positive correlation between the aerobic plate count, the aerobic Bacillus abundance, and the thermophilic aerobic Bacillus count; however, the alkaline phosphatase activity had a negative correlation with the aerobic plate count, the aerobic Bacillus abundance, and the thermophilic aerobic Bacillus abundance. These results facilitate the awareness of public health safety issues and the involvement of dairy product regulatory agencies in China.

Synergistic interactions in multispecies biofilm combinations of bacterial isolates recovered from diverse food processing industries

Most biofilms within the food industry are formed by multiple bacterial species which co-exist on surfaces as a result of interspecies interactions. These ecological interactions often make these communities tolerant against antimicrobials. Our previous work led to the identification of a large number (327) of highly diverse bacterial species on food contact surfaces of the dairy, meat, and egg industries after routine cleaning and disinfection (C&D) regimes. In the current study, biofilm-forming ability of 92 bacterial strains belonging to 26 genera and 42 species was assessed and synergistic interactions in biofilm formation were investigated by coculturing species in all possible four-species combinations. Out of the total 455 four-species biofilm combinations, greater biofilm mass production, compared to the sum of biofilm masses of individual species in monoculture, was observed in 34 combinations. Around half of the combinations showed synergy in biofilm mass > 1.5-fold and most of the combinations belonged to dairy strains. The highest synergy (3.13-fold) was shown by a combination of dairy strains comprising Stenotrophomonas rhizophila, Bacillus licheniformis, Microbacterium lacticum, and Calidifontibacter indicus. The observed synergy in mixed biofilms turned out to be strain-specific rather than species-dependent. All biofilm combinations showing remarkable synergy appeared to have certain common species in all combinations which shows there are keystone industry-specific bacterial species which stimulate synergy or antagonism and this may have implication for biofilm control in the concerned food industries.

A combined treatment of Proteinase K and biosynthesized ZnO-NPs for eradication of dairy biofilm of sporeformers

Biofilms of sporeformers found in the dairy industry are the major contaminants during processing, as they withstand heat and chemical treatment that are used to control microbes. The present work is aimed to remove these resistant forms of bacterial community (biofilm) present in dairy production lines using ecofriendly agents based on proteinase K (Prot-K) coupled with Zinc oxide nanoparticles (ZnO-NPs). Some metal/metal oxide (Ag, CuO and ZnO) NPs were prepared microbially, and ZnO-NPs were characterized as the most effective ones among them. The produced ZnO-NPs were 15-25 nm in size with spherical shape, and FTIR analysis confirmed the presence of proteins and alkanes surrounding particles as capping agents. Application of Prot-K for eradication (removal) of a model biofilm of mixed sporeformers on food-grade stainless steel resulted in an 83% reduction in the absorbance of crystal violet-stained biofilm. When Prot-K was mixed with the biosynthesized NPs ZnO_G240, the reduction increased to 99.19%. This finding could contribute to an efficient cleaning approach combined with CIP to remove the recalcitrant biofilms in dairy production lines.

Biofilms as a microbial hazard in the food industry: A scoping review

Biofilms pose a serious public health hazard with a significant economic impact on the food industry. The present scoping review is designed to analyze the literature published during 2001-2020 on biofilm formation of microbes, their detection methods, and association with antimicrobial resistance (if any). The peer-reviewed articles retrieved from 04 electronic databases were assessed using PRISMA-ScR guidelines. From the 978 preliminary search results, a total of 88 publications were included in the study. On analysis, the commonly isolated pathogens were Listeria monocytogenes, Staphylococcus aureus, Salmonella spp., Escherichia coli, Bacillus spp., Vibrio spp., Campylobacter jejuni and Clostridium perfringens. The biofilm-forming ability of microbes was found to be influenced by various factors such as attachment surfaces, temperature, presence of other species, nutrient availability etc. A total of 18 studies characterized the biofilm-forming genes, particularly for S. aureus, Salmonella spp., and E. coli. In most studies, polystyrene plate and/or stainless-steel coupons were used for biofilm formation, and the detection was carried out by crystal violet assays and/or by plate counting method. The strain-specific significant differences in biofilm formation were observed in many studies, and few studies carried out analysis of multi-species biofilms. The association between biofilm formation and antimicrobial resistance wasn't clearly defined. Further, viable but non-culturable (VBNC) form of the foodborne pathogens is posing an unseen (by conventional cultivation techniques) but potent threat food safety. The present review recommends the need for carrying out systematic surveys and risk analysis of biofilms in food chain to highlight the evidence-based public health concerns, especially in regions where microbiological food hazards are quite prevalent.

Enzymatic Disruption of Biofilms During Cheese Manufacturing: A Mini Review

Bacteria are capable of colonizing industrial processing surfaces creating biofilms on them which may adversely affect the quality and safety of products. Traditional cleaning-in-place (CIP) treatments using caustic and nitric acid solutions have been known to exhibit variable efficiency in eliminating biofilm bacteria. Here, we introduce enzymes as an alternative to traditional CIP treatments and discuss their mechanism of action against bacterial biofilms in cheese manufacturing. In addition, we discuss research gaps namely thermal stability, substrate specificity and residual activity of enzymes that may play a vital role in the selection of enzymes with optimal effectiveness against multi species biofilms. The outcome of this mini review will aid in the development of a novel and sustainable enzyme-based CIP treatment during cheese manufacturing in the future.

Development of multi-species biofilm formed by thermophilic bacteria on stainless steel immerged in skimmed milk

Thermophilic bacteria, such as Bacillus licheniformis, Geobacillus stearothermophilus, Bacillus Subtilis and Anoxybacillus flavithermus, are detected frequently in milk powder products. Biofilms of those strains act as a major contamination to milk powder manufactures and pose potential risks in food safety. In this study, we explored the developing process of multi-species biofilm formed by the four thermophilic bacteria on stainless steel immerged in skimmed milk. The results showed that the thermophilic strains possessed strong capacities to decompose proteins and lactose in skimmed milk, and the spoilage effects were superimposed from multiple strains. B. licheniformis was the most predominant species in the mixed-species biofilm after 12-h incubation. From 24 h to 48 h, G. stearothermophilus occupied the highest proportion. Within the multi-species biofilm, competitive relation existed between B. licheniformis and G. stearothermophilus, while synergistic impacts were observed between B. licheniformis and A. flavithermus. The interspecies mutual influences on biofilm development provided important evidences for understanding colonization of the predominant thermophilic bacteria during milk powder processing.

Isolation, identification, and characterization of lignocellulose-degrading Geobacillus thermoleovorans from Yellowstone National Park

The microbial degradation of lignocellulose in natural ecosystems presents numerous biotechnological opportunities, including biofuel production from agricultural waste and feedstock biomass. To explore the degradation potential of specific thermophiles, we have identified and characterized extremophilic microorganisms isolated from hot springs environments that are capable of biodegrading lignin and cellulose substrates under thermoalkaline conditions, using a combination of culturing, genomics and metabolomics techniques. Organisms that can use lignin and cellulose as a sole carbon source at 60-75°C were isolated from sediment slurry of thermoalkaline hot springs (71-81°C and pH 8-9) of Yellowstone National Park. Full-length 16S rRNA gene sequencing indicated that these isolates were closely related to Geobacillus thermoleovorans. Interestingly, most of these isolates demonstrated biofilm formation on lignin, a phenotype that is correlated with increased bioconversion. Assessment of metabolite level changes in two Geobacillus isolates from two representative springs were undertaken to characterize the metabolic responses associated with growth on glucose versus lignin carbon source as a function of pH and temperature. Overall, results from this study support that thermoalkaline springs harbor G. thermoleovorans microorganisms with lignocellulosic biomass degradation capabilities and potential downstream biotechnological applications. IMPORTANCE As lignocellulosic biomass represents a major agro-industrial waste and renewable resource, its potential to replace non-renewable petroleum-based products for energy production is considerable. Microbial ligninolytic and cellulolytic enzymes are of high interest in bio-refineries for the valorization of lignocellulosic biomass, as they can withstand the extreme conditions (e.g., high temperature, high pH) required for processing. Of high interest is the ligninolytic potential of specific Geobacillus thermoleovorans isolates to function at a broad range of pH and temperatures, as lignin is the bottleneck in the bioprocessing of lignocellulose. In this study, results obtain from G. thermolerovorans isolates originating from YNP springs are significant as very few microorganisms from alkaline thermal environments have been discovered to have lignin and cellulose biodegrading capabilities, and this work opens new avenues for the biotechnological valorization of lignocellulosic biomass at an industrial scale.

Synergistic interactions prevail in multispecies biofilms formed by the human gut microbiota on mucin

Bacterial species in the human gut predominantly exist in the form of mixed-species biofilms on mucosal surfaces. In this study, the biofilm-forming ability of many human gut bacterial strains (133 strains recovered from human faeces) on mucin-coated and non-coated polystyrene surfaces was determined. A significant variation (P < 0.05) in the biofilm-forming ability of many bacterial species on both surfaces was noticed. Based on some preliminary trials, four bacterial species were selected (Bifidobacterium bifidum, Bifidobacterium longum subsp. infantis, Parabacteroides distasonis and Bacteroides ovatus), which could not form any abundant biofilm individually under the in vitro conditions investigated, but produced abundant biofilms when co-cultured in different combinations of two, three and four species, giving an evidence of synergistic interactions in multispecies biofilm formation. There was a 4.74-fold increase in the biofilm mass when all strains developed a biofilm together. Strain-specific qPCR analysis showed that B. bifidum was the most dominant species (56%) in the four-species biofilm after 24 h, followed by B. longum subsp. infantis (36.2%). Study involving cell free supernatant of the cooperating strains showed that cell viability as well as physical presence of cooperating cells were prerequisites for the observed synergy in biofilms. The molecular mechanism behind these interactions and subsequent effects on the functionality of the strains involved were not determined in our study but merit further work.

Molecular Characterization and Biofilm Formation Study of Contaminant Bacteria Isolated from Domiaty and Hungarian Cheeses in Jeddah City

The aim was to study the microbiological quality of Domiaty and Hungarian cheeses, molecular identification and biofilm formation of some selected contaminant bacteria. Samples were collected from two M and P big markets in Jeddah City through the period from February to October 2018, nine visits for two types of natural cheese. Results showed that the total bacterial counts (CFU/ml) from Domiaty cheese from two markets (M and P) were 0.1 x 105, 8 x 105 and 1 x 10 5 CFU/ml respectively (3 visits of M market) and 4 x 106, 0.4 x 106, 6.5 x 103, 1 x 103, 0.1 x 103 and 0.1 x 103 CFU/ml respectively (six samples from 6 visits from P market). Results showed that the total bacterial counts (CFU/ml) from Hungarian cheese were 1.5 x 10 5, 1x 10 4, 11 x 10 4 and 4 x10 6 CFU/ml respectively from (4 visits of M market) and 0.18 x 104, 3 x 106, 22 x 106, 6 x 106 and 5 x 104 CFU/ml respectively (5 visits from P market).Different bacterial isolates from cheese were identified by morphology and biochemical test. Bacterial isolates from cheeses were identified by VITEK MS as follow: Serratia liquefaciens (D6-1, D6-2, D14-1, D13-1 and D13-2), and Pseudomonas fluorescens (D14-2) were isolated from Domiaty cheese while Enterococcus faecium (H11-2), Serratia liquefaciens (H15-1) and Streptococcus thermophilus (H14-1) were isolated from Hungarian cheese. Some selected bacterial isolates were identified by 16S rRNA. Isolates were belong to MK757978 (Raoultilla terrigena (D15-1)), MK757979 (Bacillus cereus (D16-1)), MK757980 (Enterococcus faecalis (H10-2)), MK757982 (Enterococcus fiscalism (H11-1)), MK757981 (Serratia liquefactions (H13-1)), MK757984 (Anoxybacillus flavithermus (H17-1). All bacterial isolates have been tested for the formation of biofilm using a Tissue Culture Plate (TCP). Results revealed 12.5% and 46.15% of high biofilm formation respectively for bacterial isolates of Domiaty and Hungarian cheeses.

Mathematical Models for the Biofilm Formation of Geobacillus and Anoxybacillus on Stainless Steel Surface in Whole Milk

Biofilm formation of Geobacillus thermodenitrificans, Geobacillus thermoglucosidans and Anoxybacillus flavithermus in milk on stainless steel were monitored at 55°C, 60°C, and 65°C for various incubation times. Although species of Geobacillus showed a rapid response and produced biofilm within 4 h on stainless steel, a delay (lag time) was observed for Anoxybacillus. A hyperbolic equation and a hyperbolic equation with lag could be used to describe the biofilm formation of Geobacillus and Anoxybacillus, respectively. The highest biofilm formation amount was obtained at 60°C for both Geobacillus and Anoxybacillus. However, the biofilm formation rates indicated that the lowest rates of formation were obtained at 60°C for Geobacillus. Moreover, biofilm formation rates of G. thermodenitrificans (1.2–1.6 Log₁₀CFU/mL·h) were higher than G. thermoglucosidans (0.4–0.7 Log₁₀CFU/mL·h). Although A. flavithermus had the highest formation rate values (2.7–3.6 Log₁₀CFU/mL·h), this was attained after the lag period (4 or 5 h). This study revealed that modeling could be used to describe the biofilm formation of thermophilic bacilli in milk.

Community-wide changes reflecting bacterial interspecific interactions in multispecies biofilms

Existence of most bacterial species, in natural, industrial, and clinical settings in the form of surface-adhered communities or biofilms has been well acknowledged for decades. Research predominantly focusses on single-species biofilms as these are relatively easy to study. However, microbiologists are now interested in studying multispecies biofilms and revealing interspecific interactions in these communities because of the existence of a plethora of different bacterial species together in almost all natural settings. Multispecies biofilms-led emergent properties are triggered by bacterial social interactions which have huge implication for research and practical knowledge useful for the control and manipulation of these microbial communities. Here, we discuss some important bacterial interactions that take place in multispecies biofilm communities and provide insights into community-wide changes that indicate bacterial interactions and elucidate underlying mechanisms.

Microbial Biofilms in the Food Industry-A Comprehensive Review

Biofilms, present as microorganisms and surviving on surfaces, can increase food cross-contamination, leading to changes in the food industry’s cleaning and disinfection dynamics. Biofilm is an association of microorganisms that is irreversibly linked with a surface, contained in an extracellular polymeric substance matrix, which poses a formidable challenge for food industries. To avoid biofilms from forming, and to eliminate them from reversible attachment and irreversible stages, where attached microorganisms improve surface adhesion, a strong disinfectant is required to eliminate bacterial attachments. This review paper tackles biofilm problems from all perspectives, including biofilm-forming pathogens in the food industry, disinfectant resistance of biofilm, and identification methods. As biofilms are largely responsible for food spoilage and outbreaks, they are also considered responsible for damage to food processing equipment. Hence the need to gain good knowledge about all of the factors favouring their development or growth, such as the attachment surface, food matrix components, environmental conditions, the bacterial cells involved, and electrostatic charging of surfaces. Overall, this review study shows the real threat of biofilms in the food industry due to the resistance of disinfectants and the mechanisms developed for their survival, including the intercellular signalling system, the cyclic nucleotide second messenger, and biofilm-associated proteins.

Understanding of food biofilms by the application of omics techniques

Biofilms constitute a protective barrier for foodborne pathogens to survive under stressful food processing conditions. Therefore, studies into the development and control of biofilms by novel techniques are vital for the food industry. In recent years, foodomics techniques have been developed for biofilm studies, which contributed to a better understanding of biofilm behavior, physiology, composition, as well as their response to antibiofilm methods at different molecular levels including genes, RNA, proteins and metabolic metabolites. Throughout this review, the main studies where foodomics tools used to explore the mechanisms for biofilm formation, dispersal and elimination were reviewed. The data summarized from relevant studies are important to design novel and appropriate biofilm elimination methods for enhancing food safety at any point of food processing lines.

Effect of Temperature-Dependent Bacterial Growth during Milk Protein Fractionation by Means of 0.1 µM Microfiltration on the Length of Possible Production Cycle Times

This study determined the maximum possible filtration time per filtration cycle and the cumulated number of operational hours per year as a function of the processing temperature during milk protein fractionation by 0.1 µm microfiltration (MF) of pasteurized skim milk. The main stopping criteria were the microbial count (max. 105 cfu/mL) and the slope of the pH change as a function of filtration time. A membrane system in a feed and bleed configuration with partial recirculation of the retentate was installed, resembling an industrial plants' operational mode. Filtration temperatures of 10, 14, 16, 20, and 55 °C were investigated to determine the flux, pH, and bacterial count. While the processing time was limited to 420 min at a 55 °C filtration temperature, it could exceed 1440 min at 10 °C. These data can help to minimize the use of cleaning agents or mixing phase losses by reducing the frequency of cleaning cycles, thus maximizing the active production time and reducing the environmental impact.

Strain variability in biofilm formation: A food safety and quality perspective

The inherent differences in microbial behavior among identically treated strains of the same microbial species, referred to as "strain variability", are regarded as an important source of variability in microbiological studies. Biofilms are defined as the structured multicellular communities with complex architecture that enable microorganisms to grow adhered to abiotic or living surfaces and constitute a fundamental aspect of microbial ecology. The research studies assessing the strain variability in biofilm formation are relatively few compared to the ones evaluating other aspects of microbial behavior such as virulence, growth and stress resistance. Among the available research data on intra-species variability in biofilm formation, compiled and discussed in the present review, most of them refer to foodborne pathogens as compared to spoilage microorganisms. Molecular and physiological aspects of biofilm formation potentially related to strain-specific responses, as well as information on the characterization and quantitative description of this type of biological variability are presented and discussed. Despite the considerable amount of available information on the strain variability in biofilm formation, there are certain data gaps and still-existing challenges that future research should cover and address. Current and future advances in systems biology and omics technologies are expected to aid significantly in the explanation of phenotypic strain variability, including biofilm formation variability, allowing for its integration in microbiological risk assessment.

Interspecies Interactions in Dual-Species Biofilms Formed by Psychrotrophic Bacteria and the Tolerance of Sessile Communities to Disinfectants

ABSTRACT

Biofilms on the surface of food processing equipment act as potential reservoirs of microbial contamination. Bacterial interactions are believed to play key roles in both biofilm formation and antimicrobial tolerance. In this study, Aeromonas hydrophila, Chryseobacterium oncorhynchi, and Pseudomonas libanensis, which were previously isolated from Chinese raw milk samples, were selected to establish two dual-species biofilm models (P. libanensis plus A. hydrophila and P. libanensis plus C. oncorhynchi) on stainless steel at 7°C. Subsequently, three disinfectants, hydrogen peroxide (100 ppm), peracetic acid (100 ppm), and sodium hypochlorite (100 ppm), were used to treat the developed sessile communities for 10 min. Structural changes after exposure to disinfectants were analyzed with confocal laser scanning microscopy. The cell numbers of both A. hydrophila and C. oncorhynchi recovered from surfaces increased when grown as dual species biofilms with P. libanensis. Dual-species biofilms were more tolerant of disinfectants than were each single-species biofilm. Peracetic acid was the most effective disinfectant for removing biofilms, followed by hydrogen peroxide and sodium hypochlorite. The results expand the knowledge of mixed-species biofilms formed by psychrotrophic bacteria and will be helpful for developing effective strategies to eliminate bacterial mixed-species biofilms.

HIGHLIGHTS

Short communication: Dynamic changes in bacterial diversity during the production of powdered infant formula by PCR-DGGE and high-throughput sequencing

Microorganisms such as thermophilic and psychrotrophic bacteria cause spoilage of milk and milk products [e.g., powdered infant formula (PIF)], mainly because they produce heat-stable extracellular enzymes. However, the dynamic changes in microbial diversity during PIF production are still not well understood. We used denaturing gradient gel electrophoresis (DGGE) and high-throughput sequencing (HTS) to investigate bacterial community structure and distribution during the major stages of PIF production: raw milk, pasteurization, mixing, evaporation, and spray-drying. Our PCR-DGGE analysis indicated that Lactobacillus and Pseudomonas spp. were the dominant bacteria at the raw milk and pasteurization stages; Lactococcus, Streptococcus, Enterococcus, and Lactobacillus spp. were abundant during mixing, evaporation, and spray-drying. Our HTS analysis showed that Pseudomonas had an abundance of 96.79% at the raw milk stage. Lactobacillus, Streptococcus, Thermus, Acinetobacter, and Bacteroides spp. were most common after pasteurization. The index of bacterial diversity was highest at the evaporation stage, suggesting a high potential risk of microbial contamination. The results from DGGE and HTS were consistent in reflecting changes in dominant flora, but different in reflecting the richness of bacterial communities present during PIF production: HTS revealed a much higher richness of bacterial species than DGGE. Our findings from DGGE and HTS showed that psychrophilic and thermophilic bacteria were the main flora present during PIF production: psychrophilic bacteria were mainly Pseudomonas spp. and thermophilic bacteria were mainly Lactobacillus, Streptococcus, and Bacillus spp. To our knowledge, this is the first study to report dynamic changes in microbial communities during PIF production. Our results provide insight into bacterial communities and identify potential contamination sources that could serve as a guide for reducing microbial risk.

Genomic comparison of anoxybacillus flavithermus AK1, a thermophilic bacteria, with other strains

From ecological and industrial perspectives, Anoxybacillus flavithermus species that lives in a thermophilic environment, are extremely important bacteria due to their potential in producing highly interesting compounds and enzymes. In order to understand the genetic makeup of these thermophiles, we have performed a comparative genomics study of 12 genome-sequenced strains of Anoxybacillus flavithermus bacteria. The genome size of Anoxybacillus flavithermus strains is from 2.5Mbp to 3.7Mbp and on average containing a low percentage of G + C genomic content (˜41.9%). We show that, on the basis of the total gene-content, Anoxybacillus flavithermus strains are grouped in three different subgroups. In the future, it would be interesting to explore these strain subgroups to further understand the lifestyle of thermophilic bacteria. Focussing on the Anoxybacillus flavithermus AK1 strain, which was isolated from a Hot Spring in Saudi Arabia and closely related to A. flavithermus NBRC strain, we identified a unique list of 75 genes specific to AK1 strain, of which 63 of them have homologs in other taxonomically related species. We speculate that these AK1-specific genes might be resulted due to horizontal gene transfer from other bacteria in order to adapt to the extreme environmental conditions. Moreover, we predicted three potential secondary metabolite gene clusters in the AK1 strain that further need to be experimentally characterised. Genomic annotation, secondary metabolite gene clusters and outcomes of the strain genomic comparisons from this study would be the basis for the strain-specific mathematical model for exploiting the metabolism for the industrial and ecological applications.

Molecular regulation of adhesion and biofilm formation in high and low biofilm producers of Bacillus licheniformis using RNA-Seq

RNA sequencing was used to reveal transcriptional changes during the motile-to-sessile switch in high and low biofilm-forming dairy strains of B. licheniformis isolated from Chinese milk powders. A significant part of the whole gene content was affected during this transition in both strains. In terms of the Kyoto Encyclopedia of Genes and Genomes (KEGG) database, seven metabolic pathways were significantly downregulated in the planktonic state compared to the biofilm state in both strains. Lipid and sugar metabolism seemed to play an important role in matrix production. Several genes involved in adhesion, matrix production and the matrix coating were either absent or less expressed in the biofilm state of the low biofilm producer compared to the high biofilm producer. Genes related to sporulation and the production of extracellular polymeric substances were concomitantly expressed in the biofilm state of both strains. These comprehensive insights will be helpful for future research into mechanisms and targets.

Biofilms in Food Processing Environments: Challenges and Opportunities

This review examines the impact of microbial communities colonizing food processing environments in the form of biofilms on food safety and food quality. The focus is both on biofilms formed by pathogenic and spoilage microorganisms and on those formed by harmless or beneficial microbes, which are of particular relevance in the processing of fermented foods. Information is presented on intraspecies variability in biofilm formation, interspecies relationships of cooperativism or competition within biofilms, the factors influencing biofilm ecology and architecture, and how these factors may influence removal. The effect on the biofilm formation ability of particular food components and different environmental conditions that commonly prevail during food processing is discussed. Available tools for the in situ monitoring and characterization of wild microbial biofilms in food processing facilities are explored. Finally, research on novel agents or strategies for the control of biofilm formation or removal is summarized.

A systematic characterization of the distribution, biofilm-forming potential and the resistance of the biofilms to the CIP processes of the bacteria in a milk powder processing factory

Owing to the resistance to conventional cleaning and sanitizing agents, biofilms formed on surfaces of dairy processing equipment pose a hazard to the dairy industry. The objective of this study was to evaluate the diversity of the microflora attached to various surfaces of the processing lines of a milk powder processing factory based on 16S rRNA gene sequence analysis. The production of biofilms by the bacterial strains was evaluated on polystyrene (PS) and stainless-steel (SS) surfaces by crystal violet staining method. Especially, effects of temperatures (e.g., 37 °C and 55 °C) and growth mediums (e.g., nutrient broth, NB; tryptic soy broth, TSB) on the production of biofilms by these strains on PS surfaces were explored. Besides, the tolerance of the biofilms of the strains to CIP processes (1.5% v/v HNO₃ solution or 2.0% w/v NaOH solution at 80 °C) were analyzed. Forty-five isolates from eleven interior surfaces of the facilities were identified and the distribution of strains had high species diversity, which indicated that multiple spoilage and pathogenic microorganisms remained in milk powder processing lines after CIP processes. Bacteria showed higher biofilm-forming abilities on SS compared to PS surfaces under the same condition. Moreover, effects of the incubation temperature and growth medium on biofilm formation varied between genera, species, and strains. One strain of each species with biofilm-forming abilities on SS surfaces was selected to check the resistance of their biofilms formed on SS coupons to the CIP processes. Biofilms of all of the nine strains were highly or moderately alkali and acid resistant, posing a threat to the milk powder production. These results suggested that organisms within the biofilm might withstand temperature and pH changes better than planktonic organisms. More research is needed to investigate different species isolated from different facilities of the processing lines and to improve the key controlling points in the CIP processes.