Culture dependent and independent genomic identification of Alicyclobacillus species in contaminated commercial fruit juices

Alicyclobacillus spp. in fruit-based products: Isolation, identification, quantitative assessment (SPME/GC-MS) of spoilage compounds and spore's resistance to thermal shocks

Alicyclobacillus spp. is the cause of great concern for the food industry due to their spores' resistance (thermal and chemical) and the spoilage potential of some species. Despite this, not all Alicyclobacillus strains can spoil fruit juices. Thus, this study aimed to identify Alicyclobacillus spp. strains isolated from fruit-based products produced in Argentina, Brazil, and Italy by DNA sequencing. All Alicyclobacillus isolates were tested for guaiacol production by the peroxidase method. Positive strains for guaiacol production were individually inoculated at concentration of 103 CFU/mL in 10 mL of orange (pH 3.90) and apple (pH 3.50) juices adjusted to 11°Brix, following incubation at 45 °C for at least 5 days to induce the production of the following spoilage compounds: Guaiacol, 2,6-dichlorophenol (2,6-DCP) and 2,6-dibromophenol (2,6-DBP). The techniques of micro-solid phase extraction by headspace (HS-SPME) and gas-chromatography with mass spectrometry (GC-MS) were used to identify and quantify the spoilage compounds. All GC-MS data was analyzed by principal component analysis (PCA). The effects of different thermal shock conditions on the recovery of Alicyclobacillus spores inoculated in orange and apple juice (11°Brix) were also tested. A total of 484 strains were isolated from 48 brands, and the species A. acidocaldarius and A. acidoterrestris were the most found among all samples analyzed. In some samples from Argentina, the species A. vulcanalis and A. mali were also identified. The incidence of these two main species of Alicyclobacillus in this study was mainly in products from pear (n = 108; 22.3 %), peach (n = 99; 20.5 %), apple (n = 86; 17.8 %), and tomato (n = 63; 13 %). The results indicated that from the total isolates from Argentina (n = 414), Brazil (n = 54) and Italy (n = 16) were able to produce guaiacol: 107 (25.8 %), 33 (61.1 %) and 13 (81.2 %) isolates from each country, respectively. The PCA score plot indicated that the Argentina and Brazil isolates correlate with higher production of guaiacol and 2,6-DCP/2,6-DBP, respectively. Heatmaps of cell survival after heat shock demonstrated that strains with different levels of guaiacol production present different resistances according to spoilage ability. None of the Alicyclobacillus isolates survived heat shocks at 120 °C for 3 min. This work provides insights into the incidence, spoilage potential, and thermal shock resistance of Alicyclobacillus strains isolated from fruit-based products.

Antibacterial effects of various molecular weight chitosans against Alicyclobacillus acidoterrestris in orange juice

Alicyclobacillus acidoterrestris has been gaining attention due to its unique thermo-acidophilic properties and being associated with the deterioration of pasteurized beverages. The objective of this study was to evaluate the antibacterial activity of chitosan with various molecular weights (MWs) (164, 85, 29.2, and 7.1 kDa) and concentrations (0-100 μg/mL) against A. acidoterrestris and its effect on guaiacol production. Various chitosan MWs were co-incubated for 7 days, and the bacterial growth, guaiacol, and vanillic acid contents during storage were determined. The chitosans performed antibacterial effects against A. acidoterrestris. Further, 164 kDa chitosan showed excellent results in controlling the growth and guaiacol formation in A. acidoterrestris. These findings demonstrated the efficacy of chitosan antibacterial activity against A. acidoterrestris and mitigating the guaiacol formation. Chitosan's antibacterial properties are attributed to the elimination of cells and suppression of guaiacol production. This study introduces a new approach for reducing A. acidoterrestris contamination in fruit juices, with potential product quality and safety advantages.

Detection of Alicyclobacillus spp. and Identification of Guaiacol Production Using the GENE-UP® PRO ACB, IFU Method No. 12, and Cosmo Bio Assays

Some species of Alicyclobacillus spoil beverages by producing guaiacol. Current culture-based methods detect the presence of Alicyclobacillus spp. and a subsequent peroxidase assay determines if the isolate can produce guaiacol. However, these methods are time-consuming and can yield false negatives due to differences in growth optima among species. The purpose of this study was to compare a RT-PCR-based method, the GENE-UP® PRO ACB assay, to the IFU Method No. 12 Enumeration and Enrichment methods. Ten species of Alicyclobacillus were detected using the tested RT-PCR assay, while A. dauci and A. kakegewensis were not detected using either IFU protocol. Low concentrations (1-10, 10-100, and 100-1,000 CFU/10 mL) of A. acidoterrestris, A. suci, and A. acidocaldarius were tested in five matrices. The proportion of positive samples identified using the tested RT-PCR assay (62/84) or the IFU Enrichment protocol (62/84) did not differ significantly from the proportion of inoculated samples (63/84). However, the IFU Enumeration method (32/84) detected statistically fewer positives. Additionally, methods identifying guaiacol production were compared. The proportion of correctly identified guaiacol producers using the tested RT-PCR assay (51/63) was not significantly different than those identified using the 3 h Cosmo Bio assay (54/63). Finally, four commercial samples of orange juice and sucrose solution were tested. Alicyclobacillus spp. were identified in all four samples using the IFU Enrichment method and in two samples using the tested RT-PCR assay. However, Alicyclobacillus was not detected in any sample using the IFU Enumeration method. Overall, this study showed consistent detection of Alicyclobacillus spp. using either the IFU Enrichment protocol or the tested RT-PCR assay, which both outperformed the IFU Enumeration protocol. Both the 3 h guaiacol bioassay and the tested RT-PCR assays consistently differentiated guaiacol-producing and nonproducing strains.

Fruit Juice Spoilage by Alicyclobacillus: Detection and Control Methods—A Comprehensive Review

Fruit juices have an important place in humans’ healthy diet. They are considered to be shelf stable products due to their low pH that prevents the growth of most bacteria. However thermo-acidophilic endospore forming bacteria of the genus Alicyclobacillus have the potential to cause spoilage of commercially pasteurized fruit juices. The flat sour type spoilage, with absence of gas production but presence of chemical spoilage compounds (mostly guaiacol) and the ability of Alicyclobacillus spores to survive after pasteurization and germinate under favorable conditions make them a major concern for the fruit juice industry worldwide. Their special characteristics and presence in the fruit juice industry has resulted in the development of many isolation and identification methods based on cell detection (plating methods, ELISA, flow cytometry), nucleic acid analysis (PCR, RAPD-PCR, ERIC-PCR, DGGE-PCR, RT-PCR, RFLP-PCR, IMS-PCR, qPCR, and 16S rRNA sequencing) and measurement of their metabolites (HPLC, GC, GC-MS, GC-O, GC-SPME, Electronic nose, and FTIR). Early detection is a big challenge that can reduce economic loss in the industry while the development of control methods targeting the inactivation of Alicyclobacillus is of paramount importance as well. This review includes a discussion of the various chemical (oxidants, natural compounds of microbial, animal and plant origin), physical (thermal pasteurization), and non-thermal (High Hydrostatic Pressure, High Pressure Homogenization, ultrasound, microwaves, UV-C light, irradiation, ohmic heating and Pulse Electric Field) treatments to control Alicyclobacillus growth in order to ensure the quality and the extended shelf life of fruit juices.

Assessment of Foodborne Disease Hazards in Beverages Consumed in Nigeria: A Systematic Literature Review

Risk assessment is a formal process of identifying hazards and assessing the risk associated with them (risk is a combination of the severity of illness and the probability of occurrence). This review highlights foodborne disease hazards reported in beverages consumed in Nigeria for the period between 2000 and 2020. Based on a preregistered protocol and search syntax, studies were retrieved from the PubMed, Google Scholar, and ScienceDirect databases. Rayyan QCRI software was used to screen the articles. Data were then extracted from the included full-text articles, into a standardized excel workbook. A total of 18,762 articles were identified, from which 126 were included in the final analyses. The common beverages studied were sachet water (14.9%), borehole/well water (13.9%), cereal-based beverages (12.1%), raw/fresh milk (8.3%) and nono/nunu, which is a fermented milk-cereal beverage (7.2%). Sufficient data were available to undertake pooled prevalence estimates for some hazards within select beverages and revealed contamination rates for Staphylococcus spp. in raw/fresh milk, 12.3% (95% CI 6.3–20.0); Salmonella spp. in borehole/well water, 19.8% (95% CI 13.1–27.4); Klebsiella spp. in sachet water, 40.0% (95% CI 12.4–71.7); Staphylococcus spp. in nono/nunu, 32.6% (95% CI 14.7–53.8), and Escherichia spp. in nono/nunu, 30.7% (95% CI 21.9–40.2). Heterogeneity was present in the aggregate summary estimates. This review has highlighted the presence of several hazards of high importance to public health in commonly consumed beverages in Nigeria. The data presented here provide an entry point for future quantitative risk assessments both to determine the level of exposure of the community to these hazards and also for the identification of the most effective mitigation strategies to reduce these risks and improve health outcomes in Nigeria.

Integrated analysis of transcriptome and proteome for exploring the mechanism of guaiacol production by Alicyclobacillus acidoterrestris

Alicyclobacillus spp. can cause commercially pasteurized fruit juices/beverages to spoil and the spoilage is characterized by the formation of a distinct medicinal or antiseptic off-odor attributed to guaiacol. The aim of this study was to reveal the mechanism of guaiacol production in A. acidoterrestris by combining transcriptomic and proteomic approaches. RNA-sequencing and iTRAQ analyses were conducted to investigate differences in expression levels of genes and proteins in A. acidoterrestris when producing (with 500 μM vanillic acid) and not producing (without vanillic acid) guaiacol. A total of 225 differentially expressed genes and 77 differentially expressed proteins were identified. The transcription of genes vdcBCD encoding subunits of vanillic acid decarboxylase were 626.47, 185.01 and 52.81-fold up-regulated, respectively; they were the most up-regulated genes involved in guaiacol production. Expressions of the benzoate membrane transport protein, fusaric acid resistance protein, resistance-nodulation- division transporter, some ATP-binding cassette transporters and major facilitator superfamily transporters were increased at either mRNA, protein or both levels, indicating that they participated in the uptake of vanillic acid and extrusion of guaiacol. In the metabolic process of vanillic acid to guaiacol in A. acidoterrestris, genes related to the pathway of tricarboxylic acid cycle and ribosome were up-regulated, while the expression of some genes associated with valine, leucine and isoleucine biosynthesis was decreased. These findings provide novel insight to understand the mechanism of guaiacol production in A. acidoterrestris, which will serve as an important guide for developing strategies for the control of A. acidoterrestris problems in the fruit juice industry.

Viability, Sublethal Injury, and Release of Cellular Components From Alicyclobacillus acidoterrestris Spores and Cells After the Application of Physical Treatments, Natural Extracts, or Their Components

Alicyclobacillus acidoterrestris is a spoiling microorganism regarded as one of the most important causes of spoilage of fruit juices and acidic products. In this paper, four strains of A. acidoterrestris (type strain-DSM 3922; two wild strains isolated from soil-C8 and C24; wild strain isolated from a spoiled pear juice CB1) were treated through natural extracts/active compounds from essential oils (EOs), and physical treatments were used to assess their susceptibility and the presence of sublethal injury. The characterization of damage was also performed. The results suggest that it is possible to control A. acidoterrestris through alternative approaches, although the effect relied upon the age of spores. In addition to the mere antimicrobial effect, some treatments could cause a sublethal injury on spores. Lemon extract was the most effective treatment for both the antimicrobial effect and the sublethal injury, as evidenced by the release of proteins, and calcium dipicolinate [dipicolinic acid (DPA)] by fresh spores and only DPA (with an exception for C8) by old spores. A sublethal injury with protein release was also found for physical treatments [US (ultrasound) or heating]. For the first time, this paper reports on the existence of a sublethal injury for A. acidoterrestris, and this evidence could also be a challenge, because injured microorganisms could restore their metabolism, or an opportunity to design new preserving treatments.

DNA electrochemical biosensor for detection of Alicyclobacillus acidoterrestris utilizing Hoechst 33258 as indicator

Alicyclobacillus acidoterrestris is an acidophilic and thermophilic bacterium present in the soil, often associated with the spoilage of acidic juices, such as orange juice. Their spores resist pasteurization and, when reactivated, modify the organoleptic properties of the juice, making it unsuitable for consumption, due mainly to production of guaiacol. Biosensors are detection devices that respond quickly and are easy to handle, with great potential for use in the juice production chain. In this context, this work reports an electrochemical genosensor for detection of A. acidoterrestris, based on a graphite electrode modified with electrochemically reduced graphene oxide, a polymer derived from 3-hydroxybenzoic acid and a specific DNA probe sequence complementary with the genomic DNA of A. acidoterrestris. Detection of the target was performed by monitoring the oxidation peak of the Hoechst 33258, a common DNA stainer. The genosensor detection limit was 12 ng mL^-1 and it kept 77% of response after ten weeks, and a test showed that orange juice does not interfere with bacteria lysate detection. This biosensor is the first platform for electrochemical detection of the genomic DNA of A. acidoterrestris in the literature, and the first to use Hoechst 33258 as indicator with whole genomic DNA molecules.

Targeting the vanillic acid decarboxylase gene for Alicyclobacillus acidoterrestris quantification and guaiacol assessment in apple juices using real time PCR

Alicyclobacillus spp. has recently received much attention due to its implication in the spoilage of pasteurized fruit juices, which is characterized by the formation of guaiacol. Previous researches indicate that not all Alicyclobacillus spp. are able to produce guaiacol. The aim of this study was to identify possible differences in the vanillic acid decarboxylase gene involved in guaiacol biosynthesis and then develop specific detection methods for guaiacol producing Alicyclobacillus. Agarose gel electrophoresis results showed that the partial vdcC gene was present in all the guaiacol producing Alicyclobacillus, but absent in non-guaicaol producing strains apart from A. fastidiosus DSM 17978. On the basis of the vdcC gene sequence, a primer pair specific to A. acidoterrestris was designed; then a SYBR Green I real time PCR was established for the direct quantification of A. acidoterrestris in apple juice, and the detection limit was 2.6 × 10¹ CFU/mL. The developed real time PCR system was used to detect A. acidoterrestris in 36 artificially contaminated apple juice samples and guaiacol production in the sample was also analyzed by GC-MS. The Gompertz model was employed to describe the relationship between A. acidoterrestris cell concentration and guaiacol content, and the value of R² was 0.854. This work provides an alternative to conventional methods of guaiacol quantification and A. acidoterrestris detection and could be very useful for the early recognition of A. acidoterrestris contamination in fruit juices.

Heat resistance and genomics of spoilage Alicyclobacillus spp. Isolated from fruit juice and fruit-based beverages

Alicyclobacillus acidoterrestris is a spore-forming bacterium of importance to the fruit juice industry due to its remarkable heat resistance and production of guaiacol taint. Whole genome sequencing analysis reveals species demarcation corresponds to the two major genotypic groups to which A. acidoterrestris isolates belong. Heat resistance was significantly different between genotypic groups 1 and 2 with D₉₀ values of 15.5 and 9.3 min, respectively (p < 0.01). Comparison of squalene-hopene cyclase (shc) encoding sequences reveals non-synonymous changes and the alteration of glutamine residues. Glutamine absence may link to the stability reinforcement of the enzyme structure against thermal denaturation. Genomic islands harbouring heavy metal resistance genes are found in the majority of genotypic group 1 genomes (63%) but occurs in only one genome (5%) of genotypic group 2. Distribution of the genomic islands in the genotypic groups 1 and 2 is also consistent with phylogenetic trees and ANI and dDDH values. Subsequently, we propose genotypic group 1 as a new species closely related to A. acidoterrestris that possesses enhanced heat resistance.

Control of the growth of Alicyclobacillus acidoterrestris in industrialized orange juice using rosemary essential oil and nisin

The use of rosemary essential oil (RO) and its combination with nisin (RO+N) in preventing the multiplication of Alicyclobacillus acidoterrestris in orange juice was evaluated. The minimum inhibitory and bactericidal concentrations (MIC and MBC) for RO were both 125 μg ml^-1 while RO+N displayed a synergistic effect. The use of RO and RO+N at concentrations of 1, 4 and 8× MIC in orange juice for 96 h was evaluated in terms of their sporicidal effectiveness. With regard to the action against A. acidoterrestris spores, RO at 8× MIC was sporostatic, whereas RO+N at 1× MIC was sporicidal. Morphological changes in the structure of the micro-organism after treatment were also observed by microscopy. Furthermore, flow cytometric analysis showed that most cells were damaged or killed after treatment. In general, the antioxidant activity after addition of RO+N decreased with time. The results demonstrate that using the combination of RO and nisin can prevent the A. acidoterrestris growth in orange juice.

Development of the Saltatory Rolling Circle Amplification Assay for Rapid and Visual Detection of Alicyclobacillus acidoterrestris in Apple Juice

A novel nucleic acid isothermal amplification method based on saltatory rolling circle amplification (SRCA) for rapid and visual detection of Alicyclobacillus acidoterrestris in apple juice was established. Fourteen A. acidoterrestris strains and 44 non-A. acidoterrestris strains were used to confirm the specificity. The sensitivity of SRCA was 4.5 × 10¹ CFU/mL by observing the white precipitate with the naked eye, while it was 4.5 × 10⁰ CFU/mL by fluorescence visualization. The detection limit of SRCA in artificially inoculated apple juice was 7.1 × 10¹ and 7.1 × 10⁰ CFU/mL via visualization of the white precipitate and fluorescence, respectively. Compared with the traditional PCR method, SRCA exhibited at least a 100-fold higher sensitivity and 100-fold lower detection limit. Seventy samples were investigated for A. acidoterrestris contamination, and the results showed 100% sensitivity, 97.01% specificity, and 97.14% accuracy compared with those by the conventional microbiological cultivation method. Overall, this method is a potentially useful tool for visual and rapid detection of A. acidoterrestris.

Genetic Heterogeneity of Alicyclobacillus Strains Revealed by RFLP Analysis of vdc Region and rpoB Gene

PCR-RFLP targeting of the 16S rDNA and rpoB genes, as well as the vdc region, was applied to identify and differentiate between the spoilage and non-spoilage Alicyclobacillus species. Eight reference strains and 75 strains isolated from spoiled juices, juice concentrates, drinks, its intermediates, and fresh apples were subject to study. Hin6I restriction patterns of the 16S rDNA gene enabled distinguishing between all the species analyzed, while the rpoB gene and vdc gene cluster analysis also revealed that there were two major types among the A. acidoterrestris isolates, one similar to the reference strain A. acidoterrestris DSM 2498, and the other similar to the reference strain A. acidoterrestris ATCC 49025. Heterogeneity was also observed among the A. acidocaldarius isolates. RFLP analysis of the 16S rDNA and rpoB genes, as well as vdc region, can be used successfully in the identification and research of intraspecies heterogeneity of the Alicyclobacillus species.