Enumeration and detection of acetic acid bacteria by real-time PCR and nested PCR

Development and application of a real-time loop-mediated isothermal amplification method for quantification of Acetobacter aceti in red wine

This study reports the development and optimization of a real-time loop-mediated isothermal amplification (qLAMP) method for rapid detection of Acetobacter aceti strain in red wine samples. Our results showed that the primers and probes designed for 16S rRNA were effective for A. aceti detection. The quantification limit of real-time polymerase chain reaction (qPCR) and qLAMP in pure culture was 2.05 × 101 colony forming units (CFU) mL-1. qLAMP had a sensitivity of 6.88 × 101 CFU mL-1 in artificially contaminated Changyu dry red wine (CDRW) and Changyu red wine (CRW), and 6.88 × 102 CFU mL-1 in artificially contaminated Greatwall dry red wine (GDRW), which was 10 times higher than that of qPCR. In conclusion, this newly developed qLAMP is a reliable, rapid and accurate method for the detection and quantification of A. aceti species in red wine samples. Furthermore, our work provides a standard reference method for the quantitative detection of A. aceti and other acetic acid bacteria during the fermentation and storage of red wine samples.

On metal and 'spoiled' wine: analysing psimythion (synthetic cerussite) pellets (5th-3rd centuries BCE) and hypothesising gas-metal reactions over a fermenting liquid within a Greek pot

A Pb-based synthetic mineral referred to as psimythion (pl. psimythia) was manufactured in the Greek world at least since the 6th c BCE and routinely by the 4th c BCE. Theophrastus (On Stones, 56) describes its preparation from metallic Pb suspended over a fermenting liquid. Psimythion is considered the precursor of one of western art's most prominent white pigments, i.e. lead white (basic lead carbonate or synthetic hydrocerussite). However, so far, and for that early period, published analyses of psimythia suggest that they consisted primarily of synthetic cerussite. In this paper, we set out to investigate how it was possible to manufacture pure cerussite, to the near exclusion of other phases. We examined the chemical and mineralogical composition (pXRF/XRD) of a small number of psimythion pellets found within ceramic pots (pyxis) from Athens and Boeotia (5th-4th c BCE) in the collection of the National Archaeological Museum (NAM), Athens. Analyses showed that the NAM pellets consisted primarily of Pb/cerussite with small amounts of Ca (some samples) and a host of metallic trace elements. We highlight the reference in the Theophrastus text to 'spoiled wine' (oxos), rather than 'vinegar', as has been previously assumed, the former including a strong biotic component. We carried out DNA sequencing of the pellets in an attempt to establish presence of microorganisms (Acetic Acid Bacteria). None was found. Subsequently, and as a working hypothesis, we propose a series of (biotic/abiotic) reactions which were likely to have taken place in the liquid and vapour phases and on the metal surface. The hypothesis aims to demonstrate that CO₂ would be microbially induced and would increase, as a function of time, resulting in cerussite forming over and above hydrocerussite/other Pb-rich phases. Psimythion has for long been valued as a white pigment. What has perhaps been not adequately appreciated is the depth of empirical understanding from the part of psimythion manufacturers of the reactions between abiotic and biotic components within 'oxos'/pot, as key drivers of minerals synthesis. Ultimately, psimythion manufacture may rest in understanding the nature of 'oxos', antiquity's relatively little researched strongest acid.

A Culture-Independent Method for Enumeration of Viable Load of Lactobacillus acidophilus NCFM by using Real-Time PCR

The study was performed to develop a non-culture method to quantify viable loads of Lactobacillus acidophilus NCFM using RNA-based molecular technique. The ‘growth curve’ and ‘cycle threshold curve’ were developed respectively by plate counting and using cycle threshold (CT) values. ‘Standard curve’ was constructed using cells per milliliter and relative CT values. A maximum viable count (1.5 ± 0.15) × 1010 cells/mL with a minimum CT value 20.18 ± 0.56 was achieved following 18 h of growth. The two parameters were inversely proportional to each other over the exponential growth. The ‘standard curve’ corresponded to equation y = 2E + 28e−2.034x (y = cells/mL, x = CT value; R2 = 0.993), and no sample showed significant difference between ‘plate count’ and relative ‘PCR count’ following the validation process. Industrial adaptation of this method in dairy processing could potentially contribute to a faster enumeration of viable L. acidophilus NCFM compared to plate counting.

Acetic Acid Bacteria in the Food Industry: Systematics, Characteristics and Applications

The group of Gram-negative bacteria capable of oxidising ethanol to acetic acid is called acetic acid bacteria (AAB). They are widespread in nature and play an important role in the production of food and beverages, such as vinegar and kombucha. The ability to oxidise ethanol to acetic acid also allows the unwanted growth of AAB in other fermented beverages, such as wine, cider, beer and functional and soft beverages, causing an undesirable sour taste. These bacteria are also used in the production of other metabolic products, for example, gluconic acid, l-sorbose and bacterial cellulose, with potential applications in the food and biomedical industries. The classification of AAB into distinct genera has undergone several modifications over the last years, based on morphological, physiological and genetic characteristics. Therefore, this review focuses on the history of taxonomy, biochemical aspects and methods of isolation, identification and quantification of AAB, mainly related to those with important biotechnological applications.

Cells-qPCR as a direct quantitative PCR method to avoid microbial DNA extractions in grape musts and wines

A novel quantitative PCR assay called Cells-qPCR has been developed for the rapid detection and quantification of yeasts, lactic acid bacteria (LAB) and acetic acid bacteria (AAB) directly from grape must and wine that does not require DNA extraction. The assay was tested on Brettanomyces bruxellensis, Saccharomyces cerevisiae, Lactobacillus plantarum, Oenococcus oeni, Acetobacter aceti and Gluconobacter oxydans in culture media, and in white and red grape musts and wines. Standard curves were constructed from DNA and cells for the six target species in all the matrices. Good efficiencies were obtained for both when comparing DNA and cells standard curves. No reaction inhibition was observed between matrices for each species. Cells quantification was linear over a range of cell concentrations (7, 5 or 4 orders of magnitude) and detected as few as one cell per reaction in all the matrices. The developed Cells-qPCR assay is a robust, reliable, fast and specific method to detect and quantify different yeasts, LAB and AAB species in grape must and wine that avoids DNA extraction and overcomes the presence of inhibitors like polyphenols and ethanol.

Using real-time polymerase chain reaction as an alternative rapid method for enumeration of colony count in live Brucella vaccines

Aim::

Brucellosis is a major bacterial zoonosis of global importance affecting a range of animal species and man worldwide. It has economic, public health, and bio-risk importance. Control and prevention of animal brucellosis mainly depend on accurate diagnostic tools and implementation of effective and safe animal vaccination program. There are three types of animal Brucella live vaccines - Brucella melitensis Rev-1 vaccine, Brucella abortus S19, and B. abortus RB51. Evaluation of these vaccines depends mainly on enumeration of Brucella viable count. At present, used colony count method is time consuming, costly and requires especial skills. Hence, the aim of this study is to use and standardize real-time polymerase chain reaction (RT-PCR) as an alternative, quantitative, sensitive, and rapid method to detect the colony count of Brucella in live Brucella vaccine.

Materials and Methods::

Four batches of different live Brucella vaccines were evaluated using of conventional bacterial count and RT-quantitative PCR (RT-qPCR) using BSCP31 gene specific primers and probe. Standard curve was generated from DNA template extracted from 10-fold serial dilution of living B. abortus RB51 vaccine to evaluate the sensitivity of RT-qPCR.

Results::

Results revealed that three batches of living Brucella vaccines were acceptable for Brucella colony count when traditional bacterial enumeration method was used. Results of RT-qPCR were identical to that of conventional bacterial count.

Conclusions::

Results concluded that RT-qPCR was relatively sensitive compared to traditional bacterial colony count of these vaccines.

Evaluation of method bias for determining bacterial populations in bacterial community analyses

Various methods are used for analyzing a bacterial community. We recently developed a method for quantifying each bacterium constituting the microbiota by combining a next-generation sequencing (NGS) analysis with a quantitative polymerase chain reaction (NGS-qPCR) assay. Our NGS-qPCR method is useful for analyzing a comprehensive bacterial community because it is enables the easy calculation of the amounts of each bacterium constituting the microbiota. However, it has not been confirmed whether the estimated bacterial community obtained using this NGS-qPCR method corresponds to the results obtained using conventional methods. Accordingly, we prepared model bacterial community samples and analyzed them by several methods (NGS-qPCR, species-specific qPCR, flow cytometry, total direct counting by epifluorescent microscopy [TDC], and plate count). The total bacterial cell densities determined by the PCR-based methods were largely consistent with those determined by the TDC method. There was a difference between the amounts of each bacterium analyzed by NGS-qPCR and species-specific qPCR, although the same trend was shown by both species-specific qPCR and NGS-qPCR. Our findings also demonstrated that there is a strong positive correlation between the cell densities of a specific bacterial group in craft beer samples determined by group-specific qPCR and NGS-qPCR, and there were no significant differences among quantification methods (we tested two bacterial groups: lactic acid bacteria and acetic acid bacteria). Thus, the NGS-qPCR method is a practical method for analyzing a comprehensive bacterial community based on a bacterial cell density.

LAMP, PCR, and real-time PCR detection of Acetobacter aceti in yogurt

Acetic acid bacteria (AAB) can spoil food. Acetobacter aceti as a core subgroup of AAB is usually isolated from yogurt. A. aceti should be timely and effectively detected to prevent yogurt contamination. The present study focused on A. aceti to establish an assay that can be performed to detect AAB in yogurt. LAMP, PCR, and real-time PCR were applied and compared for detecting A. aceti from pure culture and artificially contaminated yogurt samples. In pure culture, LAMP showed the highest detection sensitivity with 10-1 CFU/mL. For yogurt samples, the sensitivity limit of LAMP was 102 CFU/mL, which was lower than that of real-time PCR (101 CFU/mL). The results indicated that these methods could be quickly and efficiently applied to detect A. aceti. As LAMP technology has low cost and high detection efficiency, it can potentially be applied for detecting A. aceti in production and quality control programs of yogurt.

Effect of chitosan and SO2 on viability of Acetobacter strains in wine

Wine spoilage is an important concern for winemakers to preserve the quality of their final product and avoid contamination throughout the production process. The use of sulphur dioxide (SO₂) is highly recommended to prevent wine spoilage due to its antimicrobial activity. However, SO₂ has a limited effect on the viability of acetic acid bacteria (AAB). Currently, the use of SO₂ alternatives is favoured in order to reduce the use of chemicals and improve stabilization in winemaking. Chitosan is a biopolymer that is approved by the European authorities and the International Organization of Vine and Wine to be used as a fining agent and antimicrobial in wines. However, its effectiveness in AAB prevention has not been studied. Two strains of Acetobacter, adapted to high ethanol environments, were analysed in this study. Both chitosan and SO₂ effects were compared in artificially contaminated wines. Both molecules reduced the metabolic activity of both AAB strains. Although AAB populations were detected by culture independent techniques, their numbers were reduced with time, and their viability decreased following the application of both products, especially with chitosan.

Design and Performance Testing of a DNA Extraction Assay for Sensitive and Reliable Quantification of Acetic Acid Bacteria Directly in Red Wine Using Real Time PCR

Although strategies exist to prevent AAB contamination, the increased interest for wines with low sulfite addition leads to greater AAB spoilage. Hence, there is a real need for a rapid, specific, sensitive, and reliable method for detecting these spoilage bacteria. All these requirements are met by real time Polymerase Chain Reaction (or quantitative PCR; qPCR). Here, we compare existing methods of isolating DNA and their adaptation to a red wine matrix. Two different protocols for isolating DNA and three PCR mix compositions were tested to select the best method. The addition of insoluble polyvinylpolypyrrolidone (PVPP) at 1% (v/v) during DNA extraction using a protocol succeeded in eliminating PCR inhibitors from red wine. We developed a bacterial internal control which was efficient in avoiding false negative results due to decreases in the efficiency of DNA isolation and/or amplification. The specificity, linearity, repeatability, and reproducibility of the method were evaluated. A standard curve was established for the enumeration of AAB inoculated into red wines. The limit of quantification in red wine was 3.7 log AAB/mL and about 2.8 log AAB/mL when the volume of the samples was increased from 1 to 10 mL. Thus, the DNA extraction method developed in this paper allows sensitive and reliable AAB quantification without underestimation thanks to the presence of an internal control. Moreover, monitoring of both the AAB population and the amount of acetic acid in ethanol medium and red wine highlighted that a minimum about 6.0 log cells/mL of AAB is needed to significantly increase the production of acetic acid leading to spoilage.

Acetic acid bacteria and the production and quality of wine vinegar

The production of vinegar depends on an oxidation process that is mainly performed by acetic acid bacteria. Despite the different methods of vinegar production (more or less designated as either “fast” or “traditional”), the use of pure starter cultures remains far from being a reality. Uncontrolled mixed cultures are normally used, but this review proposes the use of controlled mixed cultures. The acetic acid bacteria species determine the quality of vinegar, although the final quality is a combined result of technological process, wood contact, and aging. This discussion centers on wine vinegar and evaluates the effects of these different processes on its chemical and sensory properties.

Acetobacter malorum and Acetobacter cerevisiae identification and quantification by Real-Time PCR with TaqMan-MGB probes

The identification and quantification of Acetobacter malorum and Acetobacter cerevisiae in wine and vinegar were performed using the Real-Time PCR (RT-PCR) with two TaqMan-MGB probes designed to amplify the internal transcribed spacer (ITS) region between the 16S-23S rRNA genes. The primers and probes were highly specific, with a detection limit of 10² cells/ml for both species, and the efficiency of the technique was >80%. The RT-PCR technique with these two new TaqMan-MGB probes, together with the five (Acetobacter aceti, Acetobacter pasteurianus, Gluconobacter oxydans, Gluconacetobacter hansenii and Gluconacetobacter europaeus) that are already available (Torija et al., 2010), were validated on known concentrations of Acetic Acid Bacteria (AAB) grown in glucose medium (GY) and in inoculated matrices of wine and vinegar. Furthermore, this technique was applied to evaluate the AAB population in real wine samples collected in the Canary Islands. PCR enrichment performed prior to RT-PCR increased the accuracy of quantification and produced results similar to those detected with SYBR-Green. In real wine samples, the total AAB enumeration ranged from 9 × 10² to 10⁶ cells/ml, and the seven AAB species tested were detected in more than one sample. However, AAB recovery on plates was poor; the isolates obtained on plates were A. malorum, G. oxydans, A. cerevisiae and A. pasteurianus species. RT-PCR with TaqMan-MGB probes is an accurate, specific and fast method for the identification and quantification of AAB species commonly found in wine and vinegar.

The microbial ecology of wine grape berries

Grapes have a complex microbial ecology including filamentous fungi, yeasts and bacteria with different physiological characteristics and effects upon wine production. Some species are only found in grapes, such as parasitic fungi and environmental bacteria, while others have the ability to survive and grow in wines, constituting the wine microbial consortium. This consortium covers yeast species, lactic acid bacteria and acetic acid bacteria. The proportion of these microorganisms depends on the grape ripening stage and on the availability of nutrients. Grape berries are susceptible to fungal parasites until véraison after which the microbiota of truly intact berries is similar to that of plant leaves, which is dominated by basidiomycetous yeasts (e.g. Cryptococcus spp., Rhodotorula spp. Sporobolomyces spp.) and the yeast-like fungus Aureobasidium pullulans. The cuticle of visually intact berries may bear microfissures and softens with ripening, increasing nutrient availability and explaining the possible dominance by the oxidative or weakly fermentative ascomycetous populations (e.g. Candida spp., Hanseniaspora spp., Metschnikowia spp., Pichia spp.) approaching harvest time. When grape skin is clearly damaged, the availability of high sugar concentrations on the berry surface favours the increase of ascomycetes with higher fermentative activity like Pichia spp. and Zygoascus hellenicus, including dangerous wine spoilage yeasts (e.g. Zygosaccharomyces spp., Torulaspora spp.), and of acetic acid bacteria (e.g. Gluconobacter spp., Acetobacter spp.). The sugar fermenting species Saccharomyces cerevisiae is rarely found on unblemished berries, being favoured by grape damage. Lactic acid bacteria are minor partners of grape microbiota and while being the typical agent of malolactic fermentation, Oenococcus oeni has been seldom isolated from grapes in the vineyard. Environmental ubiquitous bacteria of the genus Enterobacter spp., Enterococcus spp., Bacillus spp., Burkholderia spp., Serratia spp., Staphylococcus spp., among others, have been isolated from grapes but do not have the ability to grow in wines. Saprophytic moulds, like Botrytis cinerea, causing grey rot, or Aspergillus spp., possibly producing ochratoxin, are only active in the vineyard, although their metabolites may affect wine quality during grape processing. The impact of damaged grapes in yeast ecology has been underestimated mostly because of inaccurate grape sampling. Injured berries hidden in apparently sound bunches explain the recovery of a higher number of species when whole bunches are picked. Grape health status is the main factor affecting the microbial ecology of grapes, increasing both microbial numbers and species diversity. Therefore, the influence of abiotic (e.g. climate, rain, hail), biotic (e.g. insects, birds, phytopathogenic and saprophytic moulds) and viticultural (e.g. fungicides) factors is dependent on their primary damaging effect.

Biotechnological applications of acetic acid bacteria

The acetic acid bacteria (AAB) have important roles in food and beverage production, as well as in the bioproduction of industrial chemicals. In recent years, there have been major advances in understanding their taxonomy, molecular biology, and physiology, and in methods for their isolation and identification. AAB are obligate aerobes that oxidize sugars, sugar alcohols, and ethanol with the production of acetic acid as the major end product. This special type of metabolism differentiates them from all other bacteria. Recently, the AAB taxonomy has been strongly rearranged as new techniques using 16S rRNA sequence analysis have been introduced. Currently, the AAB are classified in ten genera in the family Acetobacteriaceae. AAB can not only play a positive role in the production of selected foods and beverages, but they can also spoil other foods and beverages. AAB occur in sugar- and alcohol-enriched environments. The difficulty of cultivation of AAB on semisolid media in the past resulted in poor knowledge of the species present in industrial processes. The first step of acetic acid production is the conversion of ethanol from a carbohydrate carried out by yeasts, and the second step is the oxidation of ethanol to acetic acid carried out by AAB. Vinegar is traditionally the product of acetous fermentation of natural alcoholic substrates. Depending on the substrate, vinegars can be classified as fruit, starch, or spirit substrate vinegars. Although a variety of bacteria can produce acetic acid, mostly members of Acetobacter, Gluconacetobacter, and Gluconobacter are used commercially. Industrial vinegar manufacturing processes fall into three main categories: slow processes, quick processes, and submerged processes. AAB also play an important role in cocoa production, which represents a significant means of income for some countries. Microbial cellulose, produced by AAB, possesses some excellent physical properties and has potential for many applications. Other products of biotransformations by AAB or their enzymes include 2-keto-L-gulonic acid, which is used for the production of vitamin C; D-tagatose, which is used as a bulking agent in food and a noncalorific sweetener; and shikimate, which is a key intermediate for a large number of antibiotics. Recently, for the first time, a pathogenic acetic acid bacterium was described, representing the newest and tenth genus of AAB.

Nucleic acid techniques in bacterial systematics and identification

Systematics and identification play central roles in any discipline of microbiology. The current prokaryotic taxonomic framework as proposed in Bergey's Manual of Systematic Bacteriology is mainly based on small subunit rRNA data. Alternative markers representing the conserved core of the prokaryotic genomes roughly support rRNA based phylogenetic inference. Consequently, many of the nucleic acid based techniques for identification target these molecules: i.e. comparative sequencing, specific probing, diagnostic PCR, and pattern techniques. For studies at species and lower taxonomic ranks, however, alternative less conserved targets have to be chosen. An overview of commonly used targets and methods for identification or differentiation is given below.

Validation of the (GTG)(5)-rep-PCR fingerprinting technique for rapid classification and identification of acetic acid bacteria, with a focus on isolates from Ghanaian fermented cocoa beans

Amplification of repetitive bacterial DNA elements through the polymerase chain reaction (rep-PCR fingerprinting) using the (GTG)(5) primer, referred to as (GTG)(5)-PCR fingerprinting, was found a promising genotypic tool for rapid and reliable speciation of acetic acid bacteria (AAB). The method was evaluated with 64 AAB reference strains, including 31 type strains, and 132 isolates from Ghanaian, fermented cocoa beans, and was validated with DNA:DNA hybridization data. Most reference strains, except for example all Acetobacter indonesiensis strains and Gluconacetobacter liquefaciens LMG 1509, grouped according to their species designation, indicating the usefulness of this technique for identification to the species level. Moreover, exclusive patterns were obtained for most strains, suggesting that the technique can also be used for characterization below species level or typing of AAB strains. The (GTG)(5)-PCR fingerprinting allowed us to differentiate four major clusters among the fermented cocoa bean isolates, namely A. pasteurianus (cluster I, 100 isolates), A. syzygii- or A. lovaniensis-like (cluster II, 23 isolates), and A. tropicalis-like (clusters III and IV containing 4 and 5 isolates, respectively). A. syzygii-like and A. tropicalis-like strains from cocoa bean fermentations were reported for the first time. Validation of the method and indications for reclassifications of AAB species and existence of new Acetobacter species were obtained through 16S rRNA sequencing analyses and DNA:DNA hybridizations. Reclassifications refer to A. aceti LMG 1531, Ga. xylinus LMG 1518, and Ga. xylinus subsp. sucrofermentans LMG 18788(T).

Dynamics and biodiversity of populations of lactic acid bacteria and acetic acid bacteria involved in spontaneous heap fermentation of cocoa beans in Ghana

The Ghanaian cocoa bean heap fermentation process was studied through a multiphasic approach, encompassing both microbiological and metabolite target analyses. A culture-dependent (plating and incubation, followed by repetitive-sequence-based PCR analyses of picked-up colonies) and culture-independent (denaturing gradient gel electrophoresis [DGGE] of 16S rRNA gene amplicons, PCR-DGGE) approach revealed a limited biodiversity and targeted population dynamics of both lactic acid bacteria (LAB) and acetic acid bacteria (AAB) during fermentation. Four main clusters were identified among the LAB isolated: Lactobacillus plantarum, Lactobacillus fermentum, Leuconostoc pseudomesenteroides, and Enterococcus casseliflavus. Other taxa encompassed, for instance, Weissella. Only four clusters were found among the AAB identified: Acetobacter pasteurianus, Acetobacter syzygii-like bacteria, and two small clusters of Acetobacter tropicalis-like bacteria. Particular strains of L. plantarum, L. fermentum, and A. pasteurianus, originating from the environment, were well adapted to the environmental conditions prevailing during Ghanaian cocoa bean heap fermentation and apparently played a significant role in the cocoa bean fermentation process. Yeasts produced ethanol from sugars, and LAB produced lactic acid, acetic acid, ethanol, and mannitol from sugars and/or citrate. Whereas L. plantarum strains were abundant in the beginning of the fermentation, L. fermentum strains converted fructose into mannitol upon prolonged fermentation. A. pasteurianus grew on ethanol, mannitol, and lactate and converted ethanol into acetic acid. A newly proposed Weissella sp., referred to as "Weissella ghanaensis," was detected through PCR-DGGE analysis in some of the fermentations and was only occasionally picked up through culture-based isolation. Two new species of Acetobacter were found as well, namely, the species tentatively named "Acetobacter senegalensis" (A. tropicalis-like) and "Acetobacter ghanaensis" (A. syzygii-like).