Identification, isolation and quantification of representative bacteria from fermented cassava dough using an integrated approach of culture-dependent and culture-independent methods

Exploring microbial diversity in Kermanshah province's Kermanshahi oil through DGGE and sequencing analysis

BACKGROUND

Ghee, known as "roghane heiwâni," or "Kermanshahi oil" is a traditional fermented butter-like product highly esteemed for its nutritional value. Ghee is prepared using traditional methods and has substantial potential as a reservoir of probiotic microorganisms. Previous research delved into isolating and identifying lactic acid bacteria (LAB) in Kermanshahi through culture and PCR sequencing. This study seeks to elucidate the microbial profiles and diversity within Kermanshahi using culture, Denaturing Gradient Gel Electrophoresis (DGGE), and sequencing methodologies.

METHODS

Twenty samples of Kermanshahi oil were meticulously gathered from diverse locales across Kermanshah province. These samples were cultivated under specialized conditions in MRS and M17 environments spanning 24 to 72 h. Following DNA extraction, amplification of the 16SrRNA gene sequences was performed, culminating in sequencing for conclusive identification of the isolates. Furthermore, the DGGE technique was directly employed to separate and identify various species present in the oil samples utilizing bioinformatics software.

RESULTS

Sequencing outcomes revealed a diverse array of microorganisms among the isolates, with Lactobacillus constituting 43%, Streptococcus comprising 27.6%, Enterococcus at 4.61%, and yeasts at 7.6%. Other species exhibited lower frequencies, encompassing Rhizobium, Bacillus coagulans, and Staphylococcus hominis.

CONCLUSIONS

The isolation of a diverse spectrum of probiotic microorganisms underscores their potential utility in the realm of industrial dairy product production. These findings allude to the possibility of integrating these valuable microorganisms, which have historically been associated with traditional products, into the contemporary dairy industry. As consumer interest in probiotic-enriched products surges, the insights gained from this study pave the way for harnessing the benefits of Kermanshahi-derived probiotics.

Analysis of bacterial communities of three cassava-based traditionally fermented Nigerian foods (abacha, fufu and garri)

Globally, cassava is an important food crop that contributes significantly to food security. In Nigeria, cassava can be traditionally processed into abacha (fermented strips), fufu (submerged-fermented porridge) and garri (solid-state fermented farinated granules) for human consumption. Despite the widespread consumption of these foods, there is a major knowledge gap in understanding their core bacterial diversity. This study, therefore, applied next-generation sequencing of 16S rRNA gene to delineate the bacterial diversity in abacha, fufu and garri. Amplicon sequence variants belonging to nine phyla were present in the three foods. Firmicutes dominated the bacterial community of abacha and fufu, whereas, Proteobacteria was the dominant phylum in garri. At genus level taxa, Lactococcus, Lysinibacillus and Pseudomonas dominated the bacterial community in abacha, fufu and garri, respectively. Other dominant phylotypes reported in the foods belonged to Bacillus, Clostridium sensu stricto (cluster 1), Cupriavidus, Enterobacter, Sphingomonas and Staphylococcus. To the best of our knowledge, Clostridium sensu stricto cluster 1 and Lysinibacillus in fufu, and Brevundimonas, Cupriavidus, Sphingomonas and Strenotrophomomas in garri are reported for the first time. Although some potential pathogenic genera were recorded, the foods contained potentially functional species that could be explored to improve artisanal food production, food security and safeguard consumer health.

Metataxonomic analysis of bacterial communities and mycotoxin reduction during processing of three millet varieties into ogi, a fermented cereal beverage

Ogi is a fermented cereal beverage, made primarily from maize (Zea mays) and rarely from millets. Unlike maize-based ogi, little is known about the bacterial community and mycotoxin profile during the production of millet-based ogi. Therefore, the bacterial community dynamics and mycotoxin reduction during ogi processing from three millet varieties were investigated using next-generation sequencing of the 16S rRNA gene and liquid chromatography-tandem mass spectrometry, respectively. A total of 1163 amplicon sequence variants (ASVs) were obtained, with ASV diversity across time intervals influenced by processing stage and millet variety. ASV distribution among samples suggested that the souring stage was more influenced by millet variety than the steeping stage, and that souring may be crucial for the quality attributes of the ogi. Furthermore, bacterial community structure during steeping and souring was significantly differentiated (PERMANOVA, P < 0.05) between varieties, with close associations observed for closely-related millet varieties. Taxonomically, Firmicutes, followed by Actinobacteria, Bacteroidetes, Cyanobacteria and Proteobacteria phyla were relatively abundant (>1%). Lactic acid bacteria, such as Burkholderia-Caballeronia-Paraburkholderia, Lactobacillus, Lactococcus and Pediococcus, dominated most fermentation stages, suggesting their roles as key fermentative and functional bacteria in relation to mycotoxin reduction. About 52-100%, 58-100% and 100% reductions in mycotoxin (aflatoxins, beauvericin, citrinin, moniliformin, sterigmatocystin and zearalenone) concentrations were recorded after processing of white fonio, brown fonio and finger millet, respectively, into ogi. This study provides new knowledge of the dominant bacterial genera vital for the improvement of millet-based ogi through starter culture development and as well, elucidates the role of processing in reducing mycotoxins in millet ogi.

Shifts in Bacterial Diversity During the Spontaneous Fermentation of Maize Meal as Revealed by Targeted Amplicon Sequencing

Maize meal was allowed to undergo uncontrolled fermentation in the laboratory, in simulation of the traditional method of fermentation as practised in most African households. During the fermentation process, samples were collected daily for 11 days. Physico-chemical analysis of the fermenting slurry and metagenomics analysis of the microbial community using 16S rRNA demonstrated an interrelationship between the changes in the properties of the fermentation environment and the successional interplay of the microbial community. The first 24 h of fermentation at pH of 6.5 was characterised by the proliferation of probiotic Lactobacillus and Bifidobacterium, with their relative abundance being 40.7% and 29.9%, respectively. However, prolonged fermentation and a drop in pH from 5.3 to 3.7 caused a decline and finally an absence of these probiotic bacteria which were replaced by Clostridium spp. with a relative abundance of between 97% and 99% from day 5 to day 11. This study demonstrated that prolonged fermentation of maize meal is not ideally suited for the proliferation of probiotic nutritionally beneficial bacteria.

Characterization of Pediococcus acidilactici PFC69 and Lactococcus lactis PFC77 Bacteriocins and Their Antimicrobial Activities in Tarhana Fermentation

Tarhana is a traditional cereal product fermented by lactic acid bacteria (LAB) and yeast strains that has gained special interest recently as an infant nutrition. Tarhana contains wheat flour, yogurt, and various vegetables that might create a microbiological toxicological risk, especially for Bacillus cereus and Staphylococcus aureus. In this study, characterization of the metabolites responsible for antibacterial activity of Pediococcus acidilactici PFC69 and Lactococcus lactis PFC77 strains obtained from tarhana was performed, and antibacterial effects were detected against B. cereus ATCC 11778 and S. aureus ATCC 29213 during the fermentation. A total of 12,800 AU/mL antibacterial activity was observed for the supernatants of the PFC69 and PFC77 strains that were found to be stable at high temperature and in low pH conditions and sensitive to proteases, suggesting the antimicrobial metabolite is a bacteriocin. These bacteriocins were further purified and their molecular sizes were determined as 4.5 and 3.5 kDa, respectively. Importantly, inoculation of PFC69 and PFC77 to tarhana dough significantly decreased B. cereus ATCC 11778 and S. aureus ATCC 29213 amounts from the fifth day of fermentation compared to the control dough samples. P. acidilactici PFC69 and L. lactis PFC77 strains were concluded as bioprotective cultures for tarhana and these strains were offered for other cereal-based fermentations.

Microbiological characterization of traditional dough fermentation starter (Jiaozi) for steamed bread making by culture-dependent and culture-independent methods

In this study, the microbial composition of two types of Jiaozi (a dough fermentation starter in making steamed bread) was investigated using both culture-dependent and culture-independent (PCR-DGGE) methods. The numbers of the cultivable bacteria on MRS at 30°C and yeast on YPD at 28°C in the maize flour Jiaozi (MFJ) were 9.21±0.16 Log CFU/g and 9.18±0.05 Log CFU/g, respectively, which were higher than that in the rice flour Jiaozi (RFJ) (P<0.05). A total of 140 bacteria and 124 yeasts were isolated and identified on the basis of the sequences of their 16S rRNA gene and ITS region. The culture-dependent method showed that Acetobacter tropicalis and Enterococcus durans were the predominant bacteria strains in MFJ, and accounted for 45.7% and 25.7% of the bacteria, and Lactobacillus plantarum and Pediococcus pentosaceus represented 12.8% and 8.6%. In the RFJ sample, the most prominent isolate was P. pentosaceus (38.6%), followed by L. plantarum (24.3%), A. tropicalis (22.8%), and E. durans (5.7%). P. pentosaceus and L. plantarum were also detected in both starters by PCR-DGGE, while some bacteria species such as A. tropicalis and E. durans, recovered as pure cultures, were not detected by direct PCR-DGGE. On the other hand, Lactobacillus brevis, Weissella sp. and Lactobacillus alimentarius detected by PCR-DGGE were not recovered in any of the media and conditions used. In the MFJ sample, the isolated main yeast species were identified as Wickerhamomyces anomalus (67.2%), Saccharomyces cerevisiae (27.9%) and Torulaspora delbrueckii (4.9%). In addition to S. cerevisiae (42.9%), W. anomalus (27.0%) and T. delbrueckii (7.9%), Saccharomycopsis fibuligera was also identified as the predominant isolate in RFJ samples and accounted for 22.2%. PCR-DGGE also indicated the presence of W. anomalus and S. cerevisiae in both MFJ and RFJ starters and S. fibuligera was also detected in RFJ, but T. delbrueckii was not detected in both samples.

The role of abiotic environmental conditions and herbivory in shaping bacterial community composition in floral nectar

Identifying the processes that drive community assembly has long been a central theme in ecology. For microorganisms, a traditional prevailing hypothesis states that “everything is everywhere, but the environment selects”. Although the bacterial community in floral nectar may be affected by both atmosphere (air-borne bacteria) and animals as dispersal vectors, the environmental and geographic factors that shape microbial communities in floral nectar are unknown. We studied culturable bacterial communities in Asphodelus aestivus floral nectar and in its typical herbivorous bug Capsodes infuscatus, along an aridity gradient. Bacteria were sampled from floral nectar and bugs at four sites, spanning a geographical range of 200 km from Mediterranean to semi-arid conditions, under open and bagged flower treatments. In agreement with the niche assembly hypothesis, the differences in bacterial community compositions were explained by differences in abiotic environmental conditions. These results suggest that microbial model systems are useful for addressing macro-ecological questions. In addition, similar bacterial communities were found in the nectar and on the surface of the bugs that were documented visiting the flowers. These similarities imply that floral nectar bacteria dispersal is shaped not only by air borne bacteria and nectar consumers as previously reported, but also by visiting vectors like the mirid bugs.

The dominant microbial community associated with fermentation of Obushera (sorghum and millet beverages) determined by culture-dependent and culture-independent methods

Obushera includes four fermented cereal beverages from Uganda namely: Obutoko, Enturire, Ekitiribita and Obuteire, whose microbial diversity has not hitherto been fully investigated. Knowledge of the microbial diversity and dynamics in these products is crucial for understanding their safety and development of appropriate starter cultures for controlled industrial processing. Culture-dependent and culture-independent techniques including denaturating gradient gel electrophoresis (DGGE) and mixed DNA sequencing of polymerase chain reaction (PCR) amplified ribosomal RNA genes were used to study the bacteria and yeast diversity of Obushera. The pH dropped from 6.0-4.6 to 3.5-4.0 within 1-2 days for Obutoko, Enturire and Obuteire whereas that of Ekitiribita decreased to 4.4 after 4 days. Counts of lactic acid bacteria (LAB) increased from 5.0 to 11.0 log cfug(-1) and yeasts increased from 3.4 to 7.1 log cfug(-1) while coliform counts decreased from 2.0 to <1 log cfug(-1) during four days of fermentation. LAB and yeast isolates were identified by rRNA gene sequence analysis. LAB isolates included: Enterococcus spp., Lactobacillus (Lb.) plantarum, Lb. fermentum, Lb. delbrueckii, Lactococcus lactis, Leuconostoc lactis, Streptococcus (S.) infantarius subsp. infantarius, Pediococcus pentosaceus and Weisella (W.) confusa. DGGE indicated predominance of S. gallolyticus, S. infantarius subsp. infantarius, Lb. fermentum, Lb. delbrueckii, W. confusa, Lb. reuteri, Fructobacillus spp., L. lactis and L. lactis. Yeast isolates included Clavispora lusitaniae, Cyberlindnera fabianii, Issatchenkia orientalis and Saccharomyces cerevisiae. DGGE indicated predominance of S. cerevisiae in Obutoko, Enturire and Obuteire and also detected Pichia spp. and I. orientalis in Obutoko. Obushera produced in the laboratory was initially dominated by Enterobacteriaceae and later by Lactococcus spp. Enterobacteriaceae and Bacillus spp. were also detected in Ekitiribita. Development of starters for Obushera may require combinations of LAB and S. cerevisiae for Obutoko, Enturire and Obuteire and LAB for Ekitiribita.

Bacterial diversity and spoilage-related microbiota associated with freshly prepared chicken products under aerobic conditions at 4°C

This study analyzed the bacterial diversity and spoilage-related microbiota associated with freshly prepared chicken products stored aerobically at 4°C, using "bone and chicken string," a product popular in the People's Republic of China, as the study subject. Samples collected from three different factories were tray packaged with cling film and stored at 4°C. Bacterial diversity and dominant bacteria were analyzed using PCR amplification and denaturing gradient gel electrophoresis. Combined with selective cultivation of the dominant bacteria and correlation analysis, the dominant spoilage microbiota was determined. The results showed that bacterial diversity varied with different manufacturers. Such bacteria as Acinetobacter sp., Carnobacterium sp., Rahnella sp., Pseudomonas sp., Brochothrix sp., and Weissella sp. were detected in freshly prepared chicken products during storage. And Carnobacterium sp., Pseudomonas sp., and Brochothrix sp. bacteria were the common dominant spoilage bacteria groups in most freshly prepared chicken products from different factories. Carnobacterium was, for the first time, shown to be an important contributor to the spoilage-related microflora of freshly prepared chicken products stored aerobically under refrigeration. Our work shows the bacterial diversity and dominant spoilage microbiota of freshly prepared chicken products stored aerobically under refrigeration.

Microbiological and physicochemical characterisation of caxiri, an alcoholic beverage produced by the indigenous Juruna people of Brazil

Caxiri is a traditional fermented alcoholic beverage produced from cassava and sweet potatoes by the indigenous Juruna or Yudjá people in Brazil. Our results showed that caxiri fermentation is invariably associated with the following: (i) an increase in the total microbial population, with yeast being the largest group detected; (ii) a decrease in reducing sugars, malic, tartaric, succinic, oxalic and propionic acid; and (iii) a final product characterised by a high content of ethanol and a high concentration of lactic acid. The microbial community dynamics were investigated by culture-based and culture-independent approaches. Fermentation was assisted by a complex microbial community that changed in structure and composition during the fermentative process. The bacterial population ranged from 3.05 to 5.33 log/mL, and the yeast population varied from 3.27 log CFU/mL to 7.34 log CFU/mL, showing that yeasts dominated the fermentation process after 48 h. A total of 343 colonies of bacteria and 205 colonies of yeasts were isolated and initially grouped by Amplified Ribosomal DNA Restriction Analysis (ARDRA) and by biochemical features. Phylogenetic analysis of the 16S rRNA gene sequences of representative isolates showed that the bacteria were mainly represented by endospore-forming low-G+C content Gram-positive bacilli (Bacillus spp.; 61.5% of the isolates), with Bacillus pumilus, Bacillus spp. (Bacillus cereus group), and Bacillus subtilis being the main species identified. The species Sphingomonas sp. and Pediococcus acidilactici were also found. The dominant yeast identified was Saccharomyces cerevisiae. Rhodotorula mucilaginosa, Pichia membranifaciens, Pichia guilliermondii and Cryptococcus luteolus were also found. According to the Polymerase Chain Reaction and Denaturing Gradient Gel Electrophoresis (PCR-DGGE) analysis, the microbial communities present during fermentation were probably from the raw materials, ambient or present on the utensils used during beverage preparation. The results indicated the necessity to combine both culture-dependent and culture-independent methods for a better description of the microbial communities in indigenous starch fermentations. Also, pH values decreased from 4.76 to 3.15 during fermentation. The ethanol concentration was 83.9 g/L and lactic acid reached 27.89 g/L by the end of the fermentation process.

Soil dissipation of juvenile hormone analog insecticide pyriproxyfen and its effect on the bacterial community

This investigation was undertaken to examine the dissipation rate of pyriproxyfen as well as the change in the soil bacterial community. Residues of pyriproxyfen were measured using high performance liquid chromatography (HPLC) and the changes in bacterial community were determined by comparing the 16S rDNA bands on patterns by denaturing gradient gel electrophoresis (DGGE). The dissipation of pyriproxyfen was affected by both the concentration applied and incubation temperature. Lower concentrations (1 mg Kg(-1)) and higher incubation temperatures (30 and 40°C) showed more rapid dissipation rates. The population of microbial community decreased rapidly after incubation with 10 mg Kg(-1) of pyriproxyfen for 91 days, indicating the toxicity of pyriproxyfen toward bacterial communities in a closed soil ecosystem. Lower concentrations of pyriproxyfen showed less toxicity toward the microbial community. From cluster analysis, the structure of the bacterial community showed roughly a 60 % similarity throughout the experiment period in the control experiment, indicating the stability within soil microbiota without chemical agitation. However, the similarity was lower than 50 % both in the one and 10 mg Kg(-1) of insecticide pyriproxyfen spiked experiment, indicating the soil bacterial community changed after the insecticide pyriproxyfen was applied.

Diversity and dynamics of bacterial populations during spontaneous sorghum fermentations used to produce ting, a South African food

Ting is a spontaneously fermented sorghum food that is popular for its sour taste and unique flavour. Insight of the microbial diversity and population dynamics during sorghum fermentations is an essential component of the development of starter cultures for commercial production of ting. In this study, bacterial populations associated with spontaneous sorghum fermentations were examined using a culture-independent strategy based on denaturing gradient gel electrophoresis and sequence analysis of V3-16S rRNA gene amplicons, and a culture-dependent strategy using conventional isolation based on culturing followed by 16S rRNA and/or pheS gene sequence analysis. The entire fermentation process was monitored over a 54 h period and two phases were observed with respect to pH evolution and microbial succession. The first phase of the process (0-6h) was characterized by relatively high pH conditions and the presence of Enterococcus mundtii, albeit that this species was only detected with the culture-dependent approach. The second phase of the fermentation process (12-54 h) was characterized by increased acidity and the predominance of a broader range of lactic acid bacteria, including Lactococcus lactis, Lactobacillus fermentum, Lactobacillus plantarum, Lactobacillus rhamnosus, Weissella cibaria, Enterococcus faecalis, and a close relative of Lactobacillus curvatus, as well as some members of the Enterobacteriaceae family. The Lb. curvatus-like species was only detected with PCR-DGGE, while the majority of the other species was only detected using the culture-dependent approach. These findings highlighted the fact that a combination of both approaches was essential in revealing the microbial diversity and dynamics during spontaneous sorghum fermentations.

Soil bacterial communities in constructed wetlands treated with swine wastewater using PCR-DGGE technique

Marsh-pond-marsh (MPM) constructed wetlands were designed for the treatment of swine wastewater. The goal of this study was to characterize bacterial communities in these wetlands and determine the nutrient removal from influent to effluent. Surface soil samples were collected and analyzed by culture-dependent and culture-independent techniques. The results showed that the bacterial colony forming units (CFU) and the average concentrations of total nitrogen, NH(4)(+), total phosphorous (TP) and PO(4)(3-) from the influent to the effluent decreased. The NH(4)(+) and the PO(4)(3-) concentrations showed the most dramatic changes, with decreases of 39.97% and 16.92%, respectively. Data of culture-independent samples produced by using PCR-denaturing gradient gel electrophoresis (DGGE) technique showed that the Shannon diversity index and richness decreased significantly (P<0.05) from influent to effluent. Bacterium species distributions strongly correlated with the concentrations of TP, NH(4)(+) and the PO(4)(3-). Sequencing of partial 16S rRNA genes fragments revealed that the total bacterial community composition was dominated by Pseudomonas sp., Arthrobacter sp., Bacillus sp. and other soil bacteria. Anammox (anaerobic ammonium oxidation) stains were detected. Phylogenetic analysis demonstrated that some of the partial 16S rRNA gene sequences had close relationships with unculturable denitrification bacteria. The activities of these bacteria might contribute to the nutrient removal in the wetlands.

Adaptability of lactic acid bacteria and yeasts to sourdoughs prepared from cereals, pseudocereals and cassava and use of competitive strains as starters

The adaptability of lactic acid bacteria (LAB) and yeasts to sourdoughs prepared from cereals, pseudocereals and cassava was investigated using PCR-DGGE and bacteriological culture combined with rRNA gene sequence analysis. Sourdoughs were prepared either from flours of the cereals wheat, rye, oat, barley, rice, maize, and millet, or from the pseudocereals amaranth, quinoa, and buckwheat, or from cassava, using a starter consisting of various species of LAB and yeasts. Doughs were propagated until a stable microbiota was established. The dominant LAB and yeast species were Lactobacillus fermentum, Lactobacillus helveticus, Lactobacillus paralimentarius, Lactobacillus plantarum, Lactobacillus pontis, Lactobacillus spicheri, Issatchenkia orientalis and Saccharomyces cerevisiae. The proportion of the species within the microbiota varied. L. paralimentarius dominated in the pseudocereal sourdoughs, L. fermentum, L. plantarum and L. spicheri in the cassava sourdough, and L. fermentum, L. helveticus and L. pontis in the cereal sourdoughs. S. cerevisiae constituted the dominating yeast, except for quinoa sourdough, where I. orientalis also reached similar counts, and buckwheat and oat sourdoughs, where no yeasts could be detected. To assess the usefulness of competitive LAB and yeasts as starters, the fermentations were repeated using flours from rice, maize, millet and the pseudocereals, and by starting the dough fermentation with selected dominant strains. At the end of fermentation, most of starter strains belonged to the dominating microbiota. For the rice, millet and quinoa sourdoughs the species composition was similar to that of the prior fermentation, whereas in the other sourdoughs, the composition differed.

Carbon utilization profiles of bacteria colonizing the headbox water of two paper machines in a Canadian mill

Forty-one bacterial strains isolated from the headbox water of two machines in a Canadian paper mill were associated with the genera Asticcacaulis, Acidovorax, Bacillus, Exiguobacterium, Hydrogenophaga, Pseudomonas, Pseudoxanthomonas, Staphylococcus, Stenotrophomonas based on the sequence of their 16S rRNA genes. The metabolic profile of these strains were determined using Biolog EcoPlate, and the bacteria were divided into four metabolic groups. Metabolic profiles of the bacterial communities colonizing the headbox water of two paper machines was also determined weekly over a 1 year period. The only compound that was not reduced by the bacterial community was 2-hydroxybenzoic acid. Utilization frequency of the other carbon sources in the Biolog EcoPlate ranged from 3 to 100%. The metabolic profiles of the bacterial community did not vary considerably between the two paper machines. However, the metabolic profile varied among the sampling dates.

Taxonomic structure and stability of the bacterial community in belgian sourdough ecosystems as assessed by culture and population fingerprinting

A total of 39 traditional sourdoughs were sampled at 11 bakeries located throughout Belgium which were visited twice with a 1-year interval. The taxonomic structure and stability of the bacterial communities occurring in these traditional sourdoughs were assessed using both culture-dependent and culture-independent methods. A total of 1,194 potential lactic acid bacterium (LAB) isolates were tentatively grouped and identified by repetitive element sequence-based PCR, followed by sequence-based identification using 16S rRNA and pheS genes from a selection of genotypically unique LAB isolates. In parallel, all samples were analyzed by denaturing gradient gel electrophoresis (DGGE) of V3-16S rRNA gene amplicons. In addition, extensive metabolite target analysis of more than 100 different compounds was performed. Both culturing and DGGE analysis showed that the species Lactobacillus sanfranciscensis, Lactobacillus paralimentarius, Lactobacillus plantarum, and Lactobacillus pontis dominated the LAB population of Belgian type I sourdoughs. In addition, DGGE band sequence analysis demonstrated the presence of Acetobacter sp. and a member of the Erwinia/Enterobacter/Pantoea group in some samples. Overall, the culture-dependent and culture-independent approaches each exhibited intrinsic limitations in assessing bacterial LAB diversity in Belgian sourdoughs. Irrespective of the LAB biodiversity, a large majority of the sugar and amino acid metabolites were detected in all sourdough samples. Principal component-based analysis of biodiversity and metabolic data revealed only little variation among the two samples of the sourdoughs produced at the same bakery. The rare cases of instability observed could generally be linked with variations in technological parameters or differences in detection capacity between culture-dependent and culture-independent approaches. Within a sampling interval of 1 year, this study reinforces previous observations that the bakery environment rather than the type or batch of flour largely determines the development of a stable LAB population in sourdoughs.

RT-TGGE as a guide for the successful isolation of phosphonoacetate degrading bacteria

AIMS

Use of molecular techniques for the isolation of bacteria capable of phosphonoacetate mineralization as carbon, phosphorus and energy source.

METHODS AND RESULTS

RNA extracts obtained at three different stages of an enrichment selecting for phosphonoacetate degrading bacteria were reverse transcribed using 16S rRNA-specific primers, amplified and analysed by temperature gradient gel electrophoresis (TGGE). This information was used to devise a strategy for the isolation of members of the enrichment that were otherwise difficult to obtain in pure culture. We were able to pull out, in total, four out of the six main microbial cultures that were detected by TGGE. Two of the isolates belonging to Mycobacterium and Agromyces genera were for the first time shown to grow in the presence of phosphonoacetate as sole carbon, phosphorus and energy source releasing almost equimolar levels of inorganic phosphate into the culture medium, and they were shown to exhibit phosphonoacetate hydrolase activity in vitro.

CONCLUSIONS

The ubiquity of pseudomonad in degradation processes is more likely a consequence of our ignorance of bacterial requirements and physiology, rather than their possession of unique metabolic properties.

SIGNIFICANCE AND IMPACT OF THE STUDY

RT-TGGE analysis can be used to guide the successful isolation of micro-organisms difficult to obtain by culture-dependent methods alone.

Culturable psychrotrophic bacterial communities in raw milk and their proteolytic and lipolytic traits

During cold storage after milk collection, psychrotrophic bacterial populations dominate the microflora, and their extracellular enzymes, mainly proteases and lipases, contribute to the spoilage of dairy products. The diversity, dynamics, and enzymatic traits of culturable psychrotrophs in raw milk from four farms were investigated over a 10-month period. About 20% of the isolates were found to be novel species, indicating that there is still much to be learned about culturable psychrotrophs in raw milk. The psychrotrophic isolates were identified and classified in seven classes. Three classes were predominant, with high species richness (18 to 21 species per class) in different seasons of the year: Gammaproteobacteria in spring and winter, Bacilli in summer, and Actinobacteria in autumn. The four minor classes were Alphaproteobacteria, Betaproteobacteria, Flavobacteria, and Sphingobacteria. The dominant classes were found in all four dairies, although every dairy had its own unique "bacterial profile." Most but not all bacterial isolates had either lipolytic or both lipolytic and proteolytic activities. Only a few isolates showed proteolytic activity alone. The dominant genera, Pseudomonas and Acinetobacter (Gammaproteobacteria), showed mainly lipolytic activity, Microbacterium (Actinobacteria) was highly lipolytic and proteolytic, and the lactic acid bacteria (Lactococcus and Leuconostoc) displayed very minor enzymatic ability. Hence, the composition of psychrotrophic bacterial flora in raw milk has an important role in the determination of milk quality. Monitoring the dominant psychrotrophic species responsible for the production of heat-stable proteolytic and lipolytic enzymes offers a sensitive and efficient tool for maintaining better milk quality in the milk industry.

Inventory and monitoring of wine microbial consortia

The evolution of the wine microbial ecosystem is generally restricted to Saccharomyces cerevisiae and Oenococcus oeni, which are the two main agents in the transformation of grape must into wine by acting during alcoholic and malolactic fermentation, respectively. But others species like the yeast Brettanomyces bruxellensis and certain ropy strains of Pediococcus parvulus can spoil the wine. The aim of this study was to address the composition of the system more precisely, identifying other components. The advantages of the polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) approach to wine microbial ecology studies are illustrated by bacteria and yeast species identification and their monitoring at each stage of wine production. After direct DNA extraction, PCR-DGGE was used to make the most exhaustive possible inventory of bacteria and yeast species found in a wine environment. Phylogenetic neighbor-joining trees were built to illustrate microbial diversity. PCR-DGGE was also combined with population enumeration in selective media to monitor microbial changes at all stages of production. Moreover, enrichment media helped to detect the appearance of spoilage species. The genetic diversity of the wine microbial community and its dynamics during winemaking were also described. Most importantly, our study provides a better understanding of the complexity and diversity of the wine microbial consortium at all stages of the winemaking process: on grape berries, in must during fermentation, and in wine during aging. On grapes, 52 different yeast species and 40 bacteria could be identified. The diversity was dramatically reduced during winemaking then during aging. Yeast and lactic acid bacteria were also isolated from very old vintages. B. bruxellensis and O. oeni were the most frequent.

Monitoring bacterial communities in raw milk and cheese by culture-dependent and -independent 16S rRNA gene-based analyses

The diversity and dynamics of bacterial populations in Saint-Nectaire, a raw-milk, semihard cheese, were investigated using a dual culture-dependent and direct molecular approach combining single-strand conformation polymorphism (SSCP) fingerprinting and sequencing of 16S rRNA genes. The dominant clones, among 125 16S rRNA genes isolated from milk, belonged to members of the Firmicutes (58% of the total clones) affiliated mainly with the orders Clostridiales and the Lactobacillales, followed by the phyla Proteobacteria (21.6%), Actinobacteria (16.8%), and Bacteroidetes (4%). Sequencing the 16S rRNA genes of 126 milk isolates collected from four culture media revealed the presence of 36 different species showing a wider diversity in the Gammaproteobacteria phylum and Staphylococcus genus than that found among clones. In cheese, a total of 21 species were obtained from 170 isolates, with dominant species belonging to the Lactobacillales and subdominant species affiliated with the Actinobacteria, Bacteroidetes (Chryseobacterium sp.), or Gammaproteobacteria (Stenotrophomonas sp.). Fingerprinting DNA isolated from milk by SSCP analysis yielded complex patterns, whereas analyzing DNA isolated from cheese resulted in patterns composed of a single peak which corresponded to that of lactic acid bacteria. SSCP fingerprinting of mixtures of all colonies harvested from plate count agar supplemented with crystal violet and vancomycin showed good potential for monitoring the subdominant Proteobacteria and Bacteroidetes (Flavobacteria) organisms in milk and cheese. Likewise, analyzing culturable subcommunities from cheese-ripening bacterial medium permitted assessment of the diversity of halotolerant Actinobacteria and Staphylococcus organisms. Direct and culture-dependent approaches produced complementary information, thus generating a more accurate view of milk and cheese microbial ecology.

Quantification of Lactobacillus in fermented milk by multivariate image analysis with least-squares support-vector machines

This paper reports an approach for quantification of Lactobacillus in fermented milk, grown in a selective medium (MRS agar), by use of digital colour images of Petri plates easily obtained by use of a flatbed scanner. A one-dimensional data vector was formed to characterize each digital image on the basis of the frequency-distribution curves of the red (R), green (G), and blue (B) colour values, and quantities derived from them, for example lightness (L), relative red (RR), relative green (RG), and relative blue (RB). The frequency distributions of hue, saturation, and intensity (HSI) were also calculated and included in the data vector used to describe each image. Multivariate non-linear modelling using the least-squares support vector machine (LS-SVM) and a linear model based on PLS regression were developed to relate the microbiological count and the frequency vector. Feasibly models were developed using the LS-SVM and errors were below than 10% for Lactobacillus quantification, indicating the proposed approach can be used for automatic counting of colonies.

Culture-independent analysis of the microbial composition of the African traditional fermented foods poto poto and dégué by using three different DNA extraction methods

The microbial composition of the traditional fermented foods poto poto (a maize dough from the Rep. of Congo) and dégué (a millet dough from Burkina Faso) was studied by a culture-independent approach using TTGE to separate the amplified target V3 region of the 16S rRNA gene from total microbial community, followed by DNA sequencing and homology search. Three different extraction methods were used. Guanidium thiocyanate-based DNA extraction provided better performance regarding purity and DNA yield, allowing the detection of a higher number of DNA bands by TTGE in poto poto. By contrast, all three methods yielded similar results for dégué samples, indicating that the performance of the DNA extraction method largely depends on the food composition. Sequencing of DNA bands from TTGE gels corresponding to poto poto samples revealed the presence of Lactobacillus gasseri, Enterococcus sp., Escherichia coli, Lactobacillus plantarum/paraplantarum, Lactobacillus acidophilus, Lactobacillus delbrueckii, Bacillus sp., Lactobacillus reuteri and Lactobacillus casei. The following bacteria were identified in dégué: L. gasseri, Enterococcus sp., E. coli, Lactobacillus fermentum, Lactobacillus brevis, and L. casei.

Changes in the spoilage-related microbiota of beef during refrigerated storage under different packaging conditions

The microbial spoilage of beef was monitored during storage at 5 degrees C under three different conditions of modified-atmosphere packaging (MAP): (i) air (MAP1), (ii) 60% O2 and 40% CO2 (MAP2), and (iii) 20% O2 and 40% CO2 (MAP3). Pseudomonas, Enterobacteriaceae, Brochothrix thermosphacta, and lactic acid bacteria were monitored by viable counts and PCR-denaturing gradient gel electrophoresis (DGGE) analysis during 14 days of storage. Moreover, headspace gas composition, weight loss, and beef color change were also determined at each sampling time. Overall, MAP2 was shown to have the best protective effect, keeping the microbial loads and color change to acceptable levels in the first 7 days of refrigerated storage. The microbial colonies from the plate counts of each microbial group were identified by PCR-DGGE of the variable V6-V8 region of the 16S rRNA gene. Thirteen different genera and at least 17 different species were identified after sequencing of DGGE fragments that showed a wide diversity of spoilage-related bacteria taking turns during beef storage in the function of the packaging conditions. The countable species for each spoilage-related microbial group were different according to packaging conditions and times of storage. In fact, the DGGE profiles displayed significant changes during time and depending on the initial atmosphere used. The spoilage occurred between 7 and 14 days of storage, and the microbial species found in the spoiled meat varied according to the packaging conditions. Rahnella aquatilis, Rahnella spp., Pseudomonas spp., and Carnobacterium divergens were identified as acting during beef storage in air (MAP1). Pseudomonas spp. and Lactobacillus sakei were found in beef stored under MAP conditions with high oxygen content (MAP2), while Rahnella spp. and L. sakei were the main species found during storage using MAP3. The identification of the spoilage-related microbiota by molecular methods can help in the effective establishment of storage conditions for fresh meat.

Microbiological study of lactic acid fermentation of Caper berries by molecular and culture-dependent methods

Fermentation of capers (the fruits of Capparis sp.) was studied by molecular and culture-independent methods. A lactic acid fermentation occurred following immersion of caper berries in water, resulting in fast acidification and development of the organoleptic properties typical of this fermented food. A collection of 133 isolates obtained at different times of fermentation was reduced to 75 after randomly amplified polymorphic DNA (RAPD)-PCR analysis. Isolates were identified by PCR or 16S rRNA gene sequencing as Lactobacillus plantarum (37 isolates), Lactobacillus paraplantarum (1 isolate), Lactobacillus pentosus (5 isolates), Lactobacillus brevis (9 isolates), Lactobacillus fermentum (6 isolates), Pediococcus pentosaceus (14 isolates), Pediococcus acidilactici (1 isolate), and Enterococcus faecium (2 isolates). Cluster analysis of RAPD-PCR patterns revealed a high degree of diversity among lactobacilli (with four major groups and five subgroups), while pediococci clustered in two closely related groups. A culture-independent analysis of fermentation samples by temporal temperature gradient electrophoresis (TTGE) also indicated that L. plantarum is the predominant species in this fermentation, in agreement with culture-dependent results. The distribution of L. brevis and L. fermentum in samples was also determined by TTGE, but identification of Pediococcus at the species level was not possible. TTGE also allowed a more precise estimation of the distribution of E. faecium, and the detection of Enterococcus casseliflavus (which was not revealed by the culture-dependent analysis). Results from this study indicate that complementary data from molecular and culture-dependent analysis provide a more accurate determination of the microbial community dynamics during caper fermentation.