PCR-DGGE fingerprinting: novel strategies for detection of microbes in food

Comprehensive survey of kombucha microbial communities of diverse origins and fermentation practices

Kombucha is a unique, naturally fermented sweetened tea produced for thousands of years, relying on a symbiotic microbiota in a floating biofilm, used for successive fermentations. The microbial communities consist of yeast and bacteria species, distributed across two phases: the liquid and the biofilm fractions. In the fermentation of kombucha, various starters of different shapes and origins are used, and there are multiple brewing practices. By metabarcoding, we explored here the consortia and their evolution from a collection of 23 starters coming from various origins summarizing the diversity of kombucha fermentation processes. A core microbiota of yeast and bacteria has been identified in these diverse kombucha symbiotic consortia, revealing consistent core taxa across symbiotic consortium of bacteria and yeasts from different starters. The common core consists of five taxa: two yeast species from the Brettanomyces genus (B. bruxellensis and B. anomalus) and bacterial taxa Komagataeibacter, Lactobacillus, and Acetobacteraceae, including the Acetobacter genus. The distribution of yeast and bacteria core taxa differs between the liquid and biofilm fractions, as well as between the "mother" and "daughter" biofilms used in successive fermentations. In terms of microbial composition, the diversity is relatively low, with only a few accessory taxa identified. Overall, our study provides a deeper understanding of the core and accessory taxa involved in kombucha fermentation.

Analysis of Microbial Diversity Dominating Nitrite Enzymatic Degradation and Acidic Degradation in the Fermentation Broth of Northeast Sauerkraut

Nitrite hazard is an important food safety issue in the production process of Chinese Northeastern sauerkraut, but this nitrite can be eliminated through microbial enzymatic degradation and acidic degradation as fermentation progresses. Therefore, analyzing the microbial diversity that dominates nitrite degradation in Chinese Northeastern sauerkraut can provide a reference for its safe production. In this study, based on the dynamic monitoring of nitrite concentration, pH, and the abundance of nitrite reductase genes (nirK and nirS) and the application of high-throughput sequencing technology and various statistical analysis methods, the microbial groups associated with nitrite enzymatic degradation and acidic degradation in Northeast sauerkraut fermentation broth were analyzed. During the nitrite peak period of Northeast sauerkraut fermentation broth, the nitrite concentration reached 32.15 mg/kg, the pH was 4.7, and the abundances of the nitrite reductase genes nirK and nirS were 3.0 × 104 and 4.9 × 104 copies/μL, respectively. At this stage, nitrite degradation was likely dominated by enzymatic activities. Microbial phyla such as Bacteroidetes (38.8%), Proteobacteria (19.2%), and the archaeal phylum Euryarchaeota (1.1%) showed strong correlations with nitrite. Among the genera within these three phyla, Chryseobacterium, Elizabethkingia, and Aeromonas exhibited significant differences in abundance compared to the late fermentation stage and were identified as the primary microbial groups likely driving the enzymatic degradation. During the nitrite degradation period, the nitrite concentration decreased to 0.04 mg/kg, the pH dropped to 3.6, and the abundances of nirK and nirS genes were reduced to 1.0 × 103 copies/μL. At this stage, the nitrite degradation was primarily driven by acid activity. The bacterial phylum Firmicutes (99%) exhibited a strong correlation with pH. Within this phylum, the genus Lactobacillus, which showed significant differences in abundance compared to the early fermentation stage, was identified as the primary microbial group indirectly contributing to acidic degradation. This study provides guidance for the isolation of food-grade prokaryotic microbial strains capable of nitrite degradation. Additionally, the findings offer a methodological reference for conducting future research on nitrite-degrading microorganisms in fermented vegetable broths.

Discoveries by the genome profiling, symbolic powers of non-next generation sequencing methods

Next-generation sequencing and other sequencing approaches have made significant progress in DNA analysis. However, there are indispensable advantages in the nonsequencing methods. They have their justifications such as being speedy, cost-effective, multi-applicable, and straightforward. Among the nonsequencing methods, the genome profiling method is worthy of reviewing because of its high potential. This article first reviews its basic properties, highlights the key concept of species identification dots (spiddos), and then summarizes its various applications.

Unexplored microbial diversity from 2,500 food metagenomes and links with the human microbiome

Complex microbiomes are part of the food we eat and influence our own microbiome, but their diversity remains largely unexplored. Here, we generated the open access curatedFoodMetagenomicData (cFMD) resource by integrating 1,950 newly sequenced and 583 public food metagenomes. We produced 10,899 metagenome-assembled genomes spanning 1,036 prokaryotic and 108 eukaryotic species-level genome bins (SGBs), including 320 previously undescribed taxa. Food SGBs displayed significant microbial diversity within and between food categories. Extension to >20,000 human metagenomes revealed that food SGBs accounted on average for 3% of the adult gut microbiome. Strain-level analysis highlighted potential instances of food-to-gut transmission and intestinal colonization (e.g., Lacticaseibacillus paracasei) as well as SGBs with divergent genomic structures in food and humans (e.g., Streptococcus gallolyticus and Limosilactobabillus mucosae). The cFMD expands our knowledge on food microbiomes, their role in shaping the human microbiome, and supports future uses of metagenomics for food quality, safety, and authentication.

Microbiological Evaluation of Two Mexican Artisanal Cheeses: Analysis of Foodborne Pathogenic Bacteria in Cotija Cheese and Bola de Ocosingo Cheese by qPCR

Cotija and Bola de Ocosingo are artisanal ripened cheeses produced in Mexico. Both are made with raw bovine milk from free-grazing cows and with no starter cultures. Unlike culture-based techniques, molecular methods for pathogen detection in food allow a shorter turnaround time, higher detection specificity, and represent a lower microbiological risk for the analyst. In the present investigation, we analyzed 111 cheese samples (95 Cotija and 16 Bola de Ocosingo) by qPCR (TaqMan®) after an enrichment-culture step specific to each foodborne bacterium. The results showed that 100% of the samples were free of DNA from Listeria monocytogenes, Brucella spp., Escherichia coli enterotoxigenic (ETEC), and O157:H7; 9% amplified Salmonella spp. DNA; and 11.7%, Staphylococcus aureus DNA. However, the threshold cycle (Ct) values of the amplified targets ranged between 23 and 30, indicating DNA from non-viable microorganisms. Plate counts supported this assumption. In conclusion, 100% of the cheeses analyzed were safe to consume, and the enrichment step before DNA extraction proved essential to discern between viable and non-viable microorganisms. Hygienic milking, milk handling, cheese manufacturing, and ripening are crucial to achieve an adequate microbiological quality of cheeses made with raw milk.

Lactic acid bacteria as an eco-friendly approach in plant production: Current state and prospects

Since the late nineteenth century, the agricultural sector has experienced a tremendous increase in chemical use in response to the growing population. Consequently, the intensive and indiscriminate use of these substances caused serious damage on several levels, including threatening human health, disrupting soil microbiota, affecting wildlife ecosystems, and causing groundwater pollution. As a solution, the application of microbial-based products presents an interesting and ecological restoration tool. The use of Plant Growth-Promoting Microbes (PGPM) affected positive production, by increasing its efficiency, reducing production costs, environmental pollution, and chemical use. Among these microbial communities, lactic acid bacteria (LAB) are considered an interesting candidate to be formulated and applied as effective microbes. Indeed, these bacteria are approved by the European Food Safety Authority (EFSA) and Food and Drug Administration (FDA) as Qualified Presumption of Safety statute and Generally Recognized as Safe for various applications. To do so, this review comes as a road map for future research, which addresses the different steps included in LAB formulation as biocontrol, bioremediation, or plant growth promoting agents from the isolation process to their field application passing by the different identification methods and their various uses. The plant application methods as well as challenges limiting their use in agriculture are also discussed.

Research progress in isolation and identification of rumen probiotics

With the increasing research on the exploitation of rumen microbial resources, rumen probiotics have attracted much attention for their positive contributions in promoting nutrient digestion, inhibiting pathogenic bacteria, and improving production performance. In the past two decades, macrogenomics has provided a rich source of new-generation probiotic candidates, but most of these "dark substances" have not been successfully cultured due to the restrictive growth conditions. However, fueled by high-throughput culture and sorting technologies, it is expected that the potential probiotics in the rumen can be exploited on a large scale, and their potential applications in medicine and agriculture can be explored. In this paper, we review and summarize the classical techniques for isolation and identification of rumen probiotics, introduce the development of droplet-based high-throughput cell culture and single-cell sequencing for microbial culture and identification, and finally introduce promising cultureomics techniques. The aim is to provide technical references for the development of related technologies and microbiological research to promote the further development of the field of rumen microbiology research.

Unravelling the genomic secrets of bacterial fish pathogens: a roadmap to aquaculture sustainability

In the field of aquaculture, bacterial pathogens pose significant challenges to fish health and production. Advancements in genomic technologies have revolutionized our understanding of bacterial fish pathogens and their interactions with their host species. This review explores the application of genomic approaches in the identification, classification, and characterization of bacterial fish pathogens. Through an extensive analysis of the literature, we have compiled valuable data on 79 bacterial fish pathogens spanning 13 different phyla, encompassing their whole genome sequences. By leveraging high-throughput sequencing techniques, researchers have gained valuable insights into the genomic makeup of these pathogens, enabling a deeper understanding of their virulence factors and mechanisms of host interaction. Furthermore, genomic approaches have facilitated the discovery of potential vaccine and drug targets, opening up new avenues for the development of effective interventions against fish pathogens. Additionally, the utilization of genomics in fish disease resistance and control in aquaculture has shown promising results, enabling the identification of genetic markers associated with disease resistance traits. This review highlights the significant contributions of genomics to the field of fish pathogen research and underscores its potential for improving disease management strategies and enhancing the sustainability of aquaculture practices.

Recent and Advanced DNA-Based Technologies for the Authentication of Probiotic, Protected Designation of Origin (PDO) and Protected Geographical Indication (PGI) Fermented Foods and Beverages

The authenticity of probiotic products and fermented foods and beverages that have the status of protected designation of origin (PDO) or geographical indication (PGI) can be assessed via numerous methods. DNA-based technologies have emerged in recent decades as valuable tools to achieve food authentication, and advanced DNA-based methods and platforms are being developed. The present review focuses on the recent and advanced DNA-based techniques for the authentication of probiotic, PDO and PGI fermented foods and beverages. Moreover, the most promising DNA-based detection tools are presented. Strain- and species-specific DNA-based markers of microorganisms used as starter cultures or (probiotic) adjuncts for the production of probiotic and fermented food and beverages have been exploited for valuable authentication in several detection methods. Among the available technologies, propidium monoazide (PMA) real-time polymerase chain reaction (PCR)-based technologies allow for the on-time quantitative detection of viable microbes. DNA-based lab-on-a-chips are promising devices that can be used for the on-site and on-time quantitative detection of microorganisms. PCR-DGGE and metagenomics, even combined with the use of PMA, are valuable tools allowing for the fingerprinting of the microbial communities, which characterize PDO and PGI fermented foods and beverages, and they are necessary for authentication besides permitting the detection of extra or mislabeled species in probiotic products. These methods, in relation to the authentication of probiotic foods and beverages, need to be used in combination with PMA, culturomics or flow cytometry to allow for the enumeration of viable microorganisms.

Yeast diversity in pit mud and related volatile compounds in fermented grains of chinese strong-flavour liquor

Chinese strong-flavour liquor is produced via a traditional solid-state fermentation strategy facilitated by live microorganisms in pit mud-based cellars. For the present analysis, pit mud samples from different spatial locations within fermentation cellars were collected, and the yeast communities therein were assessed via culture-based and denaturing gradient gel electrophoresis (DGGE) approaches. These analyses revealed significant differences in the composition of yeast communities present in different layers of pit mud. In total, 29 different yeast species were detected, and principal component analyses revealed clear differences in microbial diversity in pit mud samples taken from different cellar locations. Culture-dependent strategies similarly detected 20 different yeast species in these samples. However, while Geotrichum silvicola, Torulaspora delbrueckii, Hanseniaspora uvarum, Saturnispora silvae, Issatchenkia orientalis, Candida mucifera, Kazachstania barnettii, Cyberlindnera jadinii, Hanseniaspora spp., Alternaria tenuissima, Cryptococcus laurentii, Metschnikowia spp., and Rhodotorula dairenensis were detected via a PCR-DGGE approach, they were not detectable in culture-dependent analyses. In contrast, culture-based approaches led to the identification of Schizosaccharomyces pombe and Debaryomyces hansenii in these pit mud samples, whereas they were not detected using DGGE fingerprints profiles. An additional HS-SPME-GC-MS-based analysis of the volatile compounds present in fermented grains samples led to the identification of 66 such compounds, with the highest levels of volatile acids, esters, and alcohols being detected in fermented grains from lower layer samples. A canonical correspondence analysis (CCA) suggested they were significant correlations between pit mud yeast communities and associated volatile compounds in fermented grains.

A Comprehensive Review with Future Insights on the Processing and Safety of Fermented Fish and the Associated Changes

As an easily spoiled source of valuable proteins and lipids, fish is preserved by fermentation in many cultures. Over time, diverse types of products have been produced from fish fermentation aside from whole fish, such as fermented fish paste and sauces. The consumption of fermented fish products has been shown to improve both physical and mental health due to the composition of the products. Fermented fish products can be dried prior to the fermentation process and include various additives to enhance the flavours and aid in fermentation. At the same time, the fermentation process and its conditions play a major role in determining the quality and safety of the product as the compositions change biochemically throughout fermentation. Additionally, the necessity of certain microorganisms and challenges in avoiding harmful microbes are reviewed to further optimise fermentation conditions in the future. Although several advanced technologies have emerged to produce better quality products and easier processes, the diversity of processes, ingredients, and products of fermented fish warrants further study, especially for the sake of the consumers' health and safety. In this review, the nutritional, microbial, and sensory characteristics of fermented fish are explored to better understand the health benefits along with the safety challenges introduced by fermented fish products. An exploratory approach of the published literature was conducted to achieve the purpose of this review using numerous books and online databases, including Google Scholar, Web of Science, Scopus, ScienceDirect, and PubMed Central, with the goal of obtaining, compiling, and reconstructing information on a variety of fundamental aspects of fish fermentation. This review explores significant information from all available library databases from 1950 to 2022. This review can assist food industries involved in fermented fish commercialization to efficiently ferment and produce better quality products by easing the fermentation process without risking the health and safety of consumers.

Emulsion Polymerase Chain Reaction Coupled with Denaturing Gradient Gel Electrophoresis for Microbial Diversity Studies

Emulsion PCR-DGGE is a molecular biology technique used to amplify and analyze DNA fragments. This technique combines two processes, emulsion PCR and denaturing gradient gel electrophoresis (DGGE), to enhance the specificity and yield of the amplification process and to separate the amplified fragments based on their melting behavior. In the emulsion PCR step, a high-quality DNA template is mixed with the PCR reagents and droplet generator oil to create an oil-in-water emulsion. The emulsion is then subjected to thermal cycling to amplify the target DNA fragments. The amplified fragments are recovered from the droplets and purified to remove any impurities that may interfere with downstream applications. In the DGGE step, the purified amplicon is loaded onto a DGGE apparatus, where the DNA fragments are separated and visualized based on their melting behavior. This method allows for the concurrent amplification and separation of multiple DNA fragments, thereby enhancing the resolution and sensitivity of the analysis. It is widely used in environmental and medical microbiology research, as well as in other fields that require the identification and characterization of microorganisms, such as the study of microbial diversity in soil, water, and other natural environments, as well as in the human gut microbiome and other medical samples.

Lactobacillus plantarum and propionic acid improve the fermentation quality of high-moisture amaranth silage by altering the microbial community composition

Objective

The objective of this study was to determine the effect of Lactobacillus plantarum (L. plantarum) and propionic acid (PA) on the microbial community and fermentation performance of high-moisture amaranth silage.

Methods

Amaranth silages were rown without addition (AhGCK) as a control and with L. plantarum JYLP-002 (AhGLP) or propionic acid (AhGPA) and then were opened after 60 days of ensiling to determine the microbial community and fermentation quality.

Results

Crude protein (CP) content, lactic acid (LA) content, and lactic acid bacteria (LAB) counts were significantly higher in AhGLP and AhGPA compared with those in AhGCK (p < 0.05). In contrast, pH, acetic acid (AA) content, and yeast and aerobic bacteria counts were significantly lower in AhGLP and AhGPA compared with those in AhGCK (p < 0.05). In addition, propionic acid (PA) levels were markedly higher in AhGPA (p < 0.05). In terms of microbial communities, the silage in the additive groups showed an increased relative abundance of Lactiplantibacillus plantarum and Lentilactobacillus buchneri and a reduced relative abundance of Enterobacter cloacae and Clostridium tyrobutyricum. The abundance of Xanthomonas oryzae was significantly increased in AhGPA, but completely inhibited in the silage supplemented with L. plantarum. Spearman's correlation analysis revealed that Lentilactobacillus buchneri and Levilactobacillus brevis were positively associated with LA and negatively associated with pH. Conversely, Clostridium tyrobutyricum and Enterobacter cloacae were negatively associated with LA, but positively associated with pH and AA content. AA content was inversely correlated with Lentilactobacillus buchneri. Functional prediction analysis showed that LAB dominated the three groups of silage and the silages containing additives had improved carbohydrate and amino acid metabolism compared with the control silage; in particular, the AhGLP group had more heterotypic fermentation processes and a richer metabolic pathway. Furthermore, the epiphytic Lactiplantibacillus plantarum and Lentilactobacillus buchneri could inhibit the reproductive activity of undesirable microorganisms to a certain extent, thus slowing the spoilage process of the silage.

Conclusion

In conclusion, L. plantarum can improve fermentation characteristics by modulating the microbial community attached to high-moisture amaranth silage and will prove useful for preserving high-moisture silage.

Microbiome of rehydrated corn and sorghum grain silages treated with microbial inoculants in different fermentation periods

Due to the co-evolved intricate relationships and mutual influence between changes in the microbiome and silage fermentation quality, we explored the effects of Lactobacillus plantarum and Propionibacterium acidipropionici (Inoc1) or Lactobacillus buchneri (Inoc2) inoculants on the diversity and bacterial and fungal community succession of rehydrated corn (CG) and sorghum (SG) grains and their silages using Illumina Miseq sequencing after 0, 3, 7, 21, 90, and 360 days of fermentation. The effects of inoculants on bacterial and fungal succession differed among the grains. Lactobacillus and Weissella species were the main bacteria involved in the fermentation of rehydrated corn and sorghum grain silage. Aspergillus spp. mold was predominant in rehydrated CG fermentation, while the yeast Wickerhamomyces anomalus was the major fungus in rehydrated SG silages. The Inoc1 was more efficient than CTRL and Inoc2 in promoting the sharp growth of Lactobacillus spp. and maintaining the stability of the bacterial community during long periods of storage in both grain silages. However, the bacterial and fungal communities of rehydrated corn and sorghum grain silages did not remain stable after 360 days of storage.

The gut microbiome analysis of Anastrepha obliqua reveals inter-kingdom diversity: bacteria, fungi, and archaea

The fruit fly Anastrepha obliqua is an economically important pest. The sterile insect technique to control it involves mass production and release of sterile flies to reduce the reproduction of the wild population. As noted in different Tephritidae, the performance of sterile males may be affected by the assimilation of nutrients under mass-rearing conditions. In the wild, the fly's life cycle suggests the acquisition of different organisms that could modulate its fitness and physiology. For A. obliqua, there is no information regarding microorganisms other than bacteria. This study analyzed bacteria, fungal, and archaea communities in the A. obliqua gut through denaturing gradient gel electrophoresis (DGGE) profiles of 16S (using a different set of primers for bacteria and archaea) and 18S ribosomal DNA markers. We found that wild flies presented higher microbial diversity related to fructose assimilation than laboratory species, suggesting that microorganisms have led to a specialized metabolism to process nutrients associated with an artificial diet. We identified species that have not been previously described in this fruit fly, especially actinobacteria and archaea, by employing different primer sets aimed at the same molecular marker but targeting diverse hypervariable regions of 16S rDNA. The possibility that Archaea affect fly fitness should not be ignored. This report on the intestinal microbial (bacteria, archaea, and fungi) composition of A. obliqua contributes to our understanding of the role of microorganisms in the development and physiology of the flies.

Environmental, Microbiological, and Immunological Features of Bacterial Biofilms Associated with Implanted Medical Devices

The spread of biofilms on medical implants represents one of the principal triggers of persistent and chronic infections in clinical settings, and it has been the subject of many studies in the past few years, with most of them focused on prosthetic joint infections. We review here recent works on biofilm formation and microbial colonization on a large variety of indwelling devices, ranging from heart valves and pacemakers to urological and breast implants and from biliary stents and endoscopic tubes to contact lenses and neurosurgical implants. We focus on bacterial abundance and distribution across different devices and body sites and on the role of environmental features, such as the presence of fluid flow and properties of the implant surface, as well as on the interplay between bacterial colonization and the response of the human immune system.

Why the importance of geo-origin tracing of edible bird nests is arising?

Edible bird's nest (EBN) swiftlet existed naturally 48,000 years ago in caves as their natural dwellings. Nowadays, edible bird's nest has become a very important industry due to its high nutritional, medicinal and economic value. Additionally, edible bird's nest has a long quality guarantee period. Obviously, the nutritional components and medicinal functions vary depending on geographical origins. Recently, the global demand for edible bird's nest has markedly increased, accompanied by the increasing attention of all key players of the global food trade system, i.e., producers, consumers, traders and the authorities to obtain safe and high-quality edible bird's nest. Hence, this target can be accomplished via the enforcement of an efficient and universal geo-tracing technique. Current methods of the geo-tracking of edible bird's nest, i.e., automation, physical and analytical techniques have several limitations and all of them fail to discriminate different quality grades of edible bird's nest. Meanwhile, in many studies and applications, polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) has proven to be a "cutting edge" technique for greatly enhance food traceability from field to fork through its ability in distinguishing the food products in terms of their quality and safety. This article provides an overview of (1) edible bird's nest as a multiuse strategic food product, (2) quality issues associated with edible bird's nest including implications that the site of acquisition of the edible bird's nest has food safety implications, (3) current regulations and geo-tracking approaches to ensure the safety and quality of edible bird's nest with the special focus on polymerase chain reaction-denaturing gradient gel electrophoresis technique as a vigorous and universal geo-tracing tool to be suggested for edible bird's nest geo-traceability.

Tejuino, a Traditional Fermented Beverage: Composition, Safety Quality, and Microbial Identification

This study aims to analyze the chemical and microbial composition and characterize volatile compounds from the artisanal and commercial Tejuino beverage. For this, eight samples are analyzed (four artisanal and four commercial). The chemical and microbiological quality is determined by standard methods, and volatile compounds are determined by solid-phase microextraction. Overall, the physicochemical composition and microbiological quality are higher for artisanal Tejuino (p < 0.05). The pH values were 3.20 and 3.62, and 0.76 and 0.46 meq of lactic acid for artisanal and commercial Tejuino, respectively. With volatile compounds analyzed, esters, benzenes, and aldehydes were predominant; meanwhile, ethanol was a volatile compound with the highest concentration for all samples. Saccharomyces cerevisiae and Limosilactobacillus fermentum were identified in artisanal Tejuino; yeasts of the Pichia genera and Lactiplantibacillus plantarum, for commercial Tejuino, and Enterococcus genus were identified in both samples. The characterization of both types of Tejuino allows us to update the information available on this important Mexican beverage. In addition, the isolation of lactic acid bacteria, as representative bacteria of both drinks, offers an area of opportunity to know the potential functionality of these bacteria in traditional fermented products.

Global cocoa fermentation microbiome: revealing new taxa and microbial functions by next generation sequencing technologies

This review provides an overview of the application of next-generation sequencing (NGS) technologies for microbiome analysis of cocoa beans fermentation. The cocoa-producing regions where NGS has been applied include Brazil, Ghana, Ivory Coast, Cameroon, Nicaragua, and Colombia. The data collected were processed by principal component analysis (PCA) and Venn diagrams to perform a multivariate association between microbial diversity and cocoa-producing regions. NGS studies have confirmed the dominance of three major microbial groups revealed by culture-dependent approaches, i.e., lactic acid bacteria, acetic acid bacteria, and yeasts. However, a more complex microbial diversity has been revealed, comprising sub-dominant populations, late-growing species, and uncultivable microorganisms. A total of 99 microbial genera and species were for the first time reported in cocoa beans fermentation, such as Brevibacillus sp., Halomonas meridiana, Methylobacterium sp., Novosphingobium sp., and Paenibacillus pabuli. PCA and Venn diagrams showed that species composition is rarely fixed and often experiences fluctuations of varying degrees and at varying frequencies between different cocoa-producing regions. Understanding these differences will provide further directions for exploring the functional and metabolic activity of rare and abundant taxa, as well as their use as starter cultures to obtain high-quality cocoa beans.

Dynamics of Fermentation Parameters and Bacterial Community in High-Moisture Alfalfa Silage with or without Lactic Acid Bacteria

The aim of this study was to gain deeper insights into the dynamics of fermentation parameters and the bacterial community during the ensiling of high-moisture alfalfa. A commercial lactic acid bacteria (YX) inoculant was used as an additive. After 15 and 30 days of ensiling, the control silage (CK) exhibited a high pH and a high concentration of ammoniacal nitrogen (NH₃-N); Enterobacter and Hafnia-Obesumbacterium were the dominant genera. At 60 d, the pH value and the concentration of NH₃-N in CK silage increased compared with 15 and 30 d, propionic acid and butyric acid (BA) were detected, and Garciella had the highest abundance in the bacterial community. Compared with CK silage, inoculation of YX significantly promoted lactic acid and acetic acid accumulation and reduced pH and BA formation, did not significantly reduce the concentration of NH₃-N except at 60 d, and significantly promoted the abundance of Lactobacillus and decreased the abundance of Garciella and Anaerosporobacter, but did not significantly inhibit the growth of Enterobacter and Hafnia-Obesumbacterium. In conclusion, high-moisture alfalfa naturally ensiled is prone to rot. Adding YX can delay the process of silage spoilage by inhibiting the growth of undesirable microorganisms to a certain extent.

Analysis of Cultivable Microbial Community during Kimchi Fermentation Using MALDI-TOF MS

Kimchi, a traditional Korean fermented vegetable, has received considerable attention for its health-promoting effects. This study analyzes the cultivable microbial community in kimchi fermented at different temperatures using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) to comprehensively understand the factors affecting the quality of kimchi. Of the 5204 strains isolated from kimchi, aligned with the in-house database, 4467 (85.8%) were correctly identified at the species level. The fermentation temperature affected the microbial community by varying the pH and acidity, which was mainly caused by temperature-dependent competition between the different lactic acid bacteria (LAB) species in kimchi. LAB, such as Levilactobacillus (Lb.) brevis and Lactiplantibacillus (Lpb.) plantarum associated with rancidity and tissue softening, proliferated faster at higher temperatures than at low temperature. In addition, LAB, such as Latilactobacillus (Lat.) sakei and Leuconostoc (Leu.) mesenteroides, which produce beneficial substances and flavor, were mainly distributed in kimchi fermented at 4 °C. This study shows as a novelty that MALDI-TOF MS is a robust and economically affordable method for investigating viable microbial communities in kimchi.

Factors influencing the persistence of enteropathogenic bacteria in wetland habitats and implications for water quality

AIMS

To better understand the persistence dynamics of enteropathogenic bacteria in freshwater wetland habitats, we constructed lab-scale mesocosms planted with two different wetland plant species using a subsurface flow wetland design. Mesocosms were treated with either a high-quality or a poor-quality water source to examine the effects of water quality exposure and plant species on Escherichia coli, Salmonella spp. and Enterococcus spp. in the rhizoplane, rhizosphere and water of wetland habitats.

METHODS AND RESULTS

Quantities of study micro-organisms were detected using real-time PCR in wetland mesocosms. A combination of molecular and culture-based methods was also used to enumerate these organisms from surface water and plant material at high, medium and poor water quality sites in the field. We found that all three enteropathogenic micro-organisms were influenced by microhabitat type and plant species. Organisms differed with respect to their predominant microhabitat and the extent of persistence associated with wetland plant species in the mesocosm study. Of the monitored pathogens, only E. coli was influenced by both water quality treatment and plant species. Salmonella spp. quantities in the rhizoplane consistently increased in all treatments over the course of the mesocosm experiment.

CONCLUSIONS

Plant species selection appears to be an overlooked aspect of constructed wetland design with respect to the removal of enteropathogenic micro-organisms. Escherichia coli and Enterococcus concentrations in wetland outflow were significantly different between the two plant species tested, with Enterococcus concentrations being significantly higher in mesocosms planted with Phalaris arundinaceae and E. coli concentrations being higher in mesocosms planted with Veronica anagallis-aquatica. Furthermore, there is evidence that the rhizoplane is a significant reservoir for Salmonella spp. within wetland habitats.

SIGNIFICANCE AND IMPACT OF THE STUDY

This is the first time that Salmonella spp. has been shown to proliferate under natural conditions within the rhizoplane. This will contribute to our understanding of wetland removal mechanisms for enteropathogenic bacteria. This study identifies the rhizoplane as a potentially important reservoir for human pathogenic micro-organisms and warrants additional study to establish whether this finding is applicable in non-wetland habitats.

Computational analysis of successional changes in the microbial population and community diversity of the immobilized marine nitrifying bacterial consortium in a nitrifying packed bed bioreactor

Nitrifying bioreactor (NBR) connected to the recirculating aquaculture system (RAS), has a greater emphasis on the biological treatment of wastewater. Nitrifying bacterial consortium (NBC) formed bio-film on the substratum activating the NBR, and it was observed with high nitrification potential in shrimp maturation systems. Scanning Electron Microscopy (SEM) revealed the integrity of the biofilm substantiated with biomineralization. The fate of the matured bio-film population on subsequent operation under RAS, and the aggregated population at different points of RAS, including the rearing water were determined using fingerprints of Denaturing Gradient Gel Electrophoresis (DGGE). Altogether, 38 OTUs of biofilm sample and 35 OTUs of water samples represented the bacterial communities; the shared and unique OTUs indicated the diversity of the population at different time intervals in the operation of the NBR. The mathematical (range-weighted richness) and statistical (diversity indices) interpretation unveiled the OTUs based high bacterial diversity in the biofilm supporting the compositional changes and determined the distance between the community cluster. Ordination analyses indicated the population shift and stability of the activated bio-film till the matured biofilm community got established in the RAS. The DGGE with mathematical and statistical analysis revealed microbial diversity (high Shannon index, species richness and evenness), abundance (relative intensity), consecutive change in the population composition (OTUs, Rr index), and the dynamics (Δt) in the system during the operation.

An updated review on bacterial community composition of traditional fermented milk products: what next-generation sequencing has revealed so far?

The emergence of next-generation sequencing (NGS) technologies has revolutionized the way to investigate the microbial diversity in traditional fermentations. In the field of food microbial ecology, different NGS platforms have been used for community analysis, including 454 pyrosequencing from Roche, Illumina's instruments and Thermo Fisher's SOLiD/Ion Torrent sequencers. These recent platforms generate information about millions of rDNA amplicons in a single running, enabling accurate phylogenetic resolution of microbial taxa. This review provides a comprehensive overview of the application of NGS for microbiome analysis of traditional fermented milk products worldwide. Fermented milk products covered in this review include kefir, buttermilk, koumiss, dahi, kurut, airag, tarag, khoormog, lait caillé, and suero costeño. Lactobacillus-mainly represented by Lb. helveticus, Lb. kefiranofaciens, and Lb. delbrueckii-is the most important and frequent genus with 51 reported species. In general, dominant species detected by culturing were also identified by NGS. However, NGS studies have revealed a more complex bacterial diversity, with estimated 400-600 operational taxonomic units, comprising uncultivable microorganisms, sub-dominant populations, and late-growing species. This review explores the importance of these discoveries and address related topics on workflow, NGS platforms, and knowledge bioinformatics devoted to fermented milk products. The knowledge that has been gained is vital in improving the monitoring, manipulation, and safety of these traditional fermented foods.

Microbial Ecology of Greek Wheat Sourdoughs, Identified by a Culture-Dependent and a Culture-Independent Approach

The aim of the present study was to assess the microecosystem of 13 homemade spontaneously fermented wheat sourdoughs from different regions of Greece, through the combined use of culture-dependent (classical approach; clustering by Random Amplified Polymorphic DNA-Polymerase Chain Reaction (RAPD-PCR) and identification by PCR species-specific for Lactiplantibacillus plantarum, and sequencing of the 16S-rRNA and 26S-rRNA gene, for Lactic Acid Bacteria (LAB) and yeasts, respectively) and independent approaches [DNA- and RNA-based PCR-Denaturing Gradient Gel Electrophoresis (DGGE)]. The pH and Total Titratable Acidity (TTA) values ranged from 3.64–5.05 and from 0.50–1.59% lactic acid, respectively. Yeast and lactic acid bacteria populations ranged within 4.60–6.32 and 6.28–9.20 log CFU/g, respectively. The yeast: LAB ratio varied from 1:23–1:10,000. A total of 207 bacterial and 195 yeast isolates were obtained and a culture-dependent assessment of their taxonomic affiliation revealed dominance of Lb. plantarum in three sourdoughs, Levilactobacillus brevis in four sourdoughs and co-dominance of these species in two sourdoughs. In addition, Companilactobacillusparalimentarius dominated in two sourdoughs and Fructilactobacillussanfranciscensis and Latilactobacillus sakei in one sourdough each. Lactococcus lactis, Lb. curvatus, Leuconostoc citreum, Ln. mesenteroides and Lb. zymae were also recovered from some samples. Regarding the yeast microbiota, it was dominated by Saccharomyces cerevisiae in 11 sourdoughs and Pichia membranifaciens and P. fermentans in one sourdough each. Wickerhamomyces anomalus and Kazachstania humilis were also recovered from one sample. RNA-based PCR-DGGE provided with nearly identical results with DNA-based one; in only one sample the latter provided an additional band. In general, the limitations of this approach, namely co-migration of amplicons from different species to the same electrophoretic position and multiband profile of specific isolates, greatly reduced resolution capacity, which resulted in only partial verification of the microbial ecology detected by culture-dependent approach in the majority of sourdough samples. Our knowledge regarding the microecosystem of spontaneously fermented Greek wheat-based sourdoughs was expanded, through the study of sourdoughs originating from regions of Greece that were not previously assessed.

Silage Fermentation, Bacterial Community, and Aerobic Stability of Total Mixed Ration Containing Wet Corn Gluten Feed and Corn Stover Prepared with Different Additives

Simple Summary

Wet corn gluten feed (WCGF) is a feed containing high moisture and rapidly digestible, non-forage fiber and protein for dairy cows, that is difficult to preserve. The use of corn stover as roughage by ruminants is limited by its poor digestibility. Total mixed ration (TMR) silage is an ensiling mixed feed that can fully mix forage and concentrate in a specific ratio to satisfy the nutritional needs of dairy cows, which has become an effective method of preservation of high-moisture byproducts. The objective of this study was to investigate the effects of different additives on the fermentation quality, bacterial community, and aerobic stability of TMR silage containing WCGF and corn stover. Inoculation with lactic acid bacteria (LAB) + fibrolytic enzyme (EN) and LAB improved aerobic stability of TMR silages indicated by higher and more stable LA and AA contents, a smaller rise in pH, and yeast count than other silages. Total mixed ration silage inoculated the LAB + EN and LAB can become an effective method of preserving high-moisture WCGF and corn stover with poor digestibility.

Abstract

The objective of this study was to investigate the effects of different additives on the fermentation quality, bacterial community, and aerobic stability of total mixed ration (TMR) silage containing wet corn gluten feed (WCGF) and corn stover. The TMR was ensiled with four treatments: (1) no additive (control); (2) lactic acid bacteria (LAB); (3) fibrolytic enzyme (EN); (4) LAB + EN. The EN and LAB + EN decreased the neutral detergent fiber and acid detergent fiber contents. Additives led to a higher lactic acid (LA) content (p < 0.0001) compared to control at all ensiling times. Silages inoculated with LAB and LAB + EN had higher dry matter (p = 0.0007), LA (p < 0.0001) and acetic acid (AA) contents (p < 0.0001) compared to control. The LAB and LAB + EN had significantly lowest ammonia nitrogen among the treatments, while no significant difference occurred after days 7 of ensiling. Silages treated with LAB and LAB + EN had a higher LAB count (p < 0.0001) and a lower pH, yeast, and mold counts compared to other silages. The LAB and LAB + EN greatly increased the portions of Firmicutes and Lactobacillus (p < 0.0001, and p < 0.0001, respectively) and reduced undesirable bacteria. Inoculation with LAB + EN and LAB improved aerobic stability of TMR silages indicated by higher and more stable LA and AA contents, smaller rise in pH, and yeast count than other silages. The LAB + EN and LAB reduced microbial diversity and improved the fermentation quality and aerobic stability of TMR silage containing WCGF and corn stover.

Microbial detection and identification methods: Bench top assays to omics approaches

Rapid detection of foodborne pathogens, spoilage microbes, and other biological contaminants in complex food matrices is essential to maintain food quality and ensure consumer safety. Traditional methods involve culturing microbes using a range of nonselective and selective enrichment methods, followed by biochemical confirmation among others. The time-to-detection is a key limitation when testing foods, particularly those with short shelf lives, such as fresh meat, fish, dairy products, and vegetables. Some recent detection methods developed include the use of spectroscopic techniques, such as matrix-assisted laser desorption ionization-time of flight along with hyperspectral imaging protocols.This review presents a comprehensive overview comparing insights into the principles, characteristics, and applications of newer and emerging techniques methods applied to the detection and identification of microbes in food matrices, to more traditional benchtop approaches. The content has been developed to provide specialist scientists a broad view of bacterial identification methods available in terms of their benefits and limitations, which may be useful in the development of future experimental design. The case is also made for incorporating some of these emerging methods into the mainstream, for example, underutilized potential of spectroscopic techniques and hyperspectral imaging.

Lactobacillus commensals autochthonous to human milk have the hallmarks of potent probiotics

Maternal milk is an important source of essential nutrients for the optimal growth of infants. Breastfeeding provides a continuous supply of beneficial bacteria to colonize the infant gastrointestinal tract (GIT) and offers health benefits for disease prevention and immunity. The purpose of this study was to isolate novel probiotic strains from the breast milk of native Pakistani mothers and to evaluate their probiotic potential. We isolated 21 strains of bacteria from the colostrum and mature milk of 20 healthy mothers, who had vaginal deliveries and were not taking antibiotics. After phenotypic and genotypic characterization, these isolates were tested for survival in the GIT using in vitro acid and bile tests. Nine strains showing good acid tolerance were assessed for their growth rate, bile resistance and ability to hydrolyze bile salts. Out of the four Lactobacillus isolates adjudged to be most promising as probiotics, three were Lactobacillus fermentum strains and one was a strain of Lactobacillus oris. This study demonstrates that human milk is a viable source of commensal bacteria beneficial to both adults and babies.

Sub-Lethal Effects of Pesticides on the DNA of Soil Organisms as Early Ecotoxicological Biomarkers

This review describes the researches performed in the last years to assess the impact of pesticide sub-lethal doses on soil microorganisms and non-target organisms in agricultural soil ecosystems. The overview was developed through the careful description and a critical analysis of three methodologies based on culture-independent approaches involving DNA extraction and sequencing (denaturing gradient gel electrophoresis, DGGE; next-generation sequencing, NGS) to characterize the microbial population and DNA damage assessment (comet assay) to determine the effect on soil invertebrates. The examination of the related published articles showed a continuous improvement of the possibility to detect the detrimental effect of the pesticides on soil microorganisms and non-target organisms at sub-lethal doses, i.e., doses which have no lethal effect on the organisms. Considering the overall critical discussion on microbial soil monitoring in the function of pesticide treatments, we can confirm the usefulness of PCR-DGGE as a screening technique to assess the genetic diversity of microbial communities. Nowadays, DGGE remains a preliminary technique to highlight rapidly the main differences in microbial community composition, which is able to give further information if coupled with culture-dependent microbiological approaches, while thorough assessments must be gained by high-throughput techniques such as NGS. The comet assay represents an elective technique for assessing genotoxicity in environmental biomonitoring, being mature after decades of implementation and widely used worldwide for its direct, simple, and affordable implementation. Nonetheless, in order to promote the consistency and reliability of results, regulatory bodies should provide guidelines on the optimal use of this tool, strongly indicating the most reliable indicators of DNA damage. This review may help the European Regulation Authority in deriving new ecotoxicological endpoints to be included in the Registration Procedure of new pesticides.

Current Progression: Application of High-Throughput Sequencing Technique in Space Microbiology

During a spaceflight, astronauts need to live in a spacecraft on orbit for a long time, and the relationship between humans and microorganisms in the closed environment of space is not the same as on the ground. The dynamic study of microorganisms in confined space shows that with the extension of the isolation time, harmful bacteria gradually accumulate. Monitoring and controlling microbial pollution in a confined environment system are very important for crew health and the sustainable operation of a space life support system. Culture-based assays have been used traditionally to assess the microbial loads in a spacecraft, and uncultured-based techniques are already under way according to the NASA global exploration roadmap. High-throughput sequencing technology has been used generally to study the communities of the environment and human on the ground and shows its broad prospects applied onboard. We here review the recent application of high-throughput sequencing on space microbiology and analyze its feasibility and potential as an on-orbit detection technology.

Traceability of fruits and vegetables

Food safety and traceability are nowadays a constant concern for consumers, and indeed for all actors in the food chain, including those involved in the fruit and vegetable sector. For the EU, the principles and legal requirements of traceability are set out in Regulation 178/2002. Currently however the regulation does not describe any analytical traceability tools. Furthermore, traceability systems for fruits and vegetables face increasing competition due to market globalization. The current challenge for actors in this sector is therefore to be sufficiently competitive in terms of price, traceability, quality and safety to avoid scandal and fraud. For all these reasons, new, flexible, cheap and efficient traceability tools, as isotopic analysis, DNA fingerprinting and metabolomic profiling coupled with chemometrics are needed.

Evaluation of the Bacterial Diversity of Inner Mongolian Acidic Gruel Using Illumina MiSeq and PCR-DGGE

As a traditional fermented cereal, Inner Mongolian acidic gruel has a unique flavor and rich nutrition, but the microbial diversity of acidic gruel and the microbial differences among the products in different regions have not been reported. The bacterial diversity and the lactic acid bacteria species of 27 types of traditional handmade acidic gruel were evaluated using a combination of MiSeq high-throughput sequencing and PCR-DGGE. All 358,205 high-quality 16S rRNA reads were divided into 25,171 OTUs under the similarity of 97%. Firmicutes, Proteobacteria, and Bacteroidetes were the dominant bacterial phyla, and the core dominant genera were Lactobacillus and Acetobacter with average relative abundances of 64.06% and 24.13%, respectively. The primary genera that caused the differences in the bacterial community structure between the Bayan Nur and Ordos acidic gruel samples were Pseudomonas, Leuconostoc, and Acinetobacter as revealed by redundancy analysis (RDA). PCR-DGGE analyses revealed that the lactic acid bacteria in both the Bayan Nur and Ordos samples of acidic gruel were Lactobacillus (L.) amylolyticus, L. alimentarius, L. fermentum, L. hamsteri, L. helveticus, L. panis, L. plantarum, L. pontis, and Leuconostoc lactis. In addition, L. hamsteri was the core strain detected among all the samples. The results deepened the understanding of the microbial community composition and the diversity of acidic gruel to provide a theoretical basis for the preservation and protection of microbial resources in acidic gruel in the Inner Mongolia area.

Horizontal transfer and finalization of a reliable detection method for the olive fruit fly endosymbiont, Candidatus Erwinia dacicola

BACKGROUND

The olive fly, Bactrocera oleae, is the most important insect pest in olive production, causing economic damage to olive crops worldwide. In addition to extensive research on B. oleae control methods, scientists have devoted much effort in the last century to understanding olive fly endosymbiosis with a bacterium eventually identified as Candidatus Erwinia dacicola. This bacterium plays a relevant role in olive fly fitness. It is vertically transmitted, and it benefits both larvae and adults in wild populations; however, the endosymbiont is not present in lab colonies, probably due to the antibiotics and preservatives required for the preparation of artificial diets. Endosymbiont transfer from wild B. oleae populations to laboratory-reared ones allows olive fly mass-rearing, thus producing more competitive flies for future Sterile Insect Technique (SIT) applications.

RESULTS

We tested the hypothesis that Ca. E. dacicola might be transmitted from wild, naturally symbiotic adults to laboratory-reared flies. Several trials have been performed with different contamination sources of Ca. E. dacicola, such as ripe olives and gelled water contaminated by wild flies, wax domes containing eggs laid by wild females, cages dirtied by faeces dropped by wild flies and matings between lab and wild adults. PCR-DGGE, performed with the primer set 63F-GC/518R, demonstrated that the transfer of the endosymbiont from wild flies to lab-reared ones occurred only in the case of cohabitation.

CONCLUSIONS

Cohabitation of symbiotic wild flies and non-symbiotic lab flies allows the transfer of Ca. E. dacicola through adults. Moreover, PCR-DGGE performed with the primer set 63F-GC/518R was shown to be a consistent method for screening Ca. E. dacicola, also showing the potential to distinguish between the two haplotypes (htA and htB). This study represents the first successful attempt at horizontal transfer of Ca. E. dacicola and the first step in acquiring a better understanding of the endosymbiont physiology and its relationship with the olive fly. Our research also represents a starting point for the development of a laboratory symbiotic olive fly colony, improving perspectives for future applications of the Sterile Insect Technique.

Tracing insect pests: is there new potential in molecular techniques?

Insects are amongst the greatest pests of agriculture, horticulture and forestry worldwide, inflicting damage and economic costs both directly and by transmitting plant viruses. Many kinds of insects are now resistant or cross-resistant to pesticides. Tracking studies have become very important for combatting insect pests and for better understanding their biology (eg insect population dynamics, movements, feeding behaviour and other ecological interactions). A wide variety of tracing approaches have been used including discriminative, tracer and molecular methods. The perfect technique for insect tracking is the technique that harmonizes with insects' 'normal' biology. Furthermore, the technique should be environmentally safe, cost-effective and easy to use. This paper reviews the current techniques used for insect traceability, documents the advantages and drawbacks of each method, and puts special focus on molecular techniques, including PCR-denaturing gradient gel electrophoresis as a new and promising traceability tool that could provide insects with a unique biological barcode and thus make it possible to trace their movements.

High Throughput Sequencing Technologies as a New Toolbox for Deep Analysis, Characterization and Potentially Authentication of Protection Designation of Origin Cheeses?

Protected Designation of Origin (PDO) labeling of cheeses has been established by the European Union (EU) as a quality policy that assures the authenticity of a cheese produced in a specific region by applying traditional production methods. However, currently used scientific methods for differentiating and establishing PDO are limited in terms of time, cost, accuracy and their ability to identify through quantifiable methods PDO fraud. Cheese microbiome is a dynamic community that progressively changes throughout ripening, contributing via its metabolism to unique qualitative and sensorial characteristics that differentiate each cheese. High Throughput Sequencing (HTS) methodologies have enabled the more precise identification of the microbial communities developed in fermented cheeses, characterization of their population dynamics during the cheese ripening process, as well as their contribution to the development of specific organoleptic and physio-chemical characteristics. Therefore, their application may provide an additional tool to identify the key microbial species that contribute to PDO cheeses unique sensorial characteristics and to assist to define their typicityin order to distinguish them from various fraudulent products. Additionally, they may assist the cheese-makers to better evaluate the quality, as well as the safety of their products. In this structured literature review indications are provided on the potential for defining PDO enabling differentiating factors based on distinguishable microbial communities shaped throughout the ripening procedures associated to cheese sensorial characteristics, as revealed through metagenomic and metatranscriptomic studies. Conclusively, HTS applications, even though still underexploited, have the potential to demonstrate how the cheese microbiome can affect the ripening process and sensorial characteristics formation via the catabolism of the available nutrients and interplay with other compounds of the matrix and/or production of microbial origin metabolites and thus their further quality enhancement.

Lactic Acid Bacteria Biota and Aroma Profile of Italian Traditional Sourdoughs From the Irpinian Area in Italy

This study identified the lactic acid bacteria (LAB) biota and the volatilome profile of 28 typical sourdoughs of Irpinia—a large area of the Campania region of Southern Italy where numerous breads are produced, even today, following the ancient procedures of sourdough fermentation and for which information on the microbiological and sensory profile is lacking in literature. For this purpose, microbial quality, LAB biodiversity, chemical, and technological characteristics, as well as aroma profile by solid-phase microextraction technique (SPME)–gas chromatography/mass spectrometry (GC/MS) of Irpinian sourdoughs were investigated. The dominant LAB microbiota was examined by both culture-dependent and culture-independent methods Polymerase Chain Reaction/Denaturing Gradient Gel Electrophoresis (PCR-DGGE). Results showed a high biodiversity in LAB community whereas the most frequent lactobacilli species recognized were Lactobacillus plantarum (ca. 22% of total LAB isolates), Lactobacillus sanfranciscensis (11%), Lactobacillus paralimentarius (8%), and Lactobacillus rossiae (6.5%), whereas LAB cocci could be mainly referred to Pediococcus pentosaceus (9.5% of total LAB isolates), Leuconostoc spp. (7.8%), and Weissella cibaria (7.7%). Sourdoughs were characterized by the dominance of one or two LAB species, thus proving that the environment influences the selection and the establishment of few key LAB species and that no specific correlation can be traced between microbial composition and geographical origin of the samples. Furthermore, although sourdoughs were characterized by different qualitative and quantitative volatile organic compound (VOC) compositions, no noticeable correlation between volatilome profile and geographical origin was found. However, it emerged that for more isolated locations, it was possible to find the existence of microbial biotypes and sensory profiles with a strong identity, thus revealing the existence of highly traditional and evocative bread recipes in those geographical contexts.

Engineering Synthetic Microbial Communities through a Selective Biofilm Cultivation Device for the Production of Fermented Beverages

Production of Cambodian rice wine involves complex microbial consortia. Indeed, previous studies focused on traditional microbial starters used for this product revealed that three microbial strains with complementary metabolic activities are required for an effective fermentation, i.e., filamentous fungi (Rhizopus oryzae), yeast (Saccharomycescerevisiae), and lactic acid bacteria (Lactobacillusplantarum). Modulating the ratio between these three key players led to significant differences, not only in terms of ethanol and organic acid production, but also on the profile of volatile compounds, in comparison with natural communities. However, we observed that using an equal ratio of spores/cells of the three microbial strains during inoculation led to flavor profile and ethanol yield close to that obtained through the use of natural communities. Compartmentalization of metabolic tasks through the use of a biofilm cultivation device allows further improvement of the whole fermentation process, notably by increasing the amount of key components of the aroma profile of the fermented beverage (i.e., mainly phenylethyl alcohol, isobutyl alcohol, isoamyl alcohol, and 2-methyl-butanol) and reducing the amount of off-flavor compounds. This study is a step forward in our understanding of interkingdom microbial interactions with strong application potential in food biotechnology.

Effects of Freeze-Thaw Event on Microbial Community Dynamics During Red Clover Ensiling

Freezing damages in forages represents a major economic loss to agriculture. This study was conducted to investigate the effects of freeze–thaw (FT) event on microbial community dynamics of red clover silage. Results showed that the FT-treated material displayed higher proportions of Weissella and aerobic bacteria, while lower Pantoea and Enterobacter compared with the control material. The FT event promoted the development of Lactobacillus in silage microflora, inducing more intense lactic fermentation after an initial short lag. The aerobic bacteria were suppressed immediately after the onset of ensiling. Microbiomes of the two silages tended to be almost similar after 2 days of ensiling. However, a small number of aerobic bacteria tended to revitalize in the FT silage with prolonged ensiling time, indicated by apparent abundances of Acinetobacter and Pseudomonas at the end of ensiling. The results obtained here suggest that the FT event could promote the development of Lactobacillus during ensiling and the control of aerobe revitalization need to be concerned with silages made from the freeze-damaged forages.