DNA-based, culture-independent strategies for evaluating microbial communities in food-associated ecosystems

Duck compound probiotics fermented diet alters the growth performance by shaping the gut morphology, microbiota and metabolism

Dietary absorption and digestion are influenced by the microbiota, morphology, and digestive enzymes of intestines, and fermentation is a popular and effective technique to enhance animal rearing growth performance. This study aims to explore the pivotal role of Muscovy duck probiotics fermented feedstuff (FF) in altering the growth performance by reshaping gut morphology, microorganisms and metabolism. The findings showed that FF considerably raised the levels of fatty acids (FA) and small peptides (7-19AA) in the diet. Further feeding trial data reveals that FF greatly increased the Muscovy duck average daily gain (ADG) but had no effect on their daily feed intake (DFI), and the FCR significantly dropped (P < 0.05). Additionally, it was evident that FF improved the integrity of the intestinal mucosa in Muscovy duck by increasing villus height, villus height-to-crypt depth ratio, and lowering crypt depth. Then, in comparison to the control group (NC), there was a significant increase in the gene expression of the mucosal tight junction proteins Occludin, Claudin-1, and Zo-1 in the intestine of Muscovy duck. Additionally, there was higher expression of the mucosal transport channels SGLT-1, PepT1, AQP2, AQP3, and AQP10 in the similarly colon site, jejunum, and duodenum. Furthermore, in AB-PAS/PAS-stained duodenum, jejunum, ileum, and similarly colon site, FF markedly increased relative mucus output and goblet cells while decreasing epithelial cell apoptosis. Following 16S sequencing data indicated that the intestinal microbiota was altered and the diversity and richness of gut microbes was greatly enhanced by FF. Particularly, the boost of core probiotics, such as Rothia of duodenum, Limosilactobacillus and Lentilactobacillus of jejunum, Lactococcus and Rothia of ileum, Ligilactobacillus and Entocuccus of similarly colon site, Gallibacterium of caecum. And reduced potentially pathogenic bacteria (Campylobacter, Prevotellaceae, Clostridia-vadinBB60, and Oscillospira). Nontargeted metabolomics assay for intestinal content confirmed an increased organic acids (oxidanesulfonic acid, cholic acid, gallic acid, coumaric acid, pipecollc acid, 13s-hydroxyoctadecadienoic acid) and glycosides metabolites (5-hydroxydantrolene, 3-hydroxyguanfacine glucuronide, acetylleucine, astragalin, xanthosine, taxiphylin, sinapine, denudatine, penylalanyl-tyrosine and phenylalanyl-valine). These findings demonstrated that FF, a viable option to improve Muscovy duck growth performance through reconstructed intestinal morphology, microorganisms, and metabolism, subsequently promoted the gut health and increased diet digestion and absorption. The study that is being presented offers scientific proof that FF might be a useful strategy for improving Muscovy duck growth performance.

The bacterial succession and its role in flavor compounds formation during the fermentation of cigar tobacco leaves

Fermentation is the key process required for developing the characteristic properties of cigar tobacco leaves, complex microorganisms are involved in this process. However, the microbial fermentation mechanisms during the fermentation process have not been well-characterized. This study investigated the dynamic changes in conventional chemical composition, flavor compounds, and bacterial community during the fermentation of cigar tobacco leaves from Hainan and Sichuan provinces in China, as well as the potential roles of bacteria. Fermentation resulted in a reduction of conventional chemical components in tobacco leaves, with the exception of a noteworthy increase in insoluble protein content. Furthermore, the levels of 10 organic acids and 19 amino acids showed a significant decrease, whereas the concentration of 30 aromatic substances exhibited a unimodal trend. Before fermentation, the bacterial community structures and dominant bacteria in Hainan and Sichuan tobacco leaves differed significantly. As fermentation progressed, the community structures in the two regions became relatively similar, with Delftia, Ochrobactrum, Rhodococcus, and Stenotrophomonas being dominant. Furthermore, a total of 12 functional bacterial genera were identified in Hainan and Sichuan tobacco leaves using bidirectional orthogonal partial least squares (O2PLS) analysis. Delftia, Ochrobactrum, and Rhodococcus demonstrated a significant negative correlation with oleic acid and linoleic acid, while Stenotrophomonas and Delftia showed a significant negative correlation with undesirable amino acids, such as Ala and Glu. In addition, Bacillus showed a positive correlation with benzaldehyde, while Kocuria displayed a positive correlation with 2-acetylfuran, isophorone, 2, 6-nonadienal, and β-damascenone. The co-occurrence network analysis of microorganisms revealed a prevalence of positive correlations within the bacterial network, with non-abundant bacteria potentially contributing to the stabilization of the bacterial community. These findings can improve the overall tobacco quality and provide a novel perspective on the utilization of microorganisms in the fermentation of cigar tobacco leaves.

Metagenomics: An Effective Approach for Exploring Microbial Diversity and Functions

Various fields have been identified in the "omics" era, such as genomics, proteomics, transcriptomics, metabolomics, phenomics, and metagenomics. Among these, metagenomics has enabled a significant increase in discoveries related to the microbial world. Newly discovered microbiomes in different ecologies provide meaningful information on the diversity and functions of microorganisms on the Earth. Therefore, the results of metagenomic studies have enabled new microbe-based applications in human health, agriculture, and the food industry, among others. This review summarizes the fundamental procedures on recent advances in bioinformatic tools. It also explores up-to-date applications of metagenomics in human health, food study, plant research, environmental sciences, and other fields. Finally, metagenomics is a powerful tool for studying the microbial world, and it still has numerous applications that are currently hidden and awaiting discovery. Therefore, this review also discusses the future perspectives of metagenomics.

Methods used in microbial forensics and epidemiological investigations for stronger health systems

This review discusses microbial forensics as an emerging science that finds application in protecting human health. It is important to distinguish naturally acquired infections from those caused by the intentional release of microorganisms to the environment. This information is crucial in formulating procedures against the spread of infectious diseases and prosecuting persons who may be involved in acts of biocrime, bioterrorism, or biowarfare. A comparison between epidemiological investigations and microbial forensic investigations is provided. In addition, a discussion on how microbial forensics strengthens health systems is included in this review. Microbial forensic investigations and epidemiologic examinations employ similar concepts and involve identifying and characterising the microbe of interest. Both fields require formulating an appropriate case definition, determining a pathogen's mode of transmission, and identifying the source(s) of infection. However, the two subdisciplines differ in their objectives. An epidemiological investigation aims to identify the pathogen's source to prevent the spread of the disease. Microbial forensics focuses on source-tracking to facilitate the prosecution of persons responsible for the spread of a pathogen. Both fields use molecular techniques in analysing and comparing DNA, gene products, and biomolecules to identify and characterise the microorganisms of interest. We included case studies to show methods used in microbial forensic investigations, a brief discussion of the public significance of microbial forensic systems, and a roadmap for establishing a system at a national level. This system is expected to strengthen a country's capacity to respond to public health emergencies. Several factors must be considered in establishing national microbial forensic systems. First is the inherent ubiquity, diversity, and adaptability of microorganisms that warrants the use of robust and accurate molecular typing systems. Second, the availability of facilities and scientists who have been trained in epidemiology, molecular biology, bioinformatics, and data analytics. Human resources and infrastructure are critical requirements because formulating strategies and allocating resources in times of infectious disease outbreaks must be data-driven. Establishing and maintaining a national microbial forensic system to strengthen capacities in conducting forensic and epidemiological investigations should be prioritised by all countries, accompanied by a national policy that sets the legislative framework and provides for the system's financial requirements.

Microbial community structure and biogenic amines content variations in chilled chicken during storage

The aim of this study was to investigate the sensory indicators, biogenic amine contents, and bacterial community structure and diversity of chilled chicken stored at 4°C under aerobic conditions. Bacterial diversity and dominant bacteria were analyzed using high-throughput sequencing technique (HTS). The relationship between biogenic amine contents and microbial community structure was studied. The results showed that contents of putrescine and cadaverine increased significantly with storage time. Proteobacteria was absolutely dominant flora at the phylum level. The predominant spoilage bacteria found in chicken thighs were Pseudomonas, Acinetobacter, Aeromonas, Shewanella, and Yersinia, and the difference with chicken breasts was related to the presence of Myroides and absence of Yersinia. Myroides, Yersinia, and Shewanella were reported for the first time as an important contributor to the spoilage-related microflora. Bacterial diversity and richness indices showed fluctuating and decreasing trend with storage time. The redundancy analysis showed that the relative abundance of Pseudomonas, Yersinia, and Janthinobacterium was positively related to the contents of putrescine, cadaverine, and tyramine, while Shewanella and Aeromonas showed positive relationship with putrescine content. Furthermore, positive relationship of Myroides and Desulfovibrio with the contents of cadaverine and tyramine was proposed for the first time. The key findings of this study can provide experimental data for food safety monitoring during refrigerated storage and preservation for poultry meat products.

Microbial Dynamics of a Specialty Italian Raw Ewe's Milk Cheese Curdled with Extracts from Spontaneous and Cultivated Onopordum tauricum Willd

Milk coagulants prepared by maceration of flowers harvested from both spontaneous and cultivated Onopordum tauricum Willd. and a commercially available coagulant obtained from Cynara cardunculus L. (control) were assayed for small-scale manufacturing of Caciofiore, an Italian specialty raw ewe's milk cheese produced in a family run dairy farm located in the Marche region (Central Italy). The microbiota of the three thistle-based milk coagulants and their effect on the microbial dynamics of raw milk cheeses during fermentation and maturation (from day 0 up until day 60) were investigated through a combined approach based on viable counting and Illumina DNA sequencing. In both the control and experimental cheeses, despite the slight differences emerged depending on the coagulant used, Lactococcus lactis and Debaryomyces hansenii were the prevalent species among bacteria and fungi, respectively. Moreover, raw ewe's milk was the main factor affecting the evolution of both the bacterial and fungal microbiota in all cheeses. The overall similarities between control and experimental cheeses herein analyzed supports the exploitation of Onopordum tauricum Willd. as an alternative milk coagulating agent for production of Caciofiore and, more in general, raw ewe's milk cheeses.

16S rRNA Based Profiling of Bacterial Communities Colonizing Bakery-Production Environments

Conventional culture-based techniques are largely inadequate in elucidating the microbiota contained in an environment, due to low recovery within a complex bacterial community. This limitation has been mitigated by the use of next-generation sequencing (NGS)-based approaches thereby facilitating the identification and classification of both culturable and uncultivable microorganisms. Amplicon targeted NGS methods, such as 16S ribosomal RNA (16S rRNA) and shotgun metagenomics, are increasingly being applied in various settings such as in food production environments to decipher the microbial consortium therein. Even though multiple food matrices/food production environments have been studied, the low-moisture environment associated with bakery food production remains to be investigated. To address this knowledge gap, in this study, we investigated the microbiome associated with two bakery production sites (designated as A and B) located in Ireland using 16S rRNA-amplicon-based sequencing. Amplicons corresponding to a hypervariable region contained within the 16S rRNA gene were amplified from DNA samples purified from environmental swabs and ingredients collected at both sites at various stages (preparation, production, postproduction, and storage) across the bakery production chain, over three seasons (winter, spring, and summer). These amplicons were sequenced, and data were analyzed using the mothur pipeline and visualized using MicrobiomeAnalyst and a series of R packages. The top seven bacterial phyla identified at both sites were composed of Proteobacteria, Firmicutes, Actinobacteria, Bacteroidetes, Deinococcus-Thermus, Patescibacteria, and Verrucomicrobia. In addition, the phyla Tenericutes (Mycoplasmatota) and Acidobacteria were observed only in samples taken at site B. Different bacterial compositions were identified at each stage of production. These same bacteria were also found to be present in the final processed food suggesting the influence of the environment on the food matrix. This study is the first demonstration of the utility of 16S rRNA amplicon-based sequencing to describe the microbiota associated with bakery processing environments.

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.

Characterization of Bacterial Communities of Cold-Smoked Salmon during Storage

Cold-smoked salmon is a widely consumed ready-to-eat seafood product that is a fragile commodity with a long shelf-life. The microbial ecology of cold-smoked salmon during its shelf-life is well known. However, to our knowledge, no study on the microbial ecology of cold-smoked salmon using next-generation sequencing has yet been undertaken. In this study, cold-smoked salmon microbiotas were investigated using a polyphasic approach composed of cultivable methods, V3—V4 16S rRNA gene metabarcoding and chemical analyses. Forty-five cold-smoked salmon products processed in three different factories were analyzed. The metabarcoding approach highlighted 12 dominant genera previously reported as fish spoilers: Firmicutes Staphylococcus, Carnobacterium, Lactobacillus, β-Proteobacteria Photobacterium, Vibrio, Aliivibrio, Salinivibrio, Enterobacteriaceae Serratia,Pantoea, γ-Proteobacteria Psychrobacter, Shewanella and Pseudomonas. Specific operational taxonomic units were identified during the 28-day storage study period. Operational taxonomic units specific to the processing environment were also identified. Although the 45 cold-smoked salmon products shared a core microbiota, a processing plant signature was found. This suggest that the bacterial communities of cold-smoked salmon products are impacted by the processing environment, and this environment could have a negative effect on product quality. The use of a polyphasic approach for seafood products and food processing environments could provide better insights into residential bacteria dynamics and their impact on food safety and quality.

Impact of DNA extraction and sampling methods on bacterial communities monitored by 16S rDNA metabarcoding in cold-smoked salmon and processing plant surfaces

Amplicon sequencing approaches have been widely used in food bacterial ecology. However, choices regarding the methodology can bias results. In this study, bacterial communities associated with cold-smoked salmon products and their processing plant surfaces were monitored via sequencing of the V3-V4 region of the 16S rRNA gene. The impact of DNA extraction protocols, sampling methods (swabbing or sponging) and surface materials on bacterial communities were investigated. α and β diversity analyses revealed that DNA extraction methods mainly influence the observed cold-smoked salmon microbiota composition. Moreover, different DNA extraction methods revealed significant differences in observed community richness and evenness. β-Proteobacteria: Photobacterium, Serratia and Firmicutes: Brochothrix, Carnobacterium and Staphylococcus were identified as the dominant genera. Surface microbiota richness, diversity and composition were mainly affected by cleaning and disinfection procedures but not by DNA extraction methods. Surface community richness and evenness appeared higher when sampled by sponging compared to swabbing. β-diversity analyses highlighted that surface topology, cleaning and disinfection and sampling devices seemed to affect the bacterial community composition. The dominant surface bacteria identified were mainly Flavobacteriaceae, β-Proteobacteria and γ-Proteobacteria described as fish spoilers such as Acinetobacter, Pseudomonas and Shewanella. DNA extraction and sampling methods can have an impact on sequencing results and the ecological analysis of bacterial community structures. This study confirmed the importance of methodology standardization and the need for analytical validation before 16S rDNA metabarcoding surveys.

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 diversity of representative traditional fermented sausages in different regions of China

AIMS

The purpose of this experiment was to study the bacterial diversity of traditional fermented sausages from four typical regions of China (Chengdu, Shenzhen, Changsha and Harbin) and to further evaluate their microbiological safety.

METHODS AND RESULTS

The diversity of the microbiota of the sausages was studied using the Illumina HiSeq platform. The results showed that compared with the highest diversity of fermented bacteria in Guangdong, the bacterial diversity of fermented sausage was the lowest in Sichuan. The percentage of dominant phylum (Firmicutes, Cyanophyta, Proteobacter) were 78·39, 13·13 and 7·14% in SC, 35·47, 30·36 and 28·04% in GD, 54·81, 28·91 and 14·00% in HN, 20·20, 58·16 and 17·31% in HB respectively. The main genus distribution of fermented sausages in different regions is varied, but lactic acid bacteria and cyanobacteria are generally the main ones. Traditional fermented sausages using natural fermentation methods have poor microbiological safety, and pathogenic and spoilage micro-organisms such as Acinetobacter, Brochothrix and Pseudomonas have been detected in all four regions.

CONCLUSIONS

The results in this paper provide a microbiota profile of four typical fermented sausages in China. There is a big difference in the microbiota of sausages in different regions, and the good flavour of traditional Chinese fermented sausage is related closely with the abundant microbial resources, however, the natural fermentation method also expose to the product security threats, including spoilage, pathogenic micro-organisms and biogenic amines, etc. SIGNIFICANCE AND IMPACT OF THE STUDY: The results would offer guidance for industrial fermented sausage production with certain flavour and also improve the microbial resource utilization, and contribute to the control of harmful micro-organisms in traditional fermented sausage.

Microbiome characterization of poultry products based on the poultry part and production label

Poultry is one of the most consumed meats worldwide and there are many different types of poultry products available on the market for consumers. Many poultry producers provide a variety of labeled meats based on rearing system such as organic, free-range and antibiotic-free. However, these labels often can be misleading by implying organic products are better in safety and quality compared to poultry products without additional labels. In this study, the microbiological profiles of commercial poultry products were characterized via a next generation sequencing. A variety of poultry products including whole carcass, leg, breast and thigh were purchased from local markets and subdivided by labels indicating organic, non-antibiotic, free range and no-label. According to the microbiome analysis based on the 16S rRNA gene, similar level of species richness were observed in comparison by labels, however, different parts and producers exhibited significant differences. Also, microbial similarities among groups were measured and most samples showed relatively close clustering based on the poultry part and the producer. The results emphasize potential contamination routes and the importance of the control strategy during the pre-harvest step of poultry products. The results also envision potential opportunities to improve current production procedure being utilized by industries.

Molecular screening and genetic diversity analysis of anticancer Azurin-encoding and Azurin-like genes in human gut microbiome deduced through cultivation-dependent and cultivation-independent studies

Azurin, a bacteriocin produced by a human gut bacterium Pseudomonas aeruginosa, can reveal selectively cytotoxic and induce apoptosis in cancer cells. After overcoming two phase I trials, a functional region of Azurin called p28 has been approved as a drug for the treatment of brain tumor glioma by FDA. The present study aims to improve a screening procedure and assess genetic diversity of Azurin genes in P. aeruginosa and Azurin-like genes in the gut microbiome of a specific population in Vietnam and global populations. Firstly, both cultivation-dependent and cultivation-independent techniques based on genomic and metagenomic DNAs extracted from fecal samples of the healthy specific population were performed and optimized to detect Azurin genes. Secondly, the Azurin gene sequences were analyzed and compared with global populations by using bioinformatics tools. Finally, the screening procedure improved from the first step was applied for screening Azurin-like genes, followed by the protein synthesis and NCI in vitro screening for anticancer activity. As a result, this study has successfully optimized the annealing temperatures to amplify DNAs for screening Azurin genes and applying to Azurin-like genes from human gut microbiota. The novelty of this study is the first of its kind to classify Azurin genes into five different genotypes at a global scale and confirm the potential anticancer activity of three Azurin-like synthetic proteins (Cnazu1, Dlazu11, and Ruazu12). The results contribute to the procedure development applied for screening anticancer proteins from human microbiome and a comprehensive understanding of their therapeutic response at a genetic level.

Root-Associated Endophytic Bacterial Community Composition of Pennisetum sinese from Four Representative Provinces in China

Pennisetum sinese, a source of bio-energy with high biomass production, is a species that contains high crude protein and will be useful for solving the shortage of forage grass after the implementation of “Green for Grain” project in the Loess plateau of Northern Shaanxi in 1999. Plants may receive benefits from endophytic bacteria, such as the enhancement of plant growth or the reduction of plant stress. However, the composition of the endophytic bacterial community associated with the roots of P. sinese is poorly elucidated. In this study, P. sinese from five different samples (Shaanxi province, SX; Fujian province, FJ; the Xinjiang Uyghur autonomous prefecture, XJ and Inner Mongolia, including sand (NS) and saline-alkali land (NY), China) were investigated by high-throughput next-generation sequencing of the 16S rDNA V3-V4 hypervariable region of endophytic bacteria. A total of 313,044 effective sequences were obtained by sequencing five different samples, and 957 effective operational taxonomic units (OTUs) were yielded at 97% identity. The phylum Proteobacteria, the classes Gammaproteobacteria and Alphaproteobacteria, and the genera Pantoea, Pseudomonas, Burkholderia, Arthrobacter, Psychrobacter, and Neokomagataea were significantly dominant in the five samples. In addition, our results demonstrated that the Shaanxi province (SX) sample had the highest Shannon index values (3.795). We found that the SX (308.097) and NS (126.240) samples had the highest and lowest Chao1 richness estimator (Chao1) values, respectively. Venn graphs indicated that the five samples shared 39 common OTUs. Moreover, according to results of the canonical correlation analysis (CCA), soil total carbon, total nitrogen, effective phosphorus, and pH were the major contributing factors to the difference in the overall composition of the bacteria community in this study. Our data provide insights into the endophytic bacteria community composition and structure of roots associated with P. sinese. These results might be useful for growth promotion in different samples, and some of the strains may have the potential to improve plant production in future studies.

Quality, functionality, and microbiology of fermented fish: a review

Fermentation is a traditional food preservation method and is widely used for improving food safety, shelf life, and organoleptic and nutritional attributes. Fermented fish are produced and consumed in different parts of the world and are an integral part of many food cultures. Furthermore, fermented fish are a source of interesting microbes and are an important industry in many countries. This review tries to update the types and manufacturing processes for fermented fish around the world. The emphasis is on this work related to fermented fish and their health benefits, as well as the contribution of microorganisms to their fermentation. A variety of different approaches have been used to determine and understand microbial composition and functionality. Moreover, some challenges and future research directions regarding fermented fish are also discussed in this review. Further research into fermented fish products is of crucial importance not only for the food industry but also for human health. However, extensive in vivo and toxicological studies are essential before the application of bioactive-rich fermented fish products for human health benefits.

The heat shock protein 70 gene as a new alternative molecular marker for the taxonomic identification of Streptomyces strains

With the developments in taxonomy, the classically used highly conserved 16S rRNA molecular marker has shown some disadvantages among closely related species. For further taxonomic studies of the prokaryotes, specific PCR primers were designed from two conserved regions in the amino acid sequences of the 70-kDa heat shock protein sourced from 20 different genera in actinomycetes. These were used for the amplification of the hsp70 genes in 16 Streptomyces strains. Then, we investigated the phylogenetic relationships among these Streptomyces strains and compared the tree topology based on the hsp70 gene with those based on the previously used markers (16S rRNA and gyrB). To our knowledge, this is the first use of the hsp70 gene as a molecular marker for the taxonomic identification of Streptomyces.

Screening of microbial communities associated with endive lettuce during postharvest processing on industrial scale

In this study, the composition of the microbial community on endive lettuce (Cichorium endivia) was evaluated during different postharvest processing steps. Microbial community structure was characterized by culture-dependent and culture-independent methods. Endive lettuce was sampled exemplarily at four different stages of processing (raw material, cut endive lettuce, washed endive lettuce, and spin-dried (ready to pack) endive lettuce) and analysed by plate count analysis using non-selective and selective agar plates with subsequent identification of bacteria colonies by matrix-assisted laser desorption/ionization time-of light mass spectrometry (MALDI-TOF MS). Additionally, terminal-restriction fragment length polymorphism (TRFLP) analysis and 16S rRNA gene nucleotide sequence analysis were conducted.

The results revealed structural differences in the lettuce microbiomes during the different processing steps. The most predominant bacteria on endive lettuce were detected by almost all methods. Bacterial species belonging to the families Pseudomonadaceae, Enterobacteriaceae, Xanthomonadaceae, and Moraxellaceae were detected in most of the examined samples including some unexpected potentially human pathogenic bacteria, especially those with the potential to build resistance to antibiotics (e.g., Stenotrophomonas maltophilia (0.9 % in cut sample, 0.4 % in spin-dried sample), Acinetobacter sp. (0.6 % in raw material, 0.9 % in cut sample, 0.9 % in washed sample, 0.4 % in spin-dried sample), Morganella morganii (0.2 % in cut sample, 3 % in washed sample)) revealing the potential health risk for consumers.

However, more seldom occurring bacterial species were detected in varying range by the different methods. In conclusion, the applied methods allow the determination of the microbiome's structure and its dynamic changes during postharvest processing in detail. Such a combined approach enables the implementation of tailored control strategies including hygienic design, innovative decontamination techniques, and appropriate storage conditions for improved product safety.

Bacterial diversity of artisanal cheese from the Amazonian region of Brazil during the dry and rainy seasons

The microbiota from artisanal cheeses produced in the Amazonian region is evaluated. Samples of artisanal cheeses were obtained from markets in Conceição do Araguaia and Redenção (Pará, Brazil) over rainy and dry seasons, and their biodiversity was assessed by culture-dependent and culture-independent methods. Mean counts of lactic acid bacteria (LAB) in cheeses ranged from 7.32 to 8.84 log CFU/g, for both seasons. Members of genera Lactobacillus, Lactococcus, Weissella, Enterococcus, Pediococcus, and Leuconostoc were predominant. The amplification of the 16S rRNA V6-V9 region, followed by a temporal temperature-gradient gel electrophoresis (TTGE) and sequencing of the TTGE bands revealed important differences in the microbial composition variability between samples from the two seasons and among cheese samples analyzed. TTGE showed the presence of microorganisms that are frequently found in cheese, such as L. lactis subsp. lactis, as well as other non-usual species, such as Macrococcus caseolyticus and Corynebacterium variabile. Moreover, TTGE analysis revealed the presence of microorganisms that have been isolated from other types of foods (Paralactobacillus selangorenses) along with some not usually found in foods, such as Exiguobacterium acetylicum, plus the presence of pathogenic microorganisms (Granulicatella elegans and Aerococcus sanguinicola). The present molecular approaches combined with culture-dependent methods provided a more detailed description of the microbial ecology of traditional cheeses from the Amazonian region in northern Brazil.

Advancement in LH-PCR methodology for multiple microbial species detections in fermented foods

The length-heterogeneity PCR is a low throughput molecular biology methods explored to monitor bacteria populations in different environments. It could be more used in food microbiology analysis, not only for fingerprinting analysis, but it has been hampered until now by a limiting factor which relates to the high percentage of secondary peaks. With the aim to overcome this problem, different experiments were performed focusing on changing PCR parameters in order to obtain more specific amplicon patterns and also to reduce the complexity of community patterns. With this purpose, different annealing temperatures were tested on complex fermented food matrices taken from both animal and vegetable origin and also on the bacteria isolated from the same food source. In particular, the optimal annealing temperature identified for the fermented food samples is 59 °C and the optimal for bacterial strains varied between 63 °C and 65 °C. The approach allowed the modification of the LH-PCR protocol increasing the amplification efficiency and therefore the bacteria species discrimination. These temperatures also allowed the implementation of the previous LH-PCR published database. The modification in the level of accuracy of the LH-PCR technique could also allow an improvement in the relative species quantification by the peak area evaluation.

High-Throughput Sequencing Analysis of Endophytic Bacteria Diversity in Fruits of White and Red Pitayas from Three Different Origins

Pitaya contains various types of polyphenols, flavonoid and vitamins which are beneficial for health and it is among the most important commercial tropical fruits worldwide. Endophytic bacteria might be beneficial for plant growth and yield. However, bacterial diversity in pitaya is poorly characterized. In this study, fruits of white and red pitayas from three different origins (Thailand, Vietnam and China) were chosen for endophytic bacteria diversity investigation by using Illumina HiSeq second-generation high-throughput sequencing technology. Large number of endophytic bacteria were detected and 22 phyla, 56 classes, 81 orders, 122 families and 159 genera were identified. Endophytic bacteria diversity was uneven among pitaya fruits from different origins and bacteria structure was different between white pitaya group and red pitaya group. Phylum Bacteroidetes, classes Bacteroidia and Coriobacteriia, orders Bacteroidales and Coriobacteriales, families Prevotellaceae, Bacteroidaceae, Ruminococcaceae, Paraprevotellaceae, Rikenellaceae, Alcaligenaceae and Coriobacteriaceae, genera Prevotella, Bacteroides, Roseburia, Faecalibacterium and Sutterella were statistically significant different species (P < 0.05) between white and red pitayas. These findings might be useful for growth improvement, fruit preservation and processing of different pitaya species from different origins.

Determination of the microbial flora in traditional İzmir Tulum cheeses by Denaturing Gradient Gel Electrophoresis

In this study, it was aimed to determine microbial flora members in three traditional Tulum cheeses (C1, C2 and C3) produced in different villages and settlement areas in İzmir, Turkey. For this purpose, culture depended and 16S rRNA based culture independent methods were used. According to the results of culture depended method, Lactococcus spp., Enterococcus spp., Staphylococcus spp., Lactobacillus spp., Pediococcus spp. and yeast-mold were detected in all samples at different levels. In order to determine and identify both of the culturable and non-culturable microorganisms, denaturing gradient gel electrophoresis (DGGE) method was used. DGGE results have shown that there were eight different dominant microorganisms (Streptococcus thermophilus, Lactococcus lactis subs. lactis, Streptococcus infantarius subs. infantarius, Lactobacillus gallinarum, Streptococcus equinus, Enterococcus faecalis, Enterococcus faecium, Lactococcus garvieae) in three regionally cheese samples. Further more, total bacterial loads were monitored with real-time PCR (qPCR) method. According to the results, 3.5 × 10⁸, 3.8 × 10⁸, 8.4 × 10⁸ copy number of DNA was detected in C1, C2 and C3 cheese samples, respectively. This study is the first description for the dynamics of microbial composition of Izmir Tulum cheese after the production and brining processes.

Characterization of microbial community composition and pathogens risk assessment in typical Italian-style salami by high-throughput sequencing technology

The structure of microbial communities in a typical Italian-style salami, including bacterial and fungal diversity, was investigated by high-throughput sequencing technology. A total of 6 phyla, 7 classes, 19 orders, 20 families and 28 genera were obtained from 16S rDNA sequences, and a total of 2 phyla, 4 classes, 4 orders, 5 families, 10 genera and 12 Species were obtained from 18S rDNA sequences. The core microbiota was composed of Staphylococcaceae, representing up to 97.52% of the total 16S rRNA, and Penicillium digitatum, accounting for 99.74% of the total classified 18S rRNA. Lactobacillales and Saccharomycetales were detected with a quite low proportion of 1.71 and 0.007%, respectively. This study contributes to the knowledge of the microbial diversity involved in salami and presents high-throughput sequencing as a useful tool to evaluate microbial diversity and monitor the food-borne pathogens in fermented sausage.

Food Evolution: The Impact of Society and Science on the Fermentation of Cocoa Beans

Cocoa is part of the cultural heritage in many areas of South and Central America and has played an important role in the history of human culture there. The modern methods of cocoa bean production for the purpose of the manufacture of modern chocolate are tied to the origin and development of cocoa bean fermentation and processing methods and the science of microbiology. To date, however, there has not been a study that discusses the impacts of both science and culture on the evolution of cocoa beans and cocoa bean processing. This work provides both a detailed overview of the evolution and historical development of cocoa, from its earliest forms to modern chocolate manufacturing, an in-depth discussion of the biochemistry of cocoa bean fermentation, as well as a compilation of primary research studies with details on fermentation methods, the scientific bases of interactions in microbial fermentations, and methods for their investigation, as well as metabolites that are produced. As a result, we present here the major microorganisms among all the ones that have been identified in previous studies. This database will aid researchers seeking standardized inoculants to drive cocoa bean fermentation, as well as serve as a guide for inventorying and assessing other food evolution-related studies regarding traditional and artisanal-based food systems.

Rapid and accurate identification of Xanthomonas citri subspecies citri by fluorescence in situ hybridization

Citrus canker is an economically important disease caused by the bacterial pathogen Xanthomonas citri subsp. citri (Xcc). This organism targets a wide range of citrus plants, including sweet orange, grapefruit, lemon and lime. As Xcc is spread by environmental factors such as wind and rain, it is difficult to control its movement once the disease has established. In order to facilitate monitoring of citrus canker we sought to design a novel diagnostic protocol based on fluorescence in situ hybridization (FISH) for identification of bacterial cells directly from canker pustules without cultivation or DNA extraction. This method was validated for specificity against a range of Xanthomonas species and strains. We show that our assay is extremely rapid (typically requiring between 2 and 3 h), and possesses a similar specificity to existing PCR diagnostic tools. The sensitivity of the assay is comparable to that of an existing PCR-based technique and sufficient for identifying Xcc in symptomatic plant material. The method is easily transferable to diagnosticians without prior experience using FISH.

SIGNIFICANCE AND IMPACT OF THE STUDY

Xanthomonas citri subsp. citri (Xcc) is an aggressive and hardy pathogen of citrus plants worldwide. Outbreaks are difficult and costly to contain and the establishment of citrus canker results in restricted trade. In order to extend the existing toolkit for identification of Xcc we developed a novel diagnostic approach based on fluorescence in situ hybridization. Our approach is of comparable specificity and sensitivity to existing methods but can be performed directly on infected tissue making it significantly faster than existing PCRs, and requiring fewer laboratory resources.

The Metabolically Active Bacterial Microbiome of Tonsils and Mandibular Lymph Nodes of Slaughter Pigs

The exploration of microbiomes in lymphatic organs is relevant for basic and applied research into explaining microbial translocation processes and understanding cross-contamination during slaughter. This study aimed to investigate whether metabolically active bacteria (MAB) could be detected within tonsils and mandibular lymph nodes (MLNs) of pigs. The hypervariable V1-V2 region of the bacterial 16S rRNA genes was amplified from cDNA from tonsils and MLNs of eight clinically healthy slaughter pigs. Pyrosequencing yielded 82,857 quality-controlled sequences, clustering into 576 operational taxonomic units (OTUs), which were assigned to 230 genera and 16 phyla. The actual number of detected OTUs per sample varied highly (23–171 OTUs). Prevotella zoogleoformans and Serratia proteamaculans (best type strain hits) were most abundant (10.6 and 41.8%, respectively) in tonsils and MLNs, respectively. To explore bacterial correlation patterns between samples of each tissue, pairwise Spearman correlations (r_s) were calculated. In total, 194 strong positive and negative correlations |r_s| ≥ 0.6 were found. We conclude that (i) lymphatic organs harbor a high diversity of MAB, (ii) the occurrence of viable bacteria in lymph nodes is not restricted to pathological processes and (iii) lymphatic tissues may serve as a contamination source in pig slaughterhouses. This study confirms the necessity of the EFSA regulation with regard to a meat inspection based on visual examinations to foster a minimization of microbial contamination.

Genetic diversity analysis of isolates belonging to the Photobacterium phosphoreum species group collected from salmon products using AFLP fingerprinting

An accurate amplified fragment length polymorphism (AFLP) method, including three primer sets for the selective amplification step, was developed to display the phylogenetic position of Photobacterium isolates collected from salmon products. This method was efficient for discriminating the three species Photobacterium phosphoreum, Photobacterium iliopiscarium and Photobacterium kishitanii, until now indistinctly gathered in the P. phosphoreum species group known to be strongly responsible for seafood spoilage. The AFLP fingerprints enabled the isolates to be separated into two main clusters that, according to the type strains, were assigned to the two species P. phosphoreum and P. iliopiscarium. P. kishitanii was not found in the collection. The accuracy of the method was validated by using gyrB-gene sequencing and luxA-gene PCR amplification, which confirmed the species delineation. Most of the isolates of each species were clonally distinct and even those that were isolated from the same source showed some diversity. Moreover, this AFLP method may be an excellent tool for genotyping isolates in bacterial communities and for clarifying our knowledge of the role of the different members of the Photobacterium species group in seafood spoilage.

An Integrated Metagenomics/Metaproteomics Investigation of the Microbial Communities and Enzymes in Solid-state Fermentation of Pu-erh tea

Microbial enzymes during solid-state fermentation (SSF), which play important roles in the food, chemical, pharmaceutical and environmental fields, remain relatively unknown. In this work, the microbial communities and enzymes in SSF of Pu-erh tea, a well-known traditional Chinese tea, were investigated by integrated metagenomics/metaproteomics approach. The dominant bacteria and fungi were identified as Proteobacteria (48.42%) and Aspergillus (94.98%), through pyrosequencing-based analyses of the bacterial 16S and fungal 18S rRNA genes, respectively. In total, 335 proteins with at least two unique peptides were identified and classified into 28 Biological Processes and 35 Molecular Function categories using a metaproteomics analysis. The integration of metagenomics and metaproteomics data demonstrated that Aspergillus was dominant fungus and major host of identified proteins (50.45%). Enzymes involved in the degradation of the plant cell wall were identified and associated with the soft-rotting of tea leaves. Peroxiredoxins, catalase and peroxidases were associated with the oxidation of catechins. In conclusion, this work greatly advances our understanding of the SSF of Pu-erh tea and provides a powerful tool for studying SSF mechanisms, especially in relation to the microbial communities present.

Selection of lactic acid bacteria from Brazilian kefir grains for potential use as starter or probiotic cultures

Brazilian kefir is a homemade fermented beverage that is obtained by incubating milk or a brown sugar solution with kefir grains that contribute their different microbiological compositions. It is highly important to isolate and characterize microorganisms from Brazilian kefir grains to obtain starter cultures for the industrial production of a standardized commercial kefir. Thus, the present study aimed to isolate lactic acid bacteria from eight kefir grains that were propagated in milk or sugar solutions from five different locations in Brazil and to select Lactobacillus isolates based on desirable in vitro probiotic properties. One hundred eight isolates from both substrates were identified by amplified ribosomal DNA restriction analysis and/or 16S rRNA gene sequencing and were determined to belong to the following 11 species from the genera: Lactococcus, Leuconostoc, Lactobacillus (L.), and Oenococcus. Leuconostoc mesenteroides, Lactobacillus kefiri, and Lactobacillus kefiranofaciens were isolated only from milk grains, whereas Lactobacillus perolens, Lactobacillus parafarraginis, Lactobacillus diolivorans, and Oenococcus oeni were isolated exclusively from sugar water grains. When the microbial compositions of four kefir grains were evaluated with culture-independent analyses, L. kefiranofaciens was observed to predominant in milk grains, whereas Lactobacillus hilgardii was most abundant in sugar water kefir. Unfortunately, L. hilgardii was not isolated from any grain, although this bacteria was detected with a culture-independent methodology. Fifty-two isolated Lactobacilli were tested for gastric juice and bile salt tolerance, antagonism against pathogens, antimicrobial resistance, and surface hydrophobicity. Three Lactobacillus strains (L. kefiranofaciens 8U, L. diolivorans 1Z, and Lactobacillus casei 17U) could be classified as potential probiotics. In conclusion, several lactic acid bacteria that could be used in combination with yeasts as starter cultures for both milk kefir and sugar water kefir were characterized, and the functional properties of several of the lactobacilli isolated from the kefir grains were suggestive of their possible use as probiotics in both kefir and other dairy products.

Impact of next generation sequencing techniques in food microbiology

Understanding the Maxam-Gilbert and Sanger sequencing as the first generation, in recent years there has been an explosion of newly-developed sequencing strategies, which are usually referred to as next generation sequencing (NGS) techniques. NGS techniques have high-throughputs and produce thousands or even millions of sequences at the same time. These sequences allow for the accurate identification of microbial taxa, including uncultivable organisms and those present in small numbers. In specific applications, NGS provides a complete inventory of all microbial operons and genes present or being expressed under different study conditions. NGS techniques are revolutionizing the field of microbial ecology and have recently been used to examine several food ecosystems. After a short introduction to the most common NGS systems and platforms, this review addresses how NGS techniques have been employed in the study of food microbiota and food fermentations, and discusses their limits and perspectives. The most important findings are reviewed, including those made in the study of the microbiota of milk, fermented dairy products, and plant-, meat- and fish-derived fermented foods. The knowledge that can be gained on microbial diversity, population structure and population dynamics via the use of these technologies could be vital in improving the monitoring and manipulation of foods and fermented food products. They should also improve their safety.

Effects of Ensiling Fermentation and Aerobic Deterioration on the Bacterial Community in Italian Ryegrass, Guinea Grass, and Whole-crop Maize Silages Stored at High Moisture Content

The effects of storage period and aerobic deterioration on the bacterial community were examined in Italian ryegrass (IR), guinea grass (GG), and whole-crop maize (WM) silages. Direct-cut forages were stored in a laboratory silo for 3, 7, 14, 28, 56, and 120 d without any additives; live counts, content of fermentation products, and characteristics of the bacterial community were determined. 2,3-Butanediol, acetic acid, and lactic acid were the dominant fermentation products in the IR, GG, and WM silages, respectively. The acetic acid content increased as a result of prolonged ensiling, regardless of the type of silage crop, and the changes were distinctively visible from the beginning of GG ensiling. Pantoea agglomerans, Rahnella aquatilis, and Enterobacter sp. were the major bacteria in the IR silage, indicating that alcoholic fermentation may be due to the activity of enterobacteria. Staphylococcus sciuri and Bacillus pumilus were detected when IR silage was spoiled, whereas between aerobically stable and unstable silages, no differences were seen in the bacterial community at silo opening. Lactococcus lactis was a representative bacterium, although acetic acid was the major fermentation product in the GG silage. Lactobacillus plantarum, Lactobacillus brevis, and Morganella morganii were suggested to be associated with the increase in acetic acid due to prolonged storage. Enterobacter cloacae appeared when the GG silage was spoiled. In the WM silage, no distinctive changes due to prolonged ensiling were seen in the bacterial community. Throughout the ensiling, Weissella paramesenteroides, Weissella confusa, and Klebsiella pneumoniae were present in addition to L. plantarum, L. brevis, and L. lactis. Upon deterioration, Acetobacter pasteurianus, Klebsiella variicola, Enterobacter hormaechei, and Bacillus gibsonii were detected. These results demonstrate the diverse bacterial community that evolves during ensiling and aerobic spoilage of IR, GG, and WM silages.

Antagonistic lactic acid bacteria isolated from goat milk and identification of a novel nisin variant Lactococcus lactis

Background

The raw goat milk microbiota is considered a good source of novel bacteriocinogenic lactic acid bacteria (LAB) strains that can be exploited as an alternative for use as biopreservatives in foods. The constant demand for such alternative tools justifies studies that investigate the antimicrobial potential of such strains.

Results

The obtained data identified a predominance of Lactococcus and Enterococcus strains in raw goat milk microbiota with antimicrobial activity against Listeria monocytogenes ATCC 7644. Enzymatic assays confirmed the bacteriocinogenic nature of the antimicrobial substances produced by the isolated strains, and PCR reactions detected a variety of bacteriocin-related genes in their genomes. Rep-PCR identified broad genetic variability among the Enterococcus isolates, and close relations between the Lactococcus strains. The sequencing of PCR products from nis-positive Lactococcus allowed the identification of a predicted nisin variant not previously described and possessing a wide inhibitory spectrum.

Conclusions

Raw goat milk was confirmed as a good source of novel bacteriocinogenic LAB strains, having identified Lactococcus isolates possessing variations in their genomes that suggest the production of a nisin variant not yet described and with potential for use as biopreservatives in food due to its broad spectrum of action.