Classical Microbiological Techniques Research Articles

Isolation and Identification of Some Bacteria Associated with Biogas Production from Food Waste and Rumen Content

The goal of this study was to investigate the bacterial community associated with biogas production from food waste and rumen content. Anaerobic mono-digestion and co-digestion were performed using mixture design within Design Expert, resulting in 100 experimental runs. Parameters such as food waste and rumen content, water content, temperature, pH, number of digester agitation per day and retention time were varied during the anaerobic digestion processes. Classical microbiological techniques were used to isolate and identify strict anaerobic and facultative anaerobic bacteria from the food waste and rumen content before and after anaerobic digestion. Sixteen bacterial species belonging to 12 different generae were isolated and identified from the food waste, rumen content and composite digestates obtained from the 100 bio-digesters. These generae included Acetobacterium, Bacteroides, Clostridium, Enterobacter, Escherichia, Lactobacillus, Pseudomonas, Ruminococcus, Staphylococcus, Streptococcus, Syntrophomonas and Syntrophobacter. With the exception of Escherichia coli and Pseudomonas sp., all other bacterial species identified in the substrates were also found in samples of the composite digestates, suggesting that they may have played important roles in the anaerobic digestion process inside the 100 bio-digesters. Overall, this study provides valuable insights into the microbial community structure and function during biogas production from food waste and rumen content. The results could contribute to the development of more efficient and sustainable biogas production processes.

Microorganism community structure: A characterisation of agrosystems from Madeira Archipelago.

Microbial diversity profoundly influences soil ecosystem functions, making it vital to monitor community dynamics to comprehend its structure. Our study focused on six agrosystems in Madeira Archipelago, analysing bacteria, archaea, fungi and AMF through classical microbiology and molecular techniques. Despite distinct edaphoclimatic conditions and management practices, bacterial structures exhibited similarities, with Alphaproteobacteria at 18%-20%, Bacilli at 11%-18% and Clostridia at 9%-14%. The predominance of copiothrophic groups suggested that soil nutrient content was the driver of these communities. Regarding archaea, the communities changed among sites, and it was evident that agrosystems provided niches for methanogens. The Crenarchaeota varied between 15% and 29%, followed by two classes of Euryarchaeota, Methanomicrobia (17%-25%) and Methanococci (4%-32%). Fungal communities showed consistent composition at the class level but had differing diversity indices due to management practices and soil texture. Sordaryomycetes (21%-28%) and Agaricomycetes (15%-23%) were predominant. Conversely, AMF communities appeared to be also influenced by the agrosystem, with Glomus representing over 50% of the community in all agrosystems. These insights into microbial groups' susceptibilities to environmental conditions are crucial for maintaining healthy soil and predicting climate change effects on agrosystems' productivity, resilience and sustainability. Additionally, our findings enable the development of more robust prediction models for agricultural practices.

Investigations on Microbes Attached to the Cuticle of Phytonematodes.

Nematodes form various associations with soil microbiome. Experimental studies on nematode-attached microbes can improve mechanistic understanding of these associations and lead to new discoveries relevant for the field of nematode biocontrol. Microbial attachment to the surface of phytonematodes is very specific and influenced by a multitude of factors, including the designation of nematodes and microbes, environmental and biological factors in soil, time of incubation, and the ratio and evolutionary trajectories between nematodes and microbes. Here, we describe how the classical nematological and microbiological techniques can be coupled with the advanced molecular tools to study the microbial attachment to phytonematodes in soil. We focus on the characterization of nematode-attached microbes using classical microbiological approaches and high-throughput amplicon sequencing and on the effects of nematode-attached microbes on plant defense responses.

Fast and Non-Invasive Evaluation of Yeast Viability in Fermentation Processes Using Raman Spectroscopy and Machine Learning

Fermentation processes used for producing alcoholic beverages such as beer, wine, and cider have a long history, having been developed early on across different civilizations. In most instances, yeast strains are used for fermentation processes, e.g., at breweries and wineries. Monitoring of yeast viability, cell count, and growth behavior is essential to ensure a controlled fermentation process. However, classical microbiological techniques to monitor fermentation process parameters are time-consuming and require sampling, along with the risk of contamination. Nowadays, industries are moving toward automation and digitalization. This necessitates state-of-the-art process analytical technologies to ensure an efficient and controlled process to obtain high-quality product outputs. Hence, there is a strong need for a fast, non-invasive, and generally applicable method to evaluate the viability of yeast cells during fermentation to warrant the standardization and purity of produced products in industrial applications. The aim of our study is to discriminate between viable and non-viable yeast in various culture media using Raman spectroscopy (RS) followed by data analysis with machine learning (ML) tools. These techniques allow for rapid, non-invasive analysis addressing the limitations of traditional methods. The present work primarily focuses on the evaluation of RS combined with predictive ML models in a non-real-time setting. Our goal is to adapt these techniques for future application in real-time monitoring and determination of yeast viability in biotechnological processes. We demonstrate that RS, in combination with ML, is a promising tool for non-invasive inline monitoring of fermentation processes.

The Endophytic Microbiome of Wild Grapevines Vitis amurensis Rupr. and Vitis coignetiae Pulliat Growing in the Russian Far East.

Many grape endophytic microorganisms exhibit high potential for suppressing the development of grape diseases and stimulating grapevine growth and fitness, as well as beneficial properties of the crop. The microbiome of wild grapevines is a promising source of biocontrol agents, which can be beneficial for domesticated grapevines. Using next-generation sequencing (NGS) and classical microbiology techniques, we performed an analysis of bacterial and fungal endophytic communities of wild grapevines Vitis amurensis Rupr. and Vitis coignetiae Pulliat growing in the Russian Far East. According to the NGS analysis, 24 and 18 bacterial taxa from the class level were present in V. amurensis and V. coignetiae grapevines, respectively. Gammaproteobacteria (35%) was the predominant class of endophytic bacteria in V. amurensis and Alphaproteobacteria (46%) in V. coignetiae. Three taxa, namely Sphingomonas, Methylobacterium, and Hymenobacter, were the most common bacterial genera for V. amurensis and V. coignetiae. Metagenomic analysis showed the presence of 23 and 22 fungi and fungus-like taxa of class level in V. amurensis and V. coignetiae, respectively. The predominant fungal classes were Dothideomycetes (61-65%) and Tremellomycetes (10-11%), while Cladosporium and Aureobasidium were the most common fungal genera in V. amurensis and V. coignetiae, respectively. A comparative analysis of the endophytic communities of V. amurensis and V. coignetiae with the previously reported endophytic communities of V. vinifera revealed that the bacterial biodiversity of V. amurensis and V. coignetiae was similar in alpha diversity to V. vinifera's bacterial biodiversity. The fungal alpha diversity of V. amurensis and V. coignetiae was statistically different from that of V. vinifera. The beta diversity analysis of bacterial and fungal endophytes showed that samples of V. vinifera formed separate clusters, while V. amurensis samples formed a separate cluster including V. coignetiae samples. The data revealed that the endophytic community of bacteria and fungi from wild V. amurensis was richer than that from V. coignetiae grapes and cultivated V. vinifera grapes. Therefore, the data obtained in this work could be of high value in the search for potentially useful microorganisms for viticulture.

Tailored Gas Sensors as Rapid Technology to Support the Jams Production

Nowadays, innovation in food technologies is fundamental and consumers are increasingly aware and demanding. To create a final product that is more and more appealing, health and safety guidelines are pushing towards new challenges. It is precisely due to the high quality required by the producers that the aim discussed in this project has been conceived. Until today, the controls on the entire production line have been slowed down by the limitations of the technologies involved, including the high cost of instrumentation for microbiological analysis, the need for qualified personnel to carry them out, the long execution times and the invasiveness of the techniques themselves. This project has, therefore, proposed a user-friendly solution that is minimally invasive, fast and at a lower cost. This system makes use of classical microbiological analysis and, in parallel, use of an innovative electronic-nose small sensor system (S3+), which can be trained to recognize the volatile fingerprint of a specific product and customized for a specific use. The aim of this project was to develop a system that is able to detect the mold contamination on fruit and vegetable jams and marmalades, using a new kind of innovative metal semiconductor gas sensor (MOS) device. The application of this technology has, therefore, made it possible to classify various samples of uncontaminated and contaminated fruit and vegetable preparations. Thanks to the classification implemented by a data-driven algorithm, it has been possible to build an anomaly detector that is able to recognize the occurrence of possible contamination, thus acting as an early alert system in the food chain. All this will occur in less than 1 min once the system is trained, in contrast with classical microbiological or chemical techniques that normally require longer timeframes to obtain a result and involve the use of reagents, increasing the costs.

Study of the Impact of Lactiplantibacillus plantarum I on the Health Status of Queen Scallop Aequipecten opercularis

The objective of this research was to isolate and identify lactic acid bacteria living in the digestive tract of the queen scallop Aequipecten opercularis and further test it as a probiotic culture on the growth of the bivalve during one month in captivity. Classic microbiological techniques (API and MALDI TOF) were used and four different strains of Lactiplantibacillus and one Lactococcus were identified and further analyzed, namely: Lactiplantibacillus plantarum I, Lactiplantibacillus plantarum 1, Lactiplantibacillus plantarum 2, Lactococcus lactis, and Lactiplantibacillus brevis. The isolated cultures were further tested for the highest antimicrobial activity towards the most common marine pathogens and survival at different temperatures and pH levels. The strain Lactiplantibacillus plantarum I had the best results, with the highest antimicrobial activity (77–85% pathogen growth inhibition) and the best safety standards showing no antibiotic resistance, and no ability to synthesize biogenic amine and degrade red blood cells. Considering all the abovementioned characteristics, the strain Lpb. plantarum I was further tested on the growth and health status of the bivalve Aequipecten opercularis during a month of cultivation in captivity. The results showed that the incorporation of Lpb. plantarum I led to a decrease in the quantity of test microorganisms in the bivalve and an increase in both the growth rate weight and growth rate length of the queen scallop A. opercularis. Furthermore, the scallops fed with the algae culture + Lpb. plantarum I gained significantly higher meat yield (33.15 ± 2.63%) compared with the control scallops fed only with the algae culture (29.66 ± 2.87%). To conclude, the results from this research indicate that including Lpb. plantarum I as a dietary supplement could enhance growth performance and serve as a feasible approach to reduce pathogen levels while cultivating A. opercularis in captivity.

Differences in the composition of the bacterial element of the urinary tract microbiome in patients undergoing dialysis and patients after kidney transplantation.

The development of molecular biology methods and their application in microbial research allowed the detection of many new pathogens that cause urinary tract infections (UTIs). Despite the advances of using new research techniques, the etiopathogenesis of UTIs, especially in patients undergoing dialysis and patients after kidney transplantation, is still not fully understood. This study aimed to characterize and compare the composition of the bacterial element of the urinary tract microbiome between the groups of patients undergoing dialysis (n = 50) and patients after kidney transplantation (n = 50), with positive or negative urine culture, compared to healthy individuals (n = 50). Asymptomatic bacteriuria was observed in 30% of the urine cultures of patients undergoing dialysis and patients after kidney transplantation, with Escherichia coli as the most dominant microorganism (73%) detected with the use of classical microbiology techniques. However, differences in the bacterial composition of the urine samples between the evaluated patient groups were demonstrated using the amplicon sequencing. Finegoldia, Leptotrichia, and Corynebacterium were found to be discriminative bacteria genera in patients after dialysis and kidney transplantation compared to the control group. In addition, in all of urine samples, including those without bacteriuria in classical urine culture, many types of bacteria have been identified using 16S rRNA sequencing. The revealed microbial characteristics may form the basis in searching for new diagnostic markers in treatment of patients undergoing dialysis and patients after kidney transplantation.

Evaluation of Malolactic Starters in White and Rosé Winemaking of Moschofilero Wines

The aim of the present study was to induce malolactic fermentation (MLF) after alcoholic fermentation (AF) of must of the Moschofilero cultivar, the only ‘gris’ native grape variety that is cultivated in Greece. For this purpose, Oenococcus oeni strains Viniflora® CH16, Viniflora® Oenos and Viniflora® CiNe were inoculated after the completion of AF driven by the Saccharomyces cerevisiae strain UCLM S325. Growth of the aforementioned starter cultures was assessed during fermentation by classical microbiological techniques, and verification of their dominance was performed by (GTG)5 fingerprinting. Assessment of standard enological parameters and colorimetric analysis were performed by established approaches. Identification and quantification of organic acids, ethanol and glycerol was performed by high performance liquid chromatography (HPLC), while the solid-phase microextraction method (SPME), coupled with gas chromatography/mass spectrometry (GC/MS), was employed for the identification and quantification of volatile compounds. Finally, sensory analysis took place according to ISO 13299:2016. The suitability of the starter cultures employed to drive AF and MLF was exhibited; AF and MLF of the white and rosé wines were completed after 15 days. Upon completion of AF, substantial differences were observed in the chemical characteristics of the white and rosé wines, which were also reflected in the balance descriptor. MLF also resulted in significant changes. In all cases total acidity decreased and volatile acidity and pH value increased, while the vanilla and butter descriptors increased. Interestingly, the color intensity of the rosé wines also increased. A series of strain-dependent changes in the chemical composition and sensory analysis of both white and rosé wines was also observed.

The pig gut microbiota analysis techniques, a comparison

Abstract The gastrointestinal tract microbiota composition can be radically different among pigs with regards to their health, age, feed intake, breed, and local conditions making its investigation into an important and multifaceted tool for evaluating the effects of new breeding and feeding schemes and animal welfare. For a long time, scientists have relied upon classical microbiology techniques to identify the makeup of bacterial populations from the gastrointestinal tract. Since their conceptions, high throughput sequencing and other molecular techniques contributed immensely in better understanding the pig gut microbiota and its makeup. Since many techniques to identify and quantify the microbiota are based on bacterial gene targets, they can, be used to determine the relation between different bacterial taxons and developmental processes, how it influences the host metabolism or diseases impact. In our review, we offer an overview of the different methods employed in the assay of the gut microbiota of pigs along with differences and pitfalls.

A Peek into the Bacterial Microbiome of the Eurasian Red Squirrel (Sciurus vulgaris).

Simple SummaryThe Eurasian red squirrel can be found from Europe and Asia, but due to habitat destruction or fragmentation, other squirrel species, and infectious diseases, in some European countries, the species finds itself at the brink of extinction. In such areas, captive breeding and release into the wild may be part of the solution to repopulation. Captivity, nonetheless, has been shown to greatly influence the species’ microbiota relative to wild animals. Therefore, evaluation of the microbiota in both captive and wild squirrels could elucidate if special living conditions are needed in order to augment the survival rate of specimens reintroduced into the wild. Furthermore, the microflora profile of healthy red squirrels raised in captivity would support clinicians in addressing infectious disease episodes and also raise awareness of the zoonotic risk. Hence, this study documented the bacterial species carried by S. vulgaris, disclosing overall similarities and variability patterns of the microbiota identified in individuals from two different living environments. We predicted less diversity in the captive animals’ microbiota, due to the restrictive diet and unchanging living conditions, but a higher prevalence of zoonotic bacteria, due to the proximity of humans and of other domestic species. In this respect, samples (n = 100) were taken from five body regions of 20 red squirrels, both free-ranging and bred in captivity, processed by classical microbiology techniques and further identified by biochemical assay (VITEK®2 Compact System). A relatively poor bacterial community, comprising 62 bacterial strains belonging to 18 species and 8 different genera, was identified. Most of these microorganisms were reported for the first time in S. vulgaris. The results suggest that the resident aerobic microbiota of S. vulgaris does not differ significantly depending on living environments, neither in diversity, nor in quantity of the cultivable isolates.Sciurus vulgaris (the Eurasian red squirrel) is native to Europe and Asia, but due to habitat destruction or fragmentation, interspecific competition, and infectious diseases, especially in European island areas the species finds itself at the brink of extinction. The repopulation of such bare habitats requires healthy squirrel specimens, either translocated from other wild habitats or reintroduced to the wilderness following captive breeding. Captivity, nonetheless, has shown an immense capacity to reshape the structure of wild species’ microbiota, adapting it to the less diverse diet and fewer environmental challenges. Therefore, assessing the differences between “wild” and “captive” microbiota in this species could elucidate if special living conditions are needed in order to augment the survival rate of specimens reintroduced into the wild. Furthermore, the microflora profile of the normal flora of healthy red squirrels raised in captivity could support clinicians in addressing infectious diseases episodes and also raise awareness on the zoonotic risk. Hence, this study aimed at documenting the bacterial species carried by S. vulgaris, disclosing overall similarities and variability patterns of the microbiota identified in individuals from two different living environments. We anticipated that the bacterial community would be less diverse in individuals raised in captivity, owing to their restrictive diet and to unchanging conditions in the enclosure. We also hypothesized that there would be a higher prevalence of zoonotic microorganisms in the captive animals, due to the proximity of humans and of other domestic species. To test this, samples (n = 100) were taken from five body regions of 20 red squirrels, both free-ranging and bred in captivity, processed by classical microbiology techniques, and further identified by biochemical assay (VITEK®2 Compact System). A relatively poor bacterial community, comprising 62 bacterial strains belonging to 18 species and 8 different genera, was identified. Most of these microorganisms were reported for the first time in S. vulgaris. With no discrimination between living environments, the highest prevalence (p < 0.001), was registered in Staphylococcus sciuri (60%; 12/20), followed by Escherichia coli (45%; 9/20) and Bacillus cereus (35%; 7/20). The results suggest unremarkable differences in diversity and richness of the resident aerobic microbiota of S. vulgaris, in relation to the living environment.

The Historical Development of Cultivation Techniques for Methanogens and Other Strict Anaerobes and Their Application in Modern Microbiology.

The cultivation and investigation of strictly anaerobic microorganisms belong to the fields of anaerobic microbial physiology, microbiology, and biotechnology. Anaerobic cultivation methods differ from classic microbiological techniques in several aspects. The requirement for special instruments, which are designed to prevent the contact of the specimen with air/molecular oxygen by different means of manipulation, makes this field more challenging for general research compared to working with aerobic microorganisms. Anaerobic microbiological methods are required for many purposes, such as for the isolation and characterization of new species and their physiological examination, as well as for anaerobic biotechnological applications or medical indications. This review presents the historical development of methods for the cultivation of strictly anaerobic microorganisms focusing on methanogenic archaea, anaerobic cultivation methods that are still widely used today, novel methods for anaerobic cultivation, and almost forgotten, but still relevant, techniques.

A rotating bioreactor for the production of biofilms at the solid–air interface

Conventional bioreactors are typically developed for the production of planktonic bacteria or submerged biofilms. In contrast, reactors for the continuous production of biofilms at the solid-air interface are scarce, and they require specific conditions since the bacteria need to attach firmly to the surface and require a permanent supply of moisture and nutrients from below. Recently, research from the field of civil engineering has pinpointed an increased need for the production of terrestrial biofilms: several variants of Bacillus subtilis biofilms have been shown to be useful additives to mortar that increase the water repellency, and, thus, the lifetime of the cementitious material. The bioreactor introduced here allows for the continuous production of such bacterial biofilms at the solid-air interface, and they have virtually identical properties as biofilms cultivated via classical microbiological techniques. This is made possible by equipping a rotating cylinder with a porous membrane that acts as a solid growth substrate the bacterial biomass can form on. In this configuration, nutrient supply is enabled via diffusive transport of a suitable growth medium from the core volume of the cylindrical reactor to the membrane surface. In addition to cultivating bacterial biofilms, the versatile and adaptable set up introduced here also enables the growth of other microbial organisms including the yeast Saccharomyces cerevisiae and the fungus Penicillium chrysogenum.

Haemophilus Influenzae Type B-Diseases

Haemophilus influenzae is a small Gram negative coccobacillus colonizing the respiratory tract of humans. The bacterium may cause direct local infections like otitis media, as well as severe invasive diseases like meningitis. In the prevaccine era, of the 6 capsular serotypes (a–f), type b caused the majority of invasive disease cases, whereas “nontypeable H. influenzae” (NTHi) and other capsular types predominate today. H. influenzae infections affect mainly children &lt;5 years as well as persons &gt;60 years with underlying diseases like COPD. Diagnosis of Hib disease is performed by classical microbiological culture techniques, antigen detection tests and polymerase chain reaction from blood samples, CSF or puncture samples. If untreated or if treatment is delayed, invasive Hib diseases may result in severe consequences such as hearing loss, chronic seizures, learning disabilities, and even death. Safe and effective polysaccharide-conjugate vaccines have been available for children for almost 30 years, reducing invasive Hib-incidences from about 60 to &lt;1 / 105. Today, largely DTP-based Hib-combinations are used. After the primary series with 2 or 3 doses depending on the product and local recommendations, a booster dose in the second year of life is needed to ensure long-term protection.

The Microbiota of Grana Padano Cheese. A Review.

Grana Padano (GP) is the most appreciated and marketed cheese with Protected Designation of Origin in the world. The use of raw milk, the addition of undefined cultures (defined as ‘sieroinnesto naturale’), the peculiar manufacturing proces, and the long ripening make the cheese microbiota play a decisive role in defining the quality and the organoleptic properties of the product. The knowledge on the microbial diversity associated with GP has been the subject, in recent years, of several studies aimed at understanding its composition and characteristics in order, on the one hand, to improve its technological performances and, on the other hand, to indirectly enhance the nutritional quality of the product. This review aims to briefly illustrate the main available knowledge on the composition and properties of the GP microbiota, inferred from dozens of studies carried out by both classical microbiology techniques and metagenomic analysis. The paper will essentially, but not exclusively, be focused on the lactic acid bacteria (LAB) derived from starter (SLAB) and the non-starter bacteria, both lactic (NSLAB) and non-lactic, of milk origin.

Emerging diversity and ongoing expansion of the genus Brucella.

Remarkable genetic diversity and breadth of host species has been uncovered in the Brucella genus over the past decade, fundamentally changing our concept of what it means to be a Brucella. From ocean fishes and marine mammals, to pond dwelling amphibians, forest foxes, desert rodents, and cave-dwelling bats, Brucella have revealed a variety of previously unknown niches. Classical microbiological techniques have been able to help us classify many of these new strains but at times have limited our ability to see the true relationships among or within species. The closest relatives of Brucella are soil bacteria and the adaptations of Brucella spp. to live intracellularly suggest that the genus has evolved to live in vertebrate hosts. Several recently discovered species appear to have phenotypes that are intermediate between soil bacteria and core Brucella, suggesting that they may represent ancestral traits that were subsequently lost in the traditional species. Remarkably, the broad relationships among Brucella species using a variety of sequence and fragment-based approaches have been upheld when using comparative genomics with whole genomes. Nonetheless, genomes are required for fine-scale resolution of many of the relationships and for understanding the evolutionary history of the genus. We expect that the coming decades will reveal many more hosts and previously unknown diversity in a wide range of environments.

In silico analysis of the antimicrobial activity of phytochemicals: towards a technological breakthrough

BackgroundThe complications associated with infections from pathogens increasingly resistant to traditional drugs lead to a constant increase in the mortality rate among those affected. In such cases the fundamental purpose of the microbiology laboratory is to determine the sensitivity profile of pathogens to antimicrobial agents. This is an intense and complex work often not facilitated by the test's characteristics. Despite the evolution of the Antimicrobial Susceptibility Testing (AST) technologies, the technological breakthrough that could guide and facilitate the search for new antimicrobial agents is still missing. MethodsIn this work, we propose the experimental use of in silico instruments, particularly feedforward Multi-Layer Perceptron (MLP) Artificial Neural Network, and Genetic Programming (GP), to verify, but also to predict, the effectiveness of natural and experimental mixtures of polyphenols against several microbial strains. ResultsWe value the results in predicting the antimicrobial sensitivity profile from the mixture data. Trained MLP shows very high correlations coefficients (0,93 and 0,97) and mean absolute errors (110,70 and 56,60) in determining the Minimum Inhibitory Concentration and Minimum Microbicidal Concentration, respectively, while GP not only evidences very high correlation coefficients (0,89 and 0,96) and low mean absolute errors (6,99 and 5,60) in the same tasks, but also gives an explicit representation of the acquired knowledge about the polyphenol mixtures. ConclusionsIn silico tools can help to predict phytobiotics antimicrobial efficacy, providing an useful strategy to innovate and speed up the extant classic microbiological techniques.

A review of Listeria monocytogenes from meat and meat products: Epidemiology, virulence factors, antimicrobial resistance and diagnosis.

Listeria monocytogenes is a zoonotic food-borne pathogen that is associated with serious public health and economic implications. In animals, L. monocytogenes can be associated with clinical listeriosis, which is characterised by symptoms such as abortion, encephalitis and septicaemia. In human beings, listeriosis symptoms include encephalitis, septicaemia and meningitis. In addition, listeriosis may cause gastroenteric symptoms in human beings and still births or spontaneous abortions in pregnant women. In the last few years, a number of reported outbreaks and sporadic cases associated with consumption of contaminated meat and meat products with L. monocytogenes have increased in developing countries. A variety of virulence factors play a role in the pathogenicity of L. monocytogenes. This zoonotic pathogen can be diagnosed using both classical microbiological techniques and molecular-based methods. There is limited information about L. monocytogenes recovered from meat and meat products in African countries. This review strives to: (1) provide information on prevalence and control measures of L. monocytogenes along the meat value chain, (2) describe the epidemiology of L. monocytogenes (3) provide an overview of different methods for detection and typing of L. monocytogenes for epidemiological, regulatory and trading purposes and (4) discuss the pathogenicity, virulence traits and antimicrobial resistance profiles of L. monocytogenes.

Metagenomic analysis of the microbial community in Çal Cave soil to elucidate biotechnological potential

Turkey has a great number of karstic caves which are unexplored and have unknown microbial diversity. The biodiversity characterisation of these caves has not yet been systematically studied from the molecular point of view. Çal Cave in Trabzon, Turkey is one of the important karstic caves. In the present study, a metagenomic approach was used to explore the microbial diversity of Çal Cave for the first time to assess the potential of gene sources. Detailed taxonomic profiling was defined by sequencing all environmental genomes instead of a specific marker gene such as 16S rRNA which only targets prokaryotes. Taxonomic analysis revealed that the Çal Cave soil sample was represented as 98% Bacteria, 2% Eukaryota, 0.3% Archaea, and 0.01% Virus. Results showed that, the 31 distinct bacterial phyla represented in the Çal Cave soil sample were dominated by Actinobacteria (65%) and Proteobacteria (31%). The most dominant bacterial genus was Streptomyces. Among the 2% Eukaryotic population, the largest phylum was Ascomycota and it was mostly represented as Sordariomycetes. It was determined that 77% of Archaea was Halobacteria. The most abundant class of viruses dwelling in Çal Cave was Caudovirales. 91.61% of total readings could not be classified into any specific kingdom. Overall, classified and unclassified data verify that there exists vast microbial biodiversity in Çal Cave which could not be identified with classical microbiology techniques, and this microbial diversity provides a promising gene source for novel enzyme and bioactive compounds to be used in biotechnological applications.

External contamination of broilers by Campylobacter spp. increases from the farm to the slaughterhouse

ABSTRACT 1. In this study, classical and molecular microbiological methods for detection and quantification of Campylobacter spp. were used to estimate their prevalence in faecal samples and skin swabs collected from 31 broiler flocks (20 farms) in Portugal, and measure the impact of transport-related factors on the expected rising excretion rates from the farm to the slaughterhouse. 2. Data on husbandry practices and transport conditions were gathered, including time in transit, distance travelled or ante-mortem plant-holding time. 3. A generalised linear mixed model was used to evaluate the significance of a potential post-transport rise in Campylobacter spp. counts and to assess risk determinants. 4. At least one flock tested positive for Campylobacter spp. in 80% of the sampled farms. At the slaughterhouse, Campylobacter spp. were detected in all faecal samples, C. jejuni being the most commonly isolated. 5. A post-transport rise of Campylobacter spp. counts from skin swabs was observed using classical microbiological methods (from a mean of 1.43 to 2.40 log10 CFU/cm2) and molecular techniques (from a mean of 2.64 to 3.31 log10 genome copies/cm2). 6. None of the husbandry practices or transport-related factors were found to be associated with Campylobacter spp. counts. 7. This study highlights the need for more research to better understand the multi-factorial nature of Campylobacter spp., a public health threat that was found to be highly prevalent in a sample of Portuguese poultry farms.