Appl. Microbiol., Volume 4, Issue 4 (December 2024) – 8 articles

Salmonella has had a long and intimate relationship with humans and continues to raise concerns for human health, but this close bond also provides opportunities for new therapeutics and treatments. Although Salmonella enterica serovar Typhi is the principal organism that comes to mind in terms of death and morbidity, it is the non-typhoidal Salmonellae that have the most health and economic implications. The developed world has had a challenging relationship with Salmonella, particularly in the UK and the EC/EU, experiencing significant Salmonella outbreaks in the 1980s and 1990s. As a consequence, the research focus was on understanding the nature of infection in food animals and on developing ways and means of controlling zoonotic infections. This led to the development of numerous model systems for the study of Salmonella both in vitro and in vivo. The introduction of vaccination has all but eliminated Salmonella in eggs and reduced perceived risk held by the general public. At the same time as Salmonella in eggs was being brought under control in the UK and EU, the danger posed by antibiotic resistance was beginning to emerge. In the past, with the efficacy of antibiotics against Gram-negative bacteria being unchallenged, there was limited focus on the threat posed by antibiotic resistance in non-typhoidal Salmonella. However, the identification of Salmonella as the first ‘multidrug-resistant’ organism, the presence of invasive non-typhoidal Salmonella in North Africa and the emergence of monophasic Salmonella enterica serovar Typhimurium across Europe, Asia and the Americas have prompted renewed interest in Salmonella research, particularly in the context of non-infectious disease, biofilm studies and antibiotic resistance. At the same time, research has continued to develop ways of taking advantage of what Salmonella offers in the way of pathogenic factors and the therapeutic and treatment applications in areas such as vaccine development, cancer therapeutics and drug delivery and the role of Salmonella in non-infectious diseases supported by developments in molecular and genomic methods. Full article

This review presents an approach to the incorporation of cyanobacteria and microalgae in yogurts and explores their impact on the nutritional, rheological, sensory, and antioxidant qualities of these products. First, the yogurt market context and its relationship with nutritional quality are outlined, emphasizing the quest for functional foods that meet consumer demands for healthy and nutritious products. A discussion of the incorporation of cyanobacteria and microalgae, especially Spirulina platensis, in foods, particularly yogurt, is then presented, highlighting the nutritional and functional benefits that this type of biomass can provide to the final product. The fermentation process and the quantity of algae to be incorporated are discussed to understand their fundamental role in the characteristics of the final product. In addition, this article considers some challenges such as sensory and rheological changes in the product resulting from the interaction of milk, algal biomass, and the fermentation process. Addressing these challenges involves delineating how these interactions contribute to changes in the traditionally consumed product, while obtaining a pro- and prebiotic product is crucial for creating an innovative dairy product that diversifies the market for derived dairy products with increased functional properties. Full article

The emergence of antimicrobial resistance (AMR) in pathogens transmitted through food poses a significant threat to global public health, complicating infection treatment and increasing mortality rates. This review explores the role of resistome mapping as a crucial tool for understanding the transmission dynamics of antimicrobial resistance genes (ARGs) in foodborne pathogens, such as Salmonella, Escherichia coli, Listeria monocytogenes, and Campylobacter spp., as well as various techniques for resistome mapping, such as metagenomic sequencing, PCR-based methods, and whole-genome sequencing (WGS), highlighting the significance of horizontal gene transfer (HGT) as a key mechanism for ARG dissemination in foodborne pathogens. Additionally, we investigated the influence of agricultural practices and environmental factors on AMR development, highlighting the critical need for improved surveillance, antibiotic stewardship, and global collaboration to mitigate the spread of resistant ARGs through the food chain. The perceptions gained from resistome mapping play an essential role in developing effective approaches to address AMR and to ensure food safety. Full article

A conventional, group-specific PCR method was developed to identify each of the four previously defined major taxa (Myoviridae, Siphoviridae, Podoviridae and Microviridae) of somatic coliphages and used to classify isolates from sewage. Somatic coliphage infectivity detection, occurrence and survival in primary human sewage effluent was observed over time to further understand the presence and behavior of the groups of somatic coliphages at two environmental temperatures (4 and 25 °C). Over time, the taxonomic composition of the somatic coliphage population in sewage changed, with the Microviridae family becoming the most prevalent family in the sewage population after several weeks. Based on their persistence and prevalence in environmental waters, phages belonging to the Microviridae family provide supporting information on sewage contamination and possibly of human enteric viruses in sewage-contaminated water. Full article

This study explores the integration of genome sequencing and digital droplet polymerase chain reaction (ddPCR)-based methods for tracking the diversity of COVID-19 variants in wastewater. The research focuses on monitoring various Omicron subvariants during a period of significant viral evolution. Genome sequencing, particularly using Oxford Nanopore Technology (ONT), provides a detailed view of emerging variants, surpassing the limitations of PCR-based detection kits that rely on known sequences. Of the 43 samples analyzed, 39.5% showed matching results between the GT Molecular ddPCR kits and sequencing, though only 4% were exact matches. Some mismatches occurred due to newer subvariants like XBB and BQ.1, which the ddPCR kits could not detect. This emphasized the limitations of ddPCR kits, which rely on known variant sequences, while sequencing provides real-time data on emerging variants, offering a more comprehensive view of circulating strains. This study highlights the effectiveness of combining these methodologies to enhance early detection and inform public health strategies, especially in regions with limited clinical sequencing capabilities. Full article

V. lutrae is an emerging human pathogen attributed to increasing hospitalization cases in humans; however, its biology and epidemiology are under-explored. The present study explored V. lutrae recovery, prevalence, and biology. A two-step enrichment method (i.e., step 1, nourishment; step 2, heat, 80 °C, 20 min) and thiosulfate–citrate–bile salts–sucrose (TCBS) agar were employed for recovering V. lutrae in raw seafood. Bacterial colonies were streaked for purification before 16S rRNA bacterial identification. Confirmed V. lutrae isolates were analyzed for their culture-challenged turbidity and virulence. Of 41 bacterial isolates, 9 confirmed V. lutrae, including regular (33%; nourished 24 h) and heat-resistant (67%; nourished 48 h plus heating) isolates, were exclusively from yellow colonies (i.e., TCBS) and were exclusively recovered from nourished shrimp (78%) and crab (22%) only. The culture and virulence biology revealed that they could diversely tolerate salinity (i.e., 0–17.5% additional NaCl), pasteurization (63 °C, 8 h), oxygen availability, and antibiotic sensitivity (i.e., erythromycin, gentamicin, and vancomycin). Further, this pathogen exhibited no visible hemolytic and alkalization activities. Emerging foodborne pathogens could readily evade the established food safety regime. The present study reveals systematic investigation and diverse phenotypes of V. lutrae to enhance its detection and contribute to public health initiatives. Full article

With the anticipated population growth by 2050, the demand for high-quality protein for human consumption is set to rise. To enhance the sustainability of U.S. cattle production, producers and researchers have traditionally concentrated on improving the feed efficiency of steers through advancements in genetics, nutrition, and microbiome tools, resulting in a more marketable beef product. However, without successful pregnancies, there would be no marketable animals to feed. Despite extensive research on hormonal impacts on cattle physiology, including nutrition and reproduction, there is limited knowledge about how the rumen microbial environment is impacted by pregnancy and feed efficiency in female beef cattle. Understanding the rumen microbiome’s role in feed efficiency and its response to hormonal changes during pregnancy is crucial for advancing sustainable beef cattle production. Therefore, this review highlights the importance of understanding the microbial dynamics in the rumen of pregnant beef females. Although progress has been made, gaps remain in understanding how varying nutritional requirements throughout pregnancy affect the rumen microbiome, highlighting the need for continued research. Addressing these areas will lead to more efficient and sustainable cattle production practices, benefiting beef production and contributing to global food security. Full article

This study explores the relationship between filamentous fungi and dental caries in isolated indigenous communities in Siltepec, Chiapas, Mexico. A total of 37 oral swabs were collected, with 22 participants harboring filamentous fungi, primarily from the genus Cladosporium. Statistical analysis using Student’s t-test and the Mann–Whitney U test revealed a significant reduction in extensive and fully cavitated caries (p < 0.0001) in individuals with fungi, while those without fungi exhibited higher rates of dental decay. Participants with fungi had a higher prevalence of healthy teeth and incipient caries. The findings suggest that traditional maize-based diets, particularly fermented beverages like pozol, may promote the growth of beneficial fungi in the oral microbiome, offering a protective effect against dental caries through microbial competition and the alteration of the oral environment. These results underline the need for further research into the long-term impact of traditional diets on oral health and the potential use of natural substances, such as probiotics and plant-based antimicrobials, to maintain oral homeostasis and prevent caries. Full article