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Appl. Microbiol., Volume 4, Issue 4 (December 2024) – 21 articles

Cover Story (view full-size image): Salmonella, with its new and emerging serotypes and variants with resistance to antibiotics, as well as its ability to form biofilms, enhances its survival in hostile environments. Hence, there is potential for Salmonella as a candidate for therapeutic agents, including vaccines. Attenuated strains have potential as a delivery system for anticancer drugs and for carrying drugs or therapeutic proteins that can be released directly in the tumor microenvironment. Salmonella has potential as a vector for delivering therapeutic genes, being engineered to carry genetic material to correct genetic disorders or to enhance the body’s response to infections or tumors. However, concerns around safety remain. Advances in genetic engineering and microbiology may, in time, overcome these concerns, opening the way for Salmonella as a therapeutic tool. View this paper
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12 pages, 7794 KiB  
Article
The Effects of Red–Blue Light on the Growth and Astaxanthin Production of a Haematococcus pluvialis Strain Isolated from Southern Thailand
by Tassnapa Wongsnansilp and Manoch Khamcharoen
Appl. Microbiol. 2024, 4(4), 1745-1756; https://doi.org/10.3390/applmicrobiol4040117 - 20 Dec 2024
Abstract
Light is a crucial factor that influences algal production. Red and blue light have been widely utilized in two-stage cultivation approaches due to their significant roles in promoting algal growth and pigment accumulation. To investigate the effects of light on the growth of [...] Read more.
Light is a crucial factor that influences algal production. Red and blue light have been widely utilized in two-stage cultivation approaches due to their significant roles in promoting algal growth and pigment accumulation. To investigate the effects of light on the growth of an isolated wild strain of Haematococcus pluvialis (H. pluvialis) and its astaxanthin production, white light (30 μmol photons m−2 s−1) mixed with various light intensities of red or blue light were applied to the algal culture during the stationary phase. The results indicate that white light combined with low-intensity red light (5 μmol photons m−2 s−1) significantly enhanced algal growth, achieving a maximum biomass of 0.43 g/L. The pH values in cultures exposed to all treatments involving red-light intensities were lower than those under solely white light conditions. Furthermore, the combination of white light and low-intensity red light improved photosynthetic efficiency, carbonic anhydrase (CA) activity, and the rate of CO2 fixation. In contrast, the mixture of white light with blue light at 15 μmol photons m−2 s−1 facilitated astaxanthin production, resulting in a maximum astaxanthin content of 6.75 mg/L. Blue light was found to increase reactive oxygen species levels, leading to elevated malondialdehyde (MDA) concentrations and enhanced catalase (CAT) activity. These findings suggest that red light plays a crucial role in activating CA activity and promoting cellular CO2 fixation, which helps maintain the stability of the culture medium pH and ultimately supports algal growth. Conversely, blue light contributes to photoprotective processes by accumulating protective pigments and enhancing the activity of protective enzymes; together, these mechanisms mitigate reactive oxygen species generated by blue light exposure. Our experimental results provide valuable insights for optimizing two-stage cultivation practices for isolated strains of H. pluvialis. Full article
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16 pages, 1350 KiB  
Article
Phenotypic and Genotypic Characterization of Antimicrobial Resistance in Salmonella enterica Serovars from Colombian Pig Farms
by Iliana C. Chamorro-Tobar, Adriana Pulido-Villamarín, Ana Karina Carrascal-Camacho, Irina Barrientos-Anzola, Magdalena Wiesner, Ivonne Hernández-Toro, Lis Alban, John Elmerdahl Olsen, Anders Dalsgaard and Yaovi Mahuton Gildas Hounmanou
Appl. Microbiol. 2024, 4(4), 1729-1744; https://doi.org/10.3390/applmicrobiol4040116 - 20 Dec 2024
Abstract
Salmonella enterica is a globally important zoonotic microorganism that affects pigs and can enter the farm through various routes. This study aimed to determine the prevalence of S. enterica in water sources and pigs at Colombian pig farms, and to characterize the antimicrobial [...] Read more.
Salmonella enterica is a globally important zoonotic microorganism that affects pigs and can enter the farm through various routes. This study aimed to determine the prevalence of S. enterica in water sources and pigs at Colombian pig farms, and to characterize the antimicrobial resistance of the isolates phenotypically and genotypically. Samples were collected from 103 farms including source water (n = 104), storage tank water (n = 103), drinking water (n = 103), and individual rectal swab samples (n = 1025). The presence of Salmonella was detected/identified using MDS-3M™ agar culture medium. Isolates were serotyped, and their antibiotic susceptibility was determined by minimum inhibitory concentration (MIC). Whole genome sequencing (WGS) was performed using Illumina NovaSeq, and bioinformatics analysis focused on serovar confirmation, MLST determination, and resistance gene detection. The overall between-farm prevalence of Salmonella enterica including all types of samples was 52.4% (54/103), with 6.4% of rectal swab samples and 21.3% of water samples found to be positive. Thirty serovars were identified using WGS, with the most common being S. Typhimurium var. monophasic (1,4,[5],12:i:-) (41.2%), S. Schwarzengrund (4.2%), and S. Saintpaul (4.2%). Salmonella Typhimurium and its monophasic variant were more commonly found in rectal swabs than the remaining serotypes (relative risk = 2.9, p < 0.0001), which were commonly found in the water samples (relative risk = 5.2, p < 0.0001). High levels of phenotypic resistance were observed, particularly to amikacin (99.2%), tetracycline (59.7%), chloramphenicol (55.5%), and ampicillin (42%). All isolates carried genes conferring resistance to aminoglycosides (aac(6′)-Iaa), quinolones (qnrB19), and tetracyclines (tetA). In conclusion, S. enterica is prevalent in Colombian pig farms including the water supply, with the S. Typhimurium monophasic variant being predominant, and antimicrobial resistance is widespread. Full article
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27 pages, 9216 KiB  
Review
Bacterial Pigment Prodigiosin as Multifaceted Compound for Medical and Industrial Application
by Ivan Guryanov and Ekaterina Naumenko
Appl. Microbiol. 2024, 4(4), 1702-1728; https://doi.org/10.3390/applmicrobiol4040115 - 17 Dec 2024
Viewed by 472
Abstract
Prodigiosin is a fascinating compound that has been gaining attention in the scientific community for its diverse range of potential applications. From its vibrant red color to its unique chemical properties, prodigiosin has captured the interest of researchers looking for innovative solutions in [...] Read more.
Prodigiosin is a fascinating compound that has been gaining attention in the scientific community for its diverse range of potential applications. From its vibrant red color to its unique chemical properties, prodigiosin has captured the interest of researchers looking for innovative solutions in various fields. Prodigiosin, a red pigment produced by certain bacteria such as Serratia marcescens, has attracted interest from pharmaceutical researchers due to its promising potential in various therapeutic applications. A number of studies have demonstrated the potential of prodigiosin as an antimicrobial agent. With the rise of antibiotic resistance in the environment, prodigiosin is a promising solution to combat resistant strains and improve the effectiveness of existing antibiotic therapy. Moreover, different studies have shown that this natural pigment has anticancer properties by inhibiting the growth and proliferation of cancer cells. Prodigiosin exerts its anticancer effects by inducing apoptosis in cancer cells without causing significant damage to healthy cells. In this review, we will attempt to summarize the capabilities of prodigiosin and its prospects as a valuable tool in pharmaceutical research, and also review recent studies focusing on the various industries in which prodigiosin can be applied and the exciting possibilities it holds in the future. Full article
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25 pages, 2081 KiB  
Review
The Effect of Gut Microbiome, Neurotransmitters, and Digital Insights in Autism
by Victoria Bamicha, Pantelis Pergantis and Athanasios Drigas
Appl. Microbiol. 2024, 4(4), 1677-1701; https://doi.org/10.3390/applmicrobiol4040114 - 16 Dec 2024
Viewed by 632
Abstract
Background: Autism spectrum disorder is a multifactorial phenomenon whose genetic, biological, environmental, and nutritional factors outline the heterogeneous phenotype of the disease. A limitation in social connections with others, stereotyped reactions, and specific interests and preferences characterize the behavioral manifestations of a person [...] Read more.
Background: Autism spectrum disorder is a multifactorial phenomenon whose genetic, biological, environmental, and nutritional factors outline the heterogeneous phenotype of the disease. A limitation in social connections with others, stereotyped reactions, and specific interests and preferences characterize the behavioral manifestations of a person with autism. Also, weaknesses are found in emotional, cognitive, and metacognitive development, significantly burdening the individual’s quality of life. Lately, it has gained widespread acceptance that the gut microbiome and neurotransmission constitute two decisive etiological factors of autism both in the prenatal period and postnatally. This study aims to investigate data on the interaction between the quantitative and qualitative composition of the gut flora and neurotransmission in humans, as well as their influences on the appearance and progression of the symptoms of autism spectrum disorder. At the same time, it captures the role of digital technology in diagnosing and intervening in autism, which is mainly related to the individual subjects under study. Methods: The current research employs an exploratory review to provide a concise overview of the complex neuronal functions associated with neurotransmitter action and the homeostasis mechanisms that allow the brain and the human body to survive and perform optimally. Results: A review of 111 sources highlighted the connection of dietary habits with synthesizing and releasing neurotransmitters and their influence on the emergence of autism-related behaviors. Conclusions: The literature review’s findings revealed the importance and influence of nutritional factors on neurotransmission performance and behavioral, social, and cognitive development among individuals with autism. Moreover, it is noteworthy that combining a healthy lifestyle and the targeted use of digital tools can improve the intensity of autism symptoms. Full article
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16 pages, 2329 KiB  
Article
Carbon Metabolic Profiling as a Response to Previous Plant Mycotrophy and Soil Disturbance in Wheat Growth
by Taiana Conceição, Galdino Andrade and Isabel Brito
Appl. Microbiol. 2024, 4(4), 1661-1676; https://doi.org/10.3390/applmicrobiol4040113 - 11 Dec 2024
Viewed by 348
Abstract
Soil microorganisms play a significant role in the dynamic regulation of organic matter in soils. To assess the influence of agricultural practices on soil functional profiling, we examined the effect of soil disturbance and plant sequence with different levels of mycotrophy on wheat [...] Read more.
Soil microorganisms play a significant role in the dynamic regulation of organic matter in soils. To assess the influence of agricultural practices on soil functional profiling, we examined the effect of soil disturbance and plant sequence with different levels of mycotrophy on wheat microbiomes metabolism. Soil samples were analyzed with community-level physiological profiles (CLPP) using Biolog™ Ecoplates. The results of average well color development (AWCD) showed that the degree of mycotrophy of preceding crop and soil disturbance affected the soil microbiome, although no impact on Shannon Evenness Index was observed during the experiment. The Shannon–Wiener Diversity Index showed variations among the different preceding plants, but not in wheat analysis. The pattern of the C sources metabolism also changed differentially regarding plant type and soil disturbance during the experiment, being also different within the highly mycotrophic plants (legume and grass). In the legume, an increase in the metabolism of amine/amides and phenolic acids was observed, whilst in the grass, an increase in the metabolism of phosphate-carbons (P carbon) and carbohydrates was more evident. Principal component analysis showed that a grouping in the distinct phases of the experiment correlated with the widening of the metabolism of amino acids, carboxylic acids, and carbohydrates. The results indicate that soil functional community structure reflects soil agricultural practice conditions. Previous plant types and soil disturbance impacted the soil microbiome metabolic response (AWCD) in wheat, generating different patterns of carbon metabolism related to previous plant mycotrophy. Full article
(This article belongs to the Special Issue Microbiome in Ecosystem, 3rd Edition)
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19 pages, 1653 KiB  
Article
In Vitro Modelling of a Typical Dietary Intake in Restrictive Anorexia Nervosa Results in Changes to Gut Microbial Community and Metabolites
by Litai Liu, Carlos Poveda, Paul E. Jenkins, Ishawu Iddrisu and Gemma E. Walton
Appl. Microbiol. 2024, 4(4), 1642-1660; https://doi.org/10.3390/applmicrobiol4040112 - 10 Dec 2024
Viewed by 553
Abstract
Anorexia nervosa (AN) is a psychiatric illness with harmful physical consequences. Studies have observed differences in the faecal microbiota of patients with AN compared to healthy controls. Diet has an impact on the gut microbiota, facilitating an altered community, such changes could impact [...] Read more.
Anorexia nervosa (AN) is a psychiatric illness with harmful physical consequences. Studies have observed differences in the faecal microbiota of patients with AN compared to healthy controls. Diet has an impact on the gut microbiota, facilitating an altered community, such changes could impact the gut–brain axis. In this study, a three-stage gut model system that mimics the luminal microbiology of the large intestine was conducted to identify relationships between diet and gut microbiota. A microbial medium was developed to provide nutrients more appropriate to restricting subtype AN (R-AN). The model was inoculated with faeces and samples were taken to compare differences in the microbiota and end products following the fermentation of healthy control medium (HC) compared to R-AN medium. Then, 16S amplicon sequencing along with flow cytometry–fluorescence in situ hybridisation were used to ascertain changes in the microbiota. Gas chromatography (GC) was used to assess changes in microbial metabolites. There were reduced levels of SCFA following the fermentation of R-AN medium. The fermentation of R-AN media led to fewer total bacteria numbers, along with less bifidobacteria and Rumincoccus proximally, but more Clostridium and Enterobacteriaceae. Nutrient-deficient medium resulted in reduced neurotransmitter-producing bacteria, reduced butyrate-producing bacteria, and increased protein-utilising bacteria, all of which could be maintaining factors in AN. The model system provides a novel tool for exploring how extreme dietary changes impact the microbiota and could therefore could be useful for assessing appropriate gut–brain targeted treatments. Full article
(This article belongs to the Special Issue Applied Microbiology of Foods, 2nd Edition)
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12 pages, 835 KiB  
Review
Bacterial Resistance to Mercury: A Mini-Review
by Daniel Gonçalves de Mattos D’Avila, Rafaela Gomes Ferrari, Paloma de Almeida Rodrigues, Gabriel Lata Neves, Alexandre Mendes Ramos Filho, Rami Fanticelli Baptista Mano and Carlos Adam Conte Junior
Appl. Microbiol. 2024, 4(4), 1630-1641; https://doi.org/10.3390/applmicrobiol4040111 - 2 Dec 2024
Viewed by 611
Abstract
With the increase in mercury pollution around the world, several bacteria have been identified that are capable of resisting mercury toxicity. With this in mind, the aim of this review was to determine which genes are involved in mercury resistance, which bacterial genera [...] Read more.
With the increase in mercury pollution around the world, several bacteria have been identified that are capable of resisting mercury toxicity. With this in mind, the aim of this review was to determine which genes are involved in mercury resistance, which bacterial genera exhibit this resistance, and which bacterial isolation sources have been most reported. To answer these questions, the PICO method (population, intervention, comparison, and outcome) was used, three databases were searched, and 17 relevant articles were included. As a result, resistance is due to a set of mer genes that transcribe mer proteins. The most important genes identified were merA and merR, and their proteins confer resistance by reducing Hg to Hg+2 or Hg0. Among the bacteria studied, those of the genera Pseudomonas, Escherichia, and the phylum Cyanobacteria stand out, the most important being Escherichia coli and Synechocystis sp., which are highly efficient and fast at reducing Hg. Based on the results, Escherichia coli and Synechocystis sp. are promising candidates for reducing environmental Hg, especially in aquatic environments. However, there is a lack of studies on the mechanism of bioremediation carried out by cyanobacteria and the influence of abiotic factors on the presence and/or expression of mer genes. Full article
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14 pages, 2179 KiB  
Article
Development of Heat-Dry RT-LAMP Bioassay for Rapid Latent Detection of Botrytis cinerea
by Khadijah Ayarnah, Danielle Duanis-Assaf, Noam Alkan and Evgeni Eltzov
Appl. Microbiol. 2024, 4(4), 1616-1629; https://doi.org/10.3390/applmicrobiol4040110 - 1 Dec 2024
Viewed by 430
Abstract
The global food security crisis is emphasized by the alarming amount of food waste, where about one-third of the world’s food production, roughly 1.3 billion metric tons, is lost annually. Pathogens, such as Botrytis cinerea, contribute significantly to this loss by attacking [...] Read more.
The global food security crisis is emphasized by the alarming amount of food waste, where about one-third of the world’s food production, roughly 1.3 billion metric tons, is lost annually. Pathogens, such as Botrytis cinerea, contribute significantly to this loss by attacking stored agricultural produce. These attacks typically start when pathogens infiltrate small fruit wounds, remain dormant, and then switch to an aggressive necrotrophic stage upon ripening, causing significant postharvest food losses. In response to this challenge, this study presents an innovative application of Reverse Transcriptase Loop-Mediated Isothermal Amplification (RT-LAMP). This method is increasingly recognized for its simplicity and effectiveness, distinguishing itself from more complex molecular diagnostic techniques. This study focuses on developing a heat-dry RT-LAMP desiccation method designed to be simple, robust, rapid, sensitive, and specific in detecting Botrytis cinerea. This method lies in its utilization of a desiccation process, where heat is utilized to preserve crucial components such as primers and enzymes in the presence of trehalose. A 5% trehalose with an amplification time of 1 h and 40 min was optimal for the assay detection of latent Botrytis cinerea. This method exhibited a sensitivity of 10 femtograms and was tailored specifically to the Botrytis cinerea PLF marker. Validation was performed using RNA extracted from an infected tomato, establishing a detection threshold of 1 ng/µL, approximately 500 pg of synthesized DNA target marker. This discovery holds significant implications, suggesting the potential for developing dry RT-LAMP kits that are adaptable for both laboratory and field usage. Furthermore, this method shows promise as a diagnostic tool for other neglected pathogenic diseases, representing a substantial advancement in agricultural pathology and supporting endeavors to enhance food security. Full article
(This article belongs to the Special Issue Applied Microbiology of Foods, 2nd Edition)
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16 pages, 3988 KiB  
Article
Multi-Omics Analysis of Mouse Fecal Microbiome Reveals Supplier-Dependent Functional Differences and Novel Metagenome-Assembled Genomes
by Zachary L. McAdams, Susheel Bhanu Busi, Kevin L. Gustafson, Nathan Bivens, Craig L. Franklin, Paul Wilmes and Aaron C. Ericsson
Appl. Microbiol. 2024, 4(4), 1600-1615; https://doi.org/10.3390/applmicrobiol4040109 - 30 Nov 2024
Viewed by 595
Abstract
Host genetics and environmental factors have been associated with effects on the mouse fecal microbiome; however, the commercial source of mice remains the dominant factor. Increasing evidence indicates that supplier-specific microbiomes confer differences in disease susceptibility in models of inflammatory conditions, as well [...] Read more.
Host genetics and environmental factors have been associated with effects on the mouse fecal microbiome; however, the commercial source of mice remains the dominant factor. Increasing evidence indicates that supplier-specific microbiomes confer differences in disease susceptibility in models of inflammatory conditions, as well as baseline behavior and body morphology. However, current knowledge regarding the compositional differences between suppliers is based on targeted-amplicon sequencing data, and functional differences between these communities remain poorly defined. We applied a multi-omic (metagenomic and metatranscriptomic) approach to biomolecules extracted from murine feces representative of two U.S. suppliers of research mice, which differ in composition, and influence baseline physiology and behavior as well as disease severity in models of intestinal disease. We reconstructed high-quality metagenome-assembled genomes, frequently containing genomic content unique to each supplier. Transcriptional activity and pathway analyses revealed key functional differences between the metagenomes associated with each supplier including carbohydrate, fatty acid, and sulfite metabolism. These data provide a detailed characterization of the baseline differences in the fecal metagenome of mice from two U.S. commercial suppliers, suggesting that these functional differences are influenced by differences in the initial inoculum of colony founders, as well as additional taxa gained during growth of the production colony. Full article
(This article belongs to the Special Issue Microbiome in Ecosystem, 3rd Edition)
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18 pages, 3198 KiB  
Article
Moderate Phosphorus Addition to Field-Grown Bananas Enhanced Soil Microbial Enzyme Activities but Had Negligible Impacts on Bacterial, Fungal, and Nematode Diversity
by Anna-Belle C. Clarke, Hazel R. Lapis-Gaza, Stuart Irvine-Brown, Rebecca Lyons, Jiarui Sun, Anthony B. Pattison and Paul G. Dennis
Appl. Microbiol. 2024, 4(4), 1582-1599; https://doi.org/10.3390/applmicrobiol4040108 - 29 Nov 2024
Viewed by 410
Abstract
On commercial banana (Musa spp.) plantations, soils are often supplemented with phosphorus (P) fertiliser to optimise production. Such additions may influence the diversity and function of soil microbial communities, which play important roles in P cycling and affect plant fitness. Here, we [...] Read more.
On commercial banana (Musa spp.) plantations, soils are often supplemented with phosphorus (P) fertiliser to optimise production. Such additions may influence the diversity and function of soil microbial communities, which play important roles in P cycling and affect plant fitness. Here, we characterised the effects of P addition on the diversity and function of banana-associated microbial communities. P addition was associated with significant increases in soil P and the activities of alpha-glucosidase, chitinase, arylsulphatase, and acid phosphatase, but not beta-glucosidase or xylosidase. P addition also expedited bunch emergence and harvest, but did not influence fruit yield, plant height, or foliar P. There were no significant effects of P addition on the alpha or beta diversity of bacterial, fungal, and nematode communities, including members of the core microbiome. The only exceptions to this was an increase in the relative abundance of a Fusarium population in roots. These results indicate that phosphorus application to banana soils may stimulate microbial enzyme activities with minor or negligible effects on microbial diversity. Full article
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14 pages, 2350 KiB  
Article
Novel Epigallocatechin Gallate (EGCG) Analogs with Improved Biochemical Properties for Targeting Extracellular and Intracellular Staphylococcus aureus
by Riley Grosso, Vy Nguyen, Syed Kaleem Ahmed and Annie Wong-Beringer
Appl. Microbiol. 2024, 4(4), 1568-1581; https://doi.org/10.3390/applmicrobiol4040107 - 29 Nov 2024
Viewed by 567
Abstract
Staphylococcus aureus is a leading cause of bloodstream infection (SAB), with up to 30% mortality. Despite treatment with standard antibiotics, one in three patients develops a persistent infection, which portends a five-fold increase in the risk of death. Persistent SAB has been attributed [...] Read more.
Staphylococcus aureus is a leading cause of bloodstream infection (SAB), with up to 30% mortality. Despite treatment with standard antibiotics, one in three patients develops a persistent infection, which portends a five-fold increase in the risk of death. Persistent SAB has been attributed in part to the inability of antistaphylococcal antibiotics to eradicate intracellular S. aureus surviving inside macrophages. (-)- Epigallocatechin gallate (EGCG) is a catechin found in green tea that has been widely studied for its broad biological activities, ranging from anticancer to antibacterial activity. However, EGCG is greatly limited by its poor drug-like properties in terms of stability, membrane permeability, and bioavailability. In this study, we established through a series of in vitro experiments that structural modifications of EGCG enhanced drug-like properties while maintaining or improving its antistaphylococcal activity. Our lead EGCG analogs (MCC-1 and MCC-2) showed improved biochemical properties along with increased potency against extracellular S. aureus and restored susceptibility of β-lactam agents to methicillin-resistant S. aureus (MRSA). Importantly, the lead analogs but not EGCG potentiated macrophage- and antibiotic-mediated clearance of intracellular bacteria. Overall, EGCG analogs showed promise for further development as adjunctive therapy candidates for the treatment of SAB. Full article
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19 pages, 1575 KiB  
Review
Soil Symphony: A Comprehensive Overview of Plant–Microbe Interactions in Agricultural Systems
by Arpitha Chatchatnahalli Tharanath, Raje Siddiraju Upendra and Karthik Rajendra
Appl. Microbiol. 2024, 4(4), 1549-1567; https://doi.org/10.3390/applmicrobiol4040106 - 27 Nov 2024
Viewed by 1009
Abstract
The rhizosphere, a narrow region of soil surrounding plant roots, is an environment rich in microbial diversity that profoundly influences plants’ health, growth, and agricultural productivity. This microbial community, known as the rhizosphere microbiome, consists of a complex array of bacteria, fungi, archaea, [...] Read more.
The rhizosphere, a narrow region of soil surrounding plant roots, is an environment rich in microbial diversity that profoundly influences plants’ health, growth, and agricultural productivity. This microbial community, known as the rhizosphere microbiome, consists of a complex array of bacteria, fungi, archaea, and other microorganisms that engage in complex interactions with plant roots. These microorganisms contribute to nutrient cycling, mineral uptake facilitation, and protection against soil-borne pathogens, thereby promoting plant growth and resilience towards biotic and abiotic stresses. Additionally, microbial signaling molecules, including phytohormones such as auxins, cytokinin, gibberellins, ethylene, and abscisic acid, play a pivotal role in regulating these interactions by modulating plants’ responses to environmental stressors. Recent advancements in microbiomics have enabled a deeper understanding of the rhizosphere’s diversity, composition, and functions, paving the way for more sustainable agricultural practices. By harnessing the potential of the rhizosphere microbiome, innovative strategies can be developed to reduce dependency on synthetic agrochemicals, enhance soil fertility, and increase crop yields. This review discusses the diversity and mechanisms of plant–microbe interactions, focusing on the role of microbial signaling molecules, and explores their applications in promoting agricultural sustainability. The insights gained from microbiomics studies can revolutionize farming practices by reducing dependency on chemical inputs, enhancing crop productivity, and nurturing soil health and environmental sustainability. Full article
(This article belongs to the Special Issue Microbiome in Ecosystem, 3rd Edition)
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15 pages, 7580 KiB  
Article
Environmental and Host Characteristics Shape the Gut Microbiota of the Sand Field Cricket, Gryllus firmus
by Divya Patel, Clint D. Kelly and Cassandre Sara Lazar
Appl. Microbiol. 2024, 4(4), 1534-1548; https://doi.org/10.3390/applmicrobiol4040105 - 27 Nov 2024
Viewed by 665
Abstract
The gut microbiota plays an essential role in its host’s nutrition, development and behavior. Although crickets are becoming major ecosystemic model systems and have important societal applications, such as alternative animal proteins or biocatalysts, little is known about their gut microbiome acquisition and [...] Read more.
The gut microbiota plays an essential role in its host’s nutrition, development and behavior. Although crickets are becoming major ecosystemic model systems and have important societal applications, such as alternative animal proteins or biocatalysts, little is known about their gut microbiome acquisition and how environmental factors shape this community. Therefore, in this study, we exposed sand field crickets to soils with different characteristics and microbial communities to test the influence of these on gut microbial community composition. We used 16S/18S rRNA gene Illumina sequencing to analyze different soil and gut communities, targeting the three domains of life, Archaea, Bacteria, and Eukaryotes. Our results showed a dominance of Mucoromycota fungi and Bacteroidota in the gut microbiota. We were unable to retrieve sufficient read numbers for the Archaea. Most of the microbial taxa that were identified can degrade soil-derived complex organic matter, likely helping the host digest its food. The soil characteristics had a significant impact on the gut microbial community structure, supporting our assumption that the environment plays an essential role in gut microbiota acquisition. Host sex also had an impact on the gut community, possibly because the female guts were bigger in mass, leading to differences in oxygen concentrations. Full article
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19 pages, 1032 KiB  
Review
Salmonella: Role in Internal and External Environments and Potential as a Therapeutic Tool
by Patrick J. Naughton, Violetta R. Naughton and James S. G. Dooley
Appl. Microbiol. 2024, 4(4), 1515-1533; https://doi.org/10.3390/applmicrobiol4040104 - 8 Nov 2024
Viewed by 1387
Abstract
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 [...] Read more.
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
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22 pages, 913 KiB  
Review
Incorporation of Cyanobacteria and Microalgae in Yogurt: Formulation Challenges and Nutritional, Rheological, Sensory, and Functional Implications
by Rosana Correia Vieira Albuquerque, Carlos Eduardo de Farias Silva, Wanderson dos Santos Carneiro, Kaciane Andreola, Brígida Maria Villar da Gama and Albanise Enide da Silva
Appl. Microbiol. 2024, 4(4), 1493-1514; https://doi.org/10.3390/applmicrobiol4040103 - 30 Oct 2024
Viewed by 978
Abstract
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 [...] Read more.
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
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17 pages, 1127 KiB  
Review
Resistome Mapping in Foodborne Pathogens: Understanding Role in the Transmission Dynamics of Resistance Genes
by Muneer Oladipupo Yaqub, Chinedu Eucharia Joseph, Aashika Jain and Lekshmi K. Edison
Appl. Microbiol. 2024, 4(4), 1476-1492; https://doi.org/10.3390/applmicrobiol4040102 - 19 Oct 2024
Viewed by 1559
Abstract
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 [...] Read more.
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
(This article belongs to the Special Issue Applied Microbiology of Foods, 2nd Edition)
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12 pages, 467 KiB  
Article
Molecular Typing of Somatic Coliphage Groups and Their Occurrence and Survival in Sewage
by Heesuk Lee, Jeremy Chemla, Thomas A. Randall, Emily S. Bailey and Mark D. Sobsey
Appl. Microbiol. 2024, 4(4), 1464-1475; https://doi.org/10.3390/applmicrobiol4040101 - 19 Oct 2024
Viewed by 674
Abstract
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 [...] Read more.
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
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11 pages, 2337 KiB  
Article
Integration of Whole-Genome Sequencing with ddPCR Kit for Detection of Omicron Subvariants in Wastewater in the Upper Peninsula of Michigan
by Michelle M. Jarvie, Thu N. T. Nguyen, Benjamin Southwell and Derek Wright
Appl. Microbiol. 2024, 4(4), 1453-1463; https://doi.org/10.3390/applmicrobiol4040100 - 13 Oct 2024
Viewed by 828
Abstract
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 [...] Read more.
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
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19 pages, 2313 KiB  
Article
Recovery of Pasteurization-Resistant Vagococcus lutrae from Raw Seafoods Using a Two-Step Enrichment, Its Presumptive Prevalence, and Novel Classification Phenotypes
by Elizabeth F. Scruggs, Zaria Gulley, Guadalupe Steele, Mohammed Alahmadi, Asim Barnawi, Hussain Majrshi and Hung King Tiong
Appl. Microbiol. 2024, 4(4), 1434-1452; https://doi.org/10.3390/applmicrobiol4040099 - 4 Oct 2024
Viewed by 795
Abstract
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 [...] Read more.
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
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12 pages, 1124 KiB  
Review
The Rumen and Gastrointestinal Microbial Environment and Its Association with Feed Efficiency and Pregnancy in Female Beef Cattle
by M. Gabbi Martin, Juan F. Cordero-Llarena, Brynn H. Voy, Kyle J. McLean and Phillip R. Myer
Appl. Microbiol. 2024, 4(4), 1422-1433; https://doi.org/10.3390/applmicrobiol4040098 - 27 Sep 2024
Viewed by 1379
Abstract
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 [...] Read more.
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
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11 pages, 2040 KiB  
Article
Exploring the Intriguing World of Fungal Diversity in the Oral Cavities of a Native Community in Siltepec, Chiapas, Mexico
by Orquídea Pérez-González, Franco Valencia-Ampudia, Myriam A de la Garza-Ramos and Victor E. Aguirre-Arzola
Appl. Microbiol. 2024, 4(4), 1411-1421; https://doi.org/10.3390/applmicrobiol4040097 - 24 Sep 2024
Viewed by 894
Abstract
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 [...] Read more.
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
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