Life | Project Collection : Feature Papers in Microbiology

2024

Jump to: 2023, 2022

13 pages, 3882 KiB

Open AccessArticle

Machine Learning-Based Software for Predicting Pseudomonas spp. Growth Dynamics in Culture Media

by Fatih Tarlak

Life 2024, 14(11), 1490; https://doi.org/10.3390/life14111490 - 15 Nov 2024

Viewed by 402

Abstract

In predictive microbiology, both primary and secondary models are widely used to estimate microbial growth, often applied through two-step or one-step modelling approaches. This study focused on developing a tool to predict the growth of Pseudomonas spp., a prominent bacterial genus in food [...] Read more.

In predictive microbiology, both primary and secondary models are widely used to estimate microbial growth, often applied through two-step or one-step modelling approaches. This study focused on developing a tool to predict the growth of Pseudomonas spp., a prominent bacterial genus in food spoilage, by applying machine learning regression models, including Support Vector Regression (SVR), Random Forest Regression (RFR) and Gaussian Process Regression (GPR). The key environmental factors—temperature, water activity, and pH—served as predictor variables to model the growth of Pseudomonas spp. in culture media. To assess model performance, these machine learning approaches were compared with traditional models, namely the Gompertz, Logistic, Baranyi, and Huang models, using statistical indicators such as the adjusted coefficient of determination (R²_adj) and root mean square error (RMSE). Machine learning models provided superior accuracy over traditional approaches, with R²_adj values from 0.834 to 0.959 and RMSE values between 0.005 and 0.010, showcasing their ability to handle complex growth patterns more effectively. GPR emerged as the most accurate model for both training and testing datasets. In external validation, additional statistical indices (bias factor, B_f: 0.998 to 1.047; accuracy factor, A_f: 1.100 to 1.167) further supported GPR as a reliable alternative for microbial growth prediction. This machine learning-driven approach bypasses the need for the secondary modelling step required in traditional methods, highlighting its potential as a robust tool in predictive microbiology. Full article

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21 pages, 1553 KiB

Open AccessArticle

Selection and Effect of Plant Growth-Promoting Bacteria on Pine Seedlings (Pinus montezumae and Pinus patula)

by Francisco David Moreno-Valencia, Miguel Ángel Plascencia-Espinosa, Yolanda Elizabeth Morales-García and Jesús Muñoz-Rojas

Life 2024, 14(10), 1320; https://doi.org/10.3390/life14101320 - 17 Oct 2024

Viewed by 910

Abstract

Forest cover is deteriorating rapidly due to anthropogenic causes, making its restoration urgent. Plant growth-promoting bacteria (PGPB) could offer a viable solution to ensure successful reforestation efforts. This study aimed to select bacterial strains with mechanisms that promote plant growth and enhance seedling [...] Read more.

Forest cover is deteriorating rapidly due to anthropogenic causes, making its restoration urgent. Plant growth-promoting bacteria (PGPB) could offer a viable solution to ensure successful reforestation efforts. This study aimed to select bacterial strains with mechanisms that promote plant growth and enhance seedling development. The bacterial strains used in this study were isolated from the rhizosphere and endophyte regions of Pinus montezumae Lamb. and Pinus patula Schl. et Cham., two Mexican conifer species commonly used for reforestation purposes. Sixteen bacterial strains were selected for their ability to produce auxins, chitinase, and siderophores, perform nitrogen fixation, and solubilize inorganic phosphates; they also harbored genes encoding antimicrobial production and ACC deaminase. The adhesion to seeds, germination rate, and seedling response of P. montezumae and P. patula were performed following inoculation with 10 bacterial strains exhibiting high plant growth-promoting potential. Some strains demonstrated the capacity to enhance seedling growth. The selected strains were taxonomically characterized and belonged to the genus Serratia, Buttiauxella, and Bacillus. These strains exhibited at least two mechanisms of action, including the production of indole-3-acetic acid, biological nitrogen fixation, and phosphate solubilization, and could serve as potential alternatives for the reforestation of affected areas. Full article

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20 pages, 1206 KiB

Open AccessReview

Neonatal Gut Mycobiome: Immunity, Diversity of Fungal Strains, and Individual and Non-Individual Factors

by Alexandra Mpakosi, Rozeta Sokou, Martha Theodoraki and Christiana Kaliouli-Antonopoulou

Life 2024, 14(7), 902; https://doi.org/10.3390/life14070902 - 19 Jul 2024

Viewed by 1099

Abstract

The human gastrointestinal ecosystem, or microbiome (comprising the total bacterial genome in an environment), plays a crucial role in influencing host physiology, immune function, metabolism, and the gut–brain axis. While bacteria, fungi, viruses, and archaea are all present in the gastrointestinal ecosystem, research [...] Read more.

The human gastrointestinal ecosystem, or microbiome (comprising the total bacterial genome in an environment), plays a crucial role in influencing host physiology, immune function, metabolism, and the gut–brain axis. While bacteria, fungi, viruses, and archaea are all present in the gastrointestinal ecosystem, research on the human microbiome has predominantly focused on the bacterial component. The colonization of the human intestine by microbes during the first two years of life significantly impacts subsequent composition and diversity, influencing immune system development and long-term health. Early-life exposure to pathogens is crucial for establishing immunological memory and acquired immunity. Factors such as maternal health habits, delivery mode, and breastfeeding duration contribute to gut dysbiosis. Despite fungi’s critical role in health, particularly for vulnerable newborns, research on the gut mycobiome in infants and children remains limited. Understanding early-life factors shaping the gut mycobiome and its interactions with other microbial communities is a significant research challenge. This review explores potential factors influencing the gut mycobiome, microbial kingdom interactions, and their connections to health outcomes from childhood to adulthood. We identify gaps in current knowledge and propose future research directions in this complex field. Full article

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38 pages, 10899 KiB

Open AccessEditor’s ChoiceReview

Compaction and Segregation of DNA in Escherichia coli

by Conrad L. Woldringh

Life 2024, 14(6), 660; https://doi.org/10.3390/life14060660 - 22 May 2024

Cited by 1 | Viewed by 1119

Abstract

Theoretical and experimental approaches have been applied to study the polymer physics underlying the compaction of DNA in the bacterial nucleoid. Knowledge of the compaction mechanism is necessary to obtain a mechanistic understanding of the segregation process of replicating chromosome arms (replichores) during [...] Read more.

Theoretical and experimental approaches have been applied to study the polymer physics underlying the compaction of DNA in the bacterial nucleoid. Knowledge of the compaction mechanism is necessary to obtain a mechanistic understanding of the segregation process of replicating chromosome arms (replichores) during the cell cycle. The first part of this review discusses light microscope observations demonstrating that the nucleoid has a lower refractive index and thus, a lower density than the cytoplasm. A polymer physics explanation for this phenomenon was given by a theory discussed at length in this review. By assuming a phase separation between the nucleoid and the cytoplasm and by imposing equal osmotic pressure and chemical potential between the two phases, a minimal energy situation is obtained, in which soluble proteins are depleted from the nucleoid, thus explaining its lower density. This theory is compared to recent views on DNA compaction that are based on the exclusion of polyribosomes from the nucleoid or on the transcriptional activity of the cell. These new views prompt the question of whether they can still explain the lower refractive index or density of the nucleoid. In the second part of this review, we discuss the question of how DNA segregation occurs in Escherichia coli in the absence of the so-called active ParABS system, which is present in the majority of bacteria. How is the entanglement of nascent chromosome arms generated at the origin in the parental DNA network of the E. coli nucleoid prevented? Microscopic observations of the position of fluorescently-labeled genetic loci have indicated that the four nascent chromosome arms synthesized in the initial replication bubble segregate to opposite halves of the sister nucleoids. This implies that extensive intermingling of daughter strands does not occur. Based on the hypothesis that leading and lagging replichores synthesized in the replication bubble fold into microdomains that do not intermingle, a passive four-excluding-arms model for segregation is proposed. This model suggests that the key for segregation already exists in the structure of the replication bubble at the very start of DNA replication; it explains the different patterns of chromosome arms as well as the segregation distances between replicated loci, as experimentally observed. Full article

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16 pages, 2845 KiB

Open AccessArticle

UVC Box: An Effective Way to Quickly Decontaminate Healthcare Facilities’ Wheelchairs

by Cloé Adam, Marius Colin, Romuald Stock, Laurent Weiss and Sophie C. Gangloff

Life 2024, 14(2), 256; https://doi.org/10.3390/life14020256 - 16 Feb 2024

Viewed by 1140

Abstract

Disinfection in the hospital environment remains challenging, especially for wide and structurally complex objects such as beds or wheelchairs. Indeed, the regular disinfection of these objects with chemicals is manually carried out by healthcare workers and is fastidious and time-consuming. Alternative antibacterial techniques [...] Read more.

Disinfection in the hospital environment remains challenging, especially for wide and structurally complex objects such as beds or wheelchairs. Indeed, the regular disinfection of these objects with chemicals is manually carried out by healthcare workers and is fastidious and time-consuming. Alternative antibacterial techniques were thus proposed in the past decades, including the use of naturally antimicrobial UVC. Here, the antibacterial efficiency of a large UVC box built to accommodate wheelchairs was investigated through testing bacterial burden reductions on various parts of a wheelchair, with various support types and with several treatment durations. The results demonstrate a time-dependent antibacterial effect, with a strong burden reduction at only five minutes of treatment (>3-log median reduction in Escherichia coli and Staphylococcus epidermidis). The UVC flux and residual bacterial burden both significantly varied depending on the spatial location on the wheelchair. However, the nature of the support impacted the antibacterial efficiency even more, with residual bacterial burdens being the lowest on rigid materials (steel, plastics) and being the highest on tissue. On metallic samples, the nature of the alloy and surface treatment had various impacts on the antibacterial efficiency of the UVC. This study highlights the efficiency of the tested UVC box to efficiently and quickly decontaminate complex objects such as wheelchairs, but also gives rise to the warning to focus on rigid materials and avoid porous materials in the conception of objects, so as to ensure the efficiency of UVC decontamination. Full article

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2023

Jump to: 2024, 2022

16 pages, 1624 KiB

Open AccessEditor’s ChoiceSystematic Review

Why Does Your Uterus Become Malignant? The Impact of the Microbiome on Endometrial Carcinogenesis

by Katarzyna Morańska, Monika Englert-Golon, Magdalena Durda-Masny, Stefan Sajdak, Marlena Grabowska and Anita Szwed

Life 2023, 13(12), 2269; https://doi.org/10.3390/life13122269 - 28 Nov 2023

Cited by 1 | Viewed by 1994

Abstract

The aim of this review was to describe the uterine microbiome composition that has been analyzed so far and describe potential pathways in the carcinogenesis of the endometrium. The microbiome in the uterine environment is involved in apoptosis and proliferation during the menstruation [...] Read more.

The aim of this review was to describe the uterine microbiome composition that has been analyzed so far and describe potential pathways in the carcinogenesis of the endometrium. The microbiome in the uterine environment is involved in apoptosis and proliferation during the menstruation cycle, pregnancy maintenance, and immune system support. However, bacteria in the uterus could stimulate inflammation, which when chronic results in malignancy. An altered gut microbiota initiates an inflammatory response through microorganism-associated molecular patterns, which leads to intensified steroidogenesis in the ovaries and cancers. Moreover, intestinal bacteria secreting the enzyme β-glucuronidase may increase the level of circulating estrogen and, as a result, be influential in gynecological cancers. Both the uterine and the gut microbiota play a pivotal role in immune modulation, which is why there is a demand for further investigation from both the diagnostic and the therapeutic perspectives. Full article

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22 pages, 3698 KiB

Open AccessEditor’s ChoiceSystematic Review

The Role of Bifidobacterium in COVID-19: A Systematic Review

by Clarissa Reginato Taufer and Pabulo Henrique Rampelotto

Life 2023, 13(9), 1847; https://doi.org/10.3390/life13091847 - 31 Aug 2023

Cited by 3 | Viewed by 3892

Abstract

The COVID-19 pandemic, caused by the SARS-CoV-2 virus, mainly causes respiratory and intestinal symptoms and changes in the microbiota of patients. We performed a systematic search in major databases using “Bifidobacterium” and “COVID-19” or “SARS-CoV-2” as key terms to assess the [...] Read more.

The COVID-19 pandemic, caused by the SARS-CoV-2 virus, mainly causes respiratory and intestinal symptoms and changes in the microbiota of patients. We performed a systematic search in major databases using “Bifidobacterium” and “COVID-19” or “SARS-CoV-2” as key terms to assess the relationship of the genus to COVID-19. After the selection steps, 25 articles were analyzed. Of these, eighteen were observational, and seven were interventional articles that evaluated the use of Bifidobacterium alone or in mix as probiotics for additional treatment of patients with COVID-19. All stages and severities were contemplated, including post-COVID-19 patients. Overall, Bifidobacterium was associated with both protective effects and reduced abundance in relation to the disease. The genus has been found to be abundant in some cases and linked to disease severity. The studies evaluating the use of Bifidobacterium as probiotics have demonstrated the potential of this genus in reducing symptoms, improving pulmonary function, reducing inflammatory markers, alleviating gastrointestinal symptoms, and even contributing to better control of mortality. In summary, Bifidobacterium may offer protection against COVID-19 through its ability to modulate the immune response, reduce inflammation, compete with pathogenic microbes, and maintain gut barrier function. The findings provide valuable insights into the relationship between the disease and the genus Bifidobacterium, highlighting the potential of microbiota modulation in the treatment of COVID-19. Full article

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7 pages, 686 KiB

Open AccessOpinion

The Hypothesis of a “Living Pulse” in Cells

by Marina Walther-Antonio and Dirk Schulze-Makuch

Life 2023, 13(7), 1506; https://doi.org/10.3390/life13071506 - 4 Jul 2023

Viewed by 1344

Abstract

Motility is a great biosignature and its pattern is characteristic for specific microbes. However, motion does also occur within the cell by the myriads of ongoing processes within the cell and the exchange of gases and nutrients with the outside environment. Here, we [...] Read more.

Motility is a great biosignature and its pattern is characteristic for specific microbes. However, motion does also occur within the cell by the myriads of ongoing processes within the cell and the exchange of gases and nutrients with the outside environment. Here, we propose that the sum of these processes in a microbial cell is equivalent to a pulse in complex organisms and suggest a first approach to measure the “living pulse” in microorganisms. We emphasize that if a “living pulse” can be shown to exist, it would have far-reaching applications, such as for finding life in extreme environments on Earth and in extraterrestrial locations, as well as making sure that life is not present where it should not be, such as during medical procedures and in the food processing industry. Full article

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12 pages, 1187 KiB

Open AccessReview

Host–Parasite Coevolution in Primates

by Dietmar Zinner, Filipa M. D. Paciência and Christian Roos

Life 2023, 13(3), 823; https://doi.org/10.3390/life13030823 - 17 Mar 2023

Cited by 1 | Viewed by 3409

Abstract

Organisms adapt to their environment through evolutionary processes. Environments consist of abiotic factors, but also of other organisms. In many cases, two or more species interact over generations and adapt in a reciprocal way to evolutionary changes in the respective other species. Such [...] Read more.

Organisms adapt to their environment through evolutionary processes. Environments consist of abiotic factors, but also of other organisms. In many cases, two or more species interact over generations and adapt in a reciprocal way to evolutionary changes in the respective other species. Such coevolutionary processes are found in mutualistic and antagonistic systems, such as predator–prey and host–parasite (including pathogens) relationships. Coevolution often results in an “arms race” between pathogens and hosts and can significantly affect the virulence of pathogens and thus the severity of infectious diseases, a process that we are currently witnessing with SARS-CoV-2. Furthermore, it can lead to co-speciation, resulting in congruent phylogenies of, e.g., the host and parasite. Monkeys and other primates are no exception. They are hosts to a large number of pathogens that have shaped not only the primate immune system but also various ecological and behavioral adaptions. These pathogens can cause severe diseases and most likely also infect multiple primate species, including humans. Here, we briefly review general aspects of the coevolutionary process in its strict sense and highlight the value of cophylogenetic analyses as an indicator for coevolution. Full article

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21 pages, 1875 KiB

Open AccessArticle

Carbon Fixation in the Chemolithoautotrophic Bacterium Aquifex aeolicus Involves Two Low-Potential Ferredoxins as Partners of the PFOR and OGOR Enzymes

by Laura Prioretti, Giulia D’Ermo, Pascale Infossi, Arlette Kpebe, Régine Lebrun, Marielle Bauzan, Elisabeth Lojou, Bruno Guigliarelli, Marie-Thérèse Giudici-Orticoni and Marianne Guiral

Life 2023, 13(3), 627; https://doi.org/10.3390/life13030627 - 23 Feb 2023

Cited by 4 | Viewed by 2488

Abstract

Aquifex aeolicus is a microaerophilic hydrogen- and sulfur -oxidizing bacterium that assimilates CO₂ via the reverse tricarboxylic acid cycle (rTCA). Key enzymes of this pathway are pyruvate:ferredoxin oxidoreductase (PFOR) and 2-oxoglutarate:ferredoxin oxidoreductase (OGOR), which are responsible, respectively, for the reductive carboxylation of [...] Read more.

Aquifex aeolicus is a microaerophilic hydrogen- and sulfur -oxidizing bacterium that assimilates CO₂ via the reverse tricarboxylic acid cycle (rTCA). Key enzymes of this pathway are pyruvate:ferredoxin oxidoreductase (PFOR) and 2-oxoglutarate:ferredoxin oxidoreductase (OGOR), which are responsible, respectively, for the reductive carboxylation of acetyl-CoA to pyruvate and of succinyl-CoA to 2-oxoglutarate, two energetically unfavorable reactions that require a strong reduction potential. We have confirmed, by biochemistry and proteomics, that A. aeolicus possesses a pentameric version of these enzyme complexes ((αβγδε)₂) and that they are highly abundant in the cell. In addition, we have purified and characterized, from the soluble fraction of A. aeolicus, two low redox potential and oxygen-stable [4Fe-4S] ferredoxins (Fd6 and Fd7, E⁰ = −440 and −460 mV, respectively) and shown that they can physically interact and exchange electrons with both PFOR and OGOR, suggesting that they could be the physiological electron donors of the system in vivo. Shotgun proteomics indicated that all the enzymes assumed to be involved in the rTCA cycle are produced in the A. aeolicus cells. A number of additional enzymes, previously suggested to be part of a putative partial Wood-Ljungdahl pathway used for the synthesis of serine and glycine from CO₂ were identified by mass spectrometry, but their abundance in the cell seems to be much lower than that of the rTCA cycle. Their possible involvement in carbon assimilation is discussed. Full article

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20 pages, 2729 KiB

Open AccessArticle

Taxonomic Assignment-Based Genome Reconstruction from Apical Periodontal Metagenomes to Identify Antibiotic Resistance and Virulence Factors

by K. Swapna Kumari, Sangita Dixit, Mahendra Gaur, Dibyajyoti Uttameswar Behera, Suchanda Dey, Rajesh Kumar Sahoo, Patitapaban Dash and Enketeswara Subudhi

Life 2023, 13(1), 194; https://doi.org/10.3390/life13010194 - 9 Jan 2023

Cited by 4 | Viewed by 2424

Abstract

Primary apical periodontitis occurs due to various insults to the dental pulp including microbial infections, physical and iatrogenic trauma, whereas inadequate elimination of intraradicular infection during root canal treatment may lead to secondary apical periodontitis. We explored the complex intra-radicular microbial communities and [...] Read more.

Primary apical periodontitis occurs due to various insults to the dental pulp including microbial infections, physical and iatrogenic trauma, whereas inadequate elimination of intraradicular infection during root canal treatment may lead to secondary apical periodontitis. We explored the complex intra-radicular microbial communities and their functional potential through genome reconstruction. We applied shotgun metagenomic sequencing, binning and functional profiling to identify the significant contributors to infection at the acute and chronic apical periodontal lesions. Our analysis revealed the five classified clusters representing Enterobacter, Enterococcus, Lacticaseibacillus, Pseudomonas, Streptococcus and one unclassified cluster of contigs at the genus level. Of them, the major contributors were Pseudomonas, with 90.61% abundance in acute conditions, whereas Enterobacter followed by Enterococcus with 69.88% and 15.42% abundance, respectively, in chronic conditions. Enterobacter actively participated in antibiotic target alteration following multidrug efflux-mediated resistance mechanisms, predominant in the chronic stage. The prediction of pathways involved in the destruction of the supportive tissues of the tooth in Enterobacter and Pseudomonas support their crucial role in the manifestation of respective disease conditions. This study provides information about the differential composition of the microbiome in chronic and acute apical periodontitis. It takes a step to interpret the role of a single pathogen, solely or predominantly, in establishing endodontic infection types through genome reconstruction following high throughput metagenomic DNA analysis. The resistome prediction sheds a new light on the therapeutic treatment guidelines for endodontists. However, it needs further conclusive research to support this outcome using a larger number of samples with similar etiological conditions, but different demographic origin. Full article

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2022

Jump to: 2024, 2023

13 pages, 701 KiB

Open AccessArticle

Resistance to Some New Drugs and Prevalence of ESBL- and MBL-Producing Enterobacteriaceae Uropathogens Isolated from Diabetic Patients

by Othman M. Alzahrani, Fakhur Uddin, Samy F. Mahmoud, Amal S. Alswat, Muhammad Sohail and Mona Youssef

Life 2022, 12(12), 2125; https://doi.org/10.3390/life12122125 - 16 Dec 2022

Cited by 3 | Viewed by 2271

Abstract

Diabetes is a leading non-communicable disease and a risk factor for relapsing infections. The current study was aimed at investigating the prevalence and antibiotic susceptibility of carbapenem-resistant (CR) uropathogens of the family Enterobacteriaceae in diabetic patients. The data of 910 bacterial isolates was [...] Read more.

Diabetes is a leading non-communicable disease and a risk factor for relapsing infections. The current study was aimed at investigating the prevalence and antibiotic susceptibility of carbapenem-resistant (CR) uropathogens of the family Enterobacteriaceae in diabetic patients. The data of 910 bacterial isolates was collected from diagnostic laboratories during January 2018 to December 2018. The bacterial isolates were identified using traditional methods including colonial characteristics, biochemical tests, and API (20E). Antimicrobial susceptibility and phenotypic characterization of ESBL, MBLs, and KPC was determined by utilizing CLSI recommended methods. The phenotypically positive isolates were further analyzed for resistance-encoding genes by manual PCR and Check-MDR CT103XL microarray. Susceptibility to colistin and cefiderocol was tested in accordance with CLSI guidelines. The data revealed that most of the patients were suffering from type 2 diabetes for a duration of more than a year and with uncontrolled blood sugar levels. Escherichia coli and Klebsiella pneumoniae were the most frequently encountered pathogens, followed by Enterobacter cloacae and Proteus mirabilis. More than 50% of the isolates showed resistance to 22 antibiotics, with the highest resistance (>80%) against tetracycline, ampicillin, and cefazolin. The uropathogens showed less resistance to non-β-lactam antibiotics, including amikacin, fosfomycin, and nitrofurantoin. In the phenotypic assays, 495 (54.3%) isolates were found to be ESBL producers, while ESBL-TEM and -PER were the most prevalent ESBL types. The resistance to carbapenems was slightly less (250; 27.5%) than ESBL producers, yet more common amongst E. coli isolates. MBL production was a common feature in carbapenem-resistant isolates (71.2%); genotypic characterization also validated this trend. The isolates were found to be sensitive against the new drugs, cefiderocol and eravacycline. with 7–28% resistance, except for P. mirabilis which had 100% resistance against eravacycline. This study concludes that a few types of ESBL and carbapenemases are common in the uropathogens isolated from the diabetic patients, and antibiotic stewardship programs need to be revisited, particularly to cure UTIs in diabetic patients. Full article

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28 pages, 3500 KiB

Open AccessSystematic Review

Novel Virus Identification through Metagenomics: A Systematic Review

by Cristian Bassi, Paola Guerriero, Marina Pierantoni, Elisa Callegari and Silvia Sabbioni

Life 2022, 12(12), 2048; https://doi.org/10.3390/life12122048 - 7 Dec 2022

Cited by 17 | Viewed by 5561

Abstract

Metagenomic Next Generation Sequencing (mNGS) allows the evaluation of complex microbial communities, avoiding isolation and cultivation of each microbial species, and does not require prior knowledge of the microbial sequences present in the sample. Applications of mNGS include virome characterization, new virus discovery [...] Read more.

Metagenomic Next Generation Sequencing (mNGS) allows the evaluation of complex microbial communities, avoiding isolation and cultivation of each microbial species, and does not require prior knowledge of the microbial sequences present in the sample. Applications of mNGS include virome characterization, new virus discovery and full-length viral genome reconstruction, either from virus preparations enriched in culture or directly from clinical and environmental specimens. Here, we systematically reviewed studies that describe novel virus identification through mNGS from samples of different origin (plant, animal and environment). Without imposing time limits to the search, 379 publications were identified that met the search parameters. Sample types, geographical origin, enrichment and nucleic acid extraction methods, sequencing platforms, bioinformatic analytical steps and identified viral families were described. The review highlights mNGS as a feasible method for novel virus discovery from samples of different origins, describes which kind of heterogeneous experimental and analytical protocols are currently used and provides useful information such as the different commercial kits used for the purification of nucleic acids and bioinformatics analytical pipelines. Full article

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23 pages, 1217 KiB

Open AccessReview

Gut Microbiota and Cardiovascular System: An Intricate Balance of Health and the Diseased State

by Mujtaba Aamir Bhat, Awdhesh Kumar Mishra, Javeed Ahmad Tantray, Hanan Ali Alatawi, Mohd Saeed, Safikur Rahman and Arif Tasleem Jan

Life 2022, 12(12), 1986; https://doi.org/10.3390/life12121986 - 28 Nov 2022

Cited by 9 | Viewed by 3415

Abstract

Gut microbiota encompasses the resident microflora of the gut. Having an intricate relationship with the host, it plays an important role in regulating physiology and in the maintenance of balance between health and disease. Though dietary habits and the environment play a critical [...] Read more.

Gut microbiota encompasses the resident microflora of the gut. Having an intricate relationship with the host, it plays an important role in regulating physiology and in the maintenance of balance between health and disease. Though dietary habits and the environment play a critical role in shaping the gut, an imbalance (referred to as dysbiosis) serves as a driving factor in the occurrence of different diseases, including cardiovascular disease (CVD). With risk factors of hypertension, diabetes, dyslipidemia, etc., CVD accounts for a large number of deaths among men (32%) and women (35%) worldwide. As gut microbiota is reported to have a direct influence on the risk factors associated with CVDs, this opens up new avenues in exploring the possible role of gut microbiota in regulating the gross physiological aspects along the gut–heart axis. The present study elaborates on different aspects of the gut microbiota and possible interaction with the host towards maintaining a balance between health and the occurrence of CVDs. As the gut microbiota makes regulatory checks for these risk factors, it has a possible role in shaping the gut and, as such, in decreasing the chances of the occurrence of CVDs. With special emphasis on the risk factors for CVDs, this paper includes information on the prominent bacterial species (Firmicutes, Bacteriodetes and others) towards an advance in our understanding of the etiology of CVDs and an exploration of the best possible therapeutic modules for implementation in the treatment of different CVDs along the gut–heart axis. Full article

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9 pages, 1446 KiB

Open AccessArticle

Characterization of Cross-Species Transmission of Drosophila melanogaster Nora Virus

by Ella G. Buhlke, Alexis M. Hobbs, Sunanda Rajput, Blase Rokusek, Darby J. Carlson, Chelle Gillan and Kimberly A. Carlson

Life 2022, 12(11), 1913; https://doi.org/10.3390/life12111913 - 17 Nov 2022

Cited by 1 | Viewed by 2087

Abstract

Drosophila melanogaster Nora virus (DmNV) is a novel picorna-like virus first characterized in 2006. Since then, Nora virus has been detected in several non-Drosophila species, including insects in the Orders Hymenoptera, Lepidoptera, Coleoptera, and Orthoptera. The objective of this study was to [...] Read more.

Drosophila melanogaster Nora virus (DmNV) is a novel picorna-like virus first characterized in 2006. Since then, Nora virus has been detected in several non-Drosophila species, including insects in the Orders Hymenoptera, Lepidoptera, Coleoptera, and Orthoptera. The objective of this study was to determine if DmNV could infect individuals of other species of invertebrates besides D. melanogaster. The presence of DmNV in native invertebrates and commercially available stocks was determined. Laboratory-reared D. yakuba, D. mercatorum, Gryllodes sigillatus, Tenebrio molitor, Galleria mellonella, and Musca domestica were intentionally infected with DmNV. In addition, native invertebrates were collected and D. melanogaster stocks were purchased and screened for DmNV presence using reverse transcription-polymerase chain reaction (RT-PCR) before being intentionally infected for study. All Drosophila species and other invertebrates, except M. domestica, that were intentionally infected with DmNV ended up scoring positive for the virus via RT-PCR. DmNV infection was also detected in three native invertebrates (Spilosoma virginica, Diplopoda, and Odontotaenius disjunctus) and all commercially available stocks tested. These findings suggest that DmNV readily infects individuals of other species of invertebrates, while also appearing to be an endemic virus in both wild and laboratory D. melanogaster populations. The detection of DmNV in commercially available stocks presents a cautionary message for scientists using these stocks in studies of virology and immunology. Full article

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23 pages, 6409 KiB

Open AccessArticle

Fungal Biodeterioration of a Historical Manuscript Dating Back to the 14th Century: An Insight into Various Fungal Strains and Their Enzymatic Activities

by Gomaa Abdel-Maksoud, Mahmoud Abdel-Nasser, Mahmoud H. Sultan, Ahmed M. Eid, Saad H. Alotaibi, Saad El-Din Hassan and Amr Fouda

Life 2022, 12(11), 1821; https://doi.org/10.3390/life12111821 - 8 Nov 2022

Cited by 25 | Viewed by 2880

Abstract

This study aims to assess the deterioration aspects of a historical manuscript dating back to the 14th century that was deposited in the Library of the Arabic Language Academy, Cairo, Egypt. The study aims at the exploration of the role of various fungal [...] Read more.

This study aims to assess the deterioration aspects of a historical manuscript dating back to the 14th century that was deposited in the Library of the Arabic Language Academy, Cairo, Egypt. The study aims at the exploration of the role of various fungal strains that had colonized this deteriorated manuscript in its biodeterioration through their efficacy in the secretion of various hydrolytic enzymes. To evaluate the deterioration, various techniques, including visual inspection, attenuated total reflectance Fourier transform infrared (ATR-FTIR), scanning electron microscopy (SEM), X-Ray diffraction analysis (XRD), color change, and pH value, were utilized. The fungal strains linked to the historical document were isolated, identified, and evaluated for their deterioration activities. The findings demonstrate that the manuscript exhibits a variety of deterioration signs including color change, brittleness and weakness, erosion, and removal of the grain surface pattern in leather binding. According to the ATR-FTIR, the chemical composition of the historical paper and leather underwent some alterations. The historical paper has a lower level of cellulose crystallinity than the control sample. Penicillium chrysogenum (two isolates), P. citrinum (four isolates), Aspergillus ustus (three isolates), A. terreus (two isolates), A. chinensis (one isolate), Paecilomyces sp. (one isolate), and Induratia sp. (one isolate) were among the fourteen fungal strains identified as being associated with the historical manuscript. These fungal strains produced several hydrolytic enzymes with high activity, such as cellulase, amylase, gelatinase, and pectinase, which play a key role in biodegradation. Full article

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25 pages, 2695 KiB

Open AccessReview

Evaluating Risk: Benefit Ratio of Fat-Soluble Vitamin Supplementation to SARS-CoV-2-Infected Autoimmune and Cancer Patients: Do Vitamin–Drug Interactions Exist?

by Radwa Y. Mekky, Noha M. Elemam, Omar Eltahtawy, Yousra Zeinelabdeen and Rana A. Youness

Life 2022, 12(10), 1654; https://doi.org/10.3390/life12101654 - 20 Oct 2022

Cited by 3 | Viewed by 3164

Abstract

COVID-19 is a recent pandemic that mandated the scientific society to provide effective evidence-based therapeutic approaches for the prevention and treatment for such a global threat, especially to those patients who hold a higher risk of infection and complications, such as patients with [...] Read more.

COVID-19 is a recent pandemic that mandated the scientific society to provide effective evidence-based therapeutic approaches for the prevention and treatment for such a global threat, especially to those patients who hold a higher risk of infection and complications, such as patients with autoimmune diseases and cancer. Recent research has examined the role of various fat-soluble vitamins (vitamins A, D, E, and K) in reducing the severity of COVID-19 infection. Studies showed that deficiency in fat-soluble vitamins abrogates the immune system, thus rendering individuals more susceptible to COVID-19 infection. Moreover, another line of evidence showed that supplementation of fat-soluble vitamins during the course of infection enhances the viral clearance episode by promoting an adequate immune response. However, more thorough research is needed to define the adequate use of vitamin supplements in cancer and autoimmune patients infected with COVID-19. Moreover, it is crucial to highlight the vitamin–drug interactions of the COVID-19 therapeutic modalities and fat-soluble vitamins. With an emphasis on cancer and autoimmune patients, the current review aims to clarify the role of fat-soluble vitamins in SARS-CoV-2 infection and to estimate the risk-to-benefit ratio of a fat-soluble supplement administered to patients taking FDA-approved COVID-19 medications such as antivirals, anti-inflammatory, receptor blockers, and monoclonal antibodies. Full article

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21 pages, 2858 KiB

Open AccessArticle

Aeromonas allosaccharophila Strain AE59-TE2 Is Highly Antagonistic towards Multidrug-Resistant Human Pathogens, What Does Its Genome Tell Us?

by Sheila da Silva, Fernanda Alves de Freitas Guedes, João Ricardo Vidal Amaral, José Roberto de Assis Ribeiro, Yuri Pinheiro Alves de Souza, Ângela Correa de Freitas-Almeida, Fabiano Lopes Thompson, Rommel Thiago Jucá Ramos, Andrew Steven Whiteley, Andrew Macrae and Selma Soares de Oliveira

Life 2022, 12(10), 1492; https://doi.org/10.3390/life12101492 - 26 Sep 2022

Cited by 2 | Viewed by 2613

Abstract

Multidrug-resistant bacteria are of critical importance and a problem for human health and food preservation; the discovery of new antimicrobial substances to control their proliferation is part of the solution. This work reports on 57 antagonistic Aeromonas strains, of which 38 strains were [...] Read more.

Multidrug-resistant bacteria are of critical importance and a problem for human health and food preservation; the discovery of new antimicrobial substances to control their proliferation is part of the solution. This work reports on 57 antagonistic Aeromonas strains, of which 38 strains were antagonistic towards problematic human pathogens. The genome of the most antagonistic strain was sequenced and identified as Aeromonas allosaccharophila. Its genome was fully annotated and mined for genes that might explain that activity. Strain AE59-TE was antagonistic toward clinically relevant gram-negative and gram-positive multidrug-resistant bacteria, including Klebsiella pneumoniae KPC, Escherichia coli ESBL, Salmonella typhimurium, and Staphylococcus aureus MRSA. Strain AE59-TE2 was identified by multilocus sequence analysis. Genome mining identified four genes homologous to the bacteriocin, zoocin A from Streptococcus equi and a gene 98% similar to cvpA linked to colicin V production. A. allosaccharophila strain AE59-TE2 produced antimicrobial activity against a broad range of bacteria, including important gram-negative bacteria, not typically targeted by bacteriocins. Herewere described novel zoocin genes that are promising for industrial applications in the food and health sectors. Interesting and important antagonistic activity is described combined with the first detailed genomic analysis of the species Aeromonas allosaccharophila. Full article

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38 pages, 2616 KiB

Open AccessReview

Probiotic Mechanisms Affecting Glucose Homeostasis: A Scoping Review

by Maša Pintarič and Tomaž Langerholc

Life 2022, 12(8), 1187; https://doi.org/10.3390/life12081187 - 3 Aug 2022

Cited by 12 | Viewed by 4705

Abstract

The maintenance of a healthy status depends on the coexistence between the host organism and the microbiota. Early studies have already focused on the nutritional properties of probiotics, which may also contribute to the structural changes in the gut microbiota, thereby affecting host [...] Read more.

The maintenance of a healthy status depends on the coexistence between the host organism and the microbiota. Early studies have already focused on the nutritional properties of probiotics, which may also contribute to the structural changes in the gut microbiota, thereby affecting host metabolism and homeostasis. Maintaining homeostasis in the body is therefore crucial and is reflected at all levels, including that of glucose, a simple sugar molecule that is an essential fuel for normal cellular function. Despite numerous clinical studies that have shown the effect of various probiotics on glucose and its homeostasis, knowledge about the exact function of their mechanism is still scarce. The aim of our review was to select in vivo and in vitro studies in English published in the last eleven years dealing with the effects of probiotics on glucose metabolism and its homeostasis. In this context, diverse probiotic effects at different organ levels were highlighted, summarizing their potential mechanisms to influence glucose metabolism and its homeostasis. Variations in results due to different methodological approaches were discussed, as well as limitations, especially in in vivo studies. Further studies on the interactions between probiotics, host microorganisms and their immunity are needed. Full article

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