Microorganisms

23 pages, 4437 KiB

Open AccessReview

The Prevalence of Metallo-Beta-Lactamese-(MβL)-Producing Pseudomonas aeruginosa Isolates in Brazil: A Systematic Review and Meta-Analysis

by Pabllo Antonny Silva Dos Santos, Marcos Jessé Abrahão Silva, Maria Isabel Montoril Gouveia, Luana Nepomuceno Gondim Costa Lima, Ana Judith Pires Garcia Quaresma, Patrícia Danielle Lima De Lima, Danielle Murici Brasiliense, Karla Valéria Batista Lima and Yan Corrêa Rodrigues

Microorganisms 2023, 11(9), 2366; https://doi.org/10.3390/microorganisms11092366 - 21 Sep 2023

Cited by 1 | Viewed by 1618

Abstract

The purpose of the current study is to describe the prevalence of Pseudomonas aeruginosa (PA)-producing MβL among Brazilian isolates and the frequency of bla_SPM-1 in MβL-PA-producing isolates. From January 2009 to August 2023, we carried out an investigation on this subject in [...] Read more.

The purpose of the current study is to describe the prevalence of Pseudomonas aeruginosa (PA)-producing MβL among Brazilian isolates and the frequency of bla_SPM-1 in MβL-PA-producing isolates. From January 2009 to August 2023, we carried out an investigation on this subject in the internet databases SciELO, PubMed, Science Direct, and LILACS. A total of 20 papers that met the eligibility requirements were chosen by comprehensive meta-analysis software v2.2 for data retrieval and analysis by one meta-analysis using a fixed-effects model for the two investigations. The prevalence of MβL-producing P. aeruginosa was 35.8% or 0.358 (95% CI = 0.324–0.393). The studies’ differences were significantly different from one another (x² = 243.15; p < 0.001; I² = 92.18%), so they were divided into subgroups based on Brazilian regions. There was indication of asymmetry in the meta-analyses’ publishing bias funnel plot; so, a meta-regression was conducted by the study’s publication year. According to the findings of Begg’s test, no discernible publishing bias was found. bla_SPM-1 prevalence was estimated at 66.9% or 0.669 in MβL-PA isolates (95% CI = 0.593–0.738). The analysis of this one showed an average heterogeneity (x² = 90.93; p < 0.001; I² = 80.20%). According to the results of Begg’s test and a funnel plot, no discernible publishing bias was found. The research showed that MβL-P. aeruginosa and SPM-1 isolates were relatively common among individuals in Brazil. P. aeruginosa and other opportunistic bacteria are spreading quickly and causing severe infections, so efforts are needed to pinpoint risk factors, reservoirs, transmission pathways, and the origin of infection. Full article

(This article belongs to the Special Issue Microorganisms Associated with Infectious Disease 2.0)

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12 pages, 2288 KiB

Open AccessArticle

Impact of Protein Aggregates on Sporulation and Germination of Bacillus subtilis

by Julien Mortier, Alexander Cambré, Sina Schack, Graham Christie and Abram Aertsen

Microorganisms 2023, 11(9), 2365; https://doi.org/10.3390/microorganisms11092365 - 21 Sep 2023

Viewed by 952

Abstract

In order to improve our general understanding of protein aggregate (PA) management and impact in bacteria, different model systems and processes need to be investigated. As such, we developed an inducible synthetic PA model system to investigate PA dynamics in the Gram-positive model [...] Read more.

In order to improve our general understanding of protein aggregate (PA) management and impact in bacteria, different model systems and processes need to be investigated. As such, we developed an inducible synthetic PA model system to investigate PA dynamics in the Gram-positive model organism Bacillus subtilis. This confirmed previous observations that PA segregation in this organism seems to follow the Escherichia coli paradigm of nucleoid occlusion governing polar localization and asymmetric segregation during vegetative growth. However, our findings also revealed that PAs can readily persist throughout the entire sporulation process after encapsulation in the forespore during sporulation. Moreover, no deleterious effects of PA presence on sporulation, germination and spore survival against heat or UV stress could be observed. Our findings therefore indicate that the sporulation process is remarkably robust against perturbations by PAs and misfolded proteins. Full article

(This article belongs to the Special Issue Assembly, Structure, and Germination of Bacterial Spores)

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15 pages, 3123 KiB

Open AccessArticle

Core Endophytic Bacteria and Their Roles in the Coralloid Roots of Cultivated Cycas revoluta (Cycadaceae)

by Jiating Liu, Haiyan Xu, Zhaochun Wang, Jian Liu and Xun Gong

Microorganisms 2023, 11(9), 2364; https://doi.org/10.3390/microorganisms11092364 - 21 Sep 2023

Cited by 1 | Viewed by 1125

Abstract

As a gymnosperm group, cycads are known for their ancient origin and specialized coralloid root, which can be used as an ideal system to explore the interaction between host and associated microorganisms. Previous studies have revealed that some nitrogen-fixing cyanobacteria contribute greatly to [...] Read more.

As a gymnosperm group, cycads are known for their ancient origin and specialized coralloid root, which can be used as an ideal system to explore the interaction between host and associated microorganisms. Previous studies have revealed that some nitrogen-fixing cyanobacteria contribute greatly to the composition of the endophytic microorganisms in cycad coralloid roots. However, the roles of host and environment in shaping the composition of endophytic bacteria during the recruitment process remain unclear. Here, we determined the diversity, composition, and function prediction of endophytic bacteria from the coralloid roots of a widely cultivated cycad, Cycas revoluta Thunb. Using next-generation sequencing techniques, we comprehensively investigated the diversity and community structure of the bacteria in coralloid roots and bulk soils sampled from 11 sites in China, aiming to explore the variations in core endophytic bacteria and to predict their potential functions. We found a higher microbe diversity in bulk soils than in coralloid roots. Meanwhile, there was no significant difference in the diversity and composition of endophytic bacteria across different localities, and the same result was found after removing cyanobacteria. Desmonostoc was the most dominant in coralloid roots, followed by Nostoc, yet these two cyanobacteria were not shared by all samples. Rhodococcus, Edaphobacter, Niastella, Nordella, SH-PL14, and Virgisporangium were defined as the core microorganisms in coralloid roots. A function prediction analysis revealed that endophytic bacteria majorly participated in the plant uptake of phosphorus and metal ions and in disease resistance. These results indicate that the community composition of the bacteria in coralloid roots is affected by both the host and environment, in which the host is more decisive. Despite the very small proportion of core microbes, their interactions are significant and likely contribute to functions related to host survival. Our study contributes to an understanding of microbial diversity and composition in cycads, and it expands the knowledge on the association between hosts and symbiotic microbes. Full article

(This article belongs to the Special Issue Plant-Microbe Interaction State-of-the-Art Research in China)

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20 pages, 1806 KiB

Open AccessReview

Gut Microbiota in Diagnosis, Therapy and Prognosis of Cholangiocarcinoma and Gallbladder Carcinoma—A Scoping Review

by Ann-Kathrin Lederer, Hannah Rasel, Eva Kohnert, Clemens Kreutz, Roman Huber, Mohamed Tarek Badr, Patricia K. E. Dellweg, Fabian Bartsch and Hauke Lang

Microorganisms 2023, 11(9), 2363; https://doi.org/10.3390/microorganisms11092363 - 21 Sep 2023

Cited by 1 | Viewed by 1594

Abstract

Cancers of the biliary tract are more common in Asia than in Europe, but are highly lethal due to delayed diagnosis and aggressive tumor biology. Since the biliary tract is in direct contact with the gut via the enterohepatic circulation, this suggests a [...] Read more.

Cancers of the biliary tract are more common in Asia than in Europe, but are highly lethal due to delayed diagnosis and aggressive tumor biology. Since the biliary tract is in direct contact with the gut via the enterohepatic circulation, this suggests a potential role of gut microbiota, but to date, the role of gut microbiota in biliary tract cancers has not been elucidated. This scoping review compiles recent data on the associations between the gut microbiota and diagnosis, progression and prognosis of biliary tract cancer patients. Systematic review of the literature yielded 154 results, of which 12 studies and one systematic review were eligible for evaluation. The analyses of microbiota diversity indices were inconsistent across the included studies. In-depth analyses revealed differences between gut microbiota of biliary tract cancer patients and healthy controls, but without a clear tendency towards particular species in the studies. Additionally, most of the studies showed methodological flaws, for example non-controlling of factors that affect gut microbiota. At the current stage, there is a lack of evidence to support a general utility of gut microbiota diagnostics in biliary tract cancers. Therefore, no recommendation can be made at this time to include gut microbiota analyses in the management of biliary tract cancer patients. Full article

(This article belongs to the Special Issue Latest Review Papers in Gut Microbiota 2023)

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13 pages, 1175 KiB

Open AccessReview

Kocuria Species Infections in Humans—A Narrative Review

by Afroditi Ziogou, Ilias Giannakodimos, Alexios Giannakodimos, Stella Baliou and Petros Ioannou

Microorganisms 2023, 11(9), 2362; https://doi.org/10.3390/microorganisms11092362 - 21 Sep 2023

Cited by 4 | Viewed by 3330

Abstract

Kocuria species are catalase-positive and coagulase-negative Gram-positive coccoid bacteria that belong to the family Micrococcaceae, order Actinomycetales, and class Actinobacteria. Even though they may be relatively rare, they have been increasingly reported as the causes of human infections lately. The present study aims [...] Read more.

Kocuria species are catalase-positive and coagulase-negative Gram-positive coccoid bacteria that belong to the family Micrococcaceae, order Actinomycetales, and class Actinobacteria. Even though they may be relatively rare, they have been increasingly reported as the causes of human infections lately. The present study aims to review all published cases of Kocuria spp. infections in humans reporting data on epidemiology, microbiology, antimicrobial susceptibility, antimicrobial treatment, and mortality. A narrative review was performed based on a search of Pubmed and Scopus databases in the literature. In total, 73 studies provided data on 102 patients with Kocuria spp. infections. The mean age of patients was 47 years, and 68.3% were male. The most common types of infection were bacteremia (36.3%), skin and soft tissue infection (18.6%), endophthalmitis (15.7%), infective endocarditis (13.7%), and peritonitis (11.8%), most commonly peritoneal–dialysis-associated. The most frequently isolated species was K. kristinae (46.1%), and antimicrobial resistance was lower for vancomycin (7%) and tetracyclines (6.7%). Vancomycin (47%), cephalosporins (39.6%), and quinolones (36.6%) were the most commonly used antimicrobials. The empirical antimicrobial treatment of Kocuria spp. infections should include vancomycin as long as antimicrobial susceptibility results are pending. The infection outcome mainly depends on the type of infection and is higher for infective endocarditis. Endophthalmitis is associated with increased rates of low visual acuity after treatment. Full article

(This article belongs to the Special Issue New Trends in Medical Bacteriology: Diagnosis, Treatment and Prevention)

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17 pages, 3277 KiB

Open AccessArticle

Transcriptome and Metabolome Analyses of Thitarodes xiaojinensis in Response to Ophiocordyceps sinensis Infection

by Miaomiao Li, Jihong Zhang, Qilian Qin, Huan Zhang, Xuan Li, Hongtuo Wang and Qian Meng

Microorganisms 2023, 11(9), 2361; https://doi.org/10.3390/microorganisms11092361 - 21 Sep 2023

Viewed by 1016

Abstract

Ophiocordyceps sinensis exhibits more than 5 months of vegetative growth in Thitarodes xiaojinensis hemocoel. The peculiar development process of O. sinensis has been elucidated through morphological observation and omics technology; however, little information has been reported regarding the changes that occur in the [...] Read more.

Ophiocordyceps sinensis exhibits more than 5 months of vegetative growth in Thitarodes xiaojinensis hemocoel. The peculiar development process of O. sinensis has been elucidated through morphological observation and omics technology; however, little information has been reported regarding the changes that occur in the host T. xiaojinensis. The RNA sequencing data showed that when O. sinensis blastospores were in the proliferative stage, the greatest change in the infected larval fat body was the selectively upregulated immune recognition and antimicrobial peptide genes. When O. sinensis blastospores were in the stationary stage, the immune pathways of T. xiaojinensis reverted to normal levels, which coincides with the successful settlement of O. sinensis. Pathway enrichment analysis showed a higher expression of genes involved in energy metabolism pathway in this stage. Metabolomic analyses revealed a reduction of amino acids and lipids in hemolymph, but an upregulation of lipids in the fat body of the host larvae after O. sinensis infection. We present the first transcriptome integrated with the metabolome study of T. xiaojinensis infected by O. sinensis. It will improve our understanding of the interaction mechanisms between the host and entomopathogenic fungi, and facilitate future functional studies of genes and pathways involved in these interactions. Full article

(This article belongs to the Special Issue Fungal Biology and Interactions)

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10 pages, 522 KiB

Open AccessCommunication

Plasma Bacterial DNA Load as a Potential Biomarker for the Early Detection of Colorectal Cancer: A Case–Control Study

by Robertina Giacconi, Rossella Donghia, Graziana Arborea, Maria Teresa Savino, Mauro Provinciali, Fabrizia Lattanzio, Giusy Rita Caponio, Sergio Coletta, Antonia Bianco, Maria Notarnicola, Caterina Bonfiglio, Giuseppe Passarino, Patrizia D’Aquila, Dina Bellizzi and Pasqua Letizia Pesole

Microorganisms 2023, 11(9), 2360; https://doi.org/10.3390/microorganisms11092360 - 21 Sep 2023

Viewed by 1249

Abstract

The gut microbiota has gained increasing attention in recent years due to its significant impact on colorectal cancer (CRC) development and progression. The recent detection of bacterial DNA load in plasma holds promise as a potential non-invasive approach for early cancer detection. The [...] Read more.

The gut microbiota has gained increasing attention in recent years due to its significant impact on colorectal cancer (CRC) development and progression. The recent detection of bacterial DNA load in plasma holds promise as a potential non-invasive approach for early cancer detection. The aim of this study was to examine the quantity of bacterial DNA present in the plasma of 50 patients who have CRC in comparison to 40 neoplastic disease-free patients, as well as to determine if there is a correlation between the amount of plasma bacterial DNA and various clinical parameters. Plasma bacterial DNA levels were found to be elevated in the CRC group compared to the control group. As it emerged from the logistic analysis (adjusted for age and gender), these levels were strongly associated with the risk of CRC (OR = 1.02, p < 0.001, 95% C.I.: 1.01–1.03). Moreover, an association was identified between a reduction in tumor mass and the highest tertile of plasma bacterial DNA. Our findings indicate that individuals with CRC displayed a higher plasma bacterial DNA load compared to healthy controls. This observation lends support to the theory of heightened bacterial migration from the gastrointestinal tract to the bloodstream in CRC. Furthermore, our results establish a link between this phenomenon and the size of the tumor mass. Full article

(This article belongs to the Special Issue Gut Microbiota, Diet, and Gastrointestinal Cancer)

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13 pages, 2347 KiB

Open AccessArticle

A Comparative Analysis of the Stomach, Gut, and Lung Microbiomes in Rattus norvegicus

by Taif Shah, Yuhan Wang, Yixuan Wang, Qian Li, Jiuxuan Zhou, Yutong Hou, Binghui Wang and Xueshan Xia

Microorganisms 2023, 11(9), 2359; https://doi.org/10.3390/microorganisms11092359 - 21 Sep 2023

Cited by 1 | Viewed by 1275

Abstract

Urban rats serve as reservoirs for several zoonotic pathogens that seriously endanger public health, destroy stored food, and damage infrastructure due to their close interaction with humans and domestic animals. Here, we characterize the core microbiomes of R. norvegicus’s stomach, gut, and lung [...] Read more.

Urban rats serve as reservoirs for several zoonotic pathogens that seriously endanger public health, destroy stored food, and damage infrastructure due to their close interaction with humans and domestic animals. Here, we characterize the core microbiomes of R. norvegicus’s stomach, gut, and lung using 16S rRNA next-generation Illumina HiSeq sequencing. The USEARCH software (v11) assigned the dataset to operational taxonomic units (OTUs). The alpha diversity index was calculated using QIIME1, while the beta diversity index was determined using the Bray–Curtis and Euclidean distances between groups. Principal component analyses visualized variation across samples based on the OTU information using the R package. Linear discriminant analysis, effect sizes (LEfSe), and phylogenetic investigation were used to identify differentially abundant taxa among groups. We reported an abundance of microbiota in the stomach, and they shared some of them with the gut and lung microbiota. A close look at the microbial family level reveals abundant Lactobacillaceae and Bifidobacteriaceae in the stomach, whereas Lactobacillaceae and Erysipelotrichaceae were more abundant in the gut; in contrast, Alcaligenaceae were abundant in the lungs. At the species level, some beneficial bacteria, particularly Lactobacillus reuteri and Lactobacillus johnsonii, and some potential pathogens, such as Bordetella hinzii, Streptococcus parauberis, Porphyromonas pogonae, Clostridium perfringens, etc., were identified in stomach, gut, and lung samples. Moreover, the alpha and beta diversity indexes revealed significant differences between the groups. Further analysis revealed abundant differential taxonomic biomarkers, i.e., increased Prevotellaceae and Clostridia in the lungs, whereas Campylobacteria and Lachnospirales were richest in the stomachs. In conclusion, we identified many beneficial, opportunistic, and highly pathogenic bacteria, confirming the importance of urban rats for public health. This study recommends a routine survey program to monitor rodent distribution and the pathogens they carry and transmit to humans and other domestic mammals. Full article

(This article belongs to the Special Issue Gut Microbiome in Homeostasis and Disease)

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16 pages, 1073 KiB

Open AccessReview

The Role of Fusobacterium nucleatum in Oral and Colorectal Carcinogenesis

by Pamela Pignatelli, Federica Nuccio, Adriano Piattelli and Maria Cristina Curia

Microorganisms 2023, 11(9), 2358; https://doi.org/10.3390/microorganisms11092358 - 20 Sep 2023

Cited by 9 | Viewed by 3659

Abstract

In recent years, several studies have suggested a strong association of microorganisms with several human cancers. Two periodontopathogenic species in particular have been mentioned frequently: Fusobacterium nucleatum (F. nucleatum) and Porphyromonas gingivalis. Chronic periodontal disease has been reported to be [...] Read more.

In recent years, several studies have suggested a strong association of microorganisms with several human cancers. Two periodontopathogenic species in particular have been mentioned frequently: Fusobacterium nucleatum (F. nucleatum) and Porphyromonas gingivalis. Chronic periodontal disease has been reported to be a risk factor for oral squamous cell carcinoma (OSCC), colorectal cancer (CRC) and pancreatic cancer. F. nucleatum is a Gram-negative anaerobic bacterium that lives in the oral cavity, urogenital, intestinal and upper digestive tract. It plays a significant role as a co-aggregation factor, with almost all bacterial species that participate in oral plaque formation acting as a bridge between early and late colonizers. F. nucleatum, gives an important inflammatory contribution to tumorigenesis progression and is associated with epithelial-derived malignancies, such as OSCC and CRC. F. nucleatum produces an adhesion protein, FadA, which binds to VE-cadherin on endothelial cells and to E-cadherins on epithelial cells. The last binding activates oncogenic pathways, such as Wnt/βcatenin, in oral and colorectal carcinogenesis. F. nucleatum also affects immune response because its Fap2 protein interacts with an immune receptor named TIGIT present on some T cells and natural killer cells inhibiting immune cells activities. Morover, F. nucleatum release outer membrane vesicles (OMVs), which induce the production of proinflammatory cytokines and initiating inflammation. F. nucleatum migrates from the oral cavity and reaches the colon hematogenously but it is not known if in the bloodstream it reaches the CRC as free, erythrocyte-bound bacteria or in OMV. F. nucleatum abundance in CRC tissue has been inversely correlated with overall survival (OS). The prevention and treatment of periodontal disease through the improvement of oral hygiene should be included in cancer prevention protocols. FadA virulence factors may also serve as novel targets for therapeutic intervention of oral and colorectal cancer. Full article

(This article belongs to the Special Issue Oncogenic Role of Viruses and Bacteria)

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10 pages, 1938 KiB

Open AccessArticle

Bacteremia in Patients with Sepsis in the ICU: Does It Make a Difference?

by Tomáš Nejtek, Martin Müller, Michal Moravec, Miroslav Průcha and Roman Zazula

Microorganisms 2023, 11(9), 2357; https://doi.org/10.3390/microorganisms11092357 - 20 Sep 2023

Viewed by 1135

Abstract

Sepsis (and septic shock) is on of the most common causes of death worldwide. Bacteremia often, but not necessarily, occurs in septic patients, but the impact of true bacteremia on a patient’s clinical characteristics and outcome remains unclear. The main aim of this [...] Read more.

Sepsis (and septic shock) is on of the most common causes of death worldwide. Bacteremia often, but not necessarily, occurs in septic patients, but the impact of true bacteremia on a patient’s clinical characteristics and outcome remains unclear. The main aim of this study was to compare the characteristics and outcome of a well-defined cohort of 258 septic patients with and without bacteremia treated in the intensive care unit (ICU) of a tertiary center hospital in Prague, Czech Republic. As expected, more frequently, bacteremia was present in patients without previous antibiotic treatment. A higher proportion of bacteremia was observed in patients with infective endocarditis as well as catheter-related and soft tissue infections in contrast to respiratory sepsis. Multivariant analysis showed increased severity of clinical status and higher Charlson comorbidity index (CCI) as variables with significant influence on mortality. Bacteremia appears to be associated with higher mortality rates and length of ICU stay in comparison with nonbacteremic counterparts, but this difference did not reach statistical significance. The presence of bacteremia, apart from previous antibiotic treatment, may be related to the site of infection. Full article

(This article belongs to the Special Issue Bacterial Pathogens Associated with Bacteremia)

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16 pages, 3559 KiB

Open AccessArticle

Concurrent Brain Subregion Microgliosis in an HLA-II Mouse Model of Group A Streptococcal Skin Infection

by Suba Nookala, Santhosh Mukundan, Bryon Grove and Colin Combs

Microorganisms 2023, 11(9), 2356; https://doi.org/10.3390/microorganisms11092356 - 20 Sep 2023

Viewed by 828

Abstract

The broad range of clinical manifestations and life-threatening infections caused by the Gram-positive bacterium, Streptococcus pyogenes or Group A Streptococcus (GAS), remains a significant concern to public health, with a subset of individuals developing neurological complications. Here, we examined the concurrent neuroimmune effects [...] Read more.

The broad range of clinical manifestations and life-threatening infections caused by the Gram-positive bacterium, Streptococcus pyogenes or Group A Streptococcus (GAS), remains a significant concern to public health, with a subset of individuals developing neurological complications. Here, we examined the concurrent neuroimmune effects of subcutaneous GAS infections in an HLA-Class II (HLA) transgenic mouse model of subcutaneous GAS infection. To investigate changes in the skin–brain axis, HLA-DQ8 (DQA1*0301/DQB1*0302) mice (DQ8) were randomly divided into three groups: uninfected controls (No Inf), GAS infected and untreated (No Tx), and GAS infected with a resolution by clindamycin (CLN) treatment (CLN Tx) (10 mg/kg/5 days) and were monitored for 16 days post-infection. While the skin GAS burden was significantly reduced by CLN, the cortical and hippocampal GAS burden in the male DQ8 mice was not significantly reduced with CLN. Immunoreactivity to anti-GAS antibody revealed the presence of GAS bacteria in the vicinity of the neuronal nucleus in the neocortex of both No Tx and CLN Tx male DQ8 mice. GAS infection-mediated cortical cytokine changes were modest; however, compared to No Inf or No Tx groups, a significant increase in IL-2, IL-13, IL-22, and IL-10 levels was observed in CLN Tx females despite the lack of GAS burden. Western blot analysis of cortical and hippocampal homogenates showed significantly higher ionized calcium-binding adaptor-1 (Iba-1, microglia marker) protein levels in No Tx females and males and CLN Tx males compared to the No Inf group. Immunohistochemical analysis showed that Iba-1 immunoreactivity in the hippocampal CA3 and CA1 subregions was significantly higher in the CLN Tx males compared to the No Tx group. Our data support the possibility that the subcutaneous GAS infection communicates to the brain and is characterized by intraneuronal GAS sequestration, brain cytokine changes, Iba-1 protein levels, and concurrent CA3 and CA1 subregion-specific microgliosis, even without bacteremia. Full article

(This article belongs to the Special Issue Group A Streptococcus: Infection, Immunity and Vaccine Development)

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42 pages, 4876 KiB

Open AccessReview

Emerging and Novel Viruses in Passerine Birds

by Richard A. J. Williams, Christian J. Sánchez-Llatas, Ana Doménech, Ricardo Madrid, Sergio Fandiño, Pablo Cea-Callejo, Esperanza Gomez-Lucia and Laura Benítez

Microorganisms 2023, 11(9), 2355; https://doi.org/10.3390/microorganisms11092355 - 20 Sep 2023

Cited by 1 | Viewed by 3392

Abstract

There is growing interest in emerging viruses that can cause serious or lethal disease in humans and animals. The proliferation of cloacal virome studies, mainly focused on poultry and other domestic birds, reveals a wide variety of viruses, although their pathogenic significance is [...] Read more.

There is growing interest in emerging viruses that can cause serious or lethal disease in humans and animals. The proliferation of cloacal virome studies, mainly focused on poultry and other domestic birds, reveals a wide variety of viruses, although their pathogenic significance is currently uncertain. Analysis of viruses detected in wild birds is complex and often biased towards waterfowl because of the obvious interest in avian influenza or other zoonotic viruses. Less is known about the viruses present in the order Passeriformes, which comprises approximately 60% of extant bird species. This review aims to compile the most significant contributions on the DNA/RNA viruses affecting passerines, from traditional and metagenomic studies. It highlights that most passerine species have never been sampled. Especially the RNA viruses from Flaviviridae, Orthomyxoviridae and Togaviridae are considered emerging because of increased incidence or avian mortality/morbidity, spread to new geographical areas or hosts and their zoonotic risk. Arguably poxvirus, and perhaps other virus groups, could also be considered “emerging viruses”. However, many of these viruses have only recently been described in passerines using metagenomics and their role in the ecosystem is unknown. Finally, it is noteworthy that only one third of the viruses affecting passerines have been officially recognized. Full article

(This article belongs to the Special Issue Avian Pathogens 2.0)

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16 pages, 1458 KiB

Open AccessArticle

A Whole-Genome Sequencing-Based Approach for the Characterization of Klebsiella pneumoniae Co-Producing KPC and OXA-48-like Carbapenemases Circulating in Sardinia, Italy

by Arcadia Del Rio, Valeria Fox, Narcisa Muresu, Illari Sechi, Andrea Cossu, Alessandra Palmieri, Rossana Scutari, Claudia Alteri, Giovanni Sotgiu, Paolo Castiglia and Andrea Piana

Microorganisms 2023, 11(9), 2354; https://doi.org/10.3390/microorganisms11092354 - 20 Sep 2023

Cited by 1 | Viewed by 1050

Abstract

Background: Whole-genome sequencing (WGS) provides important information for the characterization, surveillance, and monitoring of antimicrobial resistance (AMR) determinants, particularly in cases of multi- and extensively drug-resistant microorganisms. We reported the results of a WGS analysis carried out on carbapenemases-producing Klebsiella pneumoniae, which [...] Read more.

Background: Whole-genome sequencing (WGS) provides important information for the characterization, surveillance, and monitoring of antimicrobial resistance (AMR) determinants, particularly in cases of multi- and extensively drug-resistant microorganisms. We reported the results of a WGS analysis carried out on carbapenemases-producing Klebsiella pneumoniae, which causes hospital-acquired infections (HAIs) and is characterized by a marked resistance profile. Methods: Clinical, phenotypic, and genotypic data were collected for the AMR surveillance screening program of the University Hospital of Sassari (Italy) during 2020–2021. Genomic DNA was sequenced using the Illumina Nova Seq 6000 platform. Final assemblies were manually curated and carefully verified for the detection of antimicrobial resistance genes, porin mutations, and virulence factors. A phylogenetic analysis was performed using the maximum likelihood method. Results: All 17 strains analyzed belonged to ST512, and most of them carried the bla_KPC-31 variant bla_OXA-48-like, an OmpK35 truncation, and an OmpK36 mutation. Phenotypic analysis showed a marked resistance profile to all antibiotic classes, including β-lactams, carbapenems, aminoglycosides, fluoroquinolone, sulphonamides, and novel β-lactam/β-lactamase inhibitors (BL/BLI). Conclusion: WGS characterization revealed the presence of several antibiotic resistance determinants and porin mutations in highly resistant K. pneumoniae strains responsible for HAIs. The detection of bla_KPC-31 in our hospital wards highlights the importance of genomic surveillance in hospital settings to monitor the emergence of new clones and the need to improve control and preventive strategies to efficiently contrast AMR. Full article

(This article belongs to the Special Issue 10th Anniversary of Microorganisms: Past, Present and Future)

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19 pages, 4064 KiB

Open AccessArticle

Impact of Sleeve Gastrectomy on Fecal Microbiota in Individuals with Morbid Obesity

by Danyta I. Tedjo, Jennifer A. Wilbrink, Jos Boekhorst, Harro M. Timmerman, Simon W. Nienhuijs, Arnold Stronkhorst, Paul H. M. Savelkoul, Ad A. M. Masclee, John Penders and Daisy M. A. E. Jonkers

Microorganisms 2023, 11(9), 2353; https://doi.org/10.3390/microorganisms11092353 - 20 Sep 2023

Cited by 1 | Viewed by 1157

Abstract

Background: The intestinal microbiota plays an important role in the etiology of obesity. Sleeve gastrectomy (SG) is a frequently performed and effective therapy for morbid obesity. Objective: To investigate the effect of sleeve gastrectomy on the fecal microbiota of individuals with morbid obesity [...] Read more.

Background: The intestinal microbiota plays an important role in the etiology of obesity. Sleeve gastrectomy (SG) is a frequently performed and effective therapy for morbid obesity. Objective: To investigate the effect of sleeve gastrectomy on the fecal microbiota of individuals with morbid obesity and to examine whether shifts in microbiota composition are associated with markers of inflammation and intestinal barrier function. Methods: Fecal and blood samples of healthy individuals (n = 27) and morbidly obese individuals pre-SG (n = 24), and at 2 months (n = 13) and 6 months post-SG (n = 9) were collected. The 16SrRNA gene was sequenced to assess microbiota composition. Fecal calprotectin, plasma inflammatory markers and intestinal permeability markers (multi-sugar test) were determined. Results: Fecal microbiota composition between morbidly obese and lean individuals was significantly different. The fecal microbiota composition changed significantly 2 and 6 months post-SG (p = 0.008) compared to pre-SG but not towards a more lean profile. The post-SG microbiota profile was characterized by an increase in facultative anaerobic bacteria, characteristic for the upper gastrointestinal tract. No correlations were found between inflammatory markers, intestinal permeability and microbial profile changes. Conclusions: Fecal microbiota composition in morbidly obese individuals changed significantly following SG. This change might be explained by functional changes induced by the SG procedure. Full article

(This article belongs to the Special Issue Gut Microbiota: Health, Clinical & Beyonds)

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14 pages, 3533 KiB

Open AccessArticle

Response Surface Methodology Application for Bacteriophage–Antibiotic Antibiofilm Activity Optimization

by Bartłomiej Grygorcewicz, Marta Gliźniewicz, Patrycja Olszewska, Dominika Miłek, Artur Czajkowski, Natalia Serwin, Elżbieta Cecerska-Heryć and Rafał Rakoczy

Microorganisms 2023, 11(9), 2352; https://doi.org/10.3390/microorganisms11092352 - 20 Sep 2023

Cited by 3 | Viewed by 1505

Abstract

Phage–antibiotic combination-based protocols are presently under heightened investigation. This paradigm extends to engagements with bacterial biofilms, necessitating novel computational approaches to comprehensively characterize and optimize the outcomes achievable via these combinations. This study aimed to explore the Response Surface Methodology (RSM) in optimizing [...] Read more.

Phage–antibiotic combination-based protocols are presently under heightened investigation. This paradigm extends to engagements with bacterial biofilms, necessitating novel computational approaches to comprehensively characterize and optimize the outcomes achievable via these combinations. This study aimed to explore the Response Surface Methodology (RSM) in optimizing the antibiofilm activity of bacteriophage–antibiotic combinations. We employ a combination of antibiotics (gentamicin, meropenem, amikacin, ceftazidime, fosfomycin, imipenem, and colistin) alongside the bacteriophage vB_AbaP_AGC01 to combat Acinetobacter baumannii biofilm. Based on the conducted biofilm challenge assays analyzed using the RSM, the optimal points of antibiofilm activity efficacy were effectively selected by applying this methodology, enabling the quantifiable mathematical representations. Subsequent optimization showed the synergistic potential of the anti-biofilm that arises when antibiotics are judiciously combined with the AGC01 bacteriophage, reducing biofilm biomass by up to 80% depending on the antibiotic used. The data suggest that the phage–imipenem combination demonstrates the highest efficacy, with an 88.74% reduction. Notably, the lower concentrations characterized by a high maximum reduction in biofilm biomass were observed in the phage–amikacin combination at c_A = 0.00195 and c_P = 0.38 as the option that required minimum resources. It is worth noting that only gentamicin antagonism between the phage and the antibiotic was detected. Full article

(This article belongs to the Special Issue Esther Lederberg’s 100th Anniversary: Microbial Genetics and Bacteriophages)

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15 pages, 8839 KiB

Open AccessArticle

Alpha-Naphthoflavone as a Novel Scaffold for the Design of Potential Inhibitors of the APH(3’)-IIIa Nucleotide-Binding Site of Enterococcus faecalis

by Juliana Carolina Amorim and Juan Marcelo Carpio

Microorganisms 2023, 11(9), 2351; https://doi.org/10.3390/microorganisms11092351 - 20 Sep 2023

Cited by 1 | Viewed by 939

Abstract

The spread of nosocomial infections caused by antibiotic-resistant Enterococcus faecalis is one of the major threats to global health at present. While aminoglycosides are often used to combat these infections, their effectiveness is reduced by various resistance mechanisms, including aminoglycoside modifying enzymes, and [...] Read more.

The spread of nosocomial infections caused by antibiotic-resistant Enterococcus faecalis is one of the major threats to global health at present. While aminoglycosides are often used to combat these infections, their effectiveness is reduced by various resistance mechanisms, including aminoglycoside modifying enzymes, and there are currently no drugs to inhibit these enzymes. To address this issue, this study was conducted to identify potential aminoglycoside adjuvants from a database of 462 flavones. The affinity of these molecules with the nucleotide-binding site (NBS) of aminoglycoside phosphotransferase type IIIa of E. faecalis (EfAPH(3’)-IIIa) was evaluated, and the five molecules with the highest binding energies were identified. Of these, four were naphthoflavones, suggesting that their backbone could be useful in designing potential inhibitors. The highest-ranked naphthoflavone, 2-phenyl-4H-benzo[h]chromen-4-one, was modified to generate two new derivatives (ANF2OHC and ANF2OHCC) to interact with the NBS similarly to adenine in ATP. These derivatives showed higher binding free energies, better stability in molecular dynamics analysis and superior pharmacokinetic and toxicological profiles compared to the parent molecule. These findings suggest that these alpha-naphthoflavone derivatives are potential inhibitors of EfAPH(3’)-IIIa and that this core may be a promising scaffold for developing adjuvants that restore the sensitivity of aminoglycosides. Full article

(This article belongs to the Special Issue Advances in Antibiotic and Antifungal Resistance and Related Alternative Therapies)

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12 pages, 860 KiB

Open AccessArticle

Dual-Temperature Microbiological Control of Cellular Products: A Potential Impact for Bacterial Screening of Platelet Concentrates?

by Tanja Vollmer, Cornelius Knabbe and Jens Dreier

Microorganisms 2023, 11(9), 2350; https://doi.org/10.3390/microorganisms11092350 - 20 Sep 2023

Viewed by 734

Abstract

An experimental study by the Paul-Ehrlich Institute (PEI) demonstrated that temperatures between 35 and 37 °C are too high for the growth of some bacterial strains (e.g., Pseudomonas fluorescens), leading to false negative results. Thus, the question of whether it is necessary [...] Read more.

An experimental study by the Paul-Ehrlich Institute (PEI) demonstrated that temperatures between 35 and 37 °C are too high for the growth of some bacterial strains (e.g., Pseudomonas fluorescens), leading to false negative results. Thus, the question of whether it is necessary to adapt incubation temperatures for the microbiological control of blood products, especially platelet concentrates (PCs), to enhance safety and regulatory compliance has arisen. In order to further elucidate this issue, the growth capability of different bacterial strains of interest in PCs and the detection efficacy of cultivation of these at different incubation temperatures must be taken into account. Therefore, we inoculated PCs with 46 different strains (3–6 PCs from different donors per strain) from different origins (PC isolates, reference strains) and stored PCs at 20–22 °C under constant agitation. On day three of storage, the inoculated PCs were sampled; aerobic and anaerobic culture bottles (BacT/Alert AST/NST) were each inoculated with 5 mL of sample, and culture bottles were incubated at 25 and 35 °C using the automated BacT/Alert Dual-temperature system. Bacterial proliferation was enumerated using a colony-forming assay. All strains of Enterobacteriacae (n = 5), Staphy-lococcus spp. (n = 11), Streptococcus spp. (n = 5), and Bacillus spp. (n = 4) and most Pseudomonas aeruginosa strains (4 of 5) tested showed the capability to grow in most inoculated PCs, revealing a faster time to detection (TTD) at an incubation temperature of 35 °C. The tested Pseudomonas putida (n = 3) strains showed a noticeably reduced capability to grow in PCs. Nonetheless, those with a notable growth capability revealed a faster TTD at an incubation temperature of 35 °C. Only one of the four Pseudomonas fluorescens strains tested (strain ATCC 13525) was able to grow in PCs, showing a faster TTD at an incubation temperature of 25 °C but also detection at 35 °C. The commonly detected bacteria involved in the bacterial contamination of PCs showed a superior TTD at 35 °C incubation. Only one P. fluorescens strain showed superior growth at 25 °C; however, the microbiological control at 35 °C did not fail to identify this contamination. In conclusion, the use of PC screening using a dual-temperature setting for microbiological control is presently not justified according to the observed kinetics. Full article

(This article belongs to the Special Issue Safety of Platelet Components: Past, Present and Future)

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20 pages, 1660 KiB

Open AccessArticle

Microbiome Diversity of Anaerobic Digesters Is Enhanced by Microaeration and Low Frequency Sound

by John H. Loughrin, Rohan R. Parekh, Getahun E. Agga, Philip J. Silva and Karamat R. Sistani

Microorganisms 2023, 11(9), 2349; https://doi.org/10.3390/microorganisms11092349 - 20 Sep 2023

Cited by 1 | Viewed by 1344

Abstract

Biogas is produced by a consortium of bacteria and archaea. We studied how the microbiome of poultry litter digestate was affected by time and treatments that enhanced biogas production. The microbiome was analyzed at six, 23, and 42 weeks of incubation. Starting at [...] Read more.

Biogas is produced by a consortium of bacteria and archaea. We studied how the microbiome of poultry litter digestate was affected by time and treatments that enhanced biogas production. The microbiome was analyzed at six, 23, and 42 weeks of incubation. Starting at week seven, the digesters underwent four treatments: control, microaeration with 6 mL air L⁻¹ digestate per day, treatment with a 1000 Hz sine wave, or treatment with the sound wave and microaeration. Both microaeration and sound enhanced biogas production relative to the control, while their combination was not as effective as microaeration alone. At week six, over 80% of the microbiome of the four digesters was composed of the three phyla Actinobacteria, Proteobacteria, and Firmicutes, with less than 10% Euryarchaeota and Bacteroidetes. At week 23, the digester microbiomes were more diverse with the phyla Spirochaetes, Synergistetes, and Verrucomicrobia increasing in proportion and the abundance of Actinobacteria decreasing. At week 42, Firmicutes, Bacteroidetes, Euryarchaeota, and Actinobacteria were the most dominant phyla, comprising 27.8%, 21.4%, 17.6%, and 12.3% of the microbiome. Other than the relative proportions of Firmicutes being increased and proportions of Bacteroidetes being decreased by the treatments, no systematic shifts in the microbiomes were observed due to treatment. Rather, microbial diversity was enhanced relative to the control. Given that both air and sound treatment increased biogas production, it is likely that they improved poultry litter breakdown to promote microbial growth. Full article

(This article belongs to the Special Issue Microorganisms in Biomass Conversion and Biofuel Production)

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11 pages, 866 KiB

Open AccessArticle

Detection of Fungal Diseases in Lettuce by VIR-NIR Spectroscopy in Aquaponics

by Ivaylo Sirakov, Katya Velichkova, Toncho Dinev, Desislava Slavcheva-Sirakova, Elica Valkova, Dimitar Yorgov, Petya Veleva, Vasil Atanasov and Stefka Atanassova

Microorganisms 2023, 11(9), 2348; https://doi.org/10.3390/microorganisms11092348 - 20 Sep 2023

Cited by 1 | Viewed by 1351

Abstract

One of the main challenges facing the development of aquaponics is disease control, due on one hand to the fact that plants cannot be treated with chemicals because they can lead to mortality in cultured fish. The aim of this study was to [...] Read more.

One of the main challenges facing the development of aquaponics is disease control, due on one hand to the fact that plants cannot be treated with chemicals because they can lead to mortality in cultured fish. The aim of this study was to apply the visible–near-infrared spectroscopy and vegetation index approach to test aquaponically cultivated lettuce (Lactuca sativa L.) infected with different fungal pathogens (Aspergillus niger, Fusarium oxysporum, and Alternaria alternata). The lettuces on the third leaf formation were placed in tanks (with dimensions 1 m/0.50 m/0.35 m) filled up with water from the aquaponics system every second day. In this study, we included reference fungal strains Aspergillus niger NBIMCC 3252, Fusarium oxysporum NBIMCC 125, and Alternaria alternata NBIMCC 109. Diffuse reflectance spectra of the leaves of lettuce were measured directly on the plants using a USB4000 spectrometer in the 450–1100 nm wavelength range. In near-infrared spectral range, the reflectance values of infected leaves are lower than those of the control, which indicates that some changes in cell structures occurred as a result of the fungal infection. All three investigated pathogens had a statistically significant effect on leaf water content and water band index. Vegetative indices such as Chlorophyll Absorption in Reflectance Index (CARI), Modified chlorophyll absorption in reflectance index (MCARI), Plant Senescence Reflectance Index (PSRI), Red Edge Index (REI2), Red Edge Index (REI3), and Water band index (WBI) were found to be effective in distinguishing infected plants from healthy ones, with WBI demonstrating the greatest reliability. Full article

(This article belongs to the Section Veterinary Microbiology)

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15 pages, 2614 KiB

Open AccessArticle

Humoral Immune Responses in Patients with Severe COVID-19: A Comparative Pilot Study between Individuals Infected by SARS-CoV-2 during the Wild-Type and the Delta Periods

by Maria Sukhova, Maria Byazrova, Artem Mikhailov, Gaukhar Yusubalieva, Irina Maslova, Tatyana Belovezhets, Nikolay Chikaev, Ivan Vorobiev, Vladimir Baklaushev and Alexander Filatov

Microorganisms 2023, 11(9), 2347; https://doi.org/10.3390/microorganisms11092347 - 20 Sep 2023

Viewed by 1103

Abstract

Since the onset of the COVID-19 pandemic, humanity has experienced the spread and circulation of several SARS-CoV-2 variants that differed in transmissibility, contagiousness, and the ability to escape from vaccine-induced neutralizing antibodies. However, issues related to the differences in the variant-specific immune responses [...] Read more.

Since the onset of the COVID-19 pandemic, humanity has experienced the spread and circulation of several SARS-CoV-2 variants that differed in transmissibility, contagiousness, and the ability to escape from vaccine-induced neutralizing antibodies. However, issues related to the differences in the variant-specific immune responses remain insufficiently studied. The aim of this study was to compare the parameters of the humoral immune responses in two groups of patients with acute COVID-19 who were infected during the circulation period of the D614G and the Delta variants of SARS-CoV-2. Sera from 48 patients with acute COVID-19 were tested for SARS-CoV-2 binding and neutralizing antibodies using six assays. We found that serum samples from the D614G period demonstrated 3.9- and 1.6-fold increases in RBD- and spike-specific IgG binding with wild-type antigens compared with Delta variant antigens (p < 0.01). Cluster analysis showed the existence of two well-separated clusters. The first cluster mainly consisted of D614G-period patients and the second cluster predominantly included patients from the Delta period. The results thus obtained indicate that humoral immune responses in D614G- and Delta-specific infections can be characterized by variant-specific signatures. This can be taken into account when developing new variant-specific vaccines. Full article

(This article belongs to the Special Issue Coronaviruses: Past, Present, and Future)

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12 pages, 1484 KiB

Open AccessArticle

Safety Analysis of Extended Platelet Shelf-Life with Large-Volume Delayed Sampling on BACT/ALERT^® VIRTUO^® in Australia

by Anthea Cheng, Anindita Das, Khin Chaw, Peta M. Dennington, Claire E. Styles and Iain B. Gosbell

Microorganisms 2023, 11(9), 2346; https://doi.org/10.3390/microorganisms11092346 - 19 Sep 2023

Cited by 1 | Viewed by 984

Abstract

Transfusion-transmitted bacterial infection (TTBI) is the leading cause of transfusion-transmitted infections. Platelet components are more likely to be associated with bacterial contamination due to their storage requirements. Australian Red Cross Lifeblood introduced the bacterial contamination screening (BCS) of all platelet components in 2008. [...] Read more.

Transfusion-transmitted bacterial infection (TTBI) is the leading cause of transfusion-transmitted infections. Platelet components are more likely to be associated with bacterial contamination due to their storage requirements. Australian Red Cross Lifeblood introduced the bacterial contamination screening (BCS) of all platelet components in 2008. The process was recently updated with the use of BACT/ALERT^® VIRTUO^®, a large-volume delayed sampling (LVDS) protocol and extending platelet shelf-life to seven days. This article describes the results from the routine BCS of platelet components in Australia. Use of VIRTUO has resulted in lower false-positive rates, reducing wastage and improving platelet inventory. Our findings show that the combination of LVDS and VIRTUO improves the safety of platelet transfusions through earlier time to detection, especially for pathogenic bacterial species. Pathogenic bacteria grew within 24 h of incubation with a clear delineation between pathogenic and non-pathogenic species. The data show this protocol is very safe, with no TTBI cases during this time. There were no TTBI reports in recipients of platelet components that subsequently had a positive culture with Cutibacterium species, probably due to the low pathogenic potential of these organisms and slow replication in aerobic platelet bags. We conclude there is no advantage in incubating culture bottles beyond five days. Full article

(This article belongs to the Special Issue Safety of Platelet Components: Past, Present and Future)

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15 pages, 721 KiB

Open AccessArticle

Impact of the Combination of Probiotics and Digital Poultry System on Behavior, Welfare Parameters, and Growth Performance in Broiler Chicken

by Victor A Zammit and Sang-O Park

Microorganisms 2023, 11(9), 2345; https://doi.org/10.3390/microorganisms11092345 - 19 Sep 2023

Viewed by 1139

Abstract

Recently, applied technology in the form of the combination of a probiotics and a digital poultry system, with the convergence of Information and Communications Technology and farm animals, has enabled a new strategy to overcome the livestock production crisis caused by climate change, [...] Read more.

Recently, applied technology in the form of the combination of a probiotics and a digital poultry system, with the convergence of Information and Communications Technology and farm animals, has enabled a new strategy to overcome the livestock production crisis caused by climate change, while maintaining sustainable poultry farming in terms of care, feeding, and environmental management systems for poultry. The aim of this study was to investigate the biological mechanisms of animal behavioral welfare and production improvement using the combination of a probiotics and a digital poultry system in broiler chickens. A total of 400 one-day-old male broilers (ROSS 308) were randomly divided into four treatment groups, with five replicates each (20 birds/replicate pen) in a completely randomized design: control group with a conventional poultry system without probiotics (CON), conventional poultry system with 500 ppm of probiotics (CON500), digital poultry control system without probiotics (DPCS), and digital poultry system with 500 ppm of probiotics (DPS500). All experimental animals were reared for 35 days under the same standard environmental conditions. The experimental results indicated that the animal behavioral welfare, which includes drinking, eating, locomotion, grooming, and resting, in addition to foot pads, knee burns, plumage, and gait scores, as well as the growth performance of the broiler chickens, were improved by maintaining immune function and cecal microbiota balance via interaction between the combination of a probiotics and a digital poultry system. In conclusion, it was found that the combined system showed improved broiler growth performance and animal behavioral welfare. Thus, further studies of molecular biological mechanisms by the use of such a combined system to improve the nutritional composition and quality of chicken meats are recommended. Full article

(This article belongs to the Special Issue Prebiotics, Probiotics and Gut Microbiome in Poultry)

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16 pages, 5376 KiB

Open AccessArticle

Identification, Antioxidant Capacity, and Matrix Metallopeptidase 9 (MMP-9) In Silico Inhibition of Haloarchaeal Carotenoids from Natronococcus sp. and Halorubrum tebenquichense

by Mariana Delgado-Garcia, Osvaldo Gómez-Secundino, Jorge A. Rodríguez, Juan Carlos Mateos-Díaz, Marcelo Muller-Santos, Cristobal N. Aguilar and Rosa Maria Camacho-Ruiz

Microorganisms 2023, 11(9), 2344; https://doi.org/10.3390/microorganisms11092344 - 19 Sep 2023

Cited by 2 | Viewed by 945

Abstract

Natural pigments from haloarchaea are of great interest; bacterioruberin is the major pigment, it shows higher antioxidant power when compared with β-carotene. However, characterization of bacterioruberin and its isomers along with its antioxidant and the matrix metallopeptidase 9 (MMP-9) inhibition activities in extracts [...] Read more.

Natural pigments from haloarchaea are of great interest; bacterioruberin is the major pigment, it shows higher antioxidant power when compared with β-carotene. However, characterization of bacterioruberin and its isomers along with its antioxidant and the matrix metallopeptidase 9 (MMP-9) inhibition activities in extracts from Natronoccoccus sp. TC6 and Halorubrum tebenquichense SU10 was not previously described, being the aim of this work. The carotenoids profile was performed by UV-Vis spectrophotometry, thin-layer chromatography, nuclear magnetic resonance spectroscopy, and high-resolution mass spectrometry (UPLC-ESI-MS/MS). Antioxidant capacity was determined for DPPH, ABTS, and FRAP. In addition, MMP-9 inhibition was studied using docking simulations. The carotenoid profile of studied strains was composed of bacterioruberin, some derivatives like mono, bis, and tris anhydrobacterioruberin, and also some bacterioruberin cis isomers. The carotenoid pools showed antioxidant capacity for DPPH > ABTS > FRAP; Natronococcus sp. TC6 carotenoid pool was better for ABTS and DPPH, while Halorubrum tebenquichense SU10 carotenoid pool was better for FRAP. Additionally, docking and molecular dynamics suggest that bacterioruberin inhibits MMP-9 through hydrophobic interactions near the catalytic site. Bacterioruberin shows the higher binding energy of −8.3 (kcal/mol). The carotenoids profile of both strains was elucidated, their antioxidant activity and singular participation of each carotenoid on MMP-9 in silico inhibition were evaluated. Full article

(This article belongs to the Special Issue New Insights into the Diversity and Characterization of Extremophiles)

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15 pages, 334 KiB

Open AccessArticle

Effect of Growth Stages and Lactic Acid Fermentation on Anti-Nutrients and Nutritional Attributes of Spinach (Spinacia oleracea)

by Adila Naseem, Saeed Akhtar, Tariq Ismail, Muhammad Qamar, Dur-e-shahwar Sattar, Wisha Saeed, Tuba Esatbeyoglu, Elena Bartkiene and João Miguel Rocha

Microorganisms 2023, 11(9), 2343; https://doi.org/10.3390/microorganisms11092343 - 19 Sep 2023

Cited by 1 | Viewed by 1490

Abstract

Spinach (Spinacia oleracea) is a winter-season green, leafy vegetable grown all over the world, belonging to the family Amaranthus, sub-family Chenopodiaceae. Spinach is a low-caloric food and an enormous source of micronutrients, e.g., calcium, folates, zinc, retinol, iron, ascorbic [...] Read more.

Spinach (Spinacia oleracea) is a winter-season green, leafy vegetable grown all over the world, belonging to the family Amaranthus, sub-family Chenopodiaceae. Spinach is a low-caloric food and an enormous source of micronutrients, e.g., calcium, folates, zinc, retinol, iron, ascorbic acid and magnesium. Contrarily, it also contains a variety of anti-nutritional factors, e.g., alkaloids, phytates, saponins, oxalates, tannins and many other natural toxicants which may hinder nutrient-absorption. This study was aimed at investigating the effect of fermentation on improving the nutrient-delivering potential of spinach and mitigating its burden of antinutrients and toxicants at three growth stages: the 1st growth stage as baby leaves, the 2nd growth stage at the coarse stage, and the 3rd growth stage at maturation. The results revealed the significant (p < 0.05) effect of fermentation on increasing the protein and fiber content of spinach powder from 2.53 to 3.53% and 19.33 to 22.03%, respectively, and on reducing total carbohydrate content from 52.92 to 40.52%; the effect was consistent in all three growth stages. A significant decline in alkaloids (6.45 to 2.20 mg/100 g), oxalates (0.07 mg/100 g to 0.02 mg/100 g), phytates (1.97 to 0.43 mg/100 g) and glucosinolates (201 to 10.50 µmol/g) was observed as a result of fermentation using Lactiplantibacillus plantarum. Fermentation had no impact on total phenolic content and the antioxidant potential of spinach, as evaluated using 2,2-diphenyl-1-picrylhydrazyl (DPPH) and ferric-reducing antioxidant power (FRAP) assays. This study proposes fermentation as a safer bioprocess for improving the nutrient-delivering potential of spinach, and suggests processed powders made from spinach as a cost-effective complement to existing plant proteins. Full article

(This article belongs to the Special Issue Screening and Characterization of the Diversity of Food Microorganisms and Their Metabolites 2022)

11 pages, 1141 KiB

Open AccessBrief Report

Increased Expression of lncRNA AC000120.7 and SENP3-EIF4A1 in Patients with Acute Respiratory Distress Syndrome Induced by SARS-CoV-2 Infection: A Pilot Study

by Javier González-Ramírez, Ana Gabriela Leija-Montoya, Nicolás Serafín-Higuera, Carlos A. Guzmán-Martín, Luis M. Amezcua-Guerra, Carlos Olvera-Sandoval, Jesús René Machado-Contreras, Armando Ruiz-Hernández, Adrián Hernández-Díazcouder, Julia Dolores Estrada-Guzmán and Fausto Sánchez-Muñoz

Microorganisms 2023, 11(9), 2342; https://doi.org/10.3390/microorganisms11092342 - 19 Sep 2023

Viewed by 939

Abstract

COVID-19, a disease caused by the SARS-CoV-2 virus, poses significant threats to the respiratory system and other vital organs. Long non-coding RNAs have emerged as influential epigenetic regulators and promising biomarkers in respiratory ailments. The objective of this study was to identify candidate [...] Read more.

COVID-19, a disease caused by the SARS-CoV-2 virus, poses significant threats to the respiratory system and other vital organs. Long non-coding RNAs have emerged as influential epigenetic regulators and promising biomarkers in respiratory ailments. The objective of this study was to identify candidate lncRNAs in SARS-CoV-2-positive individuals compared to SARS-CoV-2-negative individuals and investigate their potential association with ARDS-CoV-2 (acute respiratory distress syndrome). Employing qRT-PCR, we meticulously examined the expression profiles of a panel comprising 84 inflammation-related lncRNAs in individuals presenting upper respiratory infection symptoms, categorizing them into those testing negative or positive for SARS-CoV-2. Notably, first-phase PSD individuals exhibited significantly elevated levels of AC000120.7 and SENP3-EIF4A1. In addition, we measured the expression of two lncRNAs, AC000120.7 and SENP3-EIF4A1, in patients with ARDS unrelated to SARS-CoV-2 (n = 5) and patients with ARDS induced by SARS-CoV-2 (ARDS-CoV-2, n = 10), and interestingly, expression was also higher among patients with ARDS. Intriguingly, our interaction pathway analysis unveiled potential interactions between lncRNA AC000120.7, various microRNAs, and genes associated with inflammation. This study found higher expression levels of lncRNAs AC000120.7 and SENP3-EIF4A1 in the context of infection-positive COVID-19, particularly within the complex landscape of ARDS. Full article

(This article belongs to the Special Issue Coronaviruses: Past, Present, and Future)

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18 pages, 6243 KiB

Open AccessArticle

Myco-Synthesized Selenium Nanoparticles as Wound Healing and Antibacterial Agent: An In Vitro and In Vivo Investigation

by Heba El-Sayed, Mostafa Y. Morad, Hana Sonbol, Olfat A. Hammam, Rehab M. Abd El-Hameed, Rania A. Ellethy, Amina M. Ibrahim and Marwa A. Hamada

Microorganisms 2023, 11(9), 2341; https://doi.org/10.3390/microorganisms11092341 - 19 Sep 2023

Cited by 1 | Viewed by 1263

Abstract

Bacterial-associated wound infections are an obstacle for individuals and the medical industry. Developing versatile, antibiotic-free therapies helps heal wounds more quickly and efficiently. In the current study, fungal metabolites were employed as a reducing agent in fabricating selenium nanoparticles (SeNPs) for improved antibacterial [...] Read more.

Bacterial-associated wound infections are an obstacle for individuals and the medical industry. Developing versatile, antibiotic-free therapies helps heal wounds more quickly and efficiently. In the current study, fungal metabolites were employed as a reducing agent in fabricating selenium nanoparticles (SeNPs) for improved antibacterial and wound healing properties. Utilizing UV-visible spectroscopy, dynamic light scattering (DLS), zeta potential, X-ray diffraction (XRD), and electron microscopic examination, the properties of the synthesized nanoparticles were extensively evaluated. Myco-synthesized SeNPs demonstrated strong antibacterial activity against Staphylococcus aureus ATCC 6538 with a minimum inhibitory concentration of 0.3125 mg/mL, reducing cell number and shape distortion in scanning electron microscope (SEM) images. SeNPs’ topical administration significantly reduced wound area and healing time, exhibiting the least bacterial load after six days compared to controls. After six and 11 days of treatment, SeNPs could decrease proinflammatory cytokines IL-6 and TNF-α production. The histopathological investigation showed a healed ulcer with moderate infiltration of inflammatory cells after exposing mice’s skin to SeNPs for six and 11 days. The docking interaction indicated that SeNPs were highly efficient against the IL-6 and TNF-α binding receptors. These findings imply that myco-fabricated SeNPs might be used as topically applied antimicrobial agents for treating skin infections and wounds. Full article

(This article belongs to the Section Antimicrobial Agents and Resistance)

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9 pages, 1380 KiB

Open AccessProtocol

A Method for Rapid Polyethyleneimine-Based Purification of Bacteriophage-Expressed Proteins from Diluted Crude Lysates, Exemplified by Thermostable TP-84 Depolymerase

by Beata Łubkowska, Edyta Czajkowska, Ireneusz Sobolewski, Natalia Krawczun, Agnieszka Żylicz-Stachula and Piotr M. Skowron

Microorganisms 2023, 11(9), 2340; https://doi.org/10.3390/microorganisms11092340 - 19 Sep 2023

Viewed by 1170

Abstract

Purification of bacteriophage-expressed proteins poses methodological difficulties associated with the need to process entire culture medium volume upon bacteriophage-induced bacterial cell lysis. We have used novel capsule glycosylase-depolymerase (TP84_26 GD) from bacteriophage TP-84, infecting thermophilic Geobacillus stearothermophilus bacteria, as a representative enzyme to [...] Read more.

Purification of bacteriophage-expressed proteins poses methodological difficulties associated with the need to process entire culture medium volume upon bacteriophage-induced bacterial cell lysis. We have used novel capsule glycosylase-depolymerase (TP84_26 GD) from bacteriophage TP-84, infecting thermophilic Geobacillus stearothermophilus bacteria, as a representative enzyme to develop a method for rapid concentration and purification of the enzyme present in diluted crude host cell lysate. A novel variant of the polyethyleneimine (PEI)-based purification method was devised that offers a fast and effective approach for handling PEI-facilitated purification of bacteriophage-expressed native proteins. Due to the very basic nature of PEI, the method is suitable for proteins interacting with nucleic acids or acidic proteins, where either mixed PEI-DNA or RNA–protein complexes or PEI–acidic protein complexes are reversibly precipitated. (i) The method is of general use, applicable with minor modifications to a variety of bacteriophage cell lysates and proteins. (ii) In the example application, TP84_26 GD was highly purified (over 50%) in a single PEI step; subsequent chromatography yielded a homogeneous enzyme. (iii) The enzyme’s properties were examined, revealing the presence of three distinct forms of the TP84_26 GD. These forms included soluble, unbound proteins found in host cell lysate, as well as an integrated form within the TP-84 virion. Full article

(This article belongs to the Special Issue Bacteriophages of Thermophilic 'Bacillus Group' Bacteria)

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10 pages, 1176 KiB

Open AccessCommunication

First Identification and Molecular Characterization of Trichinella britovi (Nematoda: Trichinellidae) from the Pine Marten (Martes martes Linnaeus, 1758) in Romania

by Ana-Maria Marin, Ovidiu-Alexandru Mederle, Gianluca Marucci, Dan-Cornel Popovici and Narcisa Mederle

Microorganisms 2023, 11(9), 2339; https://doi.org/10.3390/microorganisms11092339 - 18 Sep 2023

Cited by 1 | Viewed by 970

Abstract

Trichinella spp. are etiological zoonotic agents spread throughout the world and affect mammals, birds, and reptiles; they evolve via two cycles: domestic and sylvatic. Martes martes is a carnivorous nocturnal mammal from the family Mustelidae. In Romania, this host is widespread in all [...] Read more.

Trichinella spp. are etiological zoonotic agents spread throughout the world and affect mammals, birds, and reptiles; they evolve via two cycles: domestic and sylvatic. Martes martes is a carnivorous nocturnal mammal from the family Mustelidae. In Romania, this host is widespread in all forests of the country. Martes martes has an extremely voracious appetite, feeding on fruit and also on a variety of small animals, including rodents such as mice and rats. The aim of this study was the identification and molecular characterization of Trichinella larvae isolated from the muscle tissue of Martes martes collected in different counties of Romania. The muscle samples were examined via artificial digestion, and the larvae were identified at the species level via multiplex PCR. The presence of larvae belonging to Trichinella britovi, a species frequently identified in wild carnivores in temperate zones, was observed. Although T. britovi has been already reported in several host species in Romania, this is the first time this species has been observed in a Martes martes specimen. This finding contributes to our knowledge about the host species involved in the maintenance of the Trichinella sylvatic cycle in Romania, and it confirms that this parasite is consistently present in the wild fauna of this country. Full article

(This article belongs to the Section Parasitology)

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11 pages, 288 KiB

Open AccessArticle

Giardia duodenalis (Styles, 1902) in Cattle: Isolation of Calves with Diarrhoea and Manure Treatment in the Lagoon Presented as Risk Factors in Latvian Herds

by Maira Mateusa, Maija Selezņova, Margarita Terentjeva and Gunita Deksne

Microorganisms 2023, 11(9), 2338; https://doi.org/10.3390/microorganisms11092338 - 18 Sep 2023

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Abstract

Giardia duodenalis is a waterborne zoonotic protozoan that causes gastrointestinal tract inflammation in humans, cattle, and other animals. The aim of the present study was to estimate the prevalence and potential risk factors for Giardia infection in cattle in Latvia. During 2020–2021, a [...] Read more.

Giardia duodenalis is a waterborne zoonotic protozoan that causes gastrointestinal tract inflammation in humans, cattle, and other animals. The aim of the present study was to estimate the prevalence and potential risk factors for Giardia infection in cattle in Latvia. During 2020–2021, a total of 973 individual faecal samples from cattle aged from 1 day to 12 years old, from 32 cattle herds, were tested for Giardia cyst presence with immunofluorescence staining followed by Giardia assemblage differentiation targeting beta-giardin gene. Using a questionnaire, information was collected to estimate the potential risk factors for G. duodenalis infection in cattle herds. Giardia was found in 8.4% of the examined cattle with a mean intensity of 5756 cysts per gram of faeces. The highest prevalence was observed in the 0 to 3-month-old calves (16.4%). At least one Giardia shedding animal was found in 27 herds with an overall prevalence of 84.4%. Significantly higher prevalence was found for cattle infected with G. duodenalis assemblage E compared to that infected with assemblage A: 88.7% and 11.3%, respectively. Protective factors such as age and rodent control and change of shoes were found to be significant for Giardia infection, while isolating calves for diarrhoea and water bodies (ponds/lakes) in pasture were potential risk factors in Latvian cattle. Full article

(This article belongs to the Special Issue Ecology, Evolution and Epidemiology of Zoonotic and Vector-Borne Infectious Diseases 2.0)

23 pages, 5838 KiB

Open AccessArticle

Characterization of Microbial Diversity of Two Tomato Cultivars through Targeted Next-Generation Sequencing 16S rRNA and ITS Techniques

by Rukayat Abiola Abdulsalam, Oluwatosin Ademola Ijabadeniyi, Errol D. Cason and Saheed Sabiu

Microorganisms 2023, 11(9), 2337; https://doi.org/10.3390/microorganisms11092337 - 18 Sep 2023

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Abstract

Even though the nutritional and economic values of Solanum lycopersicum (tomato) are substantially impacted by microbial spoilage, the available data on its microbial community, particularly during spoilage, are limited and have primarily been characterized using conventional culture-dependent methods. This study employed a targeted [...] Read more.

Even though the nutritional and economic values of Solanum lycopersicum (tomato) are substantially impacted by microbial spoilage, the available data on its microbial community, particularly during spoilage, are limited and have primarily been characterized using conventional culture-dependent methods. This study employed a targeted high-throughput next-generation sequencing method to longitudinally characterize the microbial diversity of two South African tomato cultivars (jam and round) at varied storage intervals (1, 6, and 12 days). Throughout the storage period, the bacterial communities of the two cultivars were more diverse than the fungal communities. The microbial diversity of both bacteria and fungi was greater and comparable between the cultivars on day 1, but becomes distinct as the storage period increases, with round tomatoes being more diverse than jam tomato, though, on day 12, jam tomato develops greater diversity than round tomato. Overall, the most abundant phyla (though Proteobacteria was most dominant) were Proteobacteria, Firmicutes, and Bacteriodota in the bacterial communities, while Ascomycota and Basidiomycota formed most fungal communities with Ascomycota being dominant. At the genus level, Pantoea and Klebsiella (bacteria), Hanseniaspora, Stemphylium, and Alternaria (fungi) were prevalent. Taken together, this study casts light on a broad microbial diversity profile thus, confirms the cultivars’ diversity and abundance differences. Full article

(This article belongs to the Special Issue Food Microorganisms and Genomics)

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