Microorganisms

15 pages, 2638 KiB

Open AccessArticle

Baicalin Weakens the Porcine ExPEC-Induced Inflammatory Response in 3D4/21 Cells by Inhibiting the Expression of NF-κB/MAPK Signaling Pathways and Reducing NLRP3 Inflammasome Activation

by Bingbing Zong, Yong Xiao, Mingxing Ren, Peiyi Wang, Shulin Fu and Yinsheng Qiu

Microorganisms 2023, 11(8), 2126; https://doi.org/10.3390/microorganisms11082126 - 21 Aug 2023

Cited by 1 | Viewed by 1079

Abstract

Porcine extraintestinal pathogenic Escherichia coli (ExPEC) is a leading cause of death in pigs and has led to considerable economic losses for the pig industry. Porcine ExPEC infections often cause systemic inflammatory responses in pigs, characterized by meningitis, arthritis, pneumonia, and septicemia. Baicalin [...] Read more.

Porcine extraintestinal pathogenic Escherichia coli (ExPEC) is a leading cause of death in pigs and has led to considerable economic losses for the pig industry. Porcine ExPEC infections often cause systemic inflammatory responses in pigs, characterized by meningitis, arthritis, pneumonia, and septicemia. Baicalin has been reported to possess potent anti-inflammatory activity, but its function in porcine ExPEC remains unknown. The aim of this study was to explore the protective effect and mechanism of baicalin against the porcine ExPEC-induced inflammatory responses in 3D4/21 cells. After treatment with baicalin, the effects on cell damage, the level of pro-inflammatory cytokines, the expression of nuclear factor-

κ

B (NF-

κ

B)/mitogen-activated protein kinase (MAPK) signaling pathways, and the activation of NOD-like receptor protein 3 (NLRP3) inflammasomes were examined. Our results show that baicalin significantly reduced the damage to 3D4/21 cells infected with porcine ExPEC PCN033. Further study showed that baicalin significantly reduced the transcription and expression of pro-inflammatory cytokines such as interleukin-1

β

(IL-1

β

), interleukin-6 (IL-6), and interleukin-8 (IL-8). Furthermore, baicalin inhibited the phosphorylation of proteins such as P65, nuclear factor

κ

B inhibitor

α

(I

κ

B

α

), extracellular regulated kinase (ERK), c-Jun N-terminal kinase (JNK), and P38 and reduced the expression levels of proteins such as NLRP3, apoptosis-associated speck-like protein containing a CARD (ASC), and caspase-1. These results reveal that baicalin reduced the damage to 3D4/21 cells by inhibiting the expression of NF-

κ

B/MAPK signaling pathways and blocking NLRP3 inflammasome activation in 3D4/21 cells infected with porcine ExPEC. Taken together, these results suggest that baicalin may have potential as a medicine for the treatment of porcine ExPEC-infected pigs by regulating inflammatory responses. This study provides a novel potential pharmaco-therapeutic approach to preventing porcine ExPEC infection. Full article

(This article belongs to the Special Issue Antimicrobial Resistance Bacteria in Pets, Livestock and Wild Animals)

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14 pages, 4506 KiB

Open AccessArticle

Bibliometric Analysis of Global Trends in Research on Seasonal Variations in Gut Microbiota from 2012 to 2022

by Jiancheng Zhai, Xiao Sun, Rui Lu, Xueqin Hu and Zhiqiang Huang

Microorganisms 2023, 11(8), 2125; https://doi.org/10.3390/microorganisms11082125 - 21 Aug 2023

Viewed by 1032

Abstract

Seasons are the important influencing factor for gut microbiota, which in turn affects the ecology and evolution of the host. The seasonal variation in gut microbiota has increasingly attracted the attention of researchers and professionals worldwide. However, studies of seasonal variations in gut [...] Read more.

Seasons are the important influencing factor for gut microbiota, which in turn affects the ecology and evolution of the host. The seasonal variation in gut microbiota has increasingly attracted the attention of researchers and professionals worldwide. However, studies of seasonal variations in gut microbiota have not been systematically analyzed by bibliometrics or visual analysis. This study is based on 271 publications from 2012 to 2022 in the Web of Science Core Collection database (WOSCC) to analyze hot spots and trends in this field. The collaborations between different countries, institutions, authors, journals, and keywords were bibliometrically analyzed using Excel, CiteSpace (Version 6.2. R4), and VOSviewer (version 1.6.19) software. The number of publications has been increasing rapidly and shows a general upward trend. China and the Chinese Academy of Sciences are the country and institution contributing the most, respectively. The research hotspots and trends mainly include the diversity of gut microbiota communities in different seasons, the relationship between diet and gut microbiota in seasonal changes, and the relationship between gut microbiota and evolutionary adaptation in seasonal changes. This is the first bibliometric and visualization analysis of seasonal variations in gut microbiota, which may advance this field and lay the foundation for future research. Full article

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

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15 pages, 4318 KiB

Open AccessArticle

Fungal Community Composition at the Last Remaining Wild Site of Yellow Early Marsh Orchid (Dactylorhiza incarnata ssp. ochroleuca)

by Andrea Dove, Michael D. Charters, Matthew J. Campbell, Hanna Blake, Manoj Menon and Viswambharan Sarasan

Microorganisms 2023, 11(8), 2124; https://doi.org/10.3390/microorganisms11082124 - 21 Aug 2023

Viewed by 1052

Abstract

The yellow early marsh orchid (Dactylorhiza incarnata ssp. ochroleuca) is a critically endangered terrestrial orchid in Britain. Previous attempts to translocate symbiotic seedlings to a site near the last remaining wild site demonstrated some success, with a 10% survival rate despite [...] Read more.

The yellow early marsh orchid (Dactylorhiza incarnata ssp. ochroleuca) is a critically endangered terrestrial orchid in Britain. Previous attempts to translocate symbiotic seedlings to a site near the last remaining wild site demonstrated some success, with a 10% survival rate despite adverse weather conditions over a two-year period. However, to facilitate future reintroduction efforts or conservation translocations, a more comprehensive understanding of the fungal microbiome and abiotic soil characteristics at the final remaining wild site is required. Obtaining comprehensive information on both the fungal community and soil nutrient composition from wild sites has significant benefits and may prove critical for the success of future conservation translocations involving threatened orchids. This preliminary study, conducted at the last remaining wild site, revealed a significant correlation between the relative abundance of the orchid mycorrhizal fungal order Cantharellales and the concentrations of nitrate and phosphate in the soil. Another orchid mycorrhizal fungal group, Sebacinales, was found to be distributed extensively throughout the site. The composition of fungal communities across the entire site, orchid-hosting and non-orchid-hosting soils is discussed in relation to reinforcing the current population and preventing the extinction of this orchid. Full article

(This article belongs to the Special Issue Endophytes for Managing Biotic and Abiotic Stress in Plants 2.0)

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10 pages, 836 KiB

Open AccessArticle

Pediatric Osteoarticular Kingella kingae Infections of the Hand and Wrist: A Retrospective Study

by Blaise Cochard, Elvin Gurbanov, Ludmilla Bazin, Giacomo De Marco, Oscar Vazquez, Giorgio Di Laura Frattura, Christina N. Steiger, Romain Dayer and Dimitri Ceroni

Microorganisms 2023, 11(8), 2123; https://doi.org/10.3390/microorganisms11082123 - 21 Aug 2023

Cited by 1 | Viewed by 855

Abstract

Our understanding of pediatric osteoarticular infections (OAIs) has improved significantly in recent decades. Kingella kingae is now recognized as the most common pathogen responsible for OAIs in pediatric populations younger than 4 years old. Research has provided a better understanding of the specific [...] Read more.

Our understanding of pediatric osteoarticular infections (OAIs) has improved significantly in recent decades. Kingella kingae is now recognized as the most common pathogen responsible for OAIs in pediatric populations younger than 4 years old. Research has provided a better understanding of the specific types, clinical characteristics, biological repercussions, and functional outcomes of these infections. Hands and wrists are rarely infected, with few reports available in the literature. The present study aimed to examine this specific condition in a large patient cohort, explore the implications for each anatomical area using magnetic resonance imaging (MRI), and critically evaluate the evolution of therapeutic management. Full article

(This article belongs to the Special Issue Kingella kingae: Virulence Factors, Clinical Disease, and Diagnostics)

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13 pages, 2189 KiB

Open AccessArticle

Phylogeographic Analysis of Soft-Rot-Causing Pectobacterium spp. Strains Obtained from Cabbage in Serbia

by Aleksandra Jelušić, Marco Scortichini, Sanja Marković, Petar Mitrović, Renata Iličić, Slaviša Stanković and Tatjana Popović Milovanović

Microorganisms 2023, 11(8), 2122; https://doi.org/10.3390/microorganisms11082122 - 21 Aug 2023

Viewed by 903

Abstract

The aim of this study was to establish a link between genetic diversity and the geographic origin of Pectobacterium strains belonging to three species—P. carotovorum, P. versatile, and P. odoriferum—isolated from cabbage in Serbia by comparing their sequences with [...] Read more.

The aim of this study was to establish a link between genetic diversity and the geographic origin of Pectobacterium strains belonging to three species—P. carotovorum, P. versatile, and P. odoriferum—isolated from cabbage in Serbia by comparing their sequences with those of strains sourced from different hosts and countries in Europe, Asia, and North America. Phylogeographic relatedness was reconstructed using the Templeton, Crandall, and Sing’s (TCS) haplotype network based on concatenated sequences of the housekeeping genes dnaX, icdA, mdh, and proA, while pairwise genetic distances were computed by applying the p-distance model. The obtained TCS haplotype networks indicated the existence of high intra-species genetic diversity among strains of all three species, as reflected in the 0.2–2.3%, 0.2–2.5%, and 0.1–1.7% genetic distance ranges obtained for P. carotovorum, P. versatile, and P. odoriferum, respectively. Five new haplotypes (denoted as HPc1–HPc5) were detected among cabbage strains of P. carotovorum, while one new haplotype was identified for both P. versatile (HPv1) and P. odoriferum (HPo1). None of the TCS haplotype networks provided evidence of significant correlation between geographic origin and the determined haplotypes, i.e., the infection origin. However, as haplotype network results are affected by the availability of sequencing data in public databases for the used genes and the number of analyzed strains, these findings may also be influenced by small sample size. Full article

(This article belongs to the Topic New Insights and Case Studies in Specific and Complex Plant Diseases)

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14 pages, 1894 KiB

Open AccessArticle

Heat-Labile Enterotoxin Decreases Macrophage Phagocytosis of Enterotoxigenic Escherichia coli

by Ian E. Hollifield, Natalya I. Motyka, Kaylynn A. Fernando and Jacob P. Bitoun

Microorganisms 2023, 11(8), 2121; https://doi.org/10.3390/microorganisms11082121 - 21 Aug 2023

Cited by 1 | Viewed by 1196

Abstract

Enterotoxigenic E. coli (ETEC) are endemic in low-resource settings and cause robust secretory diarrheal disease in children less than five years of age. ETEC cause secretory diarrhea by producing the heat-stable (ST) and/or heat-labile (LT) enterotoxins. Recent studies have shown that ETEC can [...] Read more.

Enterotoxigenic E. coli (ETEC) are endemic in low-resource settings and cause robust secretory diarrheal disease in children less than five years of age. ETEC cause secretory diarrhea by producing the heat-stable (ST) and/or heat-labile (LT) enterotoxins. Recent studies have shown that ETEC can be carried asymptomatically in children and adults, but how ETEC subvert mucosal immunity to establish intestinal residency remains unclear. Macrophages are innate immune cells that can be exploited by enteric pathogens to evade mucosal immunity, so we interrogated the ability of ETEC and other E. coli pathovars to survive within macrophages. Using gentamicin protection assays, we show that ETEC H10407 is phagocytosed more readily than other ETEC and non-ETEC isolates. Furthermore, we demonstrate that ETEC H10407, at high bacterial burdens, causes nitrite accumulation in macrophages, which is indicative of a proinflammatory macrophage nitric oxide killing response. However, at low bacterial burdens, ETEC H10407 remains viable within macrophages for an extended period without nitrite accumulation. We demonstrate that LT, but not ST, intoxication decreases the number of ETEC phagocytosed by macrophages. Furthermore, we now show that macrophages exposed simultaneously to LPS and LT produce IL-33, which is a cytokine implicated in promoting macrophage alternative activation, iron recycling, and intestinal repair. Lastly, iron restriction using deferoxamine induces IL-33 receptor (IL-33R) expression and allows ETEC to escape macrophages. Altogether, these data demonstrate that LT provides ETEC with the ability to decrease the perceived ETEC burden and suppresses the initiation of inflammation. Furthermore, these data suggest that host IL-33/IL-33R signaling may augment pathways that promote iron restriction to facilitate ETEC escape from macrophages. These data could help explain novel mechanisms of immune subversion that may contribute to asymptomatic ETEC carriage. Full article

(This article belongs to the Special Issue Enterotoxigenic Escherichia coli Infection and Vaccine-Mediated Immunity)

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28 pages, 3040 KiB

Open AccessReview

Seroprevalence of Infections with TORCH Agents in Romania: A Systematic Review

by Cristiana Luiza Radoi, Ovidiu Zlatian, Maria Balasoiu, Lucian Giubelan, Andreea Cristina Stoian, Livia Dragonu, Alexandru Neacsu and Dominic Gabriel Iliescu

Microorganisms 2023, 11(8), 2120; https://doi.org/10.3390/microorganisms11082120 - 20 Aug 2023

Cited by 1 | Viewed by 1549

Abstract

Maternal–fetal infectious pathology—notably the TORCH panel (Toxoplasma gondii, rubella, Cytomegalovirus, and herpes simplex viruses)—critically impacts maternal and neonatal health. This review collates data on the seroprevalence of IgG and IgM antibodies against TORCH agents in Romanian women, aiming to discern regional [...] Read more.

Maternal–fetal infectious pathology—notably the TORCH panel (Toxoplasma gondii, rubella, Cytomegalovirus, and herpes simplex viruses)—critically impacts maternal and neonatal health. This review collates data on the seroprevalence of IgG and IgM antibodies against TORCH agents in Romanian women, aiming to discern regional and population differences and identify risk factors. Twenty studies were included in the review, revealing variable seroprevalence rates across the country. Regions such as Moldavia and Banat showed higher anti-T. gondii IgG seroprevalence rates than Bihor, with notable declines in Banat. Rural, older, and multiparous women showed elevated T. gondii IgG rates. Anti-rubella vaccine introduction significantly reduced the prevalence of anti-rubella IgG antibodies, but recent vaccination coverage decreases raise concerns. CMV and HSV seroprevalence varied geographically, with rural areas generally showing higher CMV rates and HSV influenced by factors like education level and number of sexual partners. Concurrent seroprevalence of multiple TORCH components in some cases underscores potential common risk factors. This study highlights the importance of continuous monitoring and preventive measures such as vaccinations and awareness campaigns to mitigate the health impact on the pregnant population. Full article

(This article belongs to the Special Issue State-of-the-Art Parasitic and Bacterial Infections in Romania)

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13 pages, 3634 KiB

Open AccessArticle

Native Pig Neutrophil Products: Insights into Their Antimicrobial Activity

by Eric Fernández-De La Cruz, Joanna Wessely-Szponder, Miguel Viñas, Teresa Vinuesa, Alexandra Merlos, Marta Jorba, Paula Espinal and Ester Fusté

Microorganisms 2023, 11(8), 2119; https://doi.org/10.3390/microorganisms11082119 - 20 Aug 2023

Viewed by 885

Abstract

Cationic antimicrobial peptides are molecules with potential applications for treating infections due to their antimicrobial and immunomodulatory properties. The aim of this work was to explore the antimicrobial activity and mechanisms of action of a porcine neutrophil cathelicidin mixture (MPPN). Gram-positive and Gram-negative [...] Read more.

Cationic antimicrobial peptides are molecules with potential applications for treating infections due to their antimicrobial and immunomodulatory properties. The aim of this work was to explore the antimicrobial activity and mechanisms of action of a porcine neutrophil cathelicidin mixture (MPPN). Gram-positive and Gram-negative bacteria were used to determine the minimum inhibitory concentration (MIC) and experiments of both time–kill kinetics and effects on growth curves were performed. Planar black lipid bilayer conductance was measured to analyze the interaction of MPPN with lipid bilayers. Visualization of bacterial surfaces and membrane alterations was achieved using atomic force microscopy and transmission electron microscopy. The effects on the activity of efflux pumps (EPs) were studied with an intracellular accumulation of acridine orange (AO) assay. In E. coli, MPPN behaves as a bactericide at high concentrations and as a bacteriostatic at lower concentrations. The bacteriostatic effect was also observed for slightly shorter periods in S. enterica. The mixture was not active on S. aureus. The increase in AO accumulation in the presence of MPPN indicates that, at least in E. coli, the mixture causes inhibition of the EP function. Observed and detected variable conductance events demonstrate a strong MPPN effect on lipid bilayers. Damage to the structure of treated E. coli indicates that MPPN induces alterations in the bacterial surface. The use of AMPs capable of inhibiting EP can be seen as a good tool to combat antimicrobial resistance since they could be used alone or in combination with other conventional antibiotics to which bacteria have become resistant. Full article

(This article belongs to the Special Issue Advances in Novel Antibacterial Agents)

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42 pages, 4461 KiB

Open AccessReview

A Scoping Review Evaluating the Current State of Gut Microbiota Research in Africa

by Sara M. Pheeha, Jacques L. Tamuzi, Bettina Chale-Matsau, Samuel Manda and Peter S. Nyasulu

Microorganisms 2023, 11(8), 2118; https://doi.org/10.3390/microorganisms11082118 - 20 Aug 2023

Cited by 3 | Viewed by 1499

Abstract

The gut microbiota has emerged as a key human health and disease determinant. However, there is a significant knowledge gap regarding the composition, diversity, and function of the gut microbiota, specifically in the African population. This scoping review aims to examine the existing [...] Read more.

The gut microbiota has emerged as a key human health and disease determinant. However, there is a significant knowledge gap regarding the composition, diversity, and function of the gut microbiota, specifically in the African population. This scoping review aims to examine the existing literature on gut microbiota research conducted in Africa, providing an overview of the current knowledge and identifying research gaps. A comprehensive search strategy was employed to identify relevant studies. Databases including MEDLINE (PubMed), African Index Medicus (AIM), CINAHL (EBSCOhost), Science Citation index (Web of Science), Embase (Ovid), Scopus (Elsevier), WHO International Clinical Trials Registry Platform (ICTRP), and Google Scholar were searched for relevant articles. Studies investigating the gut microbiota in African populations of all age groups were included. The initial screening included a total of 2136 articles, of which 154 were included in this scoping review. The current scoping review revealed a limited number of studies investigating diseases of public health significance in relation to the gut microbiota. Among these studies, HIV (14.3%), colorectal cancer (5.2%), and diabetes mellitus (3.9%) received the most attention. The top five countries that contributed to gut microbiota research were South Africa (16.2%), Malawi (10.4%), Egypt (9.7%), Kenya (7.1%), and Nigeria (6.5%). The high number (n = 66) of studies that did not study any specific disease in relation to the gut microbiota remains a gap that needs to be filled. This scoping review brings attention to the prevalent utilization of observational study types (38.3%) in the studies analysed and emphasizes the importance of conducting more experimental studies. Furthermore, the findings reflect the need for more disease-focused, comprehensive, and population-specific gut microbiota studies across diverse African regions and ethnic groups to better understand the factors shaping gut microbiota composition and its implications for health and disease. Such knowledge has the potential to inform targeted interventions and personalized approaches for improving health outcomes in African populations. Full article

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

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11 pages, 2318 KiB

Open AccessArticle

Differences in Microbial Community Composition between Uterine Horns Ipsilateral and Contralateral to the Corpus Luteum in Beef Cows on Day 15 of the Estrous Cycle

by Madison Blake Walker, Matthew Patrick Holton, Todd Riley Callaway, Jeferson Menezes Lourenco and Pedro Levy Piza Fontes

Microorganisms 2023, 11(8), 2117; https://doi.org/10.3390/microorganisms11082117 - 20 Aug 2023

Cited by 2 | Viewed by 937

Abstract

This study evaluated differences in uterine microbiota composition between uterine horns ipsilateral and contralateral to the corpus luteum of beef cows on day 15 of the estrous cycle. Cows (n = 23) were exposed to an estrus synchronization protocol to exogenously induce [...] Read more.

This study evaluated differences in uterine microbiota composition between uterine horns ipsilateral and contralateral to the corpus luteum of beef cows on day 15 of the estrous cycle. Cows (n = 23) were exposed to an estrus synchronization protocol to exogenously induce synchronized ovulation. Cows were then euthanized on day 15 of the estrous cycle, and individual swabs were collected from uterine horns ipsilateral and contralateral to the corpus luteum using aseptic techniques. DNA was extracted, and the entire (V1–V9 hypervariable regions) 16s rRNA gene was sequenced. Sequences were analyzed, and amplicon sequence variants (ASVs) were determined. Across all samples, 2 bacterial domains, 24 phyla, and 265 genera were identified. Butyribirio, Cutibacterium, BD7-11, Bacteroidales BS11 gut group, Ruminococcus, Bacteroidales RF16 group, and Clostridia UCG-014 differed in relative abundances between uterine horns. Rikenellaceae RC9 gut group, Bacteroidales UCG-001, Lachnospiraceae AC2044 group, Burkholderia-Caballeronia-Paraburkholderia, Psudobutyribibrio, and an unidentified genus of the family Chitinophagaceae and dgA-11 gut group differed between cows that expressed estrus and those that did not. The composition of the microbial community differed between the ipsilateral and contralateral horns and between cows that expressed estrus and cows that failed to express estrus, indicating that the uterine microbiota might play a role in cow fertility. Full article

(This article belongs to the Section Veterinary Microbiology)

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21 pages, 1917 KiB

Open AccessReview

Multiomic Investigations into Lung Health and Disease

by Sarah E. Blutt, Cristian Coarfa, Josef Neu and Mohan Pammi

Microorganisms 2023, 11(8), 2116; https://doi.org/10.3390/microorganisms11082116 - 19 Aug 2023

Cited by 1 | Viewed by 1524

Abstract

Diseases of the lung account for more than 5 million deaths worldwide and are a healthcare burden. Improving clinical outcomes, including mortality and quality of life, involves a holistic understanding of the disease, which can be provided by the integration of lung multi-omics [...] Read more.

Diseases of the lung account for more than 5 million deaths worldwide and are a healthcare burden. Improving clinical outcomes, including mortality and quality of life, involves a holistic understanding of the disease, which can be provided by the integration of lung multi-omics data. An enhanced understanding of comprehensive multiomic datasets provides opportunities to leverage those datasets to inform the treatment and prevention of lung diseases by classifying severity, prognostication, and discovery of biomarkers. The main objective of this review is to summarize the use of multiomics investigations in lung disease, including multiomics integration and the use of machine learning computational methods. This review also discusses lung disease models, including animal models, organoids, and single-cell lines, to study multiomics in lung health and disease. We provide examples of lung diseases where multi-omics investigations have provided deeper insight into etiopathogenesis and have resulted in improved preventative and therapeutic interventions. Full article

(This article belongs to the Special Issue Role of Microbiome in Lung Health)

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22 pages, 1305 KiB

Open AccessReview

International Clones of High Risk of Acinetobacter Baumannii—Definitions, History, Properties and Perspectives

by Andrey Shelenkov, Vasiliy Akimkin and Yulia Mikhaylova

Microorganisms 2023, 11(8), 2115; https://doi.org/10.3390/microorganisms11082115 - 19 Aug 2023

Cited by 2 | Viewed by 1792

Abstract

Acinetobacter baumannii is a Gram-negative coccobacillus with exceptional survival skills in an unfavorable environment and the ability to rapidly acquire antibiotic resistance, making it one of the most successful hospital pathogens worldwide, representing a serious threat to public health. The global dissemination of [...] Read more.

Acinetobacter baumannii is a Gram-negative coccobacillus with exceptional survival skills in an unfavorable environment and the ability to rapidly acquire antibiotic resistance, making it one of the most successful hospital pathogens worldwide, representing a serious threat to public health. The global dissemination of A. baumannii is driven by several lineages named ‘international clones of high risk’ (ICs), two of which were first revealed in the 1970s. Epidemiological surveillance is a crucial tool for controlling the spread of this pathogen, which currently increasingly involves whole genome sequencing. However, the assignment of a particular A. baumannii isolate to some IC based on its genomic sequence is not always straightforward and requires some computational skills from researchers, while the definitions found in the literature are sometimes controversial. In this review, we will focus on A. baumannii typing tools suitable for IC determination, provide data to easily determine IC assignment based on MLST sequence type (ST) and intrinsic bla_OXA-51_-like gene variants, discuss the history and current spread data of nine known ICs, IC1-IC9, and investigate the representation of ICs in public databases. MLST and cgMLST profiles, as well as OXA-51-like presence data are provided for all isolates available in GenBank. The possible emergence of a novel A. baumannii international clone, IC10, will be discussed. Full article

(This article belongs to the Special Issue Latest Review Papers in Medical Microbiology 2023)

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17 pages, 6217 KiB

Open AccessArticle

Comparative Genomic Analyses of Virulence and Antimicrobial Resistance in Citrobacter werkmanii, an Emerging Opportunistic Pathogen

by José R. Aguirre-Sánchez, Beatriz Quiñones, José A. Ortiz-Muñoz, Rogelio Prieto-Alvarado, Inés F. Vega-López, Jaime Martínez-Urtaza, Bertram G. Lee and Cristóbal Chaidez

Microorganisms 2023, 11(8), 2114; https://doi.org/10.3390/microorganisms11082114 - 19 Aug 2023

Cited by 1 | Viewed by 1806

Abstract

Citrobacter werkmanii is an emerging and opportunistic human pathogen found in developing countries and is a causative agent of wound, urinary tract, and blood infections. The present study conducted comparative genomic analyses of a C. werkmanii strain collection from diverse geographical locations and [...] Read more.

Citrobacter werkmanii is an emerging and opportunistic human pathogen found in developing countries and is a causative agent of wound, urinary tract, and blood infections. The present study conducted comparative genomic analyses of a C. werkmanii strain collection from diverse geographical locations and sources to identify the relevant virulence and antimicrobial resistance genes. Pangenome analyses divided the examined C. werkmanii strains into five distinct clades; the subsequent classification identified genes with functional roles in carbohydrate and general metabolism for the core genome and genes with a role in secretion, adherence, and the mobilome for the shell and cloud genomes. A maximum-likelihood phylogenetic tree with a heatmap, showing the virulence and antimicrobial genes’ presence or absence, demonstrated the presence of genes with functional roles in secretion systems, adherence, enterobactin, and siderophore among the strains belonging to the different clades. C. werkmanii strains in clade V, predominantly from clinical sources, harbored genes implicated in type II and type Vb secretion systems as well as multidrug resistance to aminoglycoside, beta-lactamase, fluoroquinolone, phenicol, trimethoprim, macrolides, sulfonamide, and tetracycline. In summary, these comparative genomic analyses have demonstrated highly pathogenic and multidrug-resistant genetic profiles in C. werkmanii strains, indicating a virulence potential for this commensal and opportunistic human pathogen. Full article

(This article belongs to the Special Issue Diagnosis, Characterization and Treatment of Emerging Pathogens)

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16 pages, 3491 KiB

Open AccessArticle

Yeast Deletomics to Uncover Gadolinium Toxicity Targets and Resistance Mechanisms

by Nicolas Grosjean, Marie Le Jean, Jordan Ory and Damien Blaudez

Microorganisms 2023, 11(8), 2113; https://doi.org/10.3390/microorganisms11082113 - 19 Aug 2023

Cited by 1 | Viewed by 1615

Abstract

Among the rare earth elements (REEs), a crucial group of metals for high-technologies. Gadolinium (Gd) is the only REE intentionally injected to human patients. The use of Gd-based contrasting agents for magnetic resonance imaging (MRI) is the primary route for Gd direct exposure [...] Read more.

Among the rare earth elements (REEs), a crucial group of metals for high-technologies. Gadolinium (Gd) is the only REE intentionally injected to human patients. The use of Gd-based contrasting agents for magnetic resonance imaging (MRI) is the primary route for Gd direct exposure and accumulation in humans. Consequently, aquatic environments are increasingly exposed to Gd due to its excretion through the urinary tract of patients following an MRI examination. The increasing number of reports mentioning Gd toxicity, notably originating from medical applications of Gd, necessitates an improved risk–benefit assessment of Gd utilizations. To go beyond toxicological studies, unravelling the mechanistic impact of Gd on humans and the ecosystem requires the use of genome-wide approaches. We used functional deletomics, a robust method relying on the screening of a knock-out mutant library of Saccharomyces cerevisiae exposed to toxic concentrations of Gd. The analysis of Gd-resistant and -sensitive mutants highlighted the cell wall, endosomes and the vacuolar compartment as cellular hotspots involved in the Gd response. Furthermore, we identified endocytosis and vesicular trafficking pathways (ESCRT) as well as sphingolipids homeostasis as playing pivotal roles mediating Gd toxicity. Finally, tens of yeast genes with human orthologs linked to renal dysfunction were identified as Gd-responsive. Therefore, the molecular and cellular pathways involved in Gd toxicity and detoxification uncovered in this study underline the pleotropic consequences of the increasing exposure to this strategic metal. Full article

(This article belongs to the Special Issue Microbial Genome Analysis and Interpretation Using Computational Approaches)

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21 pages, 3730 KiB

Open AccessArticle

Physiological and Transcriptomic Analyses of Escherichia coli Serotype O157:H7 in Response to Rhamnolipid Treatment

by Shuo Yang, Lan Ma, Xiaoqing Xu, Qing Peng, Huiying Zhong, Yuxin Gong, Linbo Shi, Mengxin He, Bo Shi and Yu Qiao

Microorganisms 2023, 11(8), 2112; https://doi.org/10.3390/microorganisms11082112 - 18 Aug 2023

Viewed by 1160

Abstract

Rhamnolipid (RL) can inhibit biofilm formation of Escherichia coli O157:H7, but the associated mechanism remains unknown. We here conducted comparative physiological and transcriptomic analyses of cultures treated with RL and untreated cultures to elucidate a potential mechanism by which RL may inhibit biofilm [...] Read more.

Rhamnolipid (RL) can inhibit biofilm formation of Escherichia coli O157:H7, but the associated mechanism remains unknown. We here conducted comparative physiological and transcriptomic analyses of cultures treated with RL and untreated cultures to elucidate a potential mechanism by which RL may inhibit biofilm formation in E. coli O157:H7. Anti-biofilm assays showed that over 70% of the E. coli O157:H7 biofilm formation capacity was inhibited by treatment with 0.25–1 mg/mL of RL. Cellular-level physiological analysis revealed that a high concentration of RL significantly reduced outer membrane hydrophobicity. E. coli cell membrane integrity and permeability were also significantly affected by RL due to an increase in the release of lipopolysaccharide (LPS) from the cell membrane. Furthermore, transcriptomic profiling showed 2601 differentially expressed genes (1344 up-regulated and 1257 down-regulated) in cells treated with RL compared to untreated cells. Functional enrichment analysis indicated that RL treatment up-regulated biosynthetic genes responsible for LPS synthesis, outer membrane protein synthesis, and flagellar assembly, and down-regulated genes required for poly-N-acetyl-glucosamine biosynthesis and genes present in the locus of enterocyte effacement pathogenicity island. In summary, RL treatment inhibited E. coli O157:H7 biofilm formation by modifying key outer membrane surface properties and expression levels of adhesion genes. Full article

(This article belongs to the Special Issue Advance Research on Bacterial Biofilm)

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10 pages, 1258 KiB

Open AccessArticle

Infant Saliva Microbiome Activity Modulates Nutritional Impacts on Neurodevelopment

by Terrah Keck-Kester and Steven D. Hicks

Microorganisms 2023, 11(8), 2111; https://doi.org/10.3390/microorganisms11082111 - 18 Aug 2023

Cited by 1 | Viewed by 2442

Abstract

Neurodevelopment is influenced by complex interactions between environmental factors, including social determinants of health (SDOH), nutrition, and even the microbiome. This longitudinal cohort study of 142 infants tested the hypothesis that microbial activity modulates the effects of nutrition on neurodevelopment. Salivary microbiome activity [...] Read more.

Neurodevelopment is influenced by complex interactions between environmental factors, including social determinants of health (SDOH), nutrition, and even the microbiome. This longitudinal cohort study of 142 infants tested the hypothesis that microbial activity modulates the effects of nutrition on neurodevelopment. Salivary microbiome activity was measured at 6 months using RNA sequencing. Infant nutrition was assessed longitudinally with the Infant Feeding Practices survey. The primary outcome was presence/absence of neurodevelopmental delay (NDD) at 18 months on the Survey of Wellbeing in Young Children. A logistic regression model employing two microbial factors, one nutritional factor, and two SDOH accounted for 33.3% of the variance between neurodevelopmental groups (p < 0.001, AIC = 77.7). NDD was associated with Hispanic ethnicity (OR 18.1, 2.36–139.3; p = 0.003), no fish consumption (OR 10.6, 2.0–54.1; p = 0.003), and increased Candidatus Gracilibacteria activity (OR 1.43, 1.00–2.07; p = 0.007). Home built after 1977 (OR 0.02, 0.001–0.53; p = 0.004) and Chlorobi activity (OR 0.76, 0.62–0.93, p = 0.001) were associated with reduced risk of NDD. Microbial alpha diversity modulated the effect of fish consumption on NDD (X² = 5.7, p = 0.017). These data suggest the benefits of fish consumption for neurodevelopment may be mediated by microbial diversity. Confirmation in a larger, randomized trial is required. Full article

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

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18 pages, 2169 KiB

Open AccessArticle

The Probiotic Bacillus subtilis MB40 Improves Immunity in a Porcine Model of Listeriosis

by Sean M. Garvey, Nima K. Emami, Justin L. Guice, Nammalwar Sriranganathan, Christopher Penet, Robert P. Rhoads, Jessica L. Spears, Rami A. Dalloul and Samer W. El-Kadi

Microorganisms 2023, 11(8), 2110; https://doi.org/10.3390/microorganisms11082110 - 18 Aug 2023

Cited by 1 | Viewed by 1926

Abstract

Probiotics for humans and direct-fed microbials for livestock are increasingly popular dietary ingredients for supporting immunity. The aim of this study was to determine the effects of dietary supplementation of Bacillus subtilis MB40 (MB40) on immunity in piglets challenged with the foodborne pathogen [...] Read more.

Probiotics for humans and direct-fed microbials for livestock are increasingly popular dietary ingredients for supporting immunity. The aim of this study was to determine the effects of dietary supplementation of Bacillus subtilis MB40 (MB40) on immunity in piglets challenged with the foodborne pathogen Listeria monocytogenes (LM). Three-week-old piglets (n = 32) were randomly assigned to four groups: (1) basal diet, (2) basal diet with LM challenge, (3) MB40-supplemented diet, and (4) MB40-supplemented diet with LM challenge. Experimental diets were provided throughout a 14-day (d) period. On d8, piglets in groups 2 and 4 were intraperitoneally inoculated with LM at 10⁸ CFU/mL per piglet. Blood samples were collected at d1, d8, and d15 for biochemical and immune response profiling. Animals were euthanized and necropsied at d15 for liver and spleen bacterial counts and intestinal morphological analysis. At d15, LM challenge was associated with increased spleen weight (p = 0.017), greater circulating populations of neutrophils (p = 0.001) and monocytes (p = 0.008), and reduced ileal villus height to crypt depth ratio (p = 0.009), compared to non-challenged controls. MB40 supplementation reduced LM bacterial counts in the liver and spleen by 67% (p < 0.001) and 49% (p < 0.001), respectively, following the LM challenge, compared to the basal diet. MB40 supplementation was also associated with decreased circulating concentrations of monocytes (p = 0.007). Altogether, these data suggest that MB40 supplementation is a safe and well-tolerated approach to enhance immunity during systemic Listeria infection. Full article

(This article belongs to the Special Issue Beneficial Microorganisms and Antimicrobials)

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16 pages, 2605 KiB

Open AccessArticle

Comparison of Phenotype Nutritional Profiles and Phosphate Metabolism Genes in Four Serovars of Salmonella enterica from Water Sources

by Lisa Gorski and Ashley Aviles Noriega

Microorganisms 2023, 11(8), 2109; https://doi.org/10.3390/microorganisms11082109 - 18 Aug 2023

Cited by 1 | Viewed by 1155

Abstract

The surveillance of foods for Salmonella is hindered by bias in common enrichment media where serovars implicated in human illness are outgrown by less virulent serovars. We examined four Salmonella serovars, two common in human illness (Enteritidis and Typhimurium) and two that often [...] Read more.

The surveillance of foods for Salmonella is hindered by bias in common enrichment media where serovars implicated in human illness are outgrown by less virulent serovars. We examined four Salmonella serovars, two common in human illness (Enteritidis and Typhimurium) and two that often dominate enrichments (Give and Kentucky), for factors that might influence culture bias. The four serovars had similar growth kinetics in Tryptic Soy Broth and Buffered Peptone Water. Phenotype microarray analysis with 950 chemical substrates to assess nutrient utilization and stress resistance revealed phenotype differences between serovars. Strains of S. Enteritidis had better utilization of plant-derived sugars such as xylose, mannitol, rhamnose, and fructose, while S. Typhimurium strains were able to metabolize tagatose. Strains of S. Kentucky used more compounds as phosphorus sources and grew better with inorganic phosphate as the sole phosphorus source. The sequences of nine genes involved in phosphate metabolism were compared, and there were differences between serovars in the catalytic ATP-binding domain of the histidine kinase phoR. Analysis of the predicted PhoR amino acid sequences from additional Salmonella genomes indicated a conservation of sequences each within the Typhimurium, Give, and Enteritidis serovars. However, three different PhoR versions were observed in S. Kentucky. Full article

(This article belongs to the Section Food Microbiology)

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15 pages, 2086 KiB

Open AccessArticle

Gut Microbiota and Respiratory Infections: Insights from Mendelian Randomization

by Shengyu Huang, Jiaqi Li, Zhihao Zhu, Xiaobin Liu, Tuo Shen, Yusong Wang, Qimin Ma, Xin Wang, Guangping Yang, Guanghua Guo and Feng Zhu

Microorganisms 2023, 11(8), 2108; https://doi.org/10.3390/microorganisms11082108 - 18 Aug 2023

Cited by 1 | Viewed by 2040

Abstract

The role of the gut microbiota in modulating the risk of respiratory infections has garnered increasing attention. However, conventional clinical trials have faced challenges in establishing the precise relationship between the two. In this study, we conducted a Mendelian randomization analysis with single [...] Read more.

The role of the gut microbiota in modulating the risk of respiratory infections has garnered increasing attention. However, conventional clinical trials have faced challenges in establishing the precise relationship between the two. In this study, we conducted a Mendelian randomization analysis with single nucleotide polymorphisms employed as instrumental variables to assess the causal links between the gut microbiota and respiratory infections. Two categories of bacteria, family Lactobacillaceae and genus Family XIII AD3011, were causally associated with the occurrence of upper respiratory tract infections (URTIs). Four categories of gut microbiota existed that were causally associated with lower respiratory tract infections (LRTIs), with order Bacillales and genus Paraprevotella showing a positive association and genus Alistipes and genus Ruminococcaceae UCG009 showing a negative association. The metabolites and metabolic pathways only played a role in the development of LRTIs, with the metabolite deoxycholine acting negatively and menaquinol 8 biosynthesis acting positively. The identification of specific bacterial populations, metabolites, and pathways may provide new clues for mechanism research concerning therapeutic interventions for respiratory infections. Future research should focus on elucidating the potential mechanisms regulating the gut microbiota and developing effective strategies to reduce the incidence of respiratory infections. These findings have the potential to significantly improve global respiratory health. Full article

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

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17 pages, 2573 KiB

Open AccessArticle

Identification of Virulence Factors in Entomopathogenic Aspergillus flavus Isolated from Naturally Infected Rhipicephalus microplus

by Cesar A. Arreguin-Perez, Estefan Miranda-Miranda, Jorge Luis Folch-Mallol and Raquel Cossío-Bayúgar

Microorganisms 2023, 11(8), 2107; https://doi.org/10.3390/microorganisms11082107 - 18 Aug 2023

Viewed by 1205

Abstract

Aspergillus flavus has been found to be an effective entomopathogenic fungus for various arthropods, including ticks. In particular, natural fungal infections in cattle ticks show promise for biocontrol of the Rhipicephalus (Boophilus) microplus tick, which is a major ectoparasite affecting cattle [...] Read more.

Aspergillus flavus has been found to be an effective entomopathogenic fungus for various arthropods, including ticks. In particular, natural fungal infections in cattle ticks show promise for biocontrol of the Rhipicephalus (Boophilus) microplus tick, which is a major ectoparasite affecting cattle worldwide. Our study aimed to elucidate the specific entomopathogenic virulence factors encoded in the genome of an A. flavus strain isolated from naturally infected cattle ticks. We performed morphological and biochemical phenotyping alongside complete genome sequencing, which revealed that the isolated fungus was A. flavus related to the L morphotype, capable of producing a range of gene-coded entomopathogenic virulence factors, including ribotoxin, aflatoxin, kojic acid, chitinases, killer toxin, and satratoxin. To evaluate the efficacy of this A. flavus strain against ticks, we conducted experimental bioassays using healthy engorged female ticks. A morbidity rate of 90% was observed, starting at a concentration of 10⁵ conidia/mL. At a concentration of 10⁷ conidia/mL, we observed a 50% mortality rate and a 21.5% inhibition of oviposition. The highest levels of hatch inhibition (30.8%) and estimated reproduction inhibition (34.64%) were achieved at a concentration of 10⁸ conidia/mL. Furthermore, the tick larval progeny that hatched from the infected tick egg masses showed evident symptoms of Aspergillus infection after incubation. Full article

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

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13 pages, 2740 KiB

Open AccessArticle

The Alteration of the Gut Microbiome during Ramadan Offers a Novel Perspective on Ramadan Fasting: A Pilot Study

by YoungJae Jo, GyuDae Lee, Sajjad Ahmad, HyunWoo Son, Min-Ji Kim, Amani Sliti, Seungjun Lee, Kyeongnam Kim, Sung-Eun Lee and Jae-Ho Shin

Microorganisms 2023, 11(8), 2106; https://doi.org/10.3390/microorganisms11082106 - 18 Aug 2023

Viewed by 2097

Abstract

An intermittent fasting regimen is widely perceived to lead to various beneficial health effects, including weight loss, the alleviation of insulin resistance, and the restructuring of a healthy gut microbiome. Because it shares certain commonalities with this dietary intervention, Ramadan fasting is sometimes [...] Read more.

An intermittent fasting regimen is widely perceived to lead to various beneficial health effects, including weight loss, the alleviation of insulin resistance, and the restructuring of a healthy gut microbiome. Because it shares certain commonalities with this dietary intervention, Ramadan fasting is sometimes misinterpreted as intermittent fasting, even though there are clear distinctions between these two regimens. The main purpose of this study is to verify whether Ramadan fasting drives the same beneficial effects as intermittent fasting by monitoring alterations in the gut microbiota. We conducted a study involving 20 Muslim individuals who were practicing Ramadan rituals and assessed the composition of their gut microbiomes during the 4-week period of Ramadan and the subsequent 8-week period post-Ramadan. Fecal microbiome analysis was conducted, and short-chain fatty acids (SCFAs) were assessed using liquid-chromatography–mass spectrometry. The observed decrease in the levels of SCFAs and beneficial bacteria during Ramadan, along with the increased microbial diversity post-Ramadan, suggests that the daily diet during Ramadan may not provide adequate nutrients to maintain robust gut microbiota. Additionally, the notable disparities in the functional genes detected through the metagenomic analysis and the strong correlation between Lactobacillus and SCFAs provide further support for our hypothesis. Full article

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

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15 pages, 5430 KiB

Open AccessArticle

The Immunogenicity and Safety of Mycobacterium tuberculosis-mosR-Based Double Deletion Strain in Mice

by Rachel E. Hildebrand, Chungyi Hansen, Brock Kingstad-Bakke, Chia-Wei Wu, Marulasiddappa Suresh and Adel Talaat

Microorganisms 2023, 11(8), 2105; https://doi.org/10.3390/microorganisms11082105 - 18 Aug 2023

Viewed by 1411

Abstract

Mycobacterium tuberculosis (M. tuberculosis) remains a significant global health threat, accounting for ~1.7 million deaths annually. The efficacy of the current vaccine, M. bovis BCG, ranges from 0 to 80% in children and does not prevent adulthood tuberculosis. We explored the [...] Read more.

Mycobacterium tuberculosis (M. tuberculosis) remains a significant global health threat, accounting for ~1.7 million deaths annually. The efficacy of the current vaccine, M. bovis BCG, ranges from 0 to 80% in children and does not prevent adulthood tuberculosis. We explored the immune profile and safety of a live-attenuated M. tuberculosis construct with double deletions of the mosR and echA7 genes, where previously, single mutations were protective against an M. tuberculosis aerosol challenge. Over 32 weeks post-vaccination (WPV), immunized mice with M. tuberculosisΔmosRΔechA7 (double mutant) were sacrificed to evaluate the vaccine persistence, histopathology, and immune responses. Interestingly, despite similar tissue colonization between the vaccine double mutant and wild-type M. tuberculosis, the vaccine construct showed a greater reaction to the ESAT-6, TB.10, and Ag85B antigens with peptide stimulation. Additionally, there was a greater number of antigen-specific CD4 T cells in the vaccine group, accompanied by significant polyfunctional T-cell responses not observed in the other groups. Histologically, mild but widely distributed inflammatory responses were recorded in the livers and lungs of the immunized animals at early timepoints, which turned into organized inflammatory foci via 32WPV, a pathology not observed in BCG-immunized mice. A lower double-mutant dose resulted in significantly less tissue colonization and less tissue inflammation. Overall, the double-mutant vaccine elicited robust immune responses dominated by antigen-specific CD4 T cells, but also triggered tissue damage and vaccine persistence. The findings highlight key features associated with the immunogenicity and safety of the examined vaccine construct that can benefit the future evaluation of other live vaccines. Full article

(This article belongs to the Special Issue Mycobacterial Tuberculosis Pathogenesis and Vaccine Development)

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9 pages, 1514 KiB

Open AccessCommunication

Isolation, Identification and Evaluation of the Effects of Native Entomopathogenic Fungi from Côte d’Ivoire on Galleria mellonella

by Fatoumatou Fofana, Corentin Descombes, Assiri Patrice Kouamé and François Lefort

Microorganisms 2023, 11(8), 2104; https://doi.org/10.3390/microorganisms11082104 - 18 Aug 2023

Viewed by 1970

Abstract

The fall armyworm, Spodoptera frugiperda (Lepidoptera: Noctuidae), is a polyphagous pest highly damaging to maize and other food crops in Africa, particularly in Côte d’Ivoire. Chemical pesticides not only have often proved to be unsuccessful, but cause adverse effects on the environment and [...] Read more.

The fall armyworm, Spodoptera frugiperda (Lepidoptera: Noctuidae), is a polyphagous pest highly damaging to maize and other food crops in Africa, particularly in Côte d’Ivoire. Chemical pesticides not only have often proved to be unsuccessful, but cause adverse effects on the environment and human health; therefore, entomopathogenic fungi could represent an alternative biocontrol solution. Against this background, fungi were isolated from soil samples collected in maize fields in three regions of Côte d’Ivoire, by the methods of soil dilution and baiting with Galleria mellonella. The resulting 86 fungal isolates were phenotypically and genetically identified. The pathogenicity of seven isolates of Metarhizium spp., three isolates of Beauveria bassiana and two isolates of Trichoderma sp. was evaluated on fifth instar larvae (L5) of G. mellonella. Larval mortality rates and the median lethal time (LT₅₀) were determined seven days after inoculation for each of these selected isolates. The median lethal concentration (LC₅₀) was determined for a selection of isolates. Beauveria bassiana isolate A214b was the most effective, causing 100% mortality, with an LT₅₀ of 2.64 days and an LC₅₀ of 1.12 × 10⁴ conidia mL⁻¹. Two other promising isolates, A211 and A214a, belonging to B. bassiana, caused 100% mortality with LT₅₀ values of 3.44 and 4.04 days, respectively. Mortality caused by Metarhizium isolates varied from 65.38% to 100%, with Metarhizium anisopliae isolate T331 causing 100% mortality with an LT₅₀ of 3.08 days at an LC₅₀ of 3.33 × 10⁴ conidia mL⁻¹. Trichoderma sp. isolates were the least pathogenic ones. Beauveria bassiana and Metarhizium isolates showed to be virulent against the model Lepidopteran G. mellonella and will be tested on S. frugiperda. Full article

(This article belongs to the Special Issue Odi Et Amo: Diversity of Insect–Microbe Interactions, from Antagonism to Mutualism, and Their Manipulation for Pest Control)

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12 pages, 1327 KiB

Open AccessArticle

Microbial Recycling of Polylactic Acid Food Packaging Waste into Carboxylates via Hydrolysis and Mixed-Culture Fermentation

by David P. B. T. B. Strik and Brian Heusschen

Microorganisms 2023, 11(8), 2103; https://doi.org/10.3390/microorganisms11082103 - 18 Aug 2023

Cited by 1 | Viewed by 1988

Abstract

To establish a circular economy, waste streams should be used as a resource to produce valuable products. Biodegradable plastic waste represents a potential feedstock to be microbially recycled via a carboxylate platform. Bioplastics such as polylactic acid food packaging waste (PLA-FPW) are theoretically [...] Read more.

To establish a circular economy, waste streams should be used as a resource to produce valuable products. Biodegradable plastic waste represents a potential feedstock to be microbially recycled via a carboxylate platform. Bioplastics such as polylactic acid food packaging waste (PLA-FPW) are theoretically suitable feedstocks for producing carboxylates. Once feasible, carboxylates such as acetate, n-butyrate, or n-caproate can be used for various applications like lubricants or building blocks for making new bioplastics. In this study, pieces of industrial compostable PLA-FPW material (at 30 or 60 g/L) were added to a watery medium with microbial growth nutrients. This broth was exposed to 70 °C for a pretreatment process to support the hydrolysis of PLA into lactic acid at a maximum rate of 3.0 g/L×d. After 21 days, the broths of the hydrolysis experiments were centrifugated and a part of the supernatant was extracted and prepared for anaerobic fermentation. The mixed microbial culture, originating from a food waste fermentation bioprocess, successfully fermented the hydrolyzed PLA into a spectrum of new C2-C6 multi-carbon carboxylates. n-butyrate was the major product for all fermentations and, on average, 6.5 g/L n-butyrate was obtained from 60 g/L PLA-FPW materials. The wide array of products were likely due to various microbial processes, including lactate conversion into acetate and propionate, as well as lactate-based chain elongation to produce medium-chain carboxylates. The fermentation process did not require pH control. Overall, we showed a proof-of-concept in using real bioplastic waste as feedstock to produce valuable C2-C6 carboxylates via microbial recycling. Full article

(This article belongs to the Special Issue Microbial Advances in a Sustainable Environment: Biological Waste Treatment and Bioconversion Technology)

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10 pages, 1894 KiB

Open AccessArticle

Biofilm Removal from In Vitro Narrow Geometries Using Single and Dual Pulse Er:YAG Laser Photoacoustic Irrigation

by Saša Terlep, Iztok Dogsa, Franja Pajk and David Stopar

Microorganisms 2023, 11(8), 2102; https://doi.org/10.3390/microorganisms11082102 - 17 Aug 2023

Cited by 3 | Viewed by 1037

Abstract

The disinfection and removal of biofilm from titanium dental implants remains a great challenge in oral medicine. Here we present results of novel photoacoustic irrigation laser modalities for biofilm removal in model geometries mimicking the peri-implant pocket. The efficacy of single pulse (Er:YAG-SSP) [...] Read more.

The disinfection and removal of biofilm from titanium dental implants remains a great challenge in oral medicine. Here we present results of novel photoacoustic irrigation laser modalities for biofilm removal in model geometries mimicking the peri-implant pocket. The efficacy of single pulse (Er:YAG-SSP) and dual pulse (Er:YAG-AutoSWEEPS) photoacoustic irrigation modalities were determined for Enterococcus faecalis biofilm decontamination from titanium surfaces in narrow cylindrical and square gap geometries. The density of bacteria as well as the number of live bacteria were determined prior and after different photoacoustic treatments. Both SSP and AutoSWEEPS photoacoustic irrigation techniques removed at least 92% of biofilm bacteria during the 10 s photoacoustic treatment. The effectiveness of cleaning was better in the narrow square gap geometry compared to the cylindrical geometry. The dual pulse Er:YAG-AutoSWEEPS photoacoustic irrigation showed better results compared to SSP modality. No chemical adjuvants were needed to boost the effectiveness of the photoacoustic irrigation in the saline solution. The results imply that photoacoustic irrigation is an efficient cleaning method for debridement and decontamination in narrow geometries and should be considered as a new therapeutic option for the treatment of peri-implant diseases. Full article

(This article belongs to the Special Issue Resilient Biofilms and Their Control)

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19 pages, 6026 KiB

Open AccessArticle

Type I Interferon Pathway-Related Hub Genes as a Potential Therapeutic Target for SARS-CoV-2 Omicron Variant-Induced Symptoms

by Zhiwei Lin, Mingshan Xue, Ziman Wu, Ze Liu, Qianyue Yang, Jiaqing Hu, Jiacong Peng, Lin Yu and Baoqing Sun

Microorganisms 2023, 11(8), 2101; https://doi.org/10.3390/microorganisms11082101 - 17 Aug 2023

Viewed by 1250

Abstract

Background: The global pandemic of COVID-19 is caused by the rapidly evolving severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The clinical presentation of SARS-CoV-2 Omicron variant infection varies from asymptomatic to severe disease with diverse symptoms. However, the underlying mechanisms responsible for these [...] Read more.

Background: The global pandemic of COVID-19 is caused by the rapidly evolving severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The clinical presentation of SARS-CoV-2 Omicron variant infection varies from asymptomatic to severe disease with diverse symptoms. However, the underlying mechanisms responsible for these symptoms remain incompletely understood. Methods: Transcriptome datasets from peripheral blood mononuclear cells (PBMCs) of COVID-19 patients infected with the Omicron variant and healthy volunteers were obtained from public databases. A comprehensive bioinformatics analysis was performed to identify hub genes associated with the Omicron variant. Hub genes were validated using quantitative RT-qPCR and clinical data. DSigDB database predicted potential therapeutic agents. Results: Seven hub genes (IFI44, IFI44L, MX1, OAS3, USP18, IFI27, and ISG15) were potential biomarkers for Omicron infection’s symptomatic diagnosis and treatment. Type I interferon-related hub genes regulated Omicron-induced symptoms, which is supported by independent datasets and RT-qPCR validation. Immune cell analysis showed elevated monocytes and reduced lymphocytes in COVID-19 patients, which is consistent with retrospective clinical data. Additionally, ten potential therapeutic agents were screened for COVID-19 treatment, targeting the hub genes. Conclusions: This study provides insights into the mechanisms underlying type I interferon-related pathways in the development and recovery of COVID-19 symptoms during Omicron infection. Seven hub genes were identified as promising biological biomarkers for diagnosing and treating Omicron infection. The identified biomarkers and potential therapeutic agent offer valuable implications for Omicron’s clinical manifestations and treatment strategies. Full article

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

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16 pages, 2148 KiB

Open AccessReview

Environmental Sampling Methods for Detection of Salmonella Infections in Laying Hens: A Systematic Review and Meta-Analysis

by Ewa Pacholewicz, Henk J. Wisselink, Miriam G. J. Koene, Marleen van der Most and Jose L. Gonzales

Microorganisms 2023, 11(8), 2100; https://doi.org/10.3390/microorganisms11082100 - 17 Aug 2023

Cited by 2 | Viewed by 1711

Abstract

Salmonellosis is the second most commonly reported foodborne gastrointestinal infection in humans in the European Union (EU). Most outbreaks are caused by Salmonella Enteritidis, present in contaminated food products, particularly in egg and egg products. In recent years, an increase in the prevalence [...] Read more.

Salmonellosis is the second most commonly reported foodborne gastrointestinal infection in humans in the European Union (EU). Most outbreaks are caused by Salmonella Enteritidis, present in contaminated food products, particularly in egg and egg products. In recent years, an increase in the prevalence of Salmonella in laying hen flocks in the EU has been observed. For the effective control of infection, adequate detection is key. In laying hen flocks, the occurrence of Salmonella in the EU is monitored by the culture of environmental samples (dust, faeces, and boot swabs). The performance of sampling procedures described in the literature for the detection of Salmonella in laying hens was reviewed. In total, 924 abstracts were screened, resulting in the selection of 87 abstracts and 18 publications for qualitative and quantitative analyses, respectively. Sample sizes and sampling locations of faecal material and dust were variable and poorly described. Microbiological culture methods used to detect Salmonella were variably described in the literature and were often incomplete. Overall, the available literature indicates higher sensitivity of environmental versus individual hen matrices and points to differences in sensitivity between environmental matrices. For non-cage housing systems, boot swabs are the preferred samples, while for cage housing systems dust might be a more reliable sample. Full article

(This article belongs to the Special Issue Poultry Pathogens and Poultry Diseases)

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18 pages, 2368 KiB

Open AccessArticle

New Potential Biological Limiters of the Main Esca-Associated Fungi in Grapevine

by Francesco Mannerucci, Giovanni D’Ambrosio, Nicola Regina, Domenico Schiavone and Giovanni Luigi Bruno

Microorganisms 2023, 11(8), 2099; https://doi.org/10.3390/microorganisms11082099 - 17 Aug 2023

Viewed by 901

Abstract

The strains Trichoderma harzianum TH07.1-NC (TH), Aphanocladium album MX95 (AA), Pleurotus eryngii AL142PE (PE) and Pleurotus ostreatus ALPO (PO) were tested as biological limiters against Fomitiporia mediterranea Fme22.12 (FM), Phaeoacremonium minimum Pm22.53 (PM) and Phaeomoniella chlamydospora Pc22.65 (PC). Pathogens were obtained from naturally [...] Read more.

The strains Trichoderma harzianum TH07.1-NC (TH), Aphanocladium album MX95 (AA), Pleurotus eryngii AL142PE (PE) and Pleurotus ostreatus ALPO (PO) were tested as biological limiters against Fomitiporia mediterranea Fme22.12 (FM), Phaeoacremonium minimum Pm22.53 (PM) and Phaeomoniella chlamydospora Pc22.65 (PC). Pathogens were obtained from naturally Esca-affected ‘Nero di Troia’ vines cropped in Grumo Appula (Puglia region, Southern Italy). The antagonistic activity of each challenge organism was verified in a dual culture. TH and PO completely overgrew the three pathogens. Partial replacement characterized PE-FM, PE-PM, PE-PC and AA-PC interactions. Deadlock at mycelial contact was observed in AA-FM and AA-PM cultures. The calculated antagonism index (AI) indicated TH and PE as moderately active antagonists (10 < AI < 15), while AA and PO were weakly active (AI < 10). The maximum value of the re-isolation index (s) was associated with deadlock among AA-PM, AA-PC and PE-FM dual cultures. The tested biological limiters were always re-isolated when PO and TH completely replaced the three tested pathogens. TH and AA confirmed their efficiencies as biological limiters when inoculated on detached canes of ‘Nero di Troia’ in dual combination with FM, PC and PM. Nevertheless, additional experiments should be performed for a solid conclusion, along with validation experiments in the field. Full article

(This article belongs to the Special Issue Biological Control of the Plant Pathogens)

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14 pages, 4180 KiB

Open AccessArticle

Phage-Based Biosensing for Rapid and Specific Detection of Staphylococcus aureus

by Ruining Li, Zhiwei Li, Chenxi Huang, Yifeng Ding, Jia Wang and Xiaohong Wang

Microorganisms 2023, 11(8), 2098; https://doi.org/10.3390/microorganisms11082098 - 17 Aug 2023

Viewed by 1300

Abstract

Staphylococcus aureus (S. aureus) is a major foodborne pathogen. Rapid and specific detection is crucial for controlling staphylococcal food poisoning. This study reported a Staphylococcus phage named LSA2302 showing great potential for applications in the rapid detection of S. aureus. [...] Read more.

Staphylococcus aureus (S. aureus) is a major foodborne pathogen. Rapid and specific detection is crucial for controlling staphylococcal food poisoning. This study reported a Staphylococcus phage named LSA2302 showing great potential for applications in the rapid detection of S. aureus. Its biological characteristics were identified, including growth properties and stability under different pH and temperature conditions. The genomic analysis revealed that the phage has no genes associated with pathogenicity or drug resistance. Then, the phage-functionalized magnetic beads (pMB), serving as a biological recognition element, were integrated with ATP bioluminescence assays to establish a biosensing method for S. aureus detection. The pMB enrichment brought high specificity and a tenfold increase in analytical sensitivity during detection. The whole detection process could be completed within 30 min, with a broad linear range of 1 × 10⁴ to 1 × 10⁸ CFU/mL and a limit of detection (LOD) of 2.43 × 10³ CFU/mL. After a 2 h pre-cultivation, this method is capable of detecting bacteria as low as 1 CFU/mL. The recoveries of S. aureus in spiked skim milk and chicken samples were 81.07% to 99.17% and 86.98% to 104.62%, respectively. Our results indicated that phage-based biosensing can contribute to the detection of target pathogens in foods. Full article

(This article belongs to the Special Issue Foodborne Pathogens: Prevention, Control and Detection Strategies)

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17 pages, 2753 KiB

Open AccessArticle

Analysis of Airborne Fungal Communities on Pedestrian Bridges in Urban Environments

by Amran A. Q. A. Al-Shaarani, Ziwei M. Quach, Xiao Wang, Mohammed H. M. Muafa, Md M. H. Nafis and Lorenzo Pecoraro

Microorganisms 2023, 11(8), 2097; https://doi.org/10.3390/microorganisms11082097 - 16 Aug 2023

Cited by 2 | Viewed by 1144

Abstract

Airborne fungal spores constitute an important type of bioaerosol and are responsible for a number of negative effects on human health, including respiratory diseases and allergies. We investigated the diversity and concentration of culturable airborne fungi on pedestrian bridges in Tianjin, China, using [...] Read more.

Airborne fungal spores constitute an important type of bioaerosol and are responsible for a number of negative effects on human health, including respiratory diseases and allergies. We investigated the diversity and concentration of culturable airborne fungi on pedestrian bridges in Tianjin, China, using an HAS-100B air sampler. We compared the airborne fungal communities at the top central area of the selected pedestrian bridges and along the corresponding sidewalk, at ground level. A total of 228 fungal strains belonging to 96 species and 58 genera of Ascomycota (68.86%), Basidiomycota (30.26%), and Mucoromycota (0.88%) were isolated and identified using morphological and molecular analysis. Alternaria was the dominant genus (20.61%), followed by Cladosporium (11.48%), Schizophyllum (6.14%), Sporobolomyces (5.70%), and Sporidiobolus (4.82%). Alternaria alternata was the most frequently occurring fungal species (6.58%), followed by Schizophyllum commune (5.26%), Alternaria sp. (4.82%), Sporobolomyces carnicolor (4.39%), and Cladosporium cladosporioides (3.95%). The recorded fungal concentration ranged from 10 to 180 CFU/m³. Although there was no significant difference in the distribution and abundance of the dominant airborne fungal taxa between the two investigated bridges’ sites, numerous species detected with a low percentage of abundance belonging to well-known pathogenic fungal genera, including Alternaria, Aspergillus, Aureobasidium, Cladosporium, Penicillium, and Trichoderma, were exclusively present in one of the two sites. The relative humidity showed a stronger influence compared to the temperature on the diversity and concentration of airborne fungi in the investigated sites. Our results may provide valuable information for air quality monitoring and for assessing human health risks associated with microbial pollution. Full article

(This article belongs to the Special Issue Airborne Microbes and Their Potential Influence)

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Microorganisms, Volume 11, Issue 8 (August 2023) – 260 articles

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