Microorganisms

16 pages, 1998 KiB

Open AccessArticle

Vermicompost Supply Enhances Fragrant-Rice Yield by Improving Soil Fertility and Eukaryotic Microbial Community Composition under Environmental Stress Conditions

by Anas Iqbal, Quaid Hussain, Zhaowen Mo, Tian Hua, Abd El-Zaher M. A. Mustafa and Xiangru Tang

Microorganisms 2024, 12(6), 1252; https://doi.org/10.3390/microorganisms12061252 - 20 Jun 2024

Cited by 2 | Viewed by 1037

Abstract

Heavy-metal contamination in agricultural soil, particularly of cadmium (Cd), poses serious threats to soil biodiversity, rice production, and food safety. Soil microbes improve soil fertility by regulating soil organic matter production, plant nutrient accumulation, and pollutant transformation. Addressing the impact of Cd toxicity [...] Read more.

Heavy-metal contamination in agricultural soil, particularly of cadmium (Cd), poses serious threats to soil biodiversity, rice production, and food safety. Soil microbes improve soil fertility by regulating soil organic matter production, plant nutrient accumulation, and pollutant transformation. Addressing the impact of Cd toxicity on soil fungal community composition, soil health, and rice yield is urgently required for sustainable rice production. Vermicompost (VC) is an organic fertilizer that alleviates the toxic effects of Cd on soil microbial biodiversity and functionality and improves crop productivity sustainably. In the present study, we examined the effects of different doses of VC (i.e., 0, 3, and 6 tons ha⁻¹) and levels of Cd stress (i.e., 0 and 25 mg Cd kg⁻¹) on soil biochemical attributes, soil fungal community composition, and fragrant-rice grain yield. The results showed that the Cd toxicity significantly reduced soil fertility, eukaryotic microbial community composition and rice grain yield. However, the VC addition alleviated the Cd toxicity and significantly improved the soil fungal community; additionally, it enhanced the relative abundance of Ascomycota, Chlorophyta, Ciliophora, Basidiomycota, and Glomeromycta in Cd-contaminated soils. Moreover, the VC addition enhanced the soil’s chemical attributes, including soil pH, soil organic carbon (SOC), available nitrogen (AN), total nitrogen (TN), and microbial biomass C and N, compared to non-VC treated soil under Cd toxicity conditions. Similarly, the VC application significantly increased rice grain yield and decreased the Cd uptake in rice. One possible explanation for the reduced Cd uptake in plants is that VC amendments influence the soil’s biological properties, which ultimately reduces soil Cd bioavailability and subsequently influences the Cd uptake and accumulation in rice plants. RDA analysis determined that the leading fungal species were highly related to soil environmental attributes and microbial biomass C and N production. However, the relative abundance levels of Ascomycota, Basidiomycota, and Glomeromycta were strongly associated with soil environmental variables. Thus, the outcomes of this study reveal that the use of VC in Cd-contaminated soils could be useful for sustainable rice production and safe utilization of Cd-polluted soil. Full article

(This article belongs to the Special Issue Soil Microbial Communities under Environmental Change)

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15 pages, 3010 KiB

Open AccessArticle

Endophytic Microorganisms in Tomato Roots, Changes in the Structure and Function of the Community at Different Growing Stages

by Yufei Wei, Siyu Chen, Xinyan Zhou, Diancao Ding, Jingjing Song and Shangdong Yang

Microorganisms 2024, 12(6), 1251; https://doi.org/10.3390/microorganisms12061251 - 20 Jun 2024

Viewed by 824

Abstract

This study analyzed flower bud differentiation and fruiting stages to investigate how the structure of the plant endophytic microbial community in the roots of tomatoes changes with plant senescence. Based on high-throughput sequencing technology, the diversity and relative abundance of endophytic microorganisms (bacteria [...] Read more.

This study analyzed flower bud differentiation and fruiting stages to investigate how the structure of the plant endophytic microbial community in the roots of tomatoes changes with plant senescence. Based on high-throughput sequencing technology, the diversity and relative abundance of endophytic microorganisms (bacteria and fungi) in tomato stems at different growth stages were analyzed. At the same time, based on LEfSe analysis, the differences in endophytic microorganisms in tomato stems at different growth stages were studied. Based on PICRUSt2 function prediction and FUNGuild, we predicted the functions of endophytic bacterial and fungal communities in tomato stems at different growth stages to explore potential microbial functional traits. The results demonstrated that not only different unique bacterial genera but also unique fungal genera could be found colonizing tomato roots at different growth stages. In tomato seedlings, flower bud differentiation, and fruiting stages, the functions of colonizing endophytes in tomato roots could primarily contribute to the promotion of plant growth, stress resistance, and improvement in nutrient cycling, respectively. These results also suggest that different functional endophytes colonize tomato roots at different growth stages. Full article

(This article belongs to the Special Issue Using Microorganisms to Increase Crop Productivity and Sustainability)

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20 pages, 3554 KiB

Open AccessArticle

Metagenomic Investigation of the Short-Term Temporal and Spatial Dynamics of the Bacterial Microbiome and the Resistome Downstream of a Wastewater Treatment Plant in the Iskar River in Bulgaria

by Deyan Donchev, Ivan N. Ivanov, Ivan Stoikov and Monika Ivanova

Microorganisms 2024, 12(6), 1250; https://doi.org/10.3390/microorganisms12061250 - 20 Jun 2024

Viewed by 1116

Abstract

Waste Water Treatment Plants (WWTP) aim to reduce contamination in effluent water; however, studies indicate antimicrobial resistance genes (ARGs) persist post-treatment, potentially leading to their spread from human populated areas into the environment. This study evaluated the impact of a large WWTP serving [...] Read more.

Waste Water Treatment Plants (WWTP) aim to reduce contamination in effluent water; however, studies indicate antimicrobial resistance genes (ARGs) persist post-treatment, potentially leading to their spread from human populated areas into the environment. This study evaluated the impact of a large WWTP serving 125,000 people on the Iskar River in Bulgaria, by characterizing the spatial and short-term temporal dynamics in bacterial community dynamics and resistance profiles of the surface water. Pairs of samples were collected biweekly on four dates from two different locations, one about 800 m after the WWTP effluents and the other 10 km downstream. Taxonomic classification revealed the dominance of Pseudomonodota and Bacteriodota, notably the genera Flavobacterium, Aquirufa, Acidovorax, Polynucleobacter, and Limnohabitans. The taxonomic structure corresponded with both lentic and lotic freshwater habitats, with Flavobacterium exhibiting a significant decrease over the study period. Principal Coordinate Analysis revealed statistically significant differences in bacterial community composition between samples collected on different dates. Differential abundance analysis identified notable enrichment of Polynucleobacter and Limnohabitans. There were shifts within the enriched or depleted bacterial taxa between early and late sampling dates. High relative abundance of the genes erm(B), erm(F), mph(E), msr(E) (macrolides); tet(C), tet(O), tet(W), tet(Q) and tet(X) (tetracyclines); sul1 and sul2 (sulphonamides); and cfxA3, cfxA6 (beta-lactams) were detected, with trends of increased presence in the latest sampling dates and in the location closer to the WWTP. Of note, genes conferring resistance to carbapenems blaOXA-58 and blaIMP-33-like were identified. Co-occurrence analysis of ARGs and mobile genetic elements on putative plasmids showed few instances, and the estimated human health risk score (0.19) according to MetaCompare2.0 was low. In total, 29 metagenome-assembled genomes were recovered, with only a few harbouring ARGs. This study enhances our understanding of freshwater microbial community dynamics and antibiotic resistance profiles, highlighting the need for continued ARGs monitoring. Full article

(This article belongs to the Special Issue Water Microorganisms Associated with Human Health)

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23 pages, 2670 KiB

Open AccessArticle

Evaluation of Functional Properties of Some Lactic Acid Bacteria Strains for Probiotic Applications in Apiculture

by Adriana Cristina Urcan, Adriana Dalila Criste, Otilia Bobiș, Mihaiela Cornea-Cipcigan, Alexandru-Ioan Giurgiu and Daniel Severus Dezmirean

Microorganisms 2024, 12(6), 1249; https://doi.org/10.3390/microorganisms12061249 - 20 Jun 2024

Cited by 1 | Viewed by 1311

Abstract

This study evaluates the suitability of three lactic acid bacteria (LAB) strains—Lactiplantibacillus plantarum, Lactobacillus acidophilus, and Apilactobacillus kunkeei—for use as probiotics in apiculture. Given the decline in bee populations due to pathogens and environmental stressors, sustainable alternatives to conventional [...] Read more.

This study evaluates the suitability of three lactic acid bacteria (LAB) strains—Lactiplantibacillus plantarum, Lactobacillus acidophilus, and Apilactobacillus kunkeei—for use as probiotics in apiculture. Given the decline in bee populations due to pathogens and environmental stressors, sustainable alternatives to conventional treatments are necessary. This study aimed to assess the potential of these LAB strains in a probiotic formulation for bees through various in vitro tests, including co-culture interactions, biofilm formation, auto-aggregation, antioxidant activity, antimicrobial activity, antibiotic susceptibility, and resistance to high osmotic concentrations. This study aimed to assess both the individual effects of the strains and their combined effects, referred to as the LAB mix. Results indicated no mutual antagonistic activity among the LAB strains, demonstrating their compatibility with multi-strain probiotic formulations. The LAB strains showed significant survival rates under high osmotic stress and simulated gastrointestinal conditions. The LAB mix displayed enhanced biofilm formation, antioxidant activity, and antimicrobial efficacy against different bacterial strains. These findings suggest that a probiotic formulation containing these LAB strains could be used for a probiotic formulation, offering a promising approach to mitigating the negative effects of pathogens. Future research should focus on in vivo studies to validate the efficacy of these probiotic bacteria in improving bee health. Full article

(This article belongs to the Section Veterinary Microbiology)

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17 pages, 1990 KiB

Open AccessReview

The Function of Probiotics and Prebiotics on Canine Intestinal Health and Their Evaluation Criteria

by Junliang Xia, Yuling Cui, Yan Guo, Yuwen Liu, Baichuan Deng and Sufang Han

Microorganisms 2024, 12(6), 1248; https://doi.org/10.3390/microorganisms12061248 - 20 Jun 2024

Viewed by 1952

Abstract

Maintaining homeostasis within the intestinal microbiota is imperative for assessing the health status of hosts, and dysbiosis within the intestinal microbiota is closely associated with canine intestinal diseases. In recent decades, the modulation of canine intestinal health through probiotics and prebiotics has emerged [...] Read more.

Maintaining homeostasis within the intestinal microbiota is imperative for assessing the health status of hosts, and dysbiosis within the intestinal microbiota is closely associated with canine intestinal diseases. In recent decades, the modulation of canine intestinal health through probiotics and prebiotics has emerged as a prominent area of investigation. Evidence indicates that probiotics and prebiotics play pivotal roles in regulating intestinal health by modulating the intestinal microbiota, fortifying the epithelial barrier, and enhancing intestinal immunity. This review consolidates literature on using probiotics and prebiotics for regulating microbiota homeostasis in canines, thereby furnishing references for prospective studies and formulating evaluation criteria. Full article

(This article belongs to the Special Issue Shaping the Future of Probiotics: Novel Methodologies, Applications, and Mechanisms of Action, 2nd Edition)

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14 pages, 2625 KiB

Open AccessArticle

Whole-Genome Sequencing of Two Potentially Allelopathic Strains of Bacillus from the Roots of C. equisetifolia and Identification of Genes Related to Synthesis of Secondary Metabolites

by Ying Wang, Pan Chen, Qi Lin, Linzhi Zuo and Lei Li

Microorganisms 2024, 12(6), 1247; https://doi.org/10.3390/microorganisms12061247 - 20 Jun 2024

Viewed by 834

Abstract

The coastal Casuarina equisetifolia is the most common tree species in Hainan’s coastal protection forests. Sequencing the genomes of its allelopathic endophytes can allow the protective effects of these bacteria to be effectively implemented in protected forests. The goal of this study was [...] Read more.

The coastal Casuarina equisetifolia is the most common tree species in Hainan’s coastal protection forests. Sequencing the genomes of its allelopathic endophytes can allow the protective effects of these bacteria to be effectively implemented in protected forests. The goal of this study was to sequence the whole genomes of the endophytes Bacillus amyloliquefaciens and Bacillus aryabhattai isolated from C. equisetifolia root tissues. The results showed that the genome sizes of B. amyloliquefaciens and B. aryabhattai were 3.854 Mb and 5.508 Mb, respectively. The two strains shared 2514 common gene families while having 1055 and 2406 distinct gene families, respectively. The two strains had 283 and 298 allelochemical synthesis-associated genes, respectively, 255 of which were shared by both strains and 28 and 43 of which were unique to each strain, respectively. The genes were putatively involved in 11 functional pathways, including secondary metabolite biosynthesis, terpene carbon skeleton biosynthesis, biosynthesis of ubiquinone and other terpene quinones, tropane/piperidine and piperidine alkaloids biosynthesis, and phenylpropanoid biosynthesis. NQO1 and entC are known to be involved in the biosynthesis of ubiquinone and other terpenoid quinones, and rfbC/rmlC, rfbA/rmlA/rffH, and rfbB/rmlB/rffG are involved in the biosynthesis of polyketide glycan units. Among the B. aryabhattai-specific allelochemical synthesis-related genes, STE24 is involved in terpene carbon skeleton production, atzF and gdhA in arginine biosynthesis, and TYR in isoquinoline alkaloid biosynthesis. B. amyloliquefaciens and B. aryabhattai share the genes aspB, yhdR, trpA, trpB, and GGPS, which are known to be involved in the synthesis of carotenoids, indole, momilactones, and other allelochemicals. Additionally, these bacteria are involved in allelochemical synthesis via routes such as polyketide sugar unit biosynthesis and isoquinoline alkaloid biosynthesis. This study sheds light on the genetic basis of allelopathy in Bacillus strains associated with C. equisetifolia, highlighting the possible use of these bacteria in sustainable agricultural strategies for weed management and crop protection. Full article

(This article belongs to the Section Plant Microbe Interactions)

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17 pages, 4561 KiB

Open AccessArticle

Bacillus amyloliquefaciens LM-1 Affects Multiple Cell Biological Processes in Magnaporthe oryzae to Suppress Rice Blast

by Meiling Liang, Aiqing Feng, Congying Wang, Xiaoyuan Zhu, Jing Su, Zihan Xu, Jianyuan Yang, Wenjuan Wang, Kailing Chen, Bing Chen, Xiaopeng Lin, Jinqi Feng and Shen Chen

Microorganisms 2024, 12(6), 1246; https://doi.org/10.3390/microorganisms12061246 - 20 Jun 2024

Viewed by 987

Abstract

Magnaporthe oryzae, one of the most destructive rice pathogens, causes significant losses during the rice harvest every year. Bacillus amyloliquefaciens has been explored in many crops as a potential biocontrol agent. However, the mechanisms of B. amyloliquefaciens controled rice blast are not [...] Read more.

Magnaporthe oryzae, one of the most destructive rice pathogens, causes significant losses during the rice harvest every year. Bacillus amyloliquefaciens has been explored in many crops as a potential biocontrol agent. However, the mechanisms of B. amyloliquefaciens controled rice blast are not fully understood. Here, a biocontrol strain LM-1, isolated from a contaminated medium, was identified as B. amyloliquefaciens using morphological observation, physiological and biochemical tests, and 16S rDNA sequencing. LM-1 inhibited the growth and pathogenicity of M. oryzae and Bipolaris oryzae (Breda de Haan) Shoem. The mycelia of M. oryzae co-cultured with LM-1 were enlarged and broken by fluorescence microscopy using calcofluor white. LM-1 inhibited the mycelia of M. oryzae from producing conidia. Genes itu, srf, and fenB were detected in LM-1. Furthermore, the supernatant of LM-1 interfered with the appressorium formation of M. oryzae, blocked conidial cell death, and reduced autophagy degradation but did not affect the normal germination of rice seeds and seeding growth. Additionally, we observed hypersensitivity reactions, reactive oxygen species, and iron accumulation reduction in rice cells inoculated with supernatant. Our study reveals that LM-1 has a control effect on rice blast and affects cell wall integrity, sporulation, appressorium formation, cell death, and autophagy. Full article

(This article belongs to the Section Microbial Biotechnology)

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15 pages, 4331 KiB

Open AccessArticle

Functional Genes and Transcripts Indicate the Existent and Active Microbial Mercury-Methylating Community in Mangrove Intertidal Sediments of an Urbanized Bay

by Guofang Feng and Sanqiang Gong

Microorganisms 2024, 12(6), 1245; https://doi.org/10.3390/microorganisms12061245 - 20 Jun 2024

Viewed by 845

Abstract

Mercury (Hg) methylation in mangrove sediments can result in the accumulation of neurotoxic methylmercury (MeHg). Identification of Hg methyltransferase gene hgcA provides the means to directly characterize the microbial Hg-methylating consortia in environments. Hitherto, the microbial Hg-methylating community in mangrove sediments was scarcely [...] Read more.

Mercury (Hg) methylation in mangrove sediments can result in the accumulation of neurotoxic methylmercury (MeHg). Identification of Hg methyltransferase gene hgcA provides the means to directly characterize the microbial Hg-methylating consortia in environments. Hitherto, the microbial Hg-methylating community in mangrove sediments was scarcely investigated. An effort to assess the diversity and abundance of hgcA genes and transcripts and link them to Hg and MeHg contents was made in the mangrove intertidal sediments along the urbanized Shenzhen Bay, China. The hgcA genes and transcripts associated with Thermodesulfobacteria [mainly Geobacteraceae, Syntrophorhabdaceae, Desulfobacterales, and Desulfarculales (these four lineages were previously classified into the Deltaproteobacteria taxon)], as well as Euryarchaeota (mainly Methanomicrobia and Theionarchaea) dominated the hgcA-harboring communities, while Chloroflexota, Nitrospirota, Planctomycetota, and Lentisphaerota-like hgcA sequences accounted for a small proportion. The hgcA genes appeared in greater abundance and diversity than their transcript counterparts in each sampling site. Correlation analysis demonstrated that the MeHg content rather than Hg content significantly correlated with the structure of the existent/active hgcA-harboring community and the abundance of hgcA genes/transcripts. These findings provide better insights into the microbial Hg methylation drivers in mangrove sediments, which could be helpful for understanding the MeHg biotransformation therein. Full article

(This article belongs to the Special Issue Genomics of Marine and Aquatic Bacteria: A Focus on Novel Taxa, Diversity and Biotechnological Potential: 2nd Edition)

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12 pages, 6006 KiB

Open AccessArticle

HigA2 (Rv2021c) Is a Transcriptional Regulator with Multiple Regulatory Targets in Mycobacterium tuberculosis

by Mingyan Xu, Meikun Liu, Tong Liu, Xuemei Pan, Qi Ren, Tiesheng Han and Lixia Gou

Microorganisms 2024, 12(6), 1244; https://doi.org/10.3390/microorganisms12061244 - 20 Jun 2024

Viewed by 1131

Abstract

Toxin-antitoxin (TA) systems are the major mechanism for persister formation in Mycobacterium tuberculosis (Mtb). Previous studies found that HigBA2 (Rv2022c-Rv2021c), a predicted type II TA system of Mtb, could be activated for transcription in response to multiple stresses such as [...] Read more.

Toxin-antitoxin (TA) systems are the major mechanism for persister formation in Mycobacterium tuberculosis (Mtb). Previous studies found that HigBA2 (Rv2022c-Rv2021c), a predicted type II TA system of Mtb, could be activated for transcription in response to multiple stresses such as anti-tuberculosis drugs, nutrient starvation, endure hypoxia, acidic pH, etc. In this study, we determined the binding site of HigA2 (Rv2021c), which is located in the coding region of the upstream gene higB2 (Rv2022c), and the conserved recognition motif of HigA2 was characterized via oligonucleotide mutation. Eight binding sites of HigA2 were further found in the Mtb genome according to the conserved motif. RT-PCR showed that HigA2 can regulate the transcription level of all eight of these genes and three adjacent downstream genes. DNA pull-down experiments showed that twelve functional regulators sense external regulatory signals and may regulate the transcription of the HigBA2 system. Of these, Rv0903c, Rv0744c, Rv0474, Rv3124, Rv2603c, and Rv3583c may be involved in the regulation of external stress signals. In general, we identified the downstream target genes and possible upstream regulatory genes of HigA2, which paved the way for the illustration of the persistence establishment mechanism in Mtb. Full article

(This article belongs to the Special Issue Transcriptional Regulation in Bacteria)

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10 pages, 2182 KiB

Open AccessArticle

Parasitic Effects on the Congenital Transmission of Trypanosoma cruzi in Mother–Newborn Pairs

by Ana Gabriela Herrera Choque, Washington R. Cuna, Simona Gabrielli, Simonetta Mattiucci, Roberto Passera and Celeste Rodriguez

Microorganisms 2024, 12(6), 1243; https://doi.org/10.3390/microorganisms12061243 - 20 Jun 2024

Viewed by 865

Abstract

Maternal parasitemia and placental parasite load were examined in mother–newborn pairs to determine their effect on the congenital transmission of Trypanosoma cruzi. Parasitemia was qualitatively assessed in mothers and newborns by the microhematocrit test; parasite load was determined in the placental tissues [...] Read more.

Maternal parasitemia and placental parasite load were examined in mother–newborn pairs to determine their effect on the congenital transmission of Trypanosoma cruzi. Parasitemia was qualitatively assessed in mothers and newborns by the microhematocrit test; parasite load was determined in the placental tissues of transmitting and non-transmitting mothers by the detection of T. cruzi DNA and by histology. Compared to transmitter mothers, the frequency and prevalence of parasitemia were found to be increased in non-transmitter mothers; however, the frequency and prevalence of parasite load were higher among the transmitter mothers than among their non-transmitter counterparts. Additionally, serum levels of interferon (IFN)-γ were measured by an enzyme-linked immunosorbent assay (ELISA) in peripheral, placental, and cord blood samples. Median values of IFN-γ were significantly increased in the cord blood of uninfected newborns. The median IFN-γ values of transmitter and non-transmitter mothers were not significantly different; however, non-transmitter mothers had the highest total IFN-γ production among the group of mothers. Collectively, the results of this study suggest that the anti-T. cruzi immune response occurring in the placenta and cord is under the influence of the cytokines from the mother’s blood and results in the control of parasitemia in uninfected newborns. Full article

(This article belongs to the Special Issue Parasites and Infection: Strategies to Control, Diagnose, and Treat Parasitic Diseases)

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15 pages, 1413 KiB

Open AccessArticle

Searching for Chemical Agents Suppressing Substrate Microbiota in White-Rot Fungi Large-Scale Cultivation

by Audrius Maruška, Rūta Mickienė, Vilma Kaškonienė, Saulius Grigiškis, Mantas Stankevičius, Tomas Drevinskas, Olga Kornyšova, Enrica Donati, Nicola Tiso, Jurgita Mikašauskaitė-Tiso, Massimo Zacchini, Donatas Levišauskas, Ona Ragažinskienė, Kristina Bimbiraitė-Survilienė, Arvydas Kanopka and Gediminas Dūda

Microorganisms 2024, 12(6), 1242; https://doi.org/10.3390/microorganisms12061242 - 20 Jun 2024

Viewed by 1039

Abstract

Edible fungi are a valuable resource in the search for sustainable solutions to environmental pollution. Their ability to degrade organic pollutants, extract heavy metals, and restore ecological balance has a huge potential for bioremediation. They are also sustainable food resources. Edible fungi (basidiomycetes [...] Read more.

Edible fungi are a valuable resource in the search for sustainable solutions to environmental pollution. Their ability to degrade organic pollutants, extract heavy metals, and restore ecological balance has a huge potential for bioremediation. They are also sustainable food resources. Edible fungi (basidiomycetes or fungi from other divisions) represent an underutilized resource in the field of bioremediation. By maximizing their unique capabilities, it is possible to develop innovative approaches for addressing environmental contamination. The aim of the present study was to find selective chemical agents suppressing the growth of microfungi and bacteria, but not suppressing white-rot fungi, in order to perform large-scale cultivation of white-rot fungi in natural unsterile substrates and use it for different purposes. One application could be the preparation of a matrix composed of wooden sleeper (contaminated with PAHs) and soil for further hazardous waste bioremediation using white-rot fungi. In vitro microbiological methods were applied, such as, firstly, compatibility tests between bacteria and white-rot fungi or microfungi, allowing us to evaluate the interaction between different organisms, and secondly, the addition of chemicals on the surface of a Petri dish with a test strain of microorganisms of white-rot fungi, allowing us to determine the impact of chemicals on the growth of organisms. This study shows that white-rot fungi are not compatible to grow with several rhizobacteria or bacteria isolated from soil and bioremediated waste. Therefore, the impact of several inorganic materials, such as lime (hydrated form), charcoal, dolomite powder, ash, gypsum, phosphogypsum, hydrogen peroxide, potassium permanganate, and sodium hydroxide, was evaluated on the growth of microfungi (sixteen strains), white-rot fungi (three strains), and bacteria (nine strains) in vitro. Charcoal, dolomite powder, gypsum, and phosphogypsum did not suppress the growth either of microfungi or of bacteria in the tested substrate, and even acted as promoters of their growth. The effects of the other agents tested were strain dependent. Potassium permanganate could be used for bacteria and Candida spp. growth suppression, but not for other microfungi. Lime showed promising results by suppressing the growth of microfungi and bacteria, but it also suppressed the growth of white-rot fungi. Hydrogen peroxide showed strong suppression of microfungi, and even had a bactericidal effect on some bacteria, but did not have an impact on white-rot fungi. The study highlights the practical utility of using hydrogen peroxide up to 3% as an effective biota-suppressing chemical agent prior to inoculating white-rot fungi in the large-scale bioremediation of polluted substrates, or in the large-scale cultivation for mushroom production as a foodstuff. Full article

(This article belongs to the Section Environmental Microbiology)

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22 pages, 5205 KiB

Open AccessArticle

Sigma Factor Engineering in Actinoplanes sp. SE50/110: Expression of the Alternative Sigma Factor Gene ACSP50_0507 (σH^As) Enhances Acarbose Yield and Alters Cell Morphology

by Laura Schlüter, Tobias Busche, Laila Bondzio, Andreas Hütten, Karsten Niehaus, Susanne Schneiker-Bekel, Alfred Pühler and Jörn Kalinowski

Microorganisms 2024, 12(6), 1241; https://doi.org/10.3390/microorganisms12061241 - 20 Jun 2024

Viewed by 1298

Abstract

Sigma factors are transcriptional regulators that are part of complex regulatory networks for major cellular processes, as well as for growth phase-dependent regulation and stress response. Actinoplanes sp. SE50/110 is the natural producer of acarbose, an α-glucosidase inhibitor that is used in diabetes [...] Read more.

Sigma factors are transcriptional regulators that are part of complex regulatory networks for major cellular processes, as well as for growth phase-dependent regulation and stress response. Actinoplanes sp. SE50/110 is the natural producer of acarbose, an α-glucosidase inhibitor that is used in diabetes type 2 treatment. Acarbose biosynthesis is dependent on growth, making sigma factor engineering a promising tool for metabolic engineering. ACSP50_0507 is a homolog of the developmental and osmotic-stress-regulating Streptomyces coelicolor σH^Sc. Therefore, the protein encoded by ACSP50_0507 was named σH^As. Here, an Actinoplanes sp. SE50/110 expression strain for the alternative sigma factor gene ACSP50_0507 (sigH^As) achieved a two-fold increased acarbose yield with acarbose production extending into the stationary growth phase. Transcriptome sequencing revealed upregulation of acarbose biosynthesis genes during growth and at the late stationary growth phase. Genes that are transcriptionally activated by σH^As frequently code for secreted or membrane-associated proteins. This is also mirrored by the severely affected cell morphology, with hyperbranching, deformed and compartmentalized hyphae. The dehydrated cell morphology and upregulation of further genes point to a putative involvement in osmotic stress response, similar to its S. coelicolor homolog. The DNA-binding motif of σH^As was determined based on transcriptome sequencing data and shows high motif similarity to that of its homolog. The motif was confirmed by in vitro binding of recombinantly expressed σH^As to the upstream sequence of a strongly upregulated gene. Autoregulation of σH^As was observed, and binding to its own gene promoter region was also confirmed. Full article

(This article belongs to the Special Issue Transcriptional Regulation in Bacteria)

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16 pages, 6421 KiB

Open AccessArticle

Upper Limb Compartment Syndrome—An Extremely Rare Life-Threatening Complication of Cutaneous Anthrax

by Mihaela Pertea, Stefana Luca, Dan Cristian Moraru, Bogdan Veliceasa, Alexandru Filip, Oxana Madalina Grosu, Vladimir Poroch, Andrian Panuta, Catalina Mihaela Luca, Andrei Nicolae Avadanei and Sorinel Lunca

Microorganisms 2024, 12(6), 1240; https://doi.org/10.3390/microorganisms12061240 - 20 Jun 2024

Viewed by 1108

Abstract

(1) Background: Cutaneous anthrax is a disease caused by a Gram-positive bacillus, spore-forming Bacillus anthracis (BA). Cutaneous anthrax accounts for 95% of all anthrax cases, with mortality between 10–40% in untreated forms. The most feared complication, which can be life-threatening and is rarely [...] Read more.

(1) Background: Cutaneous anthrax is a disease caused by a Gram-positive bacillus, spore-forming Bacillus anthracis (BA). Cutaneous anthrax accounts for 95% of all anthrax cases, with mortality between 10–40% in untreated forms. The most feared complication, which can be life-threatening and is rarely encountered and described in the literature, is compartment syndrome. (2) Methods: We report a series of six cases of cutaneous anthrax from the same endemic area. In two of the cases, the disease was complicated by compartment syndrome. The systematic review was conducted according to systematic review guidelines, and the PubMed, Google Scholar, and Web of Science databases were searched for publications from 1 January 2008 to 31 December 2023. The keywords used were: “cutaneous anthrax” and “compartment syndrome by cutaneous anthrax”. (3) Results: For compartment syndrome, emergency surgical intervention for decompression was required, along with another three surgeries, with hospitalization between 21 and 23 days. In the systematic review, among the 37 articles, 29 did not contain cases focusing on compartment syndrome of the thoracic limb in cutaneous anthrax. The results were included in a Preferred Reporting Items for Systematic Reviews and Meta-Analysis (PRISMA) flow diagram. (4) Conclusions: Early recognition of the characteristic cutaneous lesions and compartment syndrome with early initiation of antibiotics and urgent surgical treatment is the lifesaving solution. Full article

(This article belongs to the Section Medical Microbiology)

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14 pages, 449 KiB

Open AccessArticle

Effect of Triticale Grain in Diets on Performance, Development of Gastrointestinal Tract and Microflora in Crop and Ileum of Broiler Chickens

by Patrycja Wróblewska, Tomasz Hikawczuk, Anna Szuba-Trznadel, Andrzej Wiliczkiewicz, Andrii Zinchuk, Agnieszka Rusiecka and Krystyna Laszki-Szcząchor

Microorganisms 2024, 12(6), 1239; https://doi.org/10.3390/microorganisms12061239 - 20 Jun 2024

Viewed by 799

Abstract

The purpose of the research was to determine the effect of the use of a diet containing 30% triticale grain. In an experiment lasting 28 days, 180 one-day Ross-308 chickens (sex ratio 1:1) with an average initial body weight in treatment of 44.6 [...] Read more.

The purpose of the research was to determine the effect of the use of a diet containing 30% triticale grain. In an experiment lasting 28 days, 180 one-day Ross-308 chickens (sex ratio 1:1) with an average initial body weight in treatment of 44.6 g were randomly assigned to 30 metabolic cages/replications, 6 birds in each. To compare the results between treatments, a one-way ANOVA was used with uneven replication numbers. The control group (I) received a standard diet containing maize and soybean meal. In the other treatments, 30% of different cereals were used: II—wheat, III—barley, and IV—triticale. Significant differences in body weight (BW) and feed conversion ratio (FCR) were observed on the 4th day of the life of broiler chickens (p < 0.05). Differences were determined between the control group (90.7 g BW and 1.32 kg of feed/kg BWG in the case of FCR) and birds receiving barley (93.0 g BW and 1.29 kg of feed/kg BWG in the case of FCR), compared to chickens fed diets with a 30% share of wheat grain (86.2 g BW and 1.53 kg feed/kg BWG in the case of FCR) and triticale (86.6 g BW and 1.53 kg feed/kg BWG in the case of FCR). Later, the differences in performance of birds between treatments did not occur (p > 0.05). In the nutrition of broiler chickens, control or 30% of the triticale diet caused a significant reduction (p < 0.01) of the number of Escherichia coli (E. coli) in the crop of broiler chickens (0 log cfu/g), compared to birds obtaining feed with 30% of wheat (1.78 log cfu/g). The diet containing triticale also reduced the number of E. coli (p < 0.05) within the ileum (0.78 log cfu/g) compared to chickens obtaining barley grain in the diet (2.12 log cfu/g). As a result of the use of triticale grain (p < 0.05), the total length of the bird intestines (199.64 cm) was compared to 30% of barley grain (209.76 cm). The increase in the length of the large intestine of broiler chickens in treatments was positively correlated (r = 0.613, p < 0.05) with the number of Lactobacillus sp. in the ileum. Triticale increased the pH in the crop of broilers chickens. The research results indicate that triticale, after longer storage, can be used in amounts of 30% of the diet without significant effect on the performance of broiler chickens, with a reduction in E. coli in crop in comparison with wheat and in ileum with barley. Full article

(This article belongs to the Section Veterinary Microbiology)

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21 pages, 1668 KiB

Open AccessArticle

The Usefulness of the C₂HEST Score in Predicting the Clinical Outcomes of COVID-19 in COPD and Non-COPD Cohorts

by Jakub Gawryś, Adrian Doroszko, Olgierd Dróżdż, Małgorzata Trocha, Damian Gajecki, Karolina Gawryś, Ewa Szahidewicz-Krupska, Maciej Rabczyński, Krzysztof Kujawa, Piotr Rola, Agata Stanek, Janusz Sokołowski, Marcin Madziarski, Ewa Anita Jankowska, Agnieszka Bronowicka-Szydełko, Dorota Bednarska-Chabowska, Edwin Kuźnik and Katarzyna Madziarska

Microorganisms 2024, 12(6), 1238; https://doi.org/10.3390/microorganisms12061238 - 20 Jun 2024

Viewed by 1314

Abstract

Patients with chronic obstructive pulmonary disease (COPD) infected with SARS-CoV-2 indicate a higher risk of severe COVID-19 course, which is defined as the need for hospitalization in the intensive care unit, mechanical ventilation, or death. However, simple tools to stratify the risk in [...] Read more.

Patients with chronic obstructive pulmonary disease (COPD) infected with SARS-CoV-2 indicate a higher risk of severe COVID-19 course, which is defined as the need for hospitalization in the intensive care unit, mechanical ventilation, or death. However, simple tools to stratify the risk in patients with COPD suffering from COVID-19 are lacking. The current study aimed to evaluate the predictive value of the C₂HEST score in patients with COPD. A retrospective analysis of medical records from 2184 patients hospitalized with COVID-19 at the University Hospital in Wroclaw from February 2020 to June 2021, which was previously used in earlier studies, assessed outcomes such as mortality during hospitalization, all-cause mortality at 3 and 6 months, non-fatal discharge, as well as adverse clinical incidents. This re-analysis specifically examines the outcomes using a COPD split. In the COPD group, 42 deaths were recorded, including 18 in-hospital deaths. In-hospital mortality rates at 3 and 6 months did not significantly differ among C₂HEST strata, nor did their impact on subsequent treatment. However, a notable association between the C₂HEST score and prognosis was observed in the non-COPD cohort comprising 2109 patients. The C₂HEST score’s predictive ability is notably lower in COPD patients compared to non-COPD subjects, with COPD itself indicating a high mortality risk. However, C₂HEST effectively identifies patients at high risk of cardiac complications during COVID-19, especially in non-COPD cases. Full article

(This article belongs to the Special Issue Advances in SARS-CoV-2 Infection—Third Edition)

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13 pages, 3026 KiB

Open AccessSystematic Review

Canine Bacterial Endocarditis: A Text Mining and Topics Modeling Analysis as an Approach for a Systematic Review

by Annalisa Previti, Vito Biondi, Annamaria Passantino, Mehmet Erman Or and Michela Pugliese

Microorganisms 2024, 12(6), 1237; https://doi.org/10.3390/microorganisms12061237 - 19 Jun 2024

Cited by 1 | Viewed by 967

Abstract

Bacterial endocarditis (BE) is a severe infection of the endocardium and cardiac valves caused by bacterial agents in dogs. Diagnosis of endocarditis is challenging due to the variety of clinical presentations and lack of definitive diagnostic tests in its early stages. This study [...] Read more.

Bacterial endocarditis (BE) is a severe infection of the endocardium and cardiac valves caused by bacterial agents in dogs. Diagnosis of endocarditis is challenging due to the variety of clinical presentations and lack of definitive diagnostic tests in its early stages. This study aims to provide a research literature analysis on BE in dogs based on text mining (TM) and topic analysis (TA) identifying dominant topics, summarizing their temporal trend, and highlighting any possible research gaps. A literature search was performed utilizing the Scopus^® database, employing keywords pertaining to BE to analyze papers published in English from 1990 to 2023. The investigation followed a systematic approach based on the PRISMA guidelines. A total of 86 records were selected for analysis following screening procedures and underwent descriptive statistics, TM, and TA. The findings revealed that the number of records published per year has increased in 2007 and 2021. TM identified the words with the highest term frequency-inverse document frequency (TF-IDF), and TA highlighted the main research areas, in the following order: causative agents, clinical findings and predisposing factors, case reports on endocarditis, outcomes and biomarkers, and infective endocarditis and bacterial isolation. The study confirms the increasing interest in BE but shows where further studies are needed. Full article

(This article belongs to the Section Veterinary Microbiology)

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13 pages, 2045 KiB

Open AccessArticle

Hunting Dynamics and Identification of Potentially Pathogenic Bacteria in European Fallow Deer (Dama dama) across Three Hunting Reserves in Western Romania

by Iulia-Maria Bucur, Alex Cristian Moza, Mirel Pop, Ileana Nichita, Cristina Mirabela Gaspar, Răzvan Cojocaru, Radu-Valentin Gros, Marius Valentin Boldea, Andreea Tirziu and Emil Tirziu

Microorganisms 2024, 12(6), 1236; https://doi.org/10.3390/microorganisms12061236 - 19 Jun 2024

Viewed by 667

Abstract

The study focused on the hunting practices and potentially pathogenic bacterial species among European fallow deer (Dama dama). Within a five-year period, three hunting grounds from Western Romania were examined. During this period, a total of 1881 deer were hunted, and [...] Read more.

The study focused on the hunting practices and potentially pathogenic bacterial species among European fallow deer (Dama dama). Within a five-year period, three hunting grounds from Western Romania were examined. During this period, a total of 1881 deer were hunted, and 240 samples were collected by rectal and nasal swabbing from 120 carcasses. Bacterial strains were identified utilizing bacteriological assays and the Vitek^® 2 Compact system. Notably, the Socodor hunting ground exhibited a significant difference in harvesting quotas between the bucks (Group M) and does/yearlings (Group F), favoring the latter. In the Chișineu Criș–Sălișteanca hunting ground, a likely correlation in harvesting quotas between the two groups was observed. The identified potentially pathogenic bacteria were Escherichia coli, Salmonella spp., Staphylococcus aureus, Listeria monocytogenes and Enterococcus faecium. These results highlight the importance of effectively managing the deer population and recognize the potential for Dama dama to spread zoonotic pathogens, emphasizing the necessity of adopting a One Health approach and maintaining ongoing surveillance of this game species’ population dynamics. Full article

(This article belongs to the Special Issue Domestic Animals and Wildlife Zoonotic Microorganisms)

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14 pages, 3191 KiB

Open AccessReview

The Role of Short-Chain Fatty Acids, Particularly Butyrate, in Oncological Immunotherapy with Checkpoint Inhibitors: The Effectiveness of Complementary Treatment with Clostridium butyricum 588

by Massimiliano Cazzaniga, Marco Cardinali, Francesco Di Pierro, Giordano Bruno Zonzini, Chiara Maria Palazzi, Aurora Gregoretti, Nicola Zerbinati, Luigina Guasti, Maria Rosaria Matera, Ilaria Cavecchia and Alexander Bertuccioli

Microorganisms 2024, 12(6), 1235; https://doi.org/10.3390/microorganisms12061235 - 19 Jun 2024

Viewed by 1606

Abstract

The discovery of immune checkpoints (CTLA-4, PD-1, and PD-L1) and their impact on the prognosis of oncological diseases have paved the way for the development of revolutionary oncological treatments. These treatments do not combat tumors with drugs “against” cancer cells but rather support [...] Read more.

The discovery of immune checkpoints (CTLA-4, PD-1, and PD-L1) and their impact on the prognosis of oncological diseases have paved the way for the development of revolutionary oncological treatments. These treatments do not combat tumors with drugs “against” cancer cells but rather support and enhance the ability of the immune system to respond directly to tumor growth by attacking the cancer cells with lymphocytes. It has now been widely demonstrated that the presence of an adequate immune response, essentially represented by the number of TILs (tumor-infiltrating lymphocytes) present in the tumor mass decisively influences the response to treatments and the prognosis of the disease. Therefore, immunotherapy is based on and cannot be carried out without the ability to increase the presence of lymphocytic cells at the tumor site, thereby limiting and nullifying certain tumor evasion mechanisms, particularly those expressed by the activity (under positive physiological conditions) of checkpoints that restrain the response against transformed cells. Immunotherapy has been in the experimental phase for decades, and its excellent results have made it a cornerstone of treatments for many oncological pathologies, especially when combined with chemotherapy and radiotherapy. Despite these successes, a significant number of patients (approximately 50%) do not respond to treatment or develop resistance early on. The microbiota, its composition, and our ability to modulate it can have a positive impact on oncological treatments, reducing side effects and increasing sensitivity and effectiveness. Numerous studies published in high-ranking journals confirm that a certain microbial balance, particularly the presence of bacteria capable of producing short-chain fatty acids (SCFAs), especially butyrate, is essential not only for reducing the side effects of chemoradiotherapy treatments but also for a better response to immune treatments and, therefore, a better prognosis. This opens up the possibility that favorable modulation of the microbiota could become an essential complementary treatment to standard oncological therapies. This brief review aims to highlight the key aspects of using precision probiotics, such as Clostridium butyricum, that produce butyrate to improve the response to immune checkpoint treatments and, thus, the prognosis of oncological diseases. Full article

(This article belongs to the Section Gut Microbiota)

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24 pages, 7844 KiB

Open AccessArticle

Diagnostic Performance of a Molecular Assay in Synovial Fluid Targeting Dominant Prosthetic Joint Infection Pathogens

by Jiyoung Lee, Eunyoung Baek, Hyesun Ahn, Heechul Park, Suchan Lee and Sunghyun Kim

Microorganisms 2024, 12(6), 1234; https://doi.org/10.3390/microorganisms12061234 - 19 Jun 2024

Viewed by 1003

Abstract

Prosthetic joint infection (PJI) is one of the most serious complications of joint replacement surgery among orthopedic surgeries and occurs in 1 to 2% of primary surgeries. Additionally, the cause of PJIs is mostly bacteria from the Staphylococcus species, accounting for more than [...] Read more.

Prosthetic joint infection (PJI) is one of the most serious complications of joint replacement surgery among orthopedic surgeries and occurs in 1 to 2% of primary surgeries. Additionally, the cause of PJIs is mostly bacteria from the Staphylococcus species, accounting for more than 98%, while fungi cause PJIs in only 1 to 2% of cases and can be difficult to manage. The current gold-standard microbiological method of culturing synovial fluid is time-consuming and produces false-negative and -positive results. This study aimed to identify a novel, accurate, and convenient molecular diagnostic method. The DreamDX primer–hydrolysis probe set was designed for the pan-bacterial and pan-fungal detection of DNA from pathogens that cause PJIs. The sensitivity and specificity of DreamDX primer–hydrolysis probes were 88.89% (95% CI, 56.50–99.43%) and 97.62% (95% CI, 87.68–99.88%), respectively, compared with the microbiological method of culturing synovial fluid, and receiver operating characteristic (ROC) area under the curve (AUC) was 0.9974 (*** p < 0.0001). It could be concluded that the DreamDX primer–hydrolysis probes have outstanding potential as a molecular diagnostic method for identifying the causative agents of PJIs, and that host inflammatory markers are useful as adjuvants in the diagnosis of PJIs. Full article

(This article belongs to the Special Issue Molecular Techniques, Novel Biomarkers and Coagulation-Based Methods in the Diagnosis of Periprosthetic Joint Infections)

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14 pages, 2633 KiB

Open AccessArticle

Swine Colibacillosis: Analysis of the Gut Bacterial Microbiome

by Wanli Sha, Emad Beshir Ata, Man Yan, Zhijie Zhang and Honggang Fan

Microorganisms 2024, 12(6), 1233; https://doi.org/10.3390/microorganisms12061233 - 19 Jun 2024

Viewed by 915

Abstract

This study aimed to evaluate the disruption of the swine gut microbiota and histopathological changes caused by infection with enterotoxigenic E. coli. Fecal samples were collected from piglets suffering from diarrhea post-recovery and healthy animals. Intestinal tissues were collected for histopathological changes. [...] Read more.

This study aimed to evaluate the disruption of the swine gut microbiota and histopathological changes caused by infection with enterotoxigenic E. coli. Fecal samples were collected from piglets suffering from diarrhea post-recovery and healthy animals. Intestinal tissues were collected for histopathological changes. The results revealed histopathological changes mainly in the ileum of the infected animals compared to those in the ileum of the control and recovered animals. The operational taxonomic units (OTUs) revealed that the E. coli diarrheal group exhibited the highest bacterial richness. Principal coordinate analysis (PCoA) corroborated the presence of dysbiosis in the gut microbiota following E. coli-induced diarrhea. While the normal control and infected groups displayed slight clustering, the recovery group formed a distinct cluster with a distinct flora. Bacteroidetes, Firmicutes, and Fusobacteria were the dominant phyla in both the healthy and recovered piglets and in the diarrheal group. LEfSe and the associated LDA score analysis revealed that the recovered group exhibited dominance of the phyla Euryarchaeota and Bacteroidota, while groups N and I showed dominance of the phyla Firmicutes and Fusobacteriota, respectively. The LDA scores highlighted a significant expression of the Muribaculacea family in group R. The obtained findings will help in understanding the microbiome during swine colibacillosis, which will support control of the outbreaks. Full article

(This article belongs to the Special Issue State-of-the-Art Veterinary Microbiology in China (2023, 2024))

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6 pages, 877 KiB

Open AccessOpinion

The Enigma of NTH2 Gene in Yeasts

by Sergi Maicas, Ruth Sánchez-Fresneda, Francisco Solano and Juan-Carlos Argüelles

Microorganisms 2024, 12(6), 1232; https://doi.org/10.3390/microorganisms12061232 - 19 Jun 2024

Viewed by 818

Abstract

The enzymatic hydrolysis of the non-reducing disaccharide trehalose in yeasts is carried out by trehalase, a highly specific

α

–glucosidase. Two types of such trehalase activity are present in yeasts, and are referred to as neutral and acid enzymes. They are encoded by [...] Read more.

The enzymatic hydrolysis of the non-reducing disaccharide trehalose in yeasts is carried out by trehalase, a highly specific

α

–glucosidase. Two types of such trehalase activity are present in yeasts, and are referred to as neutral and acid enzymes. They are encoded by distinct genes (NTH1 and ATH1, respectively) and exhibit strong differences in their biochemical and physiological properties as well as different subcellular location and regulatory mechanisms. Whereas a single gene ATH1 codes for acid trehalase, the genome of some yeasts appears to predict the existence of a second redundant neutral trehalase, encoded by the NTH2 gene, a paralog of NTH1. In S. cerevisiae the corresponding two proteins share 77% amino acid identity, leading to the suggestion that NTH2 codes for a functional trehalase activity. However, Nth2p lacks any measurable neutral trehalase activity and disruption of NTH2 gene has no effect on this activity compared to a parental strain. Likewise, single nth1

Δ

and double nth1

Δ

/nth2

Δ

null mutants display no detectable neutral activity. Furthermore, disruption of NTH2 does not cause any apparent phenotype apart from a slight involvement in thermotolerance. To date, no evidence of a duplicated NTH gene has been recorded in other archetypical yeasts, like C. albicans or C. parapsilosis, and a possible regulatory mechanism of Nth2p remains unknown. Therefore, although genomic analysis points to the existence, in some yeasts, of two distinct genes encoding trehalase activities, the large body of biochemical and physiological evidence gathered from NTH2 gene does not support this proposal. Indeed, much more experimental evidence would be necessary to firmly validate this hypothesis. Full article

(This article belongs to the Section Molecular Microbiology and Immunology)

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15 pages, 3530 KiB

Open AccessArticle

Presence and Persistence of ESKAPEE Bacteria before and after Hospital Wastewater Treatment

by Miguel Galarde-López, Maria Elena Velazquez-Meza, Elizabeth Ernestina Godoy-Lozano, Berta Alicia Carrillo-Quiroz, Patricia Cornejo-Juárez, Alejandro Sassoé-González, Alfredo Ponce-de-León, Pedro Saturno-Hernández and Celia Mercedes Alpuche-Aranda

Microorganisms 2024, 12(6), 1231; https://doi.org/10.3390/microorganisms12061231 - 19 Jun 2024

Viewed by 1419

Abstract

The metagenomic surveillance of antimicrobial resistance in wastewater has been suggested as a methodological tool to characterize the distribution, status, and trends of antibiotic-resistant bacteria. In this study, a cross-sectional collection of samples of hospital-associated raw and treated wastewater were obtained from February [...] Read more.

The metagenomic surveillance of antimicrobial resistance in wastewater has been suggested as a methodological tool to characterize the distribution, status, and trends of antibiotic-resistant bacteria. In this study, a cross-sectional collection of samples of hospital-associated raw and treated wastewater were obtained from February to March 2020. Shotgun metagenomic sequencing and bioinformatic analysis were performed to characterize bacterial abundance and antimicrobial resistance gene analysis. The main bacterial phyla found in all the samples were as follows: Proteobacteria, Bacteroides, Firmicutes, and Actinobacteria. At the species level, ESKAPEE bacteria such as E. coli relative abundance decreased between raw and treated wastewater, but S. aureus, A. baumannii, and P. aeruginosa increased, as did the persistence of K. pneumoniae in both raw and treated wastewater. A total of 172 different ARGs were detected; bla_OXA, bla_VEB, bla_KPC, bla_GES, mphE, mef, erm, msrE, AAC(6′), ant(3″), aadS, lnu, PBP-2, dfrA, vanA-G, tet, and sul were found at the highest abundance and persistence. This study demonstrates the ability of ESKAPEE bacteria to survive tertiary treatment processes of hospital wastewater, as well as the persistence of clinically important antimicrobial resistance genes that are spreading in the environment. Full article

(This article belongs to the Section Environmental Microbiology)

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14 pages, 1555 KiB

Open AccessArticle

Nisin Inhibition of Gram-Negative Bacteria

by Adam M. Charest, Ethan Reed, Samantha Bozorgzadeh, Lorenzo Hernandez, Natalie V. Getsey, Liam Smith, Anastasia Galperina, Hadley E. Beauregard, Hailey A. Charest, Mathew Mitchell and Margaret A. Riley

Microorganisms 2024, 12(6), 1230; https://doi.org/10.3390/microorganisms12061230 - 19 Jun 2024

Cited by 2 | Viewed by 2230

Abstract

Aims: This study investigates the activity of the broad-spectrum bacteriocin nisin against a large panel of Gram-negative bacterial isolates, including relevant plant, animal, and human pathogens. The aim is to generate supportive evidence towards the use/inclusion of bacteriocin-based therapeutics and open avenues for [...] Read more.

Aims: This study investigates the activity of the broad-spectrum bacteriocin nisin against a large panel of Gram-negative bacterial isolates, including relevant plant, animal, and human pathogens. The aim is to generate supportive evidence towards the use/inclusion of bacteriocin-based therapeutics and open avenues for their continued development. Methods and Results: Nisin inhibitory activity was screened against a panel of 575 strains of Gram-negative bacteria, encompassing 17 genera. Nisin inhibition was observed in 309 out of 575 strains, challenging the prevailing belief that nisin lacks effectiveness against Gram-negative bacteria. The genera Acinetobacter, Helicobacter, Erwinia, and Xanthomonas exhibited particularly high nisin sensitivity. Conclusions: The findings of this study highlight the promising potential of nisin as a therapeutic agent for several key Gram-negative plant, animal, and human pathogens. These results challenge the prevailing notion that nisin is less effective or ineffective against Gram-negative pathogens when compared to Gram-positive pathogens and support future pursuits of nisin as a complementary therapy to existing antibiotics. Significance and Impact of Study: This research supports further exploration of nisin as a promising therapeutic agent for numerous human, animal, and plant health applications, offering a complementary tool for infection control in the face of multidrug-resistant bacteria. Full article

(This article belongs to the Special Issue The Potential of Antimicrobial Activity and Antibiofilm Activity of Bacteriocins)

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16 pages, 4428 KiB

Open AccessArticle

Spatial Chromosome Organization and Adaptation of Escherichia coli under Heat Stress

by Xu-Ting Wang and Bin-Guang Ma

Microorganisms 2024, 12(6), 1229; https://doi.org/10.3390/microorganisms12061229 - 19 Jun 2024

Viewed by 1081

Abstract

The spatial organization of bacterial chromosomes is crucial for cellular functions. It remains unclear how bacterial chromosomes adapt to high-temperature stress. This study delves into the 3D genome architecture and transcriptomic responses of Escherichia coli under heat-stress conditions to unravel the intricate interplay [...] Read more.

The spatial organization of bacterial chromosomes is crucial for cellular functions. It remains unclear how bacterial chromosomes adapt to high-temperature stress. This study delves into the 3D genome architecture and transcriptomic responses of Escherichia coli under heat-stress conditions to unravel the intricate interplay between the chromosome structure and environmental cues. By examining the role of macrodomains, chromosome interaction domains (CIDs), and nucleoid-associated proteins (NAPs), this work unveils the dynamic changes in chromosome conformation and gene expression patterns induced by high-temperature stress. It was observed that, under heat stress, the short-range interaction frequency of the chromosomes decreased, while the long-range interaction frequency of the Ter macrodomain increased. Furthermore, two metrics, namely, Global Compactness (GC) and Local Compactness (LC), were devised to measure and compare the compactness of the chromosomes based on their 3D structure models. The findings in this work shed light on the molecular mechanisms underlying thermal adaptation and chromosomal organization in bacterial cells, offering valuable insights into the complex inter-relationships between environmental stimuli and genomic responses. Full article

(This article belongs to the Special Issue Molecular Mechanism of Microbial Heat Adaptation)

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15 pages, 4713 KiB

Open AccessArticle

A Genomics-Based Discovery of Secondary Metabolite Biosynthetic Gene Clusters in the Potential Novel Strain Streptomyces sp. 21So2-11 Isolated from Antarctic Soil

by Yu Du, Wei Han, Puyu Hao, Yongqiang Hu, Ting Hu and Yinxin Zeng

Microorganisms 2024, 12(6), 1228; https://doi.org/10.3390/microorganisms12061228 - 19 Jun 2024

Viewed by 1510

Abstract

Streptomyces species are attractive sources of secondary metabolites that serve as major sources of antibiotics and other drugs. In this study, genome mining was used to determine the biosynthetic potential of Streptomyces sp. 21So2-11 isolated from Antarctic soil. 16S rRNA gene sequencing revealed [...] Read more.

Streptomyces species are attractive sources of secondary metabolites that serve as major sources of antibiotics and other drugs. In this study, genome mining was used to determine the biosynthetic potential of Streptomyces sp. 21So2-11 isolated from Antarctic soil. 16S rRNA gene sequencing revealed that this strain is most closely related to Streptomyces drozdowiczii NBRC 101007^T, with a similarity of 98.02%. Genome comparisons based on average nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH) showed that strain 21So2-11 represents a novel species of the genus Streptomyces. In addition to a large number of genes related to environmental adaptation and ecological function, a total of 28 putative biosynthetic gene clusters (BGCs) responsible for the biosynthesis of known and/or novel secondary metabolites, including terpenes, lantipeptides, polyketides, nonribosomal peptides, RiPPs and siderophores, were detected in the genome of strain 21So2-11. In addition, a total of 1456 BGCs were predicted to contribute to the biosynthesis of more than 300 secondary metabolites based on the genomes of 47 Streptomyces strains originating from polar regions. The results indicate the potential of Streptomyces sp. 21So2-11 for bioactive secondary metabolite production and are helpful for understanding bacterial adaptability and ecological function in cold terrestrial environments. Full article

(This article belongs to the Section Microbial Biotechnology)

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11 pages, 2333 KiB

Open AccessArticle

The Description and Analysis of the Complete Genome of Dermacoccus barathri FBCC-B549 Strain

by Yeha Kim, Hyaekang Kim, Jina Kim, Ji-Hye Han, Eu Jin Chung, Seung Won Nam, Miyoung Shin and Woori Kwak

Microorganisms 2024, 12(6), 1227; https://doi.org/10.3390/microorganisms12061227 - 18 Jun 2024

Viewed by 1101

Abstract

Dermacoccus barathri is the first reported pathogen within the Dermacoccus genus to cause a catheter-related bloodstream infection, which occurred in 2015. In this study, the complete genome assembly of Dermacoccus barathri was constructed, and the complete genome of Dermacoccus barathri FBCC-B549 consists of [...] Read more.

Dermacoccus barathri is the first reported pathogen within the Dermacoccus genus to cause a catheter-related bloodstream infection, which occurred in 2015. In this study, the complete genome assembly of Dermacoccus barathri was constructed, and the complete genome of Dermacoccus barathri FBCC-B549 consists of a single chromosome (3,137,745 bp) without plasmids. The constructed genome of D. barathri was compared with those of two closely related species within the Dermacoccus genus. D. barathri exhibited a pattern similar to Dermacoccus abyssi in terms of gene clusters and synteny analysis. Contrary to previous studies, biosynthetic gene cluster (BGC) analysis for predicting secondary metabolites revealed the presence of the LAP biosynthesis pathway in the complete genome of D. barathri, predicting the potential synthesis of the secondary metabolite plantazolicin. Furthermore, an analysis to investigate the potential pathogenicity of D. barathri did not reveal any antibiotic resistance genes; however, nine virulence factors were identified in the Virulence Factor Database (VFDB). According to these matching results in the VFDB, despite identifying a few factors involved in biofilm formation, further research is required to determine the actual impact of D. barathri on pathogenicity. The complete genome of D. barathri is expected to serve as a valuable resource for future studies on D. barathri, which currently lack sufficient genomic sequence information. Full article

(This article belongs to the Section Microbial Biotechnology)

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13 pages, 2627 KiB

Open AccessArticle

The Utilization of Bacillus subtilis to Design Environmentally Friendly Living Paints with Anti-Mold Properties

by Yuval Dorfan, Avichay Nahami, Yael Morris, Benny Shohat and Ilana Kolodkin-Gal

Microorganisms 2024, 12(6), 1226; https://doi.org/10.3390/microorganisms12061226 - 18 Jun 2024

Viewed by 1271

Abstract

The anti-fungal properties of the probiotic bacterium Bacillus subtilis have been studied extensively in agriculture and ecology, but their applications in the built environment remain to be determined. Our work aims to utilize this biological component to introduce new diverse anti-mold properties into [...] Read more.

The anti-fungal properties of the probiotic bacterium Bacillus subtilis have been studied extensively in agriculture and ecology, but their applications in the built environment remain to be determined. Our work aims to utilize this biological component to introduce new diverse anti-mold properties into paint. “Mold” refers to the ubiquitous fungal species that generate visible multicellular filaments commonly found in household dust. The development of mold leads to severe health problems for occupants, including allergic response, hypersensitivity pneumonitis, and asthma, which have significant economic and clinical outcomes. We here demonstrate the robust effect of a commercial paint enhanced with Bacillus subtilis cells against the common mold agent, Aspergillus niger, and identify three biosynthetic clusters essential for this effect. Our results lay the foundation for bio-convergence and synthetic biology approaches to introduce renewable and environmentally friendly bio-anti-fungal agents into the built environment. Full article

(This article belongs to the Special Issue An Update on Bacillus)

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15 pages, 2185 KiB

Open AccessArticle

Periodontal Inflammation and Dysbiosis Relate to Microbial Changes in the Gut

by Angela R. Kamer, Smruti Pushalkar, Babak Hamidi, Malvin N. Janal, Vera Tang, Kumar Raghava Chowdary Annam, Leena Palomo, Deepthi Gulivindala, Lidia Glodzik and Deepak Saxena

Microorganisms 2024, 12(6), 1225; https://doi.org/10.3390/microorganisms12061225 - 18 Jun 2024

Cited by 2 | Viewed by 1316

Abstract

Periodontal disease (PerioD) is a chronic inflammatory disease of dysbiotic etiology. Animal models and few human data showed a relationship between oral bacteria and gut dysbiosis. However, the effect of periodontal inflammation and subgingival dysbiosis on the gut is unknown. We hypothesized that [...] Read more.

Periodontal disease (PerioD) is a chronic inflammatory disease of dysbiotic etiology. Animal models and few human data showed a relationship between oral bacteria and gut dysbiosis. However, the effect of periodontal inflammation and subgingival dysbiosis on the gut is unknown. We hypothesized that periodontal inflammation and its associated subgingival dysbiosis contribute to gut dysbiosis even in subjects free of known gut disorders. We evaluated and compared elderly subjects with Low and High periodontal inflammation (assessed by Periodontal Inflamed Surface Area (PISA)) for stool and subgingival derived bacteria (assayed by 16S rRNA sequencing). The associations between PISA/subgingival dysbiosis and gut dysbiosis and bacteria known to produce short-chain fatty acid (SCFA) were assessed. LEfSe analysis showed that, in Low PISA, species belonging to Lactobacillus, Roseburia, and Ruminococcus taxa and Lactobacillus zeae were enriched, while species belonging to Coprococcus, Clostridiales, and Atopobium were enriched in High PISA. Regression analyses showed that PISA associated with indicators of dysbiosis in the gut mainly reduced abundance of SCFA producing bacteria (Radj = −0.38, p = 0.03). Subgingival bacterial dysbiosis also associated with reduced levels of gut SCFA producing bacteria (Radj = −0.58, p = 0.002). These results suggest that periodontal inflammation and subgingival microbiota contribute to gut bacterial changes. Full article

(This article belongs to the Special Issue Intestine as a Hub for Host-Microbe Interactions and Its Impact on Local and Systemic Health)

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8 pages, 600 KiB

Open AccessCommunication

Impact of COVID-19 Restrictions on Incidence of Enteropathogenic Bacteria, Virus, and Parasites in Denmark: A National, Register-Based Study

by Kumanan Rune Nanthan, Eva Plantener, John Coia, Jørgen Engberg, Leif Percival Andersen, Ea Marmolin, Gitte Nyvang Hartmeyer, Hans Linde Nielsen, Christen Rune Stensvold, Anne Line Engsbro, Bente Olesen, Lars Lemming and Ming Chen

Microorganisms 2024, 12(6), 1224; https://doi.org/10.3390/microorganisms12061224 - 18 Jun 2024

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Abstract

Diarrheal diseases caused by enteric pathogens are a significant public health concern. It is widely considered that close contact between persons, poor hygiene, and consumption of contaminated food are the primary causes of gastroenteritis. Clinical microbiology laboratory observations indicate that the incidence of [...] Read more.

Diarrheal diseases caused by enteric pathogens are a significant public health concern. It is widely considered that close contact between persons, poor hygiene, and consumption of contaminated food are the primary causes of gastroenteritis. Clinical microbiology laboratory observations indicate that the incidence of enteropathogenic microorganisms may have been reduced in Denmark during the COVID-19 pandemic. All Departments of Clinical Microbiology in Denmark provided data on the monthly incidence of Salmonella spp., Escherichia coli, Campylobacter spp., Clostridioides difficile, Norovirus GI+GII, Giardia duodenalis, and Cryptosporidium from March 2018 to February 2021. The data were divided into three periods as follows: Control Period 1 (March 2018 to February 2019); Control Period 2 (March 2019 to February 2020); and the Restriction (pandemic) Period (March 2020 to February 2021). The incidences of pathogenic Salmonella spp.-, Escherichia coli-, and Campylobacter spp.-positive samples decreased by 57.3%, 48.1%, and 32.9%, respectively, during the restriction period. No decrease in C. difficile was observed. Norovirus GI+GII-positive samples decreased by 85.6%. Giardia duodenalis-positive samples decreased by 66.2%. Cryptosporidium species decreased by 59.6%. This study demonstrates a clear decrease in the incidence of enteropathogenic bacteria (except for C. difficile), viruses, and parasites during the SARS-CoV-2 restriction period in Denmark. Full article

(This article belongs to the Section Public Health Microbiology)

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17 pages, 3726 KiB

Open AccessArticle

Development of Multiplex RT qPCR Assays for Simultaneous Detection and Quantification of Faecal Indicator Bacteria in Bathing Recreational Waters

by Marina Carrasco-Acosta and Pilar Garcia-Jimenez

Microorganisms 2024, 12(6), 1223; https://doi.org/10.3390/microorganisms12061223 - 18 Jun 2024

Viewed by 1067

Abstract

In this study, we designed and validated in silico and experimentally a rapid, sensitive, and specific multiplex RT qPCR for the detection and quantification of faecal indicator bacteria (FIB) used as microbiological references in marine bathing water regulations (Escherichia coli and intestinal [...] Read more.

In this study, we designed and validated in silico and experimentally a rapid, sensitive, and specific multiplex RT qPCR for the detection and quantification of faecal indicator bacteria (FIB) used as microbiological references in marine bathing water regulations (Escherichia coli and intestinal enterococci). The 16S rRNA gene was used to quantify group-specific enterococci and Escherichia/Shigella and species-specific such as Enterococcus faecalis and E. faecium. Additionally, a ybbW gene encoding allantoin transporter protein was used to detect E. coli. An assessment of marine coastal systems (i.e., marine water and sediment) revealed that intestinal enterococci were the predominant group compared to Escherichia/Shigella. The low contribution of E. faecalis to the intestinal enterococci group was reported. As E. faecalis and E. faecium were reported at low concentrations, it is assumed that other enterococci of faecal origin are contributing to the high gene copy number of this group-specific enterococci. Moreover, low 16S rRNA gene copy numbers with respect to E. faecalis and E. faecium were reported in seawater compared to marine sediment. We conclude that marine sediments can affect the quantification of FIBs included in bathing water regulations. Valuing the quality of the marine coastal system through sediment monitoring is recommended. Full article

(This article belongs to the Collection Advances in Public Health Microbiology)

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