Microorganisms

12 pages, 4705 KiB

Open AccessCommunication

Biofilms on Plastic Debris and the Microbiome

by Yiqian Qian, Lingfeng Huang, Pei Yan, **nhong Wang and Yuanrong Luo

Microorganisms 2024, 12(7), 1362; https://doi.org/10.3390/microorganisms12071362 - 2 Jul 2024

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Plastic pollution has become a global environmental problem, and the large number of microorganisms attached to plastic debris in the environment has become a hot topic due to their rapid response to pollutants and environmental changes. In this study, we used high-throughput sequencing [...] Read more.

Plastic pollution has become a global environmental problem, and the large number of microorganisms attached to plastic debris in the environment has become a hot topic due to their rapid response to pollutants and environmental changes. In this study, we used high-throughput sequencing to investigate the microbial community structure of and explore the metagenome in the biofilm of two types of plastic debris, polystyrene (PS) and polyethylene terephthalate (PET), and compared them with a water sample collected at the sampling site. The phylum Proteobacteria dominated both the PET and PS samples, at 93.43% and 65.95%, respectively. The metagenome data indicated that the biofilm is enriched with a number of hydrocarbon (petroleum, microplastics, etc.) degrading genes. Our results show that the type of plastic determined the bacterial community structure of the biofilm, while the environment had relatively little effect. Full article

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

14 pages, 308 KiB

Open AccessReview

Overview of the Efficacy of Using Probiotics for Neurosurgical and Potential Neurosurgical Patients

by Sabina Fijan and Tomaž Šmigoc

Microorganisms 2024, 12(7), 1361; https://doi.org/10.3390/microorganisms12071361 - 2 Jul 2024

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Abstract

This review delves into the emerging field of the gut microbiota–brain axis, emphasizing its bidirectional communication and implications for neurological health, particularly in trauma and neurosurgery. While disruptions in this axis can lead to dysbiosis and hinder neurological recovery, recent studies have highlighted [...] Read more.

This review delves into the emerging field of the gut microbiota–brain axis, emphasizing its bidirectional communication and implications for neurological health, particularly in trauma and neurosurgery. While disruptions in this axis can lead to dysbiosis and hinder neurological recovery, recent studies have highlighted the therapeutic potential of interventions like probiotics in targeting this axis. This review aims to focus on the efficacy of probiotic supplementation to support the gut microbiota–brain axis in trauma, neurosurgery, or pain based on the current clinical trials to assess the complex interplays among probiotics, the gut microbiota, and the central nervous system (CNS). This comprehensive literature review identified 10 relevant publications on probiotic interventions for various neurosurgical conditions across multiple countries. These studies demonstrated diverse outcomes, with significant improvements observed in gastrointestinal mobility, inflammatory responses, and infection rates, particularly in post-traumatic brain injury and spinal surgery. Probiotics also showed promise in mitigating antibiotic-associated diarrhea and modulating inflammatory cytokines. Despite the promising findings, the complex interplays among probiotics, the gut microbiota, and the central nervous system (CNS) call for cautious interpretation. Conflicting outcomes emphasize the need for better-designed trials to understand strain-specific and disease-specific effects accurately. In conclusion, probiotics offer a promising adjuvant therapy for neurosurgical patients, traumatic brain injuries, and post-spinal surgery. However, further well-designed randomized controlled trials are essential to elucidate the intricate relationship between microbiome-modulating interventions and the CNS via the gut microbiota–brain axis. Full article

(This article belongs to the Special Issue Interactions between Probiotics and Host)

22 pages, 3640 KiB

Open AccessArticle

Differential Resha** of Skin and Intestinal Microbiota by Stocking Density and Oxygen Availability in Farmed Gilthead Sea Bream (Sparus aurata): A Behavioral and Network-Based Integrative Approach

by Socorro Toxqui-Rodríguez, Paul George Holhorea, Fernando Naya-Català, Josep Àlvar Calduch-Giner, Ariadna Sitjà-Bobadilla, Carla Piazzon and Jaume Pérez-Sánchez

Microorganisms 2024, 12(7), 1360; https://doi.org/10.3390/microorganisms12071360 - 2 Jul 2024

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Abstract

Fish were kept for six weeks at three different initial stocking densities and water O₂ concentrations (low-LD, 8.5 kg/m³ and 95–70% O₂ saturation; medium-MD, 17 kg/m³ and 55–75% O₂ saturation; high-HD, 25 kg/m³ and 60–45% O₂ [...] Read more.

Fish were kept for six weeks at three different initial stocking densities and water O₂ concentrations (low-LD, 8.5 kg/m³ and 95–70% O₂ saturation; medium-MD, 17 kg/m³ and 55–75% O₂ saturation; high-HD, 25 kg/m³ and 60–45% O₂ saturation), with water temperature increasing from 19 °C to 26–27 °C. The improvement in growth performance with the decrease in stocking density was related to changes in skin and intestinal mucosal microbiomes. Changes in microbiome composition were higher in skin, with an increased abundance of Alteromonas and Massilia in HD fish. However, these bacteria genera were mutually exclusive, and Alteromonas abundance was related to a reactive behavior and systemic growth regulation via the liver Gh/Igf system, while Massilia was correlated to a proactive behavior and a growth regulatory transition towards muscle rather than liver. At the intestinal level, microbial abundance showed an opposite trend for two bacteria taxa, rendering in a low abundance of Reyranella and a high abundance of Prauserella in HD fish. This trend was correlated with up-regulated host gene expression, affecting the immune response, epithelial cell turnover, and abiotic stress response. Most of the observed responses are adaptive in nature, and they would serve to infer new welfare indicators for increased stress resilience. Full article

(This article belongs to the Special Issue New Methods in Microbial Research 4.0)

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12 pages, 58719 KiB

Open AccessArticle

Pathogenicity of Multidrug-Resistant Salmonella typhimurium Isolated from Ducks

by Yulin Xu, Zhitong Yu, Shaopeng Wu, Mengze Song, Lulu Cui, Shuhong Sun and Jiaqiang Wu

Microorganisms 2024, 12(7), 1359; https://doi.org/10.3390/microorganisms12071359 - 2 Jul 2024

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Abstract

Salmonella typhimurium (S. typhimurium) is one of the most common Salmonella serotypes in epidemiological surveys of poultry farms in recent years. It causes growth retardation, mortality, and significant economic losses. The extensive use of antibiotics has led to the emergence of multi-drug resistance [...] Read more.

Salmonella typhimurium (S. typhimurium) is one of the most common Salmonella serotypes in epidemiological surveys of poultry farms in recent years. It causes growth retardation, mortality, and significant economic losses. The extensive use of antibiotics has led to the emergence of multi-drug resistance (MDR) in Salmonella, which has become a significant global problem and long-term challenge. In this study, we investigated the prevalence and features of S. typhimurium strains in duck embryos and cloacal swabs from large-scale duck farms in Shandong, China, including drug resistance and virulence genes and the pathogenicity of an S. typhimurium strain by animal experiment. The results demonstrated that a total of 8 S. typhimurium strains were isolated from 13,621 samples. The drug resistance results showed that three of the eight S. typhimurium strains were MDR with the dominant resistance profile of CTX-DX-CTR-TE-AMX-AMP-CAZ. In particular, the virulence genes invA, hilA, pefA, rck, and sefA showed high positive rates. Based on the analysis of the biological characteristics of bacterial biofilm formation and mobility, a strain of S. typhimurium with the strongest biofilm formation ability, designated 22SD07, was selected for animal infection experiments with broiler ducklings. The results of animal experiments demonstrated that infection with 22SD07 reduced body weight and bursa index but increased heart and liver indexes compared to the control group. Histological examination revealed desquamation of the intestinal villous epithelium, the presence of large aggregates of lymphocytes, and a decrease in goblet cells following infection. Furthermore, the expression of IL-10 was significantly increased in the liver at 3 dpi, while TNF-α was significantly increased in the spleen at 7 dpi. The above results indicate that S. typhimurium may pose a potential threat to human health through the food chain. This helps us to understand the frequency and characteristics of S. typhimurium in duck farms and emphasizes the urgent need to strengthen and implement effective continuous monitoring to control its infection and transmission. Full article

(This article belongs to the Special Issue Bacterial Infections and Antimicrobial Resistance in Animals)

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22 pages, 7852 KiB

Open AccessArticle

Effects of Dietary Multi-Strain Probiotics on Growth Performance, Antioxidant Status, Immune Response, and Intestinal Microbiota of Hybrid Groupers (Epinephelus fuscoguttatus ♀ × E. lanceolatus ♂)

by Guangting **e, **aoying Chen, Yuwei Feng, Zhide Yu, Qiuqin Lu, Manfeng Li, Ziqi Ye, Heizhao Lin, Wei Yu and Hu Shu

Microorganisms 2024, 12(7), 1358; https://doi.org/10.3390/microorganisms12071358 - 2 Jul 2024

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Abstract

This study aims to examine the effects of the mixture of Bacillus cereus G1–11 and Exiguobacterium acetylicum G1–33, isolated from the gut of hybrid groupers (Epinephelus fuscoguttatus ♀ × E. lanceolatus ♂), on the host. The hybrid groupers were divided into a [...] Read more.

This study aims to examine the effects of the mixture of Bacillus cereus G1–11 and Exiguobacterium acetylicum G1–33, isolated from the gut of hybrid groupers (Epinephelus fuscoguttatus ♀ × E. lanceolatus ♂), on the host. The hybrid groupers were divided into a control (C, without any probiotics), B. cereus (BC, 10¹⁰ cfu/g), E. acetylicum (EA, 10⁸ cfu/g), compound (mix, a 1:1 mixture of B. cereus and E. acetylicum), and positive reference group (P, Lactobacillus acidophilus, 5 × 10⁸ cfu/L). Each group had four replicates, with 30 fish per replicate (53.30 ± 0.50 g), and were fed for 60 days. The results showed that adding probiotics to the feed significantly improved the weight gain, weight growth rate, specific growth rate, and digestive enzyme activities of hybrid groupers compared to the C group. The compound group was the most significant. In addition, composite probiotics added to feed significantly upregulated the expression levels of several growth-related genes in the liver and muscles. The activities of alkaline phosphatase, catalase, glutathione peroxidase, glutathione transferase, lysozyme, and total antioxidant capacity in the serum and liver were significantly influenced through mixed probiotic feeding. Moreover, the expression levels of several immune-related genes in the liver, spleen, and head kidney were significantly enhanced by adding single and mixed probiotics to feed, with the synergy of mixed probiotics being the best. An analysis of the gut microbiota showed that adding composite bacteria enhanced the richness and diversity of the gut microbiota, significantly increasing the relative abundance of potential probiotics (Cetobacterium and Microbacterium) while decreasing the presence of potential pathogens (Mycoplasma). Overall, our findings highlighted the efficacy of mixed probiotics (B. cereus and E. acetylicum) in enhancing growth performance, nutritional value of hybrid grouper feed, antioxidant capacity, immune response, and intestinal health, in finding the best combination of functional feed additives. Full article

(This article belongs to the Special Issue Aquatic Microorganisms and Their Application in Aquaculture)

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15 pages, 712 KiB

Open AccessReview

Endophytic Fungi for Crops Adaptation to Abiotic Stresses

by Adan Topiltzin Morales-Vargas, Varinia López-Ramírez, Cesar Álvarez-Mejía and Juan Vázquez-Martínez

Microorganisms 2024, 12(7), 1357; https://doi.org/10.3390/microorganisms12071357 - 2 Jul 2024

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Abstract

Endophytic fungi (EFs) have emerged as promising modulators of plant growth and stress tolerance in agricultural ecosystems. This review synthesizes the current knowledge on the role of EFs in enhancing the adaptation of crops to abiotic stress. Abiotic stresses, such as drought, salinity, [...] Read more.

Endophytic fungi (EFs) have emerged as promising modulators of plant growth and stress tolerance in agricultural ecosystems. This review synthesizes the current knowledge on the role of EFs in enhancing the adaptation of crops to abiotic stress. Abiotic stresses, such as drought, salinity, and extreme temperatures, pose significant challenges to crop productivity worldwide. EFs have shown remarkable potential in alleviating the adverse effects of these stresses. Through various mechanisms, including the synthesis of osmolytes, the production of stress-related enzymes, and the induction of plant defense mechanisms, EFs enhance plant resilience to abiotic stressors. Moreover, EFs promote nutrient uptake and modulate the hormonal balance in plants, further enhancing the stress tolerance of the plants. Recent advancements in molecular techniques have facilitated the identification and characterization of stress-tolerant EF strains, paving the way for their utilization in agricultural practices. Furthermore, the symbiotic relationship between EFs and plants offers ecological benefits, such as improved soil health and a reduced dependence on chemical inputs. However, challenges remain in understanding the complex interactions between EFs and host plants, as well as in scaling up their application in diverse agricultural systems. Future research should focus on elucidating the mechanisms underlying endophytic-fungal-mediated stress tolerance and develo** sustainable strategies for harnessing their potential in crop production. Full article

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

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11 pages, 3900 KiB

Open AccessArticle

Oral Microbiota Alterations in Subjects with SARS-CoV-2 Displaying Prevalence of the Opportunistic Fungal Pathogen Candida albicans

by Areej A. Alfaifi, Johanna B. Holm, Tristan W. Wang, Jonathan Lim, Timothy F. Meiller, Peter Rock, Ahmed S. Sultan and Mary Ann Jabra-Rizk

Microorganisms 2024, 12(7), 1356; https://doi.org/10.3390/microorganisms12071356 - 2 Jul 2024

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Abstract

The oral cavity remains an underappreciated site for SARS-CoV-2 infection despite the myriad of oral conditions in COVID-19 patients. Recently, SARS-CoV-2 was shown to replicate in the salivary gland cells causing tissue inflammation. Given the established association between inflammation and microbiome disruption, we [...] Read more.

The oral cavity remains an underappreciated site for SARS-CoV-2 infection despite the myriad of oral conditions in COVID-19 patients. Recently, SARS-CoV-2 was shown to replicate in the salivary gland cells causing tissue inflammation. Given the established association between inflammation and microbiome disruption, we comparatively profiled oral microbial differences at a metagenomic level in a cohort of hospitalized COVID-19 patients and matched healthy controls. Specifically, we aimed to evaluate colonization by the opportunistic fungal pathogen Candida albicans, the etiologic agent of oral candidiasis. Comprehensive shotgun metagenomic analysis indicated that, overall, COVID-19 patients exhibited significantly reduced bacterial and viral diversity/richness; we identified 12 differentially abundant bacterial species to be negatively associated with COVID-19, and the functional pathways of certain bacteria to be highly associated with COVID-19 status. Strikingly, C. albicans was recovered from approximately half of the COVID-19 subjects but not from any of the healthy controls. The prevalence of Candida is likely linked to immune hypo-dysregulation caused by COVID-19 favoring Candida proliferation, warranting investigations into the interplay between Candida and SARS-CoV2 and potential therapeutic approaches directed toward oral candidiasis. Collectively, our findings prompt a reassessment of oral opportunistic infection risks during COVID-19 disease and their potential long-term impacts on oral health. Full article

(This article belongs to the Special Issue Microbial Interactions including Candida concerning Health and Disease)

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14 pages, 3415 KiB

Open AccessArticle

Evaluation of the In Vitro Capacity of Anti-Human Cytomegalovirus Antibodies to Initiate Antibody-Dependent Cell Cytotoxicity

by Piera d’Angelo, Federica Zavaglio, Elisa Gabanti, Paola Zelini, Chiara Fornara, Stefano Bernuzzi, Arsenio Spinillo, Daniele Lilleri and Fausto Baldanti

Microorganisms 2024, 12(7), 1355; https://doi.org/10.3390/microorganisms12071355 - 2 Jul 2024

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Abstract

In the setting of infectious diseases, antibodies show different functions beyond neutralizing activity. In this study, we investigated the activation of NK cells in vitro in the presence of human cytomegalovirus (HCMV)-specific antibodies and their potential role in the control of HCMV infection [...] Read more.

In the setting of infectious diseases, antibodies show different functions beyond neutralizing activity. In this study, we investigated the activation of NK cells in vitro in the presence of human cytomegalovirus (HCMV)-specific antibodies and their potential role in the control of HCMV infection through antibody-dependent cell cytotoxicity (ADCC). Retinal pigmented epithelial cells (ARPE-19) infected with the HCMV strain VR1814 were co-cultured with cytokine-activated peripheral blood mononuclear cells (PBMCs) in the presence of sera collected from 23 HCMV-seropositive and 9 HCMV-seronegative donors. Moreover, 13 pregnant women sampled 3 and 6 months after HCMV primary infection and 13 pregnant women with pre-conception immunity were tested and compared. We determined the percentage of activated NK cells via the analysis of CD107a expression as a marker of degranulation. Significantly higher levels of NK-cell activation were observed using 1/100 and 1/10 dilutions of sera from HCMV-seropositive individuals, and when cells were infected for 96 and 120 h, suggesting that NK cells are activated by antibodies directed against late antigens. In the absence of serum NK cells, activation was negligible. In seropositive subjects, the median percentages of CD107a-positive NK cells in the presence of autologous serum and pooled HCMV-positive serum were similar (14.03% [range 0.00–33.56] and 12.42% [range 1.01–46.00], respectively), while NK-cell activation was negligible using an HCMV-negative serum pool. In HCMV-seronegative subjects, the median percentage of activated NK cells was 0.90% [range 0.00–3.92] with autologous serum and 2.07% [0.00–5.76] in the presence of the HCMV-negative serum pool, while it was 8.97% [0.00–26.49] with the pool of HCMV-positive sera. NK-cell activation using hyperimmune globulin is comparable to what is obtained using autologous serum. Sera from subjects at 3 and 6 months post primary infection showed a lower capacity of NK-cell activation than sera from subjects with past infection (p < 0.001). NK activation against HCMV-infected epithelial cells is dependent on the presence of HCMV-specific antibodies. This serum activity increases with time after the onset of HCMV infection. The protective role of NK-cell activation by HCMV-specific serum antibodies should be verified in clinical settings. Full article

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17 pages, 5247 KiB

Open AccessArticle

Biofilm Formation, Motility, and Virulence of Listeria monocytogenes Are Reduced by Deletion of the Gene lmo0159, a Novel Listerial LPXTG Surface Protein

by Weidi Shi, Qiwen Zhang, Honghuan Li, Dongdong Du, Xun Ma, **g Wang, Jianjun Jiang, Caixia Liu, Lijun Kou and **g**g Ren

Microorganisms 2024, 12(7), 1354; https://doi.org/10.3390/microorganisms12071354 - 2 Jul 2024

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Abstract

Listeria monocytogenes (L. monocytogenes) is a foodborne pathogen that causes listeriosis in humans and other animals. Surface proteins with the LPXTG motif have important roles in the virulence of L. monocytogenes. Lmo0159 is one such protein, but little is known [...] Read more.

Listeria monocytogenes (L. monocytogenes) is a foodborne pathogen that causes listeriosis in humans and other animals. Surface proteins with the LPXTG motif have important roles in the virulence of L. monocytogenes. Lmo0159 is one such protein, but little is known about its role in L. monocytogenes virulence, motility, and biofilm formation. Here, we constructed and characterized a deletion mutant of lmo0159 (∆lmo0159). We analyzed not only the capacity of biofilm formation, motility, attachment, and intracellular growth in different cell types but also LD₅₀; bacterial load in mice’s liver, spleen, and brain; expression of virulence genes; and survival time of mice after challenge. The results showed that the cross-linking density of the biofilm of ∆lmo0159 strain was lower than that of WT by microscopic examination. The expression of biofilm-formation and virulence genes also decreased in the biofilm state. Subsequently, the growth and motility of ∆lmo0159 in the culture medium were enhanced. Conversely, the growth and motility of L. monocytogenes were attenuated by ∆lmo0159 at both the cellular and mouse levels. At the cellular level, ∆lmo0159 reduced plaque size; accelerated scratch healing; and attenuated the efficiency of adhesion, invasion, and intracellular proliferation in swine intestinal epithelial cells (SIEC), RAW264.7, mouse-brain microvascular endothelial cells (mBMEC), and human-brain microvascular endothelial cells (hCMEC/D3). The expression of virulence genes was also inhibited. At the mouse level, the LD₅₀ of the ∆lmo0159 strain was 10^0.97 times higher than that of the WT strain. The bacterial load of the ∆lmo0159 strain in the liver and spleen was lower than that of the WT strain. In a mouse model of intraperitoneal infection, the deletion of the lmo0159 gene significantly prolonged the survival time of the mice, suggesting that the lmo0159 deletion mutant also exhibited reduced virulence. Thus, our study identified lmo0159 as a novel virulence factor among L. monocytogenes LPXTG proteins. Full article

(This article belongs to the Special Issue Advances in Microbial Biofilm Formation)

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20 pages, 1832 KiB

Open AccessArticle

Combinations of Antibiotics Effective against Extensively- and Pandrug-Resistant Acinetobacter baumannii Patient Isolates

by Justin Halim, Rachel A. Carr, Rebecca Fliorent, Keertana Jonnalagadda, Maftuna Kurbonnazarova, Muskanjot Kaur, Ian Millstein and Valerie J. Carabetta

Microorganisms 2024, 12(7), 1353; https://doi.org/10.3390/microorganisms12071353 - 2 Jul 2024

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Abstract

Infections due to drug-resistant Acinetobacter baumannii strains are increasing and cause significant morbidity and mortality, especially in hospitalized and critically ill patients. A. baumannii rapidly develops resistance to numerous antibiotics, and antibiotics traditionally used against this deadly pathogen have been failing in recent [...] Read more.

Infections due to drug-resistant Acinetobacter baumannii strains are increasing and cause significant morbidity and mortality, especially in hospitalized and critically ill patients. A. baumannii rapidly develops resistance to numerous antibiotics, and antibiotics traditionally used against this deadly pathogen have been failing in recent years, highlighting the need to identify new treatment strategies. Treatment options that have shown promise include revisiting common antibiotics not typically used against A. baumannii, evaluating new antibiotics recently introduced to market, and identifying combinations of antibiotics that display synergistic interactions. In this study, we characterized the antibiotic susceptibility profiles of extensively (XDR) and pandrug-resistant (PDR) A. baumannii patient isolates. We examined the potency of 22 standard-of-care antibiotics and the newer antibiotics eravacycline, omadacycline, and plazomicin against these strains. Furthermore, we examined combinations of these antibiotics against our collection to identify synergistic effects. We found that this collection is highly resistant to most or all standard-of-care antibiotics, except for minocycline and rifampin. We show that eravacycline and omadacycline are effective against these strains based on minimum inhibitory concentrations. We also identified two highly effective combinations, cefepime and amikacin and cefepime and ampicillin–sulbactam, which exhibited high rates of synergy against this collection. This information is valuable in our battle against highly drug resistant and virtually untreatable A. baumannii infections. Full article

(This article belongs to the Topic Antimicrobial Agents and Nanomaterials)

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14 pages, 1143 KiB

Open AccessReview

Exploring the Agricultural Applications of Microbial Melanin

by Patricio Muñoz-Torres, Steffany Cárdenas-Ninasivincha and Yola Aguilar

Microorganisms 2024, 12(7), 1352; https://doi.org/10.3390/microorganisms12071352 - 2 Jul 2024

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Abstract

Microbial melanins are a group of pigments with protective effects against harsh conditions, showing fascinating photoprotective activities, mainly due to their capability to absorb UV radiation. In bacteria, they are produced by the oxidation of L-tyrosine, generating eumelanin and pheomelanin. Meanwhile, allomelanin is [...] Read more.

Microbial melanins are a group of pigments with protective effects against harsh conditions, showing fascinating photoprotective activities, mainly due to their capability to absorb UV radiation. In bacteria, they are produced by the oxidation of L-tyrosine, generating eumelanin and pheomelanin. Meanwhile, allomelanin is produced by fungi through the decarboxylative condensation of malonyl-CoA. Moreover, melanins possess antioxidant and antimicrobial activities, revealing significant properties that can be used in different industries, such as cosmetic, pharmaceutical, and agronomical. In agriculture, melanins have potential applications, including the development of new biological products based on this pigment for the biocontrol of phytopathogenic fungi and bacteria to reduce the excessive and toxic levels of agrochemicals used in fields. Furthermore, there are possibilities to develop and improve new bio-based pesticides that control pest insects through the use of melanin-producing and toxin-producing Bacillus thuringiensis or through the application of melanin to insecticidal proteins to generate a new product with improved resistance to UV radiation that can then be applied to the plants. Melanins and melanin-producing bacteria have potential applications in agriculture due to their ability to improve plant growth. Finally, the bioremediation of water and soils is possible through the application of melanins to polluted soils and water, removing synthetic dyes and toxic metals. Full article

(This article belongs to the Section Microbial Biotechnology)

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16 pages, 3953 KiB

Open AccessArticle

Domestication and Genetic Improvement Alter the Symbiotic Microbiome Structure and Function of Tomato Leaf and Fruit Pericarp

by Fei Li, Hongjun Lyu, Henan Li, Kuanling **, Yin Yi and Yubin Zhang

Microorganisms 2024, 12(7), 1351; https://doi.org/10.3390/microorganisms12071351 - 2 Jul 2024

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Abstract

Many studies have attempted to explore the changes in the structure and function of symbiotic microbiomes, as well as the underlying genetic mechanism during crop domestication. However, most of these studies have focused on crop root microbiomes, while those on leaf and fruit [...] Read more.

Many studies have attempted to explore the changes in the structure and function of symbiotic microbiomes, as well as the underlying genetic mechanism during crop domestication. However, most of these studies have focused on crop root microbiomes, while those on leaf and fruit are rare. In this study, we generated a comprehensive dataset including the metagenomic (leaf) and metatranscriptomic (fruit pericarp in the orange stage) data of hundreds of germplasms from three tomato clades: Solanum pimpinellifolium (PIM), cherry tomato (S. lycopersicum var. cerasiforme) (CER), and S. lycopersicum group (BIG). We investigated the effect of domestication and improvement processes on the structure of the symbiotic microbiome of tomato leaf and fruit pericarp, as well as its genetic basis. We were able to obtain the composition of the symbiotic microbiome of tomato leaf and fruit pericarp, based on which the tomato clade (PIM, CER, or BIG) was predicted with high accuracy through machine learning methods. In the processes of tomato domestication and improvement, changes were observed in the relative abundance of specific bacterial taxa, Bacillus for example, in the tomato leaf and fruit pericarp symbiotic microbiomes, as well as in the function of these symbiotic microbiomes. In addition, SNP loci that were significantly associated with microbial species that are characteristic of tomato leaf were identified. Our results show that domestication and genetic improvement processes alter the symbiotic microbiome structure and function of tomato leaf and fruit pericarp. We propose that leaf and fruit microbiomes are more suitable for revealing changes in symbiotic microbiomes during the domestication process and the underlying genetic basis for these changes due to the exclusion of the influence of environmental factors such as soil types on the microbiome structure. Full article

(This article belongs to the Special Issue Advances in the Plant Microbiome: Rhizosphere, Endosphere and Phyllosphere)

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21 pages, 1924 KiB

Open AccessArticle

Gut Microbial Adaptation to Varied Altitudes and Temperatures in Tibetan Plateau Yaks

by Yanbin Zhu, Jia Wang, Yangji Cidan, Hongzhuang Wang, Kun Li and Wangdui Basang

Microorganisms 2024, 12(7), 1350; https://doi.org/10.3390/microorganisms12071350 - 1 Jul 2024

Viewed by 243

Abstract

The yak (Bos grunniens) exhibits exceptional regional adaptability, enabling it to thrive in the distinctive ecological niches of the Qinghai–Tibet Plateau. Its survival relies on the intricate balance of its intestinal microbiome, essential for adapting to harsh environmental conditions. Despite the [...] Read more.

The yak (Bos grunniens) exhibits exceptional regional adaptability, enabling it to thrive in the distinctive ecological niches of the Qinghai–Tibet Plateau. Its survival relies on the intricate balance of its intestinal microbiome, essential for adapting to harsh environmental conditions. Despite the documented significance of bacteria and fungi in maintaining intestinal homeostasis and supporting immune functions, there is still a substantial gap in understanding how the composition and functionality of yak gut microbiota vary along altitude–temperature gradients. This study aims to fill this gap by employing 16S rRNA and ITS amplicon sequencing techniques to analyze and compare the intestinal microbiome of yaks residing at different elevations and exposed to varying temperatures. The findings demonstrate subtle variations in the diversity of intestinal bacteria and fungi, accompanied by significant changes in taxonomic composition across various altitudes and temperature gradients. Notably, Firmicutes, Actinobacteriota, and Bacteroidota emerged as the dominant phyla across all groups, with Actinobacteriota exhibiting the highest proportion (35.77%) in the LZF group. Functional prediction analysis revealed significant associations between the LZF group and metabolic pathways related to amino acid metabolism and biosynthesis. This suggests a potential role for actinomycetes in enhancing nutrient absorption and metabolism in yaks. Furthermore, our findings suggest that the microbiota of yaks may enhance energy metabolism and catabolism by modulating the Firmicutes-to-Bacteroidota ratio, potentially mitigating the effects of temperature variations. Variations in gut bacterial and fungal communities among three distinct groups were analyzed using metagenomic techniques. Our findings indicate that microbial genera exhibiting significant increases in yaks at lower altitudes are largely beneficial. To sum up, our research investigated the changes in gut bacterial and fungal populations of yaks residing across diverse altitude and temperature ranges. Moreover, these results enhance comprehension of gut microbial makeup and variability, offering perspectives on the environmental resilience of dry lot feeding yaks from a microbial angle. Full article

(This article belongs to the Section Veterinary Microbiology)

18 pages, 3847 KiB

Open AccessArticle

Diversity, Methane Oxidation Activity, and Metabolic Potential of Microbial Communities in Terrestrial Mud Volcanos of the Taman Peninsula

by Alexander I. Slobodkin, Igor I. Rusanov, Galina B. Slobodkina, Aleksandra R. Stroeva, Nikolay A. Chernyh, Nikolai V. Pimenov and Alexander Y. Merkel

Microorganisms 2024, 12(7), 1349; https://doi.org/10.3390/microorganisms12071349 - 1 Jul 2024

Viewed by 240

Abstract

Microbial communities of terrestrial mud volcanoes are involved in aerobic and anaerobic methane oxidation, but the biological mechanisms of these processes are still understudied. We have investigated the taxonomic composition, rates of methane oxidation, and metabolic potential of microbial communities in five mud [...] Read more.

Microbial communities of terrestrial mud volcanoes are involved in aerobic and anaerobic methane oxidation, but the biological mechanisms of these processes are still understudied. We have investigated the taxonomic composition, rates of methane oxidation, and metabolic potential of microbial communities in five mud volcanoes of the Taman Peninsula, Russia. Methane oxidation rates measured by the radiotracer technique varied from 2.0 to 460 nmol CH₄ cm⁻³ day⁻¹ in different mud samples. This is the first measurement of high activity of microbial methane oxidation in terrestrial mud volcanos. 16S rRNA gene amplicon sequencing has shown that Bacteria accounted for 65–99% of prokaryotic diversity in all samples. The most abundant phyla were Pseudomonadota, Desulfobacterota, and Halobacterota. A total of 32 prokaryotic genera, which include methanotrophs, sulfur or iron reducers, and facultative anaerobes with broad metabolic capabilities, were detected in relative abundance >5%. The most highly represented genus of aerobic methanotrophs was Methyloprofundus reaching 36%. The most numerous group of anaerobic methanotrophs was ANME-2a-b (Ca. Methanocomedenaceae), identified in 60% of the samples and attaining relative abundance of 54%. The analysis of the metagenome-assembled genomes of a community with high methane oxidation rate indicates the importance of CO₂ fixation, Fe(III) and nitrate reduction, and sulfide oxidation. This study expands current knowledge on the occurrence, distribution, and activity of microorganisms associated with methane cycle in terrestrial mud volcanoes. Full article

(This article belongs to the Section Environmental Microbiology)

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14 pages, 4479 KiB

Open AccessArticle

Structure and Diversity of Endophytic Bacteria in Maize Seeds and Germinating Roots

by Yang Gao, Yujun Zhang, Puchang Wang and Lili Zhao

Microorganisms 2024, 12(7), 1348; https://doi.org/10.3390/microorganisms12071348 - 1 Jul 2024

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Abstract

Seed endophytes in maize, which facilitate the transmission of microorganisms from one plant generation to the next, may play a crucial role in plant protection and growth promotion. This study aimed to investigate the effects of various maize varieties on the communities of [...] Read more.

Seed endophytes in maize, which facilitate the transmission of microorganisms from one plant generation to the next, may play a crucial role in plant protection and growth promotion. This study aimed to investigate the effects of various maize varieties on the communities of endophytic bacteria in seeds and germinating roots. This study utilized Illumina high-throughput sequencing technology to examine the structural and diversity differences of endophytic bacterial communities within seed maize (BY1507), silage maize (QQ446), and wild maize (Teosinte) in both seeds and germinating roots. The results showed that 416 bacterial genera were detected, with Pantoea, Lachnospiraceae, Pararhizobium, Enterobacteriaceae, Stenotrophomonas, and Pseudonocardia being the most prevalent (relative abundance > 10%) at the genus level. No significant difference was observed in diversity indices (Chao1, ACE, Shannon, and Simpson) of seed endophytes among BY1507, QQ446, and Teosinte. The Shannon and Simpson indices for the germinating root endophyte from the wild variety (Teosinte) were significantly higher than the domesticated varieties (BY1507 and QQ446). PCoA revealed a notable overlap in the endophytic bacterial communities from the seeds of BY1507, QQ446, and Teosinte. Yet, clustering patterns were found. Co-occurrence network analysis showed that BY1507, QQ446, and Teosinte share a notable proportion of shared endophytic bacteria (>30%) between the seeds and germinating roots. This investigation elucidates the characteristics of endophytic microbial communities of seeds and germinating roots with seed maize, silage maize, and wild maize, offering data for future research on the physiological ecological adaptation of these endophytic microbial communities. Full article

(This article belongs to the Section Plant Microbe Interactions)

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12 pages, 3818 KiB

Open AccessArticle

Population Genomics analysis of Leptosphaeria biglobosa Associated with Brassica napus in China Reveals That Geographical Distribution Influences Its Genetic Polymorphism

by Yiji Shi, Zhiting Guo, Shunjun Bao, Jiali Xu, Keqi Li, Songbai Rong, Qiangsheng Li, Aixia Xu, Duojie Zhandui, Zhen Huang and Mingguang Chu

Microorganisms 2024, 12(7), 1347; https://doi.org/10.3390/microorganisms12071347 - 1 Jul 2024

Viewed by 235

Abstract

Blackleg disease, a major threat to Brassica crops worldwide, is primarily caused by the pathogen Leptosphaeria biglobosa. Investigating the genetic variation of L. biglobosa is crucial for managing and preventing the disease in Brassica napus. To date, there is scarce genomic [...] Read more.

Blackleg disease, a major threat to Brassica crops worldwide, is primarily caused by the pathogen Leptosphaeria biglobosa. Investigating the genetic variation of L. biglobosa is crucial for managing and preventing the disease in Brassica napus. To date, there is scarce genomic variation information available for populations of L. biglobosa in China. In this study, 73 L. biglobosa strains of canola stalks were collected from 12 provinces in China and subjected to re-sequencing. The 73 assemblies averaged 1340 contigs, 72,123 bp N50, and 30.17 Mb in size. In total, 9409 core orthogroups and 867 accessory orthogroups were identified. A total of 727,724 mutation loci were identified, including 695,230 SNPs and 32,494 indels. Principal component analysis (PCA) and population structure analysis showed that these strains could be divided into seven subgroups. The strains in most provinces were clustered into a single subgroup, suggesting a strong influence of the geographic environment on strain variation. The average nucleotide diversity (θπ) of all strains was 1.03 × 10⁻³, indicating important genetic diversity among strains from different regions of China. This study provides valuable resources for future comparative genomics, gives new insights into the population evolution of L. biglobosa, and supports the development of strategies for managing blackleg disease in canola. Full article

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

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17 pages, 1971 KiB

Open AccessReview

The Marine Fish Gut Microbiome as a Source of Novel Bacteriocins

by Shona Uniacke-Lowe, Catherine Stanton, Colin Hill and R. Paul Ross

Microorganisms 2024, 12(7), 1346; https://doi.org/10.3390/microorganisms12071346 - 1 Jul 2024

Viewed by 350

Abstract

The marine environment is the largest ecological habitat on Earth, albeit one of the least explored, particularly in terms of its microbial inhabitants. The marine fish gut is host to a diverse microbial community from which diverse bioactive molecules can be sourced. Due [...] Read more.

The marine environment is the largest ecological habitat on Earth, albeit one of the least explored, particularly in terms of its microbial inhabitants. The marine fish gut is host to a diverse microbial community from which diverse bioactive molecules can be sourced. Due to the unique environmental pressures these microbial communities experience, the bioactive molecules they produce often evolve unique adaptations that give them diverse structures and activities, differentiating them from terrestrial homologues. Of particular interest, due to their structural and functional diversity, are the ribosomally-synthesized antimicrobial peptides (bacteriocins). With increasing pressure from emerging antibiotic-resistant disease and industrial demand for novel therapeutics, the marine fish gut microbiome represents a relatively untapped resource of novel bacteriocins that could prove beneficial to human health and aquaculture. This review presents an overview of the marine fish gut microbiome and explores its potential as a source of bacteriocins for human health with considerations for applications and future research in this area. Full article

(This article belongs to the Section Systems Microbiology)

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33 pages, 28272 KiB

Open AccessArticle

Microbiological and Imaging-Based Evaluations of Photodynamic Therapy Combined with Er:YAG Laser Therapy in the In Vitro Decontamination of Titanium and Zirconia Surfaces

by Ioana-Roxana Munteanu, Ruxandra-Elena Luca, Elena Hogea, Ralph-Alexandru Erdelyi, Virgil-Florin Duma, Liviu Marsavina, Amelia-Larisa Globasu, George-Dumitru Constantin and Darinca Carmen Todea

Microorganisms 2024, 12(7), 1345; https://doi.org/10.3390/microorganisms12071345 - 30 Jun 2024

Viewed by 378

Abstract

The oral cavity’s soft and hard tissues create a conducive environment for microbial proliferation and biofilm development, facilitating the colonization of prosthodontic and implant materials such as titanium (Ti) and zirconia (Zr). This study aimed to compare the efficacy of conventional decontamination methodologies [...] Read more.

The oral cavity’s soft and hard tissues create a conducive environment for microbial proliferation and biofilm development, facilitating the colonization of prosthodontic and implant materials such as titanium (Ti) and zirconia (Zr). This study aimed to compare the efficacy of conventional decontamination methodologies (i.e., chemical and mechanical, using 0.12% digluconate chlorhexidine (CHX) solution-treatment and airflow) to adjunctive laser-based interventions on Ti and Zr substrates inoculated with Staphylococcus (S.) aureus ATCC 25923. Additionally, this investigation sought to elucidate the impact of these treatments on temperature variations and surface integrity, analyzing the laser irradiation effects on these prevalent dental materials. Experimental configurations were delineated for both Ti and Zr samples across four groups: (1) a conventional treatment group (CV); (2) a photodynamic therapy group (PDT); (3) an Er:YAG laser treatment group (Er); (4) a combined PDT and Er:YAG treatment group (PDTEr). Also, a negative control group (C) that received no treatment was considered. The decontamination of the inoculated disc samples was evaluated by quantifying the microbial colonies in colony-forming units per milliliter (CFU/mL). Temperature variations on the surface of the samples were determined during laser treatments. Surface modifications were investigated using scanning electron microscopy (SEM) and optical coherence tomography (OCT). For statistical analysis, Fisher 95% confidence intervals, Hsu’s MCB method, and the Kruskal–Wallis test were applied. With regard to the 10⁵ CFU/mL of the negative control group, results indicated average values equal for each study group to (1) 2.66 CFU/mL for Ti and 2 CFU/mL for Zr for the CV group; (2) 0.33 CFU/mL for Ti and 1 CFU/mL for Zr for the PDT group; (3) 1.25 CFU/mL for Ti and 0 CFU/mL for Zr for the Er group; (4), and 0 CFU/mL for both Ti and Zr for the PDTEr group. Therefore, the combined PDT and Er:YAG treatment (PDTEr) and the singular PDT modality outperformed conventional decontamination methods in eradicating S. aureus biofilms from both Ti and Zr surfaces. Notably, the PDTEr regime achieved a comprehensive elimination of microbial colonies on treated substrates. Surface examination employing OCT demonstrated discernible alterations in the surface morphology of samples subjected to Er:YAG and combined PDT and Er:YAG treatments. Temperature checks during treatments showed no major changes, suggesting the applied laser methods are safe. In conclusion, PDTEr and PDT eliminated bacteria more effectively, but Zr surfaces were more resilient, making them better for microbe-controlling applications. Also, the study demonstrated that the (less costly but lower resolution) OCT method can replace SEM for such investigations. Full article

(This article belongs to the Special Issue Oral Microorganisms and Biofilm)

15 pages, 12286 KiB

Open AccessArticle

Spatial and Seasonal Changes in Microbial Community of Hynobius amjiensis Breeding Pools in a Sphagnum-Dominated Peatland

by Meng-Jie Yu, **an-Ting Wang, Ting Wang, Wei-Quan Huang, Ze-Dong Lang, Jia-Peng Wang and Yu-Huan Wu

Microorganisms 2024, 12(7), 1344; https://doi.org/10.3390/microorganisms12071344 - 30 Jun 2024

Viewed by 249

Abstract

Peatlands deliver a variety of beneficial ecosystem services, particularly serving as habitats for a diverse array of species. Hynobius amjiensis is a critically endangered amphibian initially discovered in a Sphagnum-dominated peatland in Anji, China. The unique habitat requirements of H. amjiensis make [...] Read more.

Peatlands deliver a variety of beneficial ecosystem services, particularly serving as habitats for a diverse array of species. Hynobius amjiensis is a critically endangered amphibian initially discovered in a Sphagnum-dominated peatland in Anji, China. The unique habitat requirements of H. amjiensis make it highly vulnerable to environmental changes. Here, we investigated the different breeding pools of H. amjiensis in the Sphagnum-dominated peatland (the type locality) for a one-year period to evaluate the interactions among the egg sacs present, water quality, and microbial communities (16S and 18S rRNA gene amplicon). The numbers of egg sacs were higher in the breeding pools located at the marginal area than those at the core area of the peatland. Similarly, the α-diversity of bacteria, fungi, and protists were lower in the core region compared to those at the edge of the peatland, perhaps due to water eutrophication. The microbial communities and water quality differed significantly among breeding pools and sampling months. The simpler microbial networks of the breeding pools in the core wetland may impact the numbers and health of the egg sacs. This study contributes to a better understanding of the effect of water quality on biodiversity in peatlands, and it can also guide regulations for wetland conservation and the protection of endangered species. Full article

(This article belongs to the Special Issue Microbial Communities in Aquatic Environments)

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16 pages, 358 KiB

Open AccessArticle

A Critical Analysis of All-Cause Deaths during COVID-19 Vaccination in an Italian Province

by Marco Alessandria, Giovanni M. Malatesta, Franco Berrino and Alberto Donzelli

Microorganisms 2024, 12(7), 1343; https://doi.org/10.3390/microorganisms12071343 - 30 Jun 2024

Viewed by 12598

Abstract

Immortal time bias (ITB) is common in cohort studies and distorts the association estimates between the treated and untreated. We used data from an Italian study on COVID-19 vaccine effectiveness, with a large cohort, long follow-up, and adjustment for confounding factors, affected by [...] Read more.

Immortal time bias (ITB) is common in cohort studies and distorts the association estimates between the treated and untreated. We used data from an Italian study on COVID-19 vaccine effectiveness, with a large cohort, long follow-up, and adjustment for confounding factors, affected by ITB, with the aim to verify the real impact of the vaccination campaign by comparing the risk of all-cause death between the vaccinated population and the unvaccinated population. We aligned all subjects on a single index date and considered the “all-cause deaths” outcome to compare the survival distributions of the unvaccinated group versus various vaccination statuses. The all-cause-death hazard ratios in univariate analysis for vaccinated people with 1, 2, and 3/4 doses versus unvaccinated people were 0.88, 1.23, and 1.21, respectively. The multivariate values were 2.40, 1.98, and 0.99. Possible explanations of this trend of the hazard ratios as vaccinations increase could be a harvesting effect; a calendar-time bias, accounting for seasonality and pandemic waves; a case-counting window bias; a healthy-vaccinee bias; or some combination of these factors. With 2 and even with 3/4 doses, the calculated Restricted Mean Survival Time and Restricted Mean Time Lost have shown a small but significant downside for the vaccinated populations. Full article

(This article belongs to the Special Issue SARS-CoV-2/COVID-19: Infection Models, Therapeutics and Vaccines, Second Edition)

11 pages, 1312 KiB

Open AccessArticle

Prevalence of Antibiotic-Resistant Escherichia coli Isolated from Beef Cattle and Dairy Cows in a Livestock Farm in Yamagata, Japan

by Tumurbaatar Khishigtuya, Hiroki Matsuyama, Kazuhito Suzuki, Toru Watanabe and Masateru Nishiyama

Microorganisms 2024, 12(7), 1342; https://doi.org/10.3390/microorganisms12071342 - 30 Jun 2024

Viewed by 394

Abstract

Antimicrobials are used on livestock farms to treat and prevent infectious animal diseases and to promote the growth of livestock. We monitored the prevalence of antibiotic-resistant Escherichia coli (AR-EC) isolates from beef cattle (BC) and dairy cows (DCs) on a livestock farm in [...] Read more.

Antimicrobials are used on livestock farms to treat and prevent infectious animal diseases and to promote the growth of livestock. We monitored the prevalence of antibiotic-resistant Escherichia coli (AR-EC) isolates from beef cattle (BC) and dairy cows (DCs) on a livestock farm in Yamagata, Japan. Fecal samples from 5 male BC and 10 male DCs were collected monthly from October 2022 to November 2023. In total, 152 and 884 E. coli isolates were obtained from the BC and DC fecal samples, respectively. Notably, 26 (17.1%) and 29 (3.3%) E. coli isolates in the BC and DC groups, respectively, were resistant to at least one antibiotic. The resistance rates to tetracycline, ampicillin, gentamicin, and chloramphenicol of the isolates were significantly higher than those to the other antimicrobials. The tetracycline resistance genes tetA (70.6%) in DCs and tetB (28%) in BC were identified, along with the bla_TEM gene in ampicillin-resistant isolates (BC: 84.2%, DCs: 42.8%). Despite significant variations in the monthly detection rates of AR-EC isolated from BC and DCs throughout the sampling period, the judicious use of antimicrobials reduced the occurrence of AR-EC in both BC and DCs, thereby minimizing their release into the environment. Full article

(This article belongs to the Special Issue Antimicrobial Resistance and the Use of Antibiotics in Animals)

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18 pages, 3507 KiB

Open AccessArticle

Effect of Probiotic Bacteria on the Gut Microbiome of Mice with Lipopolysaccharide-Induced Inflammation

by Mariya Gryaznova, Inna Burakova, Yuliya Smirnova, Polina Morozova, Egor Chirkin, Artem Gureev, Evgeny Mikhaylov, Olga Korneeva and Mikhail Syromyatnikov

Microorganisms 2024, 12(7), 1341; https://doi.org/10.3390/microorganisms12071341 - 30 Jun 2024

Viewed by 396

Abstract

The role of lipopolysaccharide (LPS) in the development of diseases is clear, but the specific mechanisms remain poorly understood. This study aimed to investigate the microbiome aberrations in the guts of mice against the background of LPS, as well as the anti-inflammatory effect [...] Read more.

The role of lipopolysaccharide (LPS) in the development of diseases is clear, but the specific mechanisms remain poorly understood. This study aimed to investigate the microbiome aberrations in the guts of mice against the background of LPS, as well as the anti-inflammatory effect of probiotic supplementation with Lactobacillus plantarum from the gut, a mix of commercial probiotic lactic acid bacteria, and Weissella confusa isolated from milk using next-generation sequencing. LPS injections were found to induce inflammatory changes in the intestinal mucosa. These morphological changes were accompanied by a shift in the microbiota. We found no significant changes in the microbiome with probiotic supplementation compared to the LPS group. However, when Lactobacillus plantarum and a mix of commercial probiotic lactic acid bacteria were used, the intestinal mucosa was restored. Weissella confusa did not contribute to the morphological changes of the intestinal wall or the microbiome. Changes in the microbiome were observed with probiotic supplementation of Lactobacillus plantarum and a mix of commercial probiotic lactic acid bacteria compared to the control group. In addition, when Lactobacillus plantarum was used, we observed a decrease in the enrichment of the homocysteine and cysteine interconversion pathways with an increase in the L-histidine degradation pathway. Full article

(This article belongs to the Special Issue Probiotics, Prebiotics, and Gut Microbes)

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13 pages, 665 KiB

Open AccessArticle

Universal Lineage-Independent Markers of Multidrug Resistance in Mycobacterium tuberculosis

by Hleliwe Hlanze, Awelani Mutshembele and Oleg N. Reva

Microorganisms 2024, 12(7), 1340; https://doi.org/10.3390/microorganisms12071340 - 30 Jun 2024

Viewed by 287

Abstract

(1) Background: This study was aimed to identify universal genetic markers of multidrug resistance (MDR) in Mycobacterium tuberculosis (Mtb) and establish statistical associations among identified mutations to enhance understanding of MDR in Mtb and inform diagnostic and treatment development. (2) Methods: GWAS analysis [...] Read more.

(1) Background: This study was aimed to identify universal genetic markers of multidrug resistance (MDR) in Mycobacterium tuberculosis (Mtb) and establish statistical associations among identified mutations to enhance understanding of MDR in Mtb and inform diagnostic and treatment development. (2) Methods: GWAS analysis and the statistical evaluation of identified polymorphic sites within protein-coding genes of Mtb were performed. Statistical associations between specific mutations and antibiotic resistance were established using attributable risk statistics. (3) Results: Sixty-four polymorphic sites were identified as universal markers of drug resistance, with forty-seven in PE/PPE regions and seventeen in functional genes. Mutations in genes such as cyp123, fadE36, gidB, and ethA showed significant associations with resistance to various antibiotics. Notably, mutations in cyp123 at codon position 279 were linked to resistance to ten antibiotics. The study highlighted the role of PE/PPE and PE_PGRS genes in Mtb’s evolution towards a ‘mutator phenotype’. The pathways of acquisition of mutations forming the epistatic landscape of MDR were discussed. (4) Conclusions: This research identifies marker mutations across the Mtb genome associated with MDR. The findings provide new insights into the molecular basis of MDR acquisition in Mtb, aiding in the development of more effective diagnostics and treatments targeting these mutations to combat MDR tuberculosis. Full article

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

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18 pages, 6929 KiB

Open AccessArticle

Combined Effects of Lactic Acid Bacteria and Protease on the Fermentation Quality and Microbial Community during 50 Kg Soybean Meal Fermentation Simulating Actual Production Scale

by Huili Pang, ** Wang, Zhen Jiao and Yimin Cai

Microorganisms 2024, 12(7), 1339; https://doi.org/10.3390/microorganisms12071339 - 30 Jun 2024

Viewed by 467

Abstract

The improvement in the utilization rate and nutritional value of soybean meal (SBM) represents a significant challenge in the feed industry. This study conducted a 50 kg SBM fermentation based on the 300 g small-scale fermentation of SBM in early laboratory research, to [...] Read more.

The improvement in the utilization rate and nutritional value of soybean meal (SBM) represents a significant challenge in the feed industry. This study conducted a 50 kg SBM fermentation based on the 300 g small-scale fermentation of SBM in early laboratory research, to explore the combined effects of lactic acid bacteria (LAB) and acid protease on fermentation quality, chemical composition, microbial population, and macromolecular protein degradation during fermentation and aerobic exposure of SBM in simulated actual production. The results demonstrated that the increase in crude protein content and reduction in crude fiber content were considerably more pronounced after fermentation for 30 days (d) and subsequent aerobic exposure, compared to 3 d. It is also noteworthy that the treated group exhibited a greater degree of macromolecular protein degradation relative to the control and 30 d of fermentation relative to 3 d. Furthermore, after 30 d of fermentation, adding LAB and protease significantly inhibited the growth of undesired microbes including coliform bacteria and aerobic bacteria. In the mixed group, the microbial diversity decreased significantly, and Firmicutes replaced Cyanobacteria for bacteria in both groups’ fermentation. Full article

(This article belongs to the Section Food Microbiology)

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14 pages, 1328 KiB

Open AccessArticle

Production of Esters in Escherichia coli Using Citrate Synthase Variants

by Jacoby C. Shipmon, Pasupathi Rathinasabapathi, Michael L. Broich II, Hemansi and Mark A. Eiteman

Microorganisms 2024, 12(7), 1338; https://doi.org/10.3390/microorganisms12071338 - 29 Jun 2024

Viewed by 360

Abstract

Acetate esters comprise a wide range of products including fragrances and industrial solvents. Biosynthesis of esters offers a promising alternative to chemical synthesis because such routes use renewable carbohydrate resources and minimize the generation of waste. One biochemical method for ester formation relies [...] Read more.

Acetate esters comprise a wide range of products including fragrances and industrial solvents. Biosynthesis of esters offers a promising alternative to chemical synthesis because such routes use renewable carbohydrate resources and minimize the generation of waste. One biochemical method for ester formation relies on the ATF1 gene from Saccharomyces cerevisiae, which encodes alcohol-O-acyltransferase (AAT) which converts acetyl-CoA and an exogenously supplied alcohol into the ester. In this study, the formation of several acetate esters via AAT was examined in Escherichia coli chromosomally expressing citrate synthase variants, which create a metabolic bottleneck at acetyl-CoA. In shake flask cultures, variant strains generated more acetate esters than the strains expressing the wild-type citrate synthase. In a controlled bioreactor, E. coli GltA[A267T] generated 3.9 g propyl acetate in 13 h, corresponding to a yield of 0.155 g propyl acetate/g glucose, which is 18% greater than that obtained by the wild-type GltA control. These results demonstrate the ability of citrate synthase variants to redistribute carbon from central metabolism into acetyl-CoA-derived biochemicals. Full article

(This article belongs to the Special Issue Microbial Biotechnology: The Biodiversity, Properties and Benefits of Microorganisms in Medical, Clinical, Food and Environmental Fields)

14 pages, 361 KiB

Open AccessReview

Infective Endocarditis Due to Corynebacterium jeikeium: Four Case Reports and Narrative Review of the Literature

by Daniel Arnés-García, Laura Lucena-Torres, Antonio Bustos-Merlo, Antonio Rosales-Castillo and Carmen Hidalgo-Tenorio

Microorganisms 2024, 12(7), 1337; https://doi.org/10.3390/microorganisms12071337 - 29 Jun 2024

Viewed by 359

Abstract

Corynebacterium jeikeium, a pleomorphic Gram-positive bacillus, is a common component of the cutaneous microbiota, usually considered as a contaminant, with little pathogenic potential. However, its role in various types of infections, such as bacteremia, sepsis, endocarditis (IE) and infection of prosthetic material [...] Read more.

Corynebacterium jeikeium, a pleomorphic Gram-positive bacillus, is a common component of the cutaneous microbiota, usually considered as a contaminant, with little pathogenic potential. However, its role in various types of infections, such as bacteremia, sepsis, endocarditis (IE) and infection of prosthetic material is gradually being proven. Few cases of IE due to Corynebacterium jeikeium have been described in the literature. The aim of this article was to describe four cases of IE due to Corynebacterium jeikeium diagnosed in our hospital between May 2021 and April 2022, as well as to conduct a narrative review of the literature on this entity. After analysis, we highlight that 65.6% were men, 81.3% were valve or intravascular device carriers, and IE cases presented early, before one year after surgery. The most affected valve was the aortic valve (68.8%), followed by the mitral valve (21.1%). Valve replacement was performed in 65.6% of cases, and the most commonly used antibiotic was vancomycin (68.8%) at a dose of 15 mg/kg/12 h. With respect to prognosis, the overall mortality rate was 21.9%. The comparative results between our series and the literature review were similar except for a higher mortality rate (50%) and the use of dalbavancin in the treatment. We go on to review previously reported cases, along with four cases described in our hospital, of C. jeikeium endocarditis and will discuss various aspects of C. jeikeium infection, focusing on microbiology, pathophysiology, and treatment. Full article

(This article belongs to the Special Issue Antimicrobial Resistance and Multidrug-Resistant Bacteria in Infectious Patients)

15 pages, 7018 KiB

Open AccessArticle

Effect of Trace Element Selenium on the Intestinal Microbial Community in Nude Mice with Colorectal Cancer

by Yintong Su, **aohua Cai, **ngxing Fan, Jiayu Ning and Mei Shen

Microorganisms 2024, 12(7), 1336; https://doi.org/10.3390/microorganisms12071336 - 29 Jun 2024

Viewed by 286

Abstract

Colorectal cancer (CRC) is the third most common cancer worldwide. The role of intestinal microbiota in carcinogenesis has also become an important research topic, and CRC is closely related to the intestinal microbiota. Selenium-containing compounds have attracted more attention as anticancer drugs as [...] Read more.

Colorectal cancer (CRC) is the third most common cancer worldwide. The role of intestinal microbiota in carcinogenesis has also become an important research topic, and CRC is closely related to the intestinal microbiota. Selenium-containing compounds have attracted more attention as anticancer drugs as they can have minimal side effects. The purpose of this study was to determine and compare the effect of sodium selenite and selenomethionine on the microbial communities of nude mice with CRC. A CRC ectopic tumorigenesis model was established by subcutaneously injecting HCT116 cells into nude mice. The mice were then intraperitoneally injected with sodium selenite and selenomethionine for 24 days to regulate their intestinal microbiota. Compared with sodium selenite, selenomethionine resulted in a greater reduction in the richness and diversity of intestinal microbiota in nude mice with CRC, and the richness and diversity were closer to healthy levels. Selenomethionine also regulated a wider variety of flora. Additionally, sodium selenite and selenomethionine produced different microorganisms, changed function and metabolic pathways in the intestinal microbiota. Both sodium selenite and selenomethionine have certain effects on restoring the intestinal microbial diversity in nude mice with CRC, and the effect of selenomethionine is better than that of sodium selenite. Full article

(This article belongs to the Section Medical Microbiology)

15 pages, 4601 KiB

Open AccessArticle

Selection and Genetic Analysis of High Polysaccharide-Producing Mutants in Inonotus obliquus

by Lanlan Hua, Hongling Shi, Qing Lin, Haozhong Wang, Yan Gao, Jun Zeng, Kai Lou and **angdong Huo

Microorganisms 2024, 12(7), 1335; https://doi.org/10.3390/microorganisms12071335 - 29 Jun 2024

Viewed by 330

Abstract

Inonotus obliquus, a medicinal fungus, has garnered significant attention in scientific research and medical applications. In this study, protoplasts of the I. obliquus HS819 strain were prepared using an enzymatic method and achieved a regeneration rate of 5.83%. To enhance polysaccharide production [...] Read more.

Inonotus obliquus, a medicinal fungus, has garnered significant attention in scientific research and medical applications. In this study, protoplasts of the I. obliquus HS819 strain were prepared using an enzymatic method and achieved a regeneration rate of 5.83%. To enhance polysaccharide production of I. obliquus HS819, atmospheric and room temperature plasma (ARTP) technology was employed for mutagenesis of the protoplasts. Through liquid fermentation, 32 mutant strains exhibiting diverse characteristics in morphology, color of the fermentation broth, mycelial pellet size, and biomass were screened. Secondary screening identified mutant strain A27, which showed a significant increase in polysaccharide production up to 1.67 g/L and a mycelial dry weight of 17.6 g/L, representing 137.67% and 15% increases compared to the HS819 strain, respectively. Furthermore, the fermentation period was reduced by 2 days, and subsequent subculture cultivation demonstrated stable polysaccharide production and mycelial dry weight. The genome resequencing analysis of the HS819 strain and mutant strain A27 revealed 3790 InDel sites and mutations affecting 612 functional genes associated with polysaccharide synthesis. We predict that our findings will be helpful for high polysaccharide production through genetic engineering of I. obliquus. Full article

(This article belongs to the Section Microbial Biotechnology)

19 pages, 690 KiB

Open AccessArticle

Response of Arugula to Integrated Use of Biological, Inorganic, and Organic Fertilization

by Aleksandra Stanojković-Sebić, Vladimir Miladinović and Radmila Pivić

Microorganisms 2024, 12(7), 1334; https://doi.org/10.3390/microorganisms12071334 - 29 Jun 2024

Viewed by 306

Abstract

This study evaluated the effects of solely and integrated application of inorganic (NPK), commercial organic (NC), and biological (MIX, mixed strains Ensifer meliloti and Azotobacter chroococcum) fertilizers on the chemical characteristics of arugula biomass and its yield, as well as changes in [...] Read more.

This study evaluated the effects of solely and integrated application of inorganic (NPK), commercial organic (NC), and biological (MIX, mixed strains Ensifer meliloti and Azotobacter chroococcum) fertilizers on the chemical characteristics of arugula biomass and its yield, as well as changes in soil microbiological parameters after the experiment in relation to the control treatment (Ø). The experiment was performed in semi-controlled greenhouse conditions, in pots, from the 4th decade of March to the 2nd decade of September, in 2023, at three cutting times/swaths, during one agricultural season, with Vertisol soil. For soil characterization, the following parameters were analysed: granulometric composition using sieving and sedimentation procedure; soil acidity—potentiometrically; SOM—soil organic matter by Kotzmann method; total N using CNS analyser; available P—spectrophotometrically; available K—flame photometrically; total number of microorganisms on an agarized soil extract medium; fungi on a solid Czapek agar; actinomycetes on a solid Krasiljnikov agar with saccharose; Azotobacter spp. on a liquid Fyodorov medium with mannitol; ammonifiers on a liquid medium with asparagine; and dehydrogenase activity—spectrophotometrically. For plant characterization, the following parameters were determined: N and C, both on CNS analyser; P on spectrophotometer; K on flame photometer; air-dried yield biomass. A stimulative effect on all microbiological parameters was found in the treatment with integrated use of organic and biological fertilizer, except for fungi, which grew better in the treatments with separate inorganic and organic fertilizers. Generally, the stimulative impact on plant chemical parameters manifested in combined inorganic and biological, organic and biological, and inorganic and organic fertilization treatments, and was inhibited in treatment without fertilization, in all three swaths, which could also be stated for the plant yield. Positive influence of all fertilization treatments on chemical parameters was observed for the second swath in relation to the first and the third. The total yield in the NPK+MIX treatment was 121%, and in the NC+MIX treatment, it was 87% higher compared to the control (Ø). In general, integrated use of inorganic and biological, organic and biological, and inorganic and organic fertilizers, respectively, could be proposed as an optimal fertilization treatment in arugula cultivation. Full article

(This article belongs to the Special Issue Microorganisms in Agriculture)

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17 pages, 9029 KiB

Open AccessArticle

The Cellular Microbiome of Visceral Organs: An Inherent Inhabitant of Parenchymal Cells

by **aowei Sun, Hua Zhang, **ao Zhang, Wenmin Gao, Caiyun Zhou, Xuanxuan Kou, **gxin Deng and Jiangang Zhang

Microorganisms 2024, 12(7), 1333; https://doi.org/10.3390/microorganisms12071333 - 29 Jun 2024

Viewed by 365

Abstract

The cell is the basic unit of life. It is composed of organelles and various organic and inorganic biomolecules. Recent 16S ribosomal ribonucleic acid (16S rRNA) gene sequencing studies have revealed the presence of tissue bacteria in both tumor and normal tissues. Recently, [...] Read more.

The cell is the basic unit of life. It is composed of organelles and various organic and inorganic biomolecules. Recent 16S ribosomal ribonucleic acid (16S rRNA) gene sequencing studies have revealed the presence of tissue bacteria in both tumor and normal tissues. Recently, we found that the liver microbiome resided in hepatocytes. Here, we further report on the cellular microbiome in the parenchymal cells of visceral organs as inherent inhabitants. We performed 16S rRNA gene sequencing on visceral organs of male adult Sprague Dawley (SD) rats, pregnant rats, newborn rats, and fetuses and placentas; then, we performed fluorescence in situ hybridization and immunofluorescence in visceral organs. Furthermore, we performed Western blotting on nuclear and cytoplasmic extractions of visceral organs of SD rats and cell lines HepG2, Huh-7, Hepa1-6, and HSC-T6. A high abundance of 16S rRNA gene was detected in the visceral organs of male adult, pregnant, newborn, and fetal rats as well as their placentas. The number of operational taxonomic units (OTUs) of visceral bacteria was higher than that of the feces and ileum bacteria. Bacterial 16S rRNA, lipopolysaccharide (LPS), and lipoteichoic acid (LTA) were found in the parenchymal cells of visceral organs, as well as in HepG2, Huh-7, HSC-T6, and Hepa1-6 cells. LPS consistently appeared in the nucleus of cells, while LTA was mainly found in the cytoplasm. In conclusion, the cellular microbiome is an intrinsic component of cells. Gram-negative bacteria are located in the nucleus, and Gram-positive bacteria are located in the cytoplasm. This differs from the gut microbiome and may be inherited. Full article

(This article belongs to the Section Medical Microbiology)

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Microorganisms, Volume 12, Issue 7 (July 2024) – 110 articles

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