Journal Description
Microbiology Research
Microbiology Research
is an international, scientific, peer-reviewed open access journal published quarterly online by MDPI (from Volume 11 Issue 2-2020).
- Open Access— free for readers, with article processing charges (APC) paid by authors or their institutions.
- High Visibility: indexed within Scopus, ESCI (Web of Science), Embase, and other databases.
- Rapid Publication: manuscripts are peer-reviewed and a first decision is provided to authors approximately 16.7 days after submission; acceptance to publication is undertaken in 3.5 days (median values for papers published in this journal in the first half of 2024).
- Recognition of Reviewers: APC discount vouchers, optional signed peer review, and reviewer names published annually in the journal.
Impact Factor:
2.1 (2023);
5-Year Impact Factor:
2.0 (2023)
Latest Articles
Cicer arietinum Extract Suppresses Lung Sepsis Induced by Cecal Ligation and Puncture in Rats
Microbiol. Res. 2024, 15(3), 1939-1958; https://doi.org/10.3390/microbiolres15030130 (registering DOI) - 23 Sep 2024
Abstract
Sepsis is characterized by multiple organ dysfunction, which is now accepted to be due to oxidative damage. The lung is the first organ exposed to this damage, and its injury is one of the leading causes of death. Therefore, many pharmacological strategies are
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Sepsis is characterized by multiple organ dysfunction, which is now accepted to be due to oxidative damage. The lung is the first organ exposed to this damage, and its injury is one of the leading causes of death. Therefore, many pharmacological strategies are employed to attenuate sepsis. This study aimed to evaluate the in silico and in vitro antibacterial activity of Cicer arietinum extract (CAE) against Staphylococcus aureus, Escherichia coli, and Pseudomonas aeruginosa and the in vivo modulatory effect of CAE against sepsis induced by cecal ligation and puncture (CLP) in rats. This study identified seven bioactive components in Cicer arietinum extract, revealing promising interactions between these components and Staphylococcus aureus-PBP2a and Pseudomonas aeruginosa-PBP3 proteins, highlighting their potential as novel antibacterial agents. After ensuring the bactericidal ability of CAE against Staphylococcus aureus and Pseudomonas aeruginosa, an in vivo study was performed. Twenty-four rats were divided into sham-operated rats, CLP-septic rats, CLP rats treated with CAE (500 mg/kg b.wt), and CLP rats treated with hydrocortisone (25 mg/ kg b.wt). CAE was administered orally for 3 days post-operation, and animals were euthanized on the fourth day. Another twenty-four rats were used to study survival for 5 days. This study revealed that CAE, like hydrocortisone, can rescue CLP rats from death by suppressing lung procalcitonin (PCT) and MDA and enhancing SOD, CAT, and GSH levels significantly, as compared with the CLP group. The histopathological results were parallel with the biochemical results since the CLP rats treated with CAE had lower histological/inflammatory scores in the lung like hydrocortisone. The beneficial role of CAE may result from its antibacterial and antioxidant activities, and CAE can be considered as a lung antiseptic extract. This study provides a novel treatment for sepsis-induced ALI. However, the beneficial impact of CAE needs extensive study to obtain evidence.
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Open AccessArticle
The Mechanism of Bacterial Endotoxin Invasion Pathways in Porcine Reproductive and Respiratory Syndrome Virus-Positive Porcine Endometrial Epithelial Cells
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Siyi Xing, Aohang Yu, Mengran Zhang and Chenchen Wu
Microbiol. Res. 2024, 15(3), 1924-1938; https://doi.org/10.3390/microbiolres15030129 - 18 Sep 2024
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Porcine reproductive and respiratory syndrome virus (PRRSV) causes abortions, stillbirths, and dummy pregnancies. Previous studies found that PRRSV can promote secondary bacterial infections and elevate bacterial endotoxin levels, further increasing the abortion rate in sows. However, the pathways by which bacterial endotoxins invade
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Porcine reproductive and respiratory syndrome virus (PRRSV) causes abortions, stillbirths, and dummy pregnancies. Previous studies found that PRRSV can promote secondary bacterial infections and elevate bacterial endotoxin levels, further increasing the abortion rate in sows. However, the pathways by which bacterial endotoxins invade the bodies of PRRSV(+) sows and aggravate their clinical symptoms are unknown. In this study, we established a model of PRRSV and lipopolysaccharide (LPS) working together on porcine endometrial epithelial cells (PEECs). We speculate that PRRSV and LPS affect PEECs through viral protein interaction with cytokines and cytokine receptors, natural killer cell-mediated cytotoxicity, and regulation of actin cytoskeleton signaling pathways by analyzing seq-RNA. The PRRSV proteins act on inflammatory factors and their receptors to activate chemokines-5 (CCL5), chemokines-4 (CCL4), and chemokines-8 (CCL8) mRNA expression, causing severe inflammatory reactions. In addition, the elevation of MEK1/2 factors and the integrins acting on NK cells promote the upregulation of VAV1/Tiam1, RAC, and IRSp53, leading to increased expression of Arp2/3 and F-actin in PEECs in the PRRSV + LPS(+) groups. However, the highly expressed cell microfilaments and cytoskeleton disrupt the original network structure, causing changes in the original physiological function of the PEECs. In summary, the PRRSV protein interacts with cytokines and cytokine receptors of PEECs, thereby enhancing virus-mediated chemokine factors and their receptor activity, accelerating bacterial endotoxin entry into the body and the invasion of cells. They destroy the cytoskeletal structure of the cells and increase damage to uterine tissue.
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Open AccessArticle
Adenovirus-Mediated Expression of Dengue Virus 2 Envelope Ferritin Nanoparticles Induced Virus-Specific Immune Responses in BALB/c Mice
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M.S.B.W.T.M. Nipuna Sudaraka Tennakoon, Ji-Hoon Ryu, Yong-Sam Jung, Yingjuan Qian and Hyun-Jin Shin
Microbiol. Res. 2024, 15(3), 1913-1923; https://doi.org/10.3390/microbiolres15030128 - 15 Sep 2024
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This study provides a preliminary background for the development of a viral vector vaccine for the dengue virus using genetic material encoded by dengue envelope ferritin nanoparticles. Adenoviruses were generated for the recombinant envelope of dengue virus 2 (DENV2) and the envelope human
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This study provides a preliminary background for the development of a viral vector vaccine for the dengue virus using genetic material encoded by dengue envelope ferritin nanoparticles. Adenoviruses were generated for the recombinant envelope of dengue virus 2 (DENV2) and the envelope human ferritin heavy chain using a two-vector adenovirus system. The primary immunostimulatory activity of the two viruses was analyzed in mice to determine the effect of envelope ferritin nanoparticles. Transfection of a shuttle vector delivered the target gene and packaging vector carrying the packaging signal, and recombinant adenoviruses (rAds) were generated and purified using an ultracentrifugation method. Transduction efficiencies of the generated adenoviruses were confirmed in A549 cells. Purified adenoviruses (8 × 106 PFU/mL) were immunized intramuscularly into 6 weeks old BALB/c mice. Subsequently, the DENV2-specific IgG titer was evaluated 1 and 4 weeks after immunization. Envelope ferritin-immunized mice showed a significant IgG response compared to envelope-only immunized mice at 1 and 4 weeks after immunization, revealing the persistence of the dengue virus-specific IgG response. This method demonstrated the capability of the viral vector vaccine to be used as a carrier for ferritin nanoparticles, instead of direct immunization with ferritin nanoparticles.
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Open AccessArticle
Nitrogen Fixation, Carbohydrate Contents, and Bacterial Microbiota in Unelongated Stem of Manure Compost-Applied Rice at Panicle Initiation
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Zhalaga Ao, Miu Tsuchiya, Juan Xia, Chie Hayakawa, Yukitsugu Takahashi, Hideaki Hirai and Isamu Maeda
Microbiol. Res. 2024, 15(3), 1900-1912; https://doi.org/10.3390/microbiolres15030127 - 15 Sep 2024
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In rice, symbiotic N2 fixation via nodule bacteroids does not take place naturally. Although N2 fixation by endophytic and associative diazotrophs has been reported in rice, the main organs and seasonal regulation for the N2 fixation have not been elucidated.
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In rice, symbiotic N2 fixation via nodule bacteroids does not take place naturally. Although N2 fixation by endophytic and associative diazotrophs has been reported in rice, the main organs and seasonal regulation for the N2 fixation have not been elucidated. In this study, seasonal changes in nitrogenase (acetylene reduction) activity and carbohydrate contents in elongated culm (EC), unelongated stem (US), and crown root (CR) were investigated in manure compost (MC)- and chemical fertilizer (CF)-applied rice. Nitrogenase activity increased after rooting (June) and reached the highest activity in US of MC-applied rice at panicle initiation (August). The sucrose content in EC continued to increase after rooting regardless of the applied materials, whereas the glucose content in US increased after rooting only in CF-applied rice, suggesting higher consumption of glucose in US of MC-applied rice. There were significant differences among bacterial microbiota in EC, US, and CR at panicle initiation. In addition, Clostridia class anaerobes were more abundant in US of MC-applied rice than in EC and CR of MC-applied rice. Such difference was not observed in US of CF-applied rice. These results suggest the suitability of US of MC-applied rice at panicle initiation as a site of N2 fixation under anaerobic conditions.
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Open AccessArticle
Unveiling the Full Protein Effectorome of the Black Sigatoka Pathogen Pseudocercospora fijiensis—An In Silico Approach
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Karla Gisel Carreón-Anguiano, Jewel Nicole Anna Todd, César De los Santos-Briones, Santy Peraza-Echeverría, Ignacio Islas-Flores and Blondy Canto-Canché
Microbiol. Res. 2024, 15(3), 1880-1899; https://doi.org/10.3390/microbiolres15030126 - 14 Sep 2024
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Pseudocercospora (previously Mycosphaerella) fijiensis is a hemibiotroph fungus and the causal agent of black Sigatoka disease, one of the most significant threats to banana production worldwide. Only a few genomics reports have paid any attention to effector proteins, which are key players
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Pseudocercospora (previously Mycosphaerella) fijiensis is a hemibiotroph fungus and the causal agent of black Sigatoka disease, one of the most significant threats to banana production worldwide. Only a few genomics reports have paid any attention to effector proteins, which are key players in pathogenicity. These reports focus on canonical effectors: small secreted proteins, rich in cysteines, containing a signal peptide and no transmembrane domain. Thus, bias in previous reports has resulted in the non-canonical effectors being, in effect, excluded from the discussion of effectors in P. fijiensis pathogenicity. Here, using WideEffHunter and EffHunter, bioinformatic tools which identify non-canonical and canonical effectors, respectively, we predict, for the first time, the full effectorome of P. fijiensis. This complete effectorome comprises 5179 proteins: 240 canonical and 4939 non-canonical effectors. Protein families related to key functions of the hemibiotrophic lifestyle, such as Salicylate hydroxylase and Isochorismatase, are widely represented families of effectors in the P. fijiensis genome. An analysis of the gene distribution in core and dispensable scaffolds of both classes of effectors revealed a novel genomic structure of the effectorome. The majority of the effectors (canonical and non-canonical) were found to be harbored in the core scaffolds, while dispensable scaffolds harbored less than 10% of the effectors, all of which were non-canonical. Additionally, we found the motifs RXLR, YFWxC, LysM, EAR, [Li]xAR, PDI, CRN, and ToxA in the effectors of P. fijiensis. This novel genomic structure of effectors (more enriched in the core than in the dispensable genome), as well as the occurrence of effector motifs which were also observed in four other fungi, evidences that these phenomena are not unique to P. fijiensis; rather, they are widely occurring characteristics of effectors in other fungi.
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Open AccessArticle
Moringa Reduces Glucose Levels and Alters Wolbachia Abundance in Drosophila melanogaster
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Michaela Schaffer, D’Andre Grant, Katherine Berge and Nana Yaw Darko Ankrah
Microbiol. Res. 2024, 15(3), 1870-1879; https://doi.org/10.3390/microbiolres15030125 - 13 Sep 2024
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Moringa oleifera Lam. (moringa) is a plant native to India, used as a nutritional and medicinal supplement in many cultures around the world. Moringa has been linked to maintaining metabolic homeostasis and is often marketed as a weight loss supplement and a potential
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Moringa oleifera Lam. (moringa) is a plant native to India, used as a nutritional and medicinal supplement in many cultures around the world. Moringa has been linked to maintaining metabolic homeostasis and is often marketed as a weight loss supplement and a potential remedy for diseases such as diabetes. Here, we investigate how moringa, a ‘superfood’ with predicted protective effects against chronic diseases such as diabetes, influences the nutritional physiology and microbiome composition of the fruit fly Drosophila melanogaster. We administered moringa as a dietary supplement to Drosophila, and quantified key nutritional indices: glucose, triacylglyceride, and protein levels, and fly weight. We showed that dietary moringa supplementation significantly reduced fly glucose levels by up to ~30% and resulted in substantial restructuring of Drosophila microbiota composition, altering both gut and intracellular bacterial populations. The effect of moringa on fly glucose levels is specific because other nutritional indices, namely, triacylglyceride and protein levels and fly weight, were not significantly affected by dietary moringa supplementation. This study highlights the importance of moringa as a modulator of host glucose metabolism.
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Open AccessArticle
Enrichment of Geobacter on Anode Biofilms from Domestic Wastewater without Posing Anode Potential in Microbial Electrochemical Cells
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Ravi Shankar Yadav, Weihua He, Dandan Liang, Chao Li, Yanling Yu and Yujie Feng
Microbiol. Res. 2024, 15(3), 1859-1869; https://doi.org/10.3390/microbiolres15030124 - 13 Sep 2024
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Microbial electrochemical cells (MxCs) offer a sustainable approach for wastewater treatment and energy recovery by harnessing the electroactive properties of microorganisms. This study explores the enrichment of Geobacter species on anode biofilms in single-(S-MxCs) and double-chambered (D-MxCs) MxCs, using domestic wastewater without an
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Microbial electrochemical cells (MxCs) offer a sustainable approach for wastewater treatment and energy recovery by harnessing the electroactive properties of microorganisms. This study explores the enrichment of Geobacter species on anode biofilms in single-(S-MxCs) and double-chambered (D-MxCs) MxCs, using domestic wastewater without an external anode potential. Stable current densities were achieved within 10 days for S-MxCs (9.52 ± 0.8 A/m2) and 14 days for D-MxCs (4.28 ± 0.9 A/m2), with S-MxCs showing a superior electrochemical performance. Hydrogen production rates were higher in D-MxCs (14.93 ± 0.66 mmol H2/L/day) compared to S-MxCs (9.46 ± 0.8 mmol H2/L/day), with cumulative production rates of 12.9 ± 1.3 mmol H2/g COD and 6.48 ± 1.4 mmol H2/g COD, respectively. Cyclic voltammetry confirmed enhanced bioelectrocatalytic activity in S-MxCs, while SEM imaging showed denser biofilms on S-MxC anodes. The novelty of this study lies in its demonstration of efficient biofilm development and microbial community resilience under non-potentialized conditions, providing insights that advance the practical application of MxCs in environmental biotechnology.
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Open AccessArticle
Genotypes and Phylogenetic Analysis of Helicobacter pylori Clinical Bacterial Isolates
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Marcela Ríos-Sandoval, Evangelina Esmeralda Quiñones-Aguilar, Guillermo Alejandro Solís-Sánchez, Jorge Bravo-Madrigal, Norma Velázquez-Guadarrama and Gabriel Rincón-Enríquez
Microbiol. Res. 2024, 15(3), 1845-1858; https://doi.org/10.3390/microbiolres15030123 - 10 Sep 2024
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Helicobacter pylori is a human pathogen bacterium associated with gastritis, peptic ulcer, and gastric cancer. It can be identified through the 16S rRNA gene and characterized through cagA and vacA virulence genes. Clinical cultures of H. pylori were isolated and identified from human
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Helicobacter pylori is a human pathogen bacterium associated with gastritis, peptic ulcer, and gastric cancer. It can be identified through the 16S rRNA gene and characterized through cagA and vacA virulence genes. Clinical cultures of H. pylori were isolated and identified from human stomach biopsies. The isolates were characterized according to their colonial and microscopic morphology, and molecular genotyping was conducted to determine the bacterial virulence. A phylogenetic analysis of the 16S rRNA gene sequencing was performed. In addition, multilocus sequence typing analysis was performed to determine the phylogeographic nature of the isolated strains. Three bacterial isolates were selected from 22 gastric biopsies, identified as H. pylori through colonial morphology, Gram staining, urease, catalase, and oxidase tests and identification of the ureC gene through end-point PCR. Amplification of 16S rRNA, urea, and tonB genes was performed, as well. Differences between the cagA and vacA genotypes were determined among the isolates. The phylogenetic analysis confirmed the identity of the three isolates as the specie Helicobacter pylori. Different genotypes were obtained for each H. pylori strain, and all the clinical isolates showed the vacA s2/m2 genotype, indicating an absence of the VacA cytotoxin. Only HCGDL-MR01 is a cagA gene carrier with a greater risk to develop a serious disease, such as stomach cancer and peptic ulcer. The multilocus sequence typing placed all the strains within the hpEurope population structure.
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Open AccessArticle
Comprehensive Microbiological and Metagenomic Analysis of the Guillain–Barré Syndrome Outbreak in Lima, 2019
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Jesús D. Rojas, Mariana Ramos, Cristopher Cruz, Kyle A. Long, Logan J. Voegtly, Rina Meza, Nereyda Espinoza, Ana Ramos Ttito, Hugo Umeres Cáceres, Alejandro Llanos Cuentas, Yocelinda Meza, Gilda Troncos, Frédéric M. Poly, Adrian C. Paskey, Matthew R. Lueder, Gregory K. Rice, Regina Z. Cer, Kimberly A. Bishop-Lilly, María Silva and Max Grogl
Microbiol. Res. 2024, 15(3), 1826-1844; https://doi.org/10.3390/microbiolres15030122 - 8 Sep 2024
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In 2018/2019, two large Guillain–Barré Syndrome (GBS) outbreaks took place in Peru. Here, we report a comprehensive analysis of biological samples from GBS patients from the 2019 outbreak. We applied metagenomic, microbiologic, and serological analyses to different biological samples collected from GBS patients.
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In 2018/2019, two large Guillain–Barré Syndrome (GBS) outbreaks took place in Peru. Here, we report a comprehensive analysis of biological samples from GBS patients from the 2019 outbreak. We applied metagenomic, microbiologic, and serological analyses to different biological samples collected from GBS patients. Further phenotypic and genomic characterization was conducted on Campylobacter jejuni isolates from GBS samples. Microbiologic and metagenomic analyses revealed several patients with multiple co-infections, yet no common infectious agents were found other than C. jejuni. Four C. jejuni isolates were isolated from rectal swabs. Twenty-one patients had detectable IgG serum antibodies related to C. jejuni, of whom seven had IgM antibodies. Genomic analyses showed that these four strains were clonal (ST2993) and contained the class A lipooligosaccharide biosynthesis locus. These results further support the idea that that C. jejuni is the etiological agent that triggered the GBS outbreak in Peru in 2019 and that the strains are not restricted to Peru, hence could be regarded as a broad public health concern. Furthermore, though we cannot delineate the role played by co-infections in GBS development, results obtained herein highlight metagenomic analysis as a potential new tool for depicting a yet unknown area of research in GBS.
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Open AccessCommunication
Characterization of Antimicrobial Resistance Mechanisms and Virulence Determinants in Colistin- and Carbapenem-Resistant Pseudomonas aeruginosa
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Ellappan Kalaiarasan, Anoop Alex, Harish Belgode Narasimha and Rakesh Sehgal
Microbiol. Res. 2024, 15(3), 1814-1825; https://doi.org/10.3390/microbiolres15030121 - 6 Sep 2024
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Antibiotics like colistin can save patients infected with carbapenem-resistant Pseudomonas aeruginosa. However, patients can succumb to such infections even if they undergo colistin therapy. This prompted us to investigate the probable antimicrobial resistance mechanisms and virulence determinants involved in colistin- and carbapenem-resistant
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Antibiotics like colistin can save patients infected with carbapenem-resistant Pseudomonas aeruginosa. However, patients can succumb to such infections even if they undergo colistin therapy. This prompted us to investigate the probable antimicrobial resistance mechanisms and virulence determinants involved in colistin- and carbapenem-resistant P. aeruginosa (CCRPA). Of the 448 P. aeruginosa clinical strains, 19 isolates were resistant to both colistin and carbapenem. Carbapenemases and efflux pump encoding genes were assessed by multiplex PCR and qPCR, respectively. blaVIM was detected among six CCRPA isolates and blaIMP in one strain. The expression levels of pmrA and phoP, as well as pmrB genes and their association with colistin resistance, were assessed by qPCR and semi-quantitate PCR, respectively. pmrA and phoP genes were significantly enhanced in three and nine CCRPA isolates, respectively. We also phenotypically evaluated biofilms, pyocyanin, and alginate production among CCRPA strains. Alginate production was observed in 15 isolates, followed by biofilm (n = 8) and pyocyanin (n = 5). Our results highlighted the coexistence of colistin and carbapenem resistance and biofilm formation among clinical isolates of CCRPA. Further studies are required to trace the source and the origin of colistin and carbapenem resistance in this specific environment.
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Open AccessArticle
Correlation between Anti-Toxoplasma gondii IgG Antibodies in Serum and Colostrum of Naturally Infected Sheep and Passive Immunization in Lambs
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Felipe Boniedj Ventura Alvares, Brendo Andrade Lima, Ana Maria Santos Lima, Samira Pereira Batista, Antônia Aniellen Raianne Moisés Aguiar, Larissa Claudino Ferreira, Welitânia Inácia Silva, Thais Ferreira Feitosa and Vinícius Longo Ribeiro Vilela
Microbiol. Res. 2024, 15(3), 1806-1813; https://doi.org/10.3390/microbiolres15030120 - 6 Sep 2024
Abstract
Toxoplasmosis, caused by Toxoplasma gondii, poses a significant threat to sheep flocks, affecting reproductive performance and meat quality, and leading to economic losses. This study aimed to evaluate the correlation between anti-T. gondii IgG antibodies in the serum and colostrum of
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Toxoplasmosis, caused by Toxoplasma gondii, poses a significant threat to sheep flocks, affecting reproductive performance and meat quality, and leading to economic losses. This study aimed to evaluate the correlation between anti-T. gondii IgG antibodies in the serum and colostrum of naturally infected ewes and to assess passive immunity in newborn lambs. Blood and colostrum samples were collected from 162 ewes and 182 lambs across 20 sheep farms in Paraíba, Brazil. Samples were tested for anti-T. gondii and anti-Neospora caninum IgG using indirect fluorescence antibody tests (IFATs), with titers ≥ 1:64 considered positive. Among the ewes, 45.1% tested positive for anti-T. gondii IgG in serum, with titers ranging from 1:64 to 1:16,384. The colostrum from 94.6% of the ewes also tested positive, although 74% had higher titers in their serum than in their colostrum. Concordance between serum and colostrum was high, with a kappa coefficient of 0.950. Lamb serum showed a perfect agreement with maternal colostrum (kappa = 0.962), demonstrating effective passive transfer of antibodies. This study confirms that colostrum is a reliable matrix for detecting anti-T. gondii antibodies and assessing passive immunity in lambs. The high concordance between serum, colostrum, and lamb titers suggests that IFATs on colostrum can be a practical tool for monitoring maternal antibody transfer, contributing to the better management of T. gondii infections in sheep flocks.
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(This article belongs to the Special Issue Veterinary Microbiology and Diagnostics)
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Open AccessArticle
Forensic Genomic Analysis Determines That RaTG13 Was Likely Generated from a Bat Mating Plug
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Steven E. Massey
Microbiol. Res. 2024, 15(3), 1784-1805; https://doi.org/10.3390/microbiolres15030119 - 5 Sep 2024
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RaTG13 is phylogenomically the closest related coronavirus to SARS-CoV-2; consequently, understanding the provenance of this high-value genome sequence is important in understanding the origin of SARS-CoV-2. While RaTG13 was described as being generated from a Rhinolophus affinis fecal swab obtained from a mine
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RaTG13 is phylogenomically the closest related coronavirus to SARS-CoV-2; consequently, understanding the provenance of this high-value genome sequence is important in understanding the origin of SARS-CoV-2. While RaTG13 was described as being generated from a Rhinolophus affinis fecal swab obtained from a mine in Mojiang, Yunnan, numerous investigators have pointed out that this is inconsistent with the low proportion of bacterial reads in the sequencing dataset. Metagenomic analysis confirms that only 10.3% of small-subunit (SSU) rRNA sequences in the dataset are bacterial, which is inconsistent with a fecal sample. In addition, the bacterial taxa present in the sample are shown to be inconsistent with fecal material. The assembly of mitochondrial SSU rRNA sequences in the dataset produces a sequence 98.7% identical to R. affinis mitochondrial SSU rRNA, indicating that the sample was generated from R. affinis or a closely related species. In addition, 87.5% of the reads in the dataset map to the Rhinolophus ferrumequinum genome, and 62.2% of these map to protein-coding genes, indicating that the dataset represents a Rhinolophus sp. transcriptome rather than a fecal swab sample. Differential gene expression analysis reveals that the pattern of expressed genes in the RaTG13 dataset is similar to that of RaTG15, which was also collected from the Mojiang mine. GO enrichment analysis reveals the overexpression of spermatogenesis- and olfaction-related genes in both datasets. This observation is consistent with a mating plug found in female Rhinolophid bats and suggests that RaTG13 was mis-sampled from such a plug. A validated natural provenance of the RaTG13 dataset throws into relief the unusual features of the SARS-CoV-2 genome.
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Open AccessArticle
Mastitis Pathogens Mannheimia haemolytica, Staphylococcus aureus, and Streptococcus uberis Selectively Alter TLR Gene Transcription in Sheep Mammary Epithelial Cells
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Riccardo Tassi, Helen Todd and Keith T. Ballingall
Microbiol. Res. 2024, 15(3), 1772-1783; https://doi.org/10.3390/microbiolres15030118 - 4 Sep 2024
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Despite the impact of mastitis on sheep production worldwide, the pathogenesis and host response to bacterial infection of the ovine mammary gland are poorly characterized. Studies in cattle highlight the significance of the mammary epithelium in pathogen recognition and the subsequent host response.
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Despite the impact of mastitis on sheep production worldwide, the pathogenesis and host response to bacterial infection of the ovine mammary gland are poorly characterized. Studies in cattle highlight the significance of the mammary epithelium in pathogen recognition and the subsequent host response. The objective of this study was to assess bacterial adherence, invasion, and Toll like receptor (TLR) gene expression in primary sheep mammary epithelial cells (pMEC) following co-culture with the three principal mastitis pathogens of sheep, Mannheimia haemolytica, Staphylococcus aureus, and Streptococcus uberis. S. aureus was 140-fold more adherent than S. uberis and 850-fold more adherent than M. haemolytica. However, only S. aureus was internalized after 3 h of co-culture. TLR1, 2, 3, 4, 6, and 9 were shown to be constitutively transcribed by pMEC. M. haemolytica induced upregulation of transcription of TLR1, 2, 3, and 4. By contrast, S. uberis and S. aureus induced concentration-dependent transcription of TLR2 and TLR4 with a higher level of transcription in cells stimulated with the bacteria at a multiplicity of infection (MOI) of 200 compared to cells stimulated with a MOI of 20. These experiments define the range of TLR genes constitutively transcribed in sheep pMEC and show that bacterial infection has the capacity to regulate transcription in a species-specific and concentration-dependent manner.
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Open AccessArticle
Detection of Bacteria with Potential to Cause Hospital-Associated Infections in a Small-Species Veterinary Hospital in Mexico
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Diego Josimar Hernández-Silva, Ana Isabel Rivera-González, Laura Karina Avilés-Benitez, Mayra M. Becerra-Reyes, Carlos Rivera-Ballesteros, Rodrigo Morales-García, Larisa García-Ramírez, Orlando Federico Chávez-Moreno, Gabriela Aguilar-Tipacamu, José Guadalupe Gómez-Soto and Juan Mosqueda
Microbiol. Res. 2024, 15(3), 1758-1771; https://doi.org/10.3390/microbiolres15030117 - 31 Aug 2024
Abstract
Hospital-Associated Infections (HAIs) are caused by microorganisms that are not present before patients are admitted to healthcare facilities, and usually have multidrug resistance profiles. There is ample information and active research in human medicine to create preventive and control measures, but there have
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Hospital-Associated Infections (HAIs) are caused by microorganisms that are not present before patients are admitted to healthcare facilities, and usually have multidrug resistance profiles. There is ample information and active research in human medicine to create preventive and control measures, but there have been fewer efforts in animal medicine, and studies in only a few countries have been examining how this problem presents in veterinary hospitals. In Mexico, there have been no studies on the presence of multidrug-resistant bacteria associated with HAIs in veterinary medicine. Therefore, the surfaces of inanimate objects and equipment in a university veterinary hospital for small species were sampled to search for bacteria with the potential to cause HAIs. After isolation, molecular identification and multidrug resistance tests were carried out. One bacterial strain was found to be resistant to carbapenems, third-generation cephalosporines, and penicillin/β-lactamase inhibitors. Additionally, other susceptible bacterial genera were identified as potential nosocomial pathogens in humans and animals. The presence of multidrug-resistant bacteria was confirmed. Further studies should be conducted to determine the isolate’s origin and its relationship with reported human clinical genotypes. This type of study highlights the importance of epidemiological surveillance and the need to not underestimate the potential risk posed by multidrug-resistant microorganisms.
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(This article belongs to the Special Issue Veterinary Microbiology and Diagnostics)
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Open AccessArticle
Complete Genome Sequence of the Butirosin-Producing Bacillus vitellinus NBRC 13296 and Its Reclassification to Paenibacillus chitinolyticus
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Kyung-A. Hyun, Seung-Young Kim, Kyung-Hwan Boo, Won-Jae Chi and Chang-Gu Hyun
Microbiol. Res. 2024, 15(3), 1747-1757; https://doi.org/10.3390/microbiolres15030116 - 30 Aug 2024
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Butirosins are naturally occurring aminoglycoside (AG) antibiotics featuring a 4,5-disubstituted 2-deoxystreptamine (2-DOS) with a (2S)-4-amino-2-hydroxybutyrate (AHBA) side chain. This side chain has been shown to confer resistance against AG-modifying enzymes, leading to ongoing studies on the butirosin biosynthetic pathway and the corresponding enzymes.
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Butirosins are naturally occurring aminoglycoside (AG) antibiotics featuring a 4,5-disubstituted 2-deoxystreptamine (2-DOS) with a (2S)-4-amino-2-hydroxybutyrate (AHBA) side chain. This side chain has been shown to confer resistance against AG-modifying enzymes, leading to ongoing studies on the butirosin biosynthetic pathway and the corresponding enzymes. Butirosin is produced by Niallia (formerly Bacillus) circulans and Bacillus vitellinus, with most research focused on the first strain. To date, no whole-genome analysis has been performed on B. vitellinus. In this study, we sequenced the complete genome of B. vitellinus NBRC 13296 and performed a comparative analysis of different butirosin biosyntheric gene clusters (BGCs), including those from N. circulans. The complete genome of B. vitellinus NBRC 13296 comprises a 6,331,192-base circular chromosome with GC content of 52.68%. The annotation revealed the presence of 5605 CDSs, 70 tRNA genes, 30 rRNA genes, and 3 ncRNA genes in NBRC 13296. The highest dDDH and ANI values between NBRC 13296 and the most closely related type strain, Paenibacillus chitinolyticus KCCM 41,400, were 97.8% and 98.66%, respectively. Based on these genome-based comparative analyses, we propose reclassifying B. vitellinus NBRC 13296 as P. chitinolyticus. Genome mining revealed 18 gene clusters encoding the biosynthesis of diverse secondary metabolites in the genome of B. vitellinus NBRC 13296, indicating the enormous biosynthetic potential of this strain. The predicted structural diversity of the secondary metabolites includes aminoglycosides, PKS, NRPS, PKS–NRPS hybrids, metallophores, phosphonates, terpenes, β-lactones, and RiPP peptides. We then comparatively characterized the butirosin BGCs previously studied in several N. circulans strains. Additionally, the comparative genome analysis revealed complete butirosin BGCs identified from P. chitinolyticus KCCM 41,400, P. chitinolyticus NRRL B-23119, P. chitinolyticus NRRL B-23120, P. chitinolyticus B-14908, P. chitinolyticus YSY-3.1, P. chitinolyticus JMW06, Paenibacillus sp. GbtcB18, Paenibacillus sp. HGH0039, and Paenibacillus sp. MZ04-78.2. Finally, we identified the core region consisting of BtrS, BtrN, BtrM, BtrL, BtrA, BtrB, BtrC, BtrD, BtrD, BtrE, BtrF, BtrG, BtrH, BtrI, BtrI, BtrJ, BtrK, BtrO, BtrP, and BtrV, followed by an upstream region organizing BtrQ, BtrW, BtrX, BtrY, and BtrZ in the same transcriptional direction and sequential genetic arrangement, and a downstream region organizing various proteins based on BtrT, BtrR2, BtrU, and BtrR1. Our study provides insights into the reclassification of B. vitellinus NBRC 13296 to P. chitinolyticus and suggests the need for continued studies on butirosin biosynthesis from an enzymatic perspective.
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Open AccessArticle
One-Pot Synthesis of Carbon Nanodots Retrieved from Motorcycle Exhaust: Antibacterial and Antibiofilm Applications
by
Stinil Sam, Jae-Wook Oh, Prasanth Venkatachalam, Manikandan Muthu and Judy Gopal
Microbiol. Res. 2024, 15(3), 1738-1746; https://doi.org/10.3390/microbiolres15030115 - 30 Aug 2024
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Carbon nanodots (CNDs) are nanoscale carbon-based materials with particle sizes typically less than 10 nm. They are characterized by their unique electronic, optical, and surface properties, as well as their bright and tunable fluorescence across the visible light spectrum. The process involved in
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Carbon nanodots (CNDs) are nanoscale carbon-based materials with particle sizes typically less than 10 nm. They are characterized by their unique electronic, optical, and surface properties, as well as their bright and tunable fluorescence across the visible light spectrum. The process involved in synthesizing carbon nanodots is rather energy-consuming, expensive, and complicated. Motorcycle exhausts have been looked at as an environmental pollutant. In this paper, the bright side of motorcycle exhausts has been projected, whereby we have extracted carbon nanodots from motorcycle exhausts, using a simple and straightforward strategy. The nanomaterial was successfully isolated and characterized. The antimicrobial activity of the indigenously prepared nanomaterial was evaluated and coatings were prepared on glass and these nanocarbon coatings were demonstrated for their anti-biofilm activity. The results confirm the innovative and sustainable recovery of antibacterial carbon nanodots from environmental pollutants such as motorcycle exhaust.
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Open AccessCase Report
Severe Localized Q Fever, a Diagnostic Challenge: Report of Two Cases and Review of the Literature
by
Monica Muntean, Amanda Radulescu, Bogdan Caloian, Ioana Hiriscau, Mihaela Lupșe and Violeta Briciu
Microbiol. Res. 2024, 15(3), 1728-1737; https://doi.org/10.3390/microbiolres15030114 - 29 Aug 2024
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Coxiella burnetii (C. burnetii) can cause asymptomatic infections and acute, chronic, or localized manifestations affecting multiple organs. Doxycycline is the most effective treatment for Q fever. We report two cases of localized C. burnetii infections with no evident epidemiological link. Case
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Coxiella burnetii (C. burnetii) can cause asymptomatic infections and acute, chronic, or localized manifestations affecting multiple organs. Doxycycline is the most effective treatment for Q fever. We report two cases of localized C. burnetii infections with no evident epidemiological link. Case reports: We present the case of a 51-year-old male patient admitted for low fever, dry cough, and malaise. The physical examination was unremarkable except for painful hepatomegaly. He was diagnosed with a liver abscess based on inflammatory markers, positive serology for C. burnetii, and abdominal computed tomography (CT) showing a large lesion (112/86/93 mm) within the right liver lobe. Blood cultures and the fluid obtained by percutaneous catheter drainage were negative. After 28 days of treatment with doxycycline, he was discharged well. At the three-month reevaluation, blood tests were normal, and a CT scan showed a minimal residual lesion. The second case was an 81-year-old female with many comorbidities, almost simultaneous acute ischemic stroke, and double-valve (native and prosthetic) infective endocarditis (IE). C. burnetii infection was confirmed by high titers of antibodies (phase I and II IgG), most probably the direct cause of both manifestations. These two cases presented with very rare manifestations of C. burnetii infections, highlighting its diagnostic difficulties. Conclusions: A clear distinction between acute and chronic Q fever is difficult in rare localized infections, as are organ abscesses. Coxiella burnetii may cause stroke and infective endocarditis, especially in the elderly. Even in the absence of epidemiological clues, in patients with localized infections, the C. burnetii etiology should be considered.
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Open AccessReview
Multifaceted Applications of Synthetic Microbial Communities: Advances in Biomedicine, Bioremediation, and Industry
by
Edgar Adrian Contreras-Salgado, Ana Georgina Sánchez-Morán, Sergio Yair Rodríguez-Preciado, Sonia Sifuentes-Franco, Rogelio Rodríguez-Rodríguez, José Macías-Barragán and Mariana Díaz-Zaragoza
Microbiol. Res. 2024, 15(3), 1709-1727; https://doi.org/10.3390/microbiolres15030113 - 29 Aug 2024
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The broad range of applications offered by synthetic biology and bioengineering has revolutionized the ability to design and redesign microorganisms to express specific functions, overcoming the limitations of natural biological systems. This advancement has been achieved through the use of mathematical models and
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The broad range of applications offered by synthetic biology and bioengineering has revolutionized the ability to design and redesign microorganisms to express specific functions, overcoming the limitations of natural biological systems. This advancement has been achieved through the use of mathematical models and genetic circuits, enabling the precise design of synthetic microbial communities. These are defined as artificially created communities through co-cultures of selected species that share similar characteristics and environments. Reprogramming an organism is carried out by inserting synthetic genetic circuits, which are designed in a controlled manner to obtain biotechnological products beneficial to humans, their health, and the environment. The potential applications in medicine, bioremediation, industry, and pharmaceuticals make the research of synthetic microbial communities a promising field for the future. However, the implementation of synthetic microbial communities carries potential risks, such as horizontal gene transfer and possible environmental impacts. It is crucial to carefully evaluate these functions and risks, considering biocontainment and the associated ethical and ecological implications.
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Open AccessArticle
Replication Kinetics and Infectivity of African Swine Fever Virus (ASFV) Variants with Different Genotypes or Levels of Virulence in Cell Culture Models of Primary Porcine Macrophages
by
Brecht Droesbeke, Nadège Balmelle, Ann Brigitte Cay, Shaojie Han, Dayoung Oh, Hans J. Nauwynck and Marylène Tignon
Microbiol. Res. 2024, 15(3), 1690-1708; https://doi.org/10.3390/microbiolres15030112 - 29 Aug 2024
Abstract
African Swine Fever (ASF) is a devastating viral hemorrhagic disease that causes high morbidity and mortality in domestic pigs and wild boars, severely impacting the swine industry. The etiologic agent, African Swine Fever virus (ASFV), mainly infects myeloid cells of the swine mononuclear
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African Swine Fever (ASF) is a devastating viral hemorrhagic disease that causes high morbidity and mortality in domestic pigs and wild boars, severely impacting the swine industry. The etiologic agent, African Swine Fever virus (ASFV), mainly infects myeloid cells of the swine mononuclear phagocytic system (MPS). For other porcine viruses, in vitro culture models with primary cells are widely used as they mimic the in vivo viral replication behavior better compared to continuous cell lines. Our study validates this possible correlation for ASFV using cell culture models established for three different porcine macrophages, isolated from the lungs (porcine alveolar macrophages), blood (monocyte-derived macrophages) and spleen (spleen macrophages). The cells were infected with two genotype I and two genotype II strains with different pathogenic potential in vivo. The highly virulent strains replicated better in general than the low-virulent strains. This was most pronounced in monocyte-derived macrophages, although only statistically significant 18 h post-infection (hpi) in the intracellular genomic ASFV copies between E70 and the low-virulent strains. For this reason, we conclude that the different replication characteristics between the strains with different virulence do not proportionally represent the differences in pathology seen between the strains in vivo. Additionally, ASFV-positive cells were observed earlier in monocyte-derived macrophages (MDMs) compared to the alveolar and spleen macrophages, subsequently leading to an earlier rise in extracellular virus, and, ultimately, more MDMs were infected at the end of sampling. For these reasons, we propose MDMs as the best-suited cell type to study ASFV.
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(This article belongs to the Special Issue African Swine Fever Vaccines: Development and Application)
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Open AccessReview
Microbial-Derived Carotenoids and Their Health Benefits
by
Chikanshi Sharma, Madhu Kamle and Pradeep Kumar
Microbiol. Res. 2024, 15(3), 1670-1689; https://doi.org/10.3390/microbiolres15030111 - 27 Aug 2024
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Natural carotenoids (CARs) such as β-carotene, astaxanthin, lutein, norbixin, bixin, capsanthin, lycopene, β-Apo-8-carotenal, canthaxanthin, β-apo-8-carotenal-ester, and zeaxanthin are being explored for possible applications in feed, food, cosmeceuticals, and nutraceuticals. Three primary areas of carotenoid research are emerging: (1) encapsulations for improved chemical and
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Natural carotenoids (CARs) such as β-carotene, astaxanthin, lutein, norbixin, bixin, capsanthin, lycopene, β-Apo-8-carotenal, canthaxanthin, β-apo-8-carotenal-ester, and zeaxanthin are being explored for possible applications in feed, food, cosmeceuticals, and nutraceuticals. Three primary areas of carotenoid research are emerging: (1) encapsulations for improved chemical and physical properties; (2) natural source carotenoid manufacturing; and (3) preclinical, epidemiological, and clinical studies of carotenoids’ potential health benefits. The recent advancements in research on the chemistry and antioxidant activity, marketing strategies, dietary sources, bioavailability, and bioaccessibility, extraction, dietary consumption, encapsulating techniques, and health advantages of carotenoids are all extensively discussed in this review. Carotenoids are pigments found naturally in most fruits and vegetables, algae, plants, and photosynthetic bacteria. Carotenoids cannot be synthesized by humans and must be consumed in the form of food or supplements. There are several roles for carotenoids in human health. Although individual carotenoids may function in different ways, their main action is to act as antioxidants. There are validated techniques for separating and purifying carotenoids, yet, industrial production requires the development of economically viable techniques for larger-scale implementation. Carotenoids have been shown to boost cognitive performance and cardiovascular health, as well as help prevent some types of cancer. Despite evidence for carotenoids’ health benefits, major population-based supplementation trials have yielded conflicting outcomes for several carotenoids. This review includes recent developments in carotenoid metabolism and nutritional and health advantages. It also offers an outlook on future directions in these areas.
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