Pub Date : 2024-07-16DOI: 10.1186/s13568-024-01741-0
Shabana Islam, Erum Akbar Hussain, Shahida Shujaat, Muhammad Umer Khan, Qurban Ali, Saif Ul Malook, Daoud Ali
The issue of antibiotic resistance in pathogenic microbes is a global concern. This study was aimed to explore in silico and in vitro analysis of the antibacterial efficacy of different natural ligands against bacterial activity. The ligands included in the study were Propolis Neoflavanoide 1, Carvacrol, Cinnamaldehyde, Thymol, p-benzoquinone, and Ciprofloxacin (standard drug S*). The outcomes of molecular docking revealed that Propolis Neoflavaniode-1 showed a highly significant binding energy of - 7.1 and - 7.2 kcal/mol for the two gram-positive bacteria, as compared to the gram-negative bacteria. All ligands demonstrated acute toxicity (oral, dermal), except for Propolis Neoflavanoide 1 and S* drugs, with a confidence score range of 50-60%. Using a molecular dynamic simulation approach, we investigated Propolis Neoflavaniode-1's potential for therapeutic use in more detail. An MD simulation lasting 100 ns was performed using the Desmond Simulation software to examine the conformational stability and steady state of Propolis Neoflavaniode-1 in protein molecule complexes. Additionally, in vitro studies confirmed the antimicrobial activity of Propolis Neoflavaniode 1 by increasing the zone of inhibition against Gram-positive bacteria, p < 0.005 as compared to gram-negative bacteria. This study revealed the promising antibacterial efficacy of Propolis Neoflavaniode 1, demonstrated through robust in silico analyses, minimal toxicity, and confirmed in vitro antimicrobial activity, suggesting its potential as a viable alternative to combat antibiotic resistance.
{"title":"Antibacterial potential of Propolis: molecular docking, simulation and toxicity analysis.","authors":"Shabana Islam, Erum Akbar Hussain, Shahida Shujaat, Muhammad Umer Khan, Qurban Ali, Saif Ul Malook, Daoud Ali","doi":"10.1186/s13568-024-01741-0","DOIUrl":"10.1186/s13568-024-01741-0","url":null,"abstract":"<p><p>The issue of antibiotic resistance in pathogenic microbes is a global concern. This study was aimed to explore in silico and in vitro analysis of the antibacterial efficacy of different natural ligands against bacterial activity. The ligands included in the study were Propolis Neoflavanoide 1, Carvacrol, Cinnamaldehyde, Thymol, p-benzoquinone, and Ciprofloxacin (standard drug S*). The outcomes of molecular docking revealed that Propolis Neoflavaniode-1 showed a highly significant binding energy of - 7.1 and - 7.2 kcal/mol for the two gram-positive bacteria, as compared to the gram-negative bacteria. All ligands demonstrated acute toxicity (oral, dermal), except for Propolis Neoflavanoide 1 and S* drugs, with a confidence score range of 50-60%. Using a molecular dynamic simulation approach, we investigated Propolis Neoflavaniode-1's potential for therapeutic use in more detail. An MD simulation lasting 100 ns was performed using the Desmond Simulation software to examine the conformational stability and steady state of Propolis Neoflavaniode-1 in protein molecule complexes. Additionally, in vitro studies confirmed the antimicrobial activity of Propolis Neoflavaniode 1 by increasing the zone of inhibition against Gram-positive bacteria, p < 0.005 as compared to gram-negative bacteria. This study revealed the promising antibacterial efficacy of Propolis Neoflavaniode 1, demonstrated through robust in silico analyses, minimal toxicity, and confirmed in vitro antimicrobial activity, suggesting its potential as a viable alternative to combat antibiotic resistance.</p>","PeriodicalId":7537,"journal":{"name":"AMB Express","volume":null,"pages":null},"PeriodicalIF":3.5,"publicationDate":"2024-07-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11252112/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141625650","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-07-11DOI: 10.1186/s13568-024-01719-y
G Vinaya Chandu Vidyasagar, P V Janardhan Reddy, M Md Ghouse, T C Venkateswarulu, P B Kavi Kishor, Prashanth Suravajhala, Rathnagiri Polavarapu
Corona virus disease 2019 (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), claimed millions globally. After the report of the first incidence of the virus, variants emerged with each posing a unique threat than its predecessors. Though many advanced diagnostic assays like real-time PCR are available for screening of SARS-CoV-2, their applications are being hindered because of accessibility and cost. With the advent of rapid assays for antigenic screening of SARS-CoV-2 made diagnostics far easy as the assays are rapid, cost-effective and can be used at point-of-care settings. In the present study, a fusion construct was made utilising highly immunogenic B cell epitopes from the three important structural proteins of SARS-CoV-2. The protein was expressed; purified capture mAbs generated and rapid antigen assay was developed. Eight hundred and forty nasopharyngeal swab samples were screened for the evaluation of the developed assay which showed 37.14% positivity, 96.51% and 100% sensitivity and specificity respectively. The assay developed was supposed to identify SARS-CoV-2 wild-type as well as variants of concern and variants of importance in real-time conditions.
{"title":"Designing and expression of novel recombinant fusion protein for efficient antigen screening of SARS-CoV-2.","authors":"G Vinaya Chandu Vidyasagar, P V Janardhan Reddy, M Md Ghouse, T C Venkateswarulu, P B Kavi Kishor, Prashanth Suravajhala, Rathnagiri Polavarapu","doi":"10.1186/s13568-024-01719-y","DOIUrl":"10.1186/s13568-024-01719-y","url":null,"abstract":"<p><p>Corona virus disease 2019 (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), claimed millions globally. After the report of the first incidence of the virus, variants emerged with each posing a unique threat than its predecessors. Though many advanced diagnostic assays like real-time PCR are available for screening of SARS-CoV-2, their applications are being hindered because of accessibility and cost. With the advent of rapid assays for antigenic screening of SARS-CoV-2 made diagnostics far easy as the assays are rapid, cost-effective and can be used at point-of-care settings. In the present study, a fusion construct was made utilising highly immunogenic B cell epitopes from the three important structural proteins of SARS-CoV-2. The protein was expressed; purified capture mAbs generated and rapid antigen assay was developed. Eight hundred and forty nasopharyngeal swab samples were screened for the evaluation of the developed assay which showed 37.14% positivity, 96.51% and 100% sensitivity and specificity respectively. The assay developed was supposed to identify SARS-CoV-2 wild-type as well as variants of concern and variants of importance in real-time conditions.</p>","PeriodicalId":7537,"journal":{"name":"AMB Express","volume":null,"pages":null},"PeriodicalIF":3.5,"publicationDate":"2024-07-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11239635/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141578733","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Urinary tract infections (UTI) by antibiotic resistant and virulent K. pneumoniae are a growing concern. Understanding the genome and validating the genomic profile along with pangenome analysis will facilitate surveillance of high-risk clones of K. pneumoniae to underpin management strategies toward early detection. The present study aims to correlate resistome with phenotypic antimicrobial resistance and virulome with pathogenicity in Klebsiella spp. The present study aimed to perform complete genome sequences of Klebsiella spp. and to analyse the correlation of resistome with phenotypic antimicrobial resistance and virulome with pathogenicity. To understand the resistome, pangenome and virulome in the Klebsiella spp, the ResFinder, CARD, IS Finder, PlasmidFinder, PHASTER, Roary, VFDB were used. The phenotypic susceptibility profiling identified the uropathogenic kp3 to exhibit multi drug resistance. The resistome and in vitro antimicrobial profiling showed concordance with all the tested antibiotics against the study strains. Hypermucoviscosity was not observed for any of the test isolates; this phenotypic character matches perfectly with the absence of rmpA and magA genes. To the best of our knowledge, this is the first report on the presence of ste, stf, stc and sti major fimbrial operons of Salmonella enterica serotype Typhimurium in K. pneumoniae genome. The study identifies the discordance of virulome and virulence in Klebsiella spp. The complete genome analysis and phenotypic correlation identify uropathogenic K. pneumoniae kp3 as a carbapenem-resistant and virulent pathogen. The Pangenome of K. pneumoniae was open suggesting high genetic diversity. Diverse K serotypes were observed. Sequence typing reveals the prevalence of K. pneumoniae high-risk clones in UTI catheterised patients. The study also highlights the concordance of resistome and in vitro susceptibility tests. Importantly, the study identifies the necessity of virulome and phenotypic virulence markers for timely diagnosis and immediate treatment for the management of high-risk K. pneumoniae clones.
由耐药性和毒性肺炎双球菌引起的尿路感染(UTI)日益受到关注。了解基因组和验证基因组图谱以及庞基因组分析将有助于监测肺炎克雷伯菌的高风险克隆,为早期发现的管理策略提供依据。本研究旨在分析克雷伯氏菌的抗药性基因组与表型抗菌药耐药性以及致病性病毒组之间的相关性。 本研究旨在对克雷伯氏菌进行完整的基因组测序,并分析抗药性基因组与表型抗菌药耐药性以及致病性病毒组之间的相关性。为了解克雷伯氏菌的耐药性组、泛基因组和病毒组,使用了 ResFinder、CARD、IS Finder、PlasmidFinder、PHASTER、Roary 和 VFDB。表型药敏谱分析发现尿路致病菌 kp3 具有多重耐药性。耐药性组和体外抗菌谱分析显示,研究菌株对所有测试过的抗生素都有一致的耐药性。在所有测试分离物中都没有观察到高粘液性;这一表型特征与 rmpA 和 magA 基因的缺失完全吻合。据我们所知,这是首次报道肺炎克氏菌基因组中存在肠炎沙门氏菌血清型鼠伤寒沙门氏菌的 ste、stf、stc 和 sti 主要fimbrial操作子。通过完整的基因组分析和表型相关性研究发现,尿路致病性肺炎克雷伯菌 kp3 是一种耐碳青霉烯类抗生素的强毒力病原体。肺炎克雷伯菌的庞基因组是开放的,表明其具有高度遗传多样性。观察到了多种 K 血清型。序列分型揭示了肺炎克氏菌高风险克隆在UTI导管插入患者中的流行情况。该研究还强调了耐药性组和体外药敏试验的一致性。重要的是,该研究确定了病毒组和表型毒力标记的必要性,以便及时诊断和立即治疗高危肺炎克隆。
{"title":"Complete genome sequence, phenotypic correlation and pangenome analysis of uropathogenic Klebsiella spp.","authors":"Abhirami Krishnamoorthy Sundaresan, Jaya Gangwar, Aravind Murugavel, Ganesh Babu Malli Mohan, Jayapradha Ramakrishnan","doi":"10.1186/s13568-024-01737-w","DOIUrl":"10.1186/s13568-024-01737-w","url":null,"abstract":"<p><p>Urinary tract infections (UTI) by antibiotic resistant and virulent K. pneumoniae are a growing concern. Understanding the genome and validating the genomic profile along with pangenome analysis will facilitate surveillance of high-risk clones of K. pneumoniae to underpin management strategies toward early detection. The present study aims to correlate resistome with phenotypic antimicrobial resistance and virulome with pathogenicity in Klebsiella spp. The present study aimed to perform complete genome sequences of Klebsiella spp. and to analyse the correlation of resistome with phenotypic antimicrobial resistance and virulome with pathogenicity. To understand the resistome, pangenome and virulome in the Klebsiella spp, the ResFinder, CARD, IS Finder, PlasmidFinder, PHASTER, Roary, VFDB were used. The phenotypic susceptibility profiling identified the uropathogenic kp3 to exhibit multi drug resistance. The resistome and in vitro antimicrobial profiling showed concordance with all the tested antibiotics against the study strains. Hypermucoviscosity was not observed for any of the test isolates; this phenotypic character matches perfectly with the absence of rmpA and magA genes. To the best of our knowledge, this is the first report on the presence of ste, stf, stc and sti major fimbrial operons of Salmonella enterica serotype Typhimurium in K. pneumoniae genome. The study identifies the discordance of virulome and virulence in Klebsiella spp. The complete genome analysis and phenotypic correlation identify uropathogenic K. pneumoniae kp3 as a carbapenem-resistant and virulent pathogen. The Pangenome of K. pneumoniae was open suggesting high genetic diversity. Diverse K serotypes were observed. Sequence typing reveals the prevalence of K. pneumoniae high-risk clones in UTI catheterised patients. The study also highlights the concordance of resistome and in vitro susceptibility tests. Importantly, the study identifies the necessity of virulome and phenotypic virulence markers for timely diagnosis and immediate treatment for the management of high-risk K. pneumoniae clones.</p>","PeriodicalId":7537,"journal":{"name":"AMB Express","volume":null,"pages":null},"PeriodicalIF":3.5,"publicationDate":"2024-07-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11224175/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141533296","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-07-04DOI: 10.1186/s13568-024-01736-x
Eon-Bee Lee, Kyubae Lee
This study investigated the antibacterial properties of Coptis rhizome, a plant traditionally used for respiratory infections, against Streptoccus pneumonia (S. pneumoniae), for which there has been minimal empirical evidence of effectiveness. The study particularly examined autolysis, indirectly associated with antibacterial resistance, when using Coptis rhizome for bacterial infections. In our methodology, Coptis rhizome was processed with ethanol and distilled water to produce four different extracts: CRET30, CRET50, CRET70, and CRDW. The antibacterial activity of these extracts were tested through Minimum Inhibitory Concentration (MIC) assays, disk diffusion tests, and time-kill assays, targeting both standard (ATCC 49619) and resistant (ATCC 70067) strains. The study also evaluated the extracts' biofilm inhibition properties and monitored the expression of the lyt gene, integral to autolysis. The results prominently showed that the CRET70 extract demonstrated remarkable antibacterial strength. It achieved an MIC of 0.125 µg/mL against both tested S. pneumoniae strains. The disk diffusion assay recorded inhibition zones of 22.17 mm for ATCC 49619 and 17.20 mm for ATCC 70067. Impressively, CRET70 resulted in a 2-log decrease in bacterial numbers for both strains, showcasing its potent bactericidal capacity. The extract was also effective in inhibiting 77.40% of biofilm formation. Additionally, the significant overexpression of the lytA gene in the presence of CRET70 pointed to a potential mechanism of action for its antibacterial effects. The outcomes provided new perspectives on the use of Coptis rhizome in combating S. pneumoniae, especially significant in an era of escalating antibiotic resistance.
{"title":"Coptis rhizome extract influence on Streptococcus pneumoniae through autolysin activation.","authors":"Eon-Bee Lee, Kyubae Lee","doi":"10.1186/s13568-024-01736-x","DOIUrl":"10.1186/s13568-024-01736-x","url":null,"abstract":"<p><p>This study investigated the antibacterial properties of Coptis rhizome, a plant traditionally used for respiratory infections, against Streptoccus pneumonia (S. pneumoniae), for which there has been minimal empirical evidence of effectiveness. The study particularly examined autolysis, indirectly associated with antibacterial resistance, when using Coptis rhizome for bacterial infections. In our methodology, Coptis rhizome was processed with ethanol and distilled water to produce four different extracts: CRET30, CRET50, CRET70, and CRDW. The antibacterial activity of these extracts were tested through Minimum Inhibitory Concentration (MIC) assays, disk diffusion tests, and time-kill assays, targeting both standard (ATCC 49619) and resistant (ATCC 70067) strains. The study also evaluated the extracts' biofilm inhibition properties and monitored the expression of the lyt gene, integral to autolysis. The results prominently showed that the CRET70 extract demonstrated remarkable antibacterial strength. It achieved an MIC of 0.125 µg/mL against both tested S. pneumoniae strains. The disk diffusion assay recorded inhibition zones of 22.17 mm for ATCC 49619 and 17.20 mm for ATCC 70067. Impressively, CRET70 resulted in a 2-log decrease in bacterial numbers for both strains, showcasing its potent bactericidal capacity. The extract was also effective in inhibiting 77.40% of biofilm formation. Additionally, the significant overexpression of the lytA gene in the presence of CRET70 pointed to a potential mechanism of action for its antibacterial effects. The outcomes provided new perspectives on the use of Coptis rhizome in combating S. pneumoniae, especially significant in an era of escalating antibiotic resistance.</p>","PeriodicalId":7537,"journal":{"name":"AMB Express","volume":null,"pages":null},"PeriodicalIF":3.5,"publicationDate":"2024-07-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11224187/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141533297","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-06-29DOI: 10.1186/s13568-024-01732-1
Anali Riahi, Hadideh Mabudi, Elahe Tajbakhsh, Laleh Roomiani, Hasan Momtaz
Pseudomonas aeruginosa is a commonly found Gram-negative bacterium in healthcare facilities and is renowned for its ability to form biofilms and its virulence factors that are controlled by quorum sensing (QS) systems. The increasing prevalence of multidrug-resistant strains of this bacterium poses a significant challenge in the field of medicine. Consequently, the exploration of novel antimicrobial agents has become a top priority. This research aims to optimize chitosan derived from white shrimp (Metapenaeus affinis) using the Response Surface Methodology (RSM) computational approach. The objective is to investigate chitosan's potential as a solution for inhibiting QS activity and biofilm formation in P. aeruginosa ATCC 10,145. Under optimized conditions, chitin was treated with NaOH (1.41 M) for 15.75 h, HCl (7.49% vol) for 2.01 h, and at a deacetylation temperature of 81.15 °C. The resulting chitosan exhibited a degree of deacetylation (DD%) exceeding 93.98%, as confirmed by Fourier-transform infrared (FTIR) spectral analysis, indicating its high purity. The extracted chitosan demonstrated a significant synergistic antibiotic effect against P. aeruginosa when combined with ceftazidime, enhancing its bactericidal activity by up to 15-fold. In addition, sub-MIC (minimum inhibitory concentration) concentrations of extracted chitosan (10 and 100 µg/mL) successfully reduced the production of pyocyanin and rhamnolipid, as well as the swimming motility, protease activity and biofilm formation ability in comparison to the control group (P < 0.05). Moreover, chitosan treatment downregulated the RhlR and LasR genes in P. aeruginosa when compared to the control group (P < 0.05). The optimized chitosan extract shows significant potential as a coating agent for surgical equipment, effectively preventing nosocomial infections caused by P. aeruginosa pathogens.
{"title":"Optimizing chitosan derived from Metapenaeus affinis: a novel anti-biofilm agent against Pseudomonas aeruginosa.","authors":"Anali Riahi, Hadideh Mabudi, Elahe Tajbakhsh, Laleh Roomiani, Hasan Momtaz","doi":"10.1186/s13568-024-01732-1","DOIUrl":"10.1186/s13568-024-01732-1","url":null,"abstract":"<p><p>Pseudomonas aeruginosa is a commonly found Gram-negative bacterium in healthcare facilities and is renowned for its ability to form biofilms and its virulence factors that are controlled by quorum sensing (QS) systems. The increasing prevalence of multidrug-resistant strains of this bacterium poses a significant challenge in the field of medicine. Consequently, the exploration of novel antimicrobial agents has become a top priority. This research aims to optimize chitosan derived from white shrimp (Metapenaeus affinis) using the Response Surface Methodology (RSM) computational approach. The objective is to investigate chitosan's potential as a solution for inhibiting QS activity and biofilm formation in P. aeruginosa ATCC 10,145. Under optimized conditions, chitin was treated with NaOH (1.41 M) for 15.75 h, HCl (7.49% vol) for 2.01 h, and at a deacetylation temperature of 81.15 °C. The resulting chitosan exhibited a degree of deacetylation (DD%) exceeding 93.98%, as confirmed by Fourier-transform infrared (FTIR) spectral analysis, indicating its high purity. The extracted chitosan demonstrated a significant synergistic antibiotic effect against P. aeruginosa when combined with ceftazidime, enhancing its bactericidal activity by up to 15-fold. In addition, sub-MIC (minimum inhibitory concentration) concentrations of extracted chitosan (10 and 100 µg/mL) successfully reduced the production of pyocyanin and rhamnolipid, as well as the swimming motility, protease activity and biofilm formation ability in comparison to the control group (P < 0.05). Moreover, chitosan treatment downregulated the RhlR and LasR genes in P. aeruginosa when compared to the control group (P < 0.05). The optimized chitosan extract shows significant potential as a coating agent for surgical equipment, effectively preventing nosocomial infections caused by P. aeruginosa pathogens.</p>","PeriodicalId":7537,"journal":{"name":"AMB Express","volume":null,"pages":null},"PeriodicalIF":3.5,"publicationDate":"2024-06-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11217230/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141465487","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-06-28DOI: 10.1186/s13568-024-01733-0
Heng Zhao, Xiao Ju, Yong Nie, Timothy Y James, Xiao-Yong Liu
Rhizopus arrhizus is a saprotrophic, sometimes clinically- and industrially-relevant mold (Mucorales) and distributed worldwide, suggesting it can assimilate a broad spectrum of substrates. Here, 69 strains of R. arrhizus were investigated by using the Biolog FF MicroPlate for the profiles of utilizing 95 carbon and nitrogen substrates. The study showed that most R. arrhizus strains were similar in average well color development (AWCD) and substrate richness (SR). Nevertheless, 13 strains were unique in principal component analyses, heatmap, AWCD, and SR analyses, which may imply a niche differentiation within R. arrhizus. The species R. arrhizus was able to utilize all the 95 carbon and nitrogen substrates, consistent with the hypothesis of a great metabolic diversity. It possessed a substrate preference of alcohols, and seven substrates were most frequently utilized, with N-acetyl-D-galactosamine and L-phenylalanine ranking at the top of the list. Eight substrates, especially L-arabinose and xylitol, were capable of promoting sporulation and being applied for rejuvenating degenerated strains. By phenotyping R. arrhizus strains in carbon and nitrogen assimilation capacity, this study revealed the extent of intra-specific variability and laid a foundation for estimating optimum substrates that may be useful for industrial applications.
根瘤菌(Rhizopus arrhizus)是一种嗜咽性霉菌(Mucorales),有时与临床和工业有关,分布于世界各地,这表明它可以吸收多种基质。在此,研究人员使用 Biolog FF 微型平板对 69 株 R. arrhizus 菌株进行了研究,以了解其利用 95 种碳和氮基质的情况。研究表明,大多数 R. arrhizus 菌株在平均井色发展(AWCD)和基质丰富度(SR)方面相似。然而,有 13 个菌株在主成分分析、热图、AWCD 和 SR 分析中是独特的,这可能意味着 R. arrhizus 的生态位分化。R. arrhizus 能利用所有 95 种碳和氮底物,这与代谢多样性的假设一致。它偏好醇类底物,最常利用的底物有 7 种,其中 N-乙酰-D-半乳糖胺和 L-苯丙氨酸位居前列。八种底物,尤其是 L-阿拉伯糖和木糖醇,能够促进孢子的产生,并可用于使退化菌株恢复活力。通过对 R. arrhizus 菌株的碳氮同化能力进行表型分析,本研究揭示了特异性内变异的程度,并为估计可能用于工业应用的最佳底物奠定了基础。
{"title":"High-throughput screening carbon and nitrogen sources to promote growth and sporulation in Rhizopus arrhizus.","authors":"Heng Zhao, Xiao Ju, Yong Nie, Timothy Y James, Xiao-Yong Liu","doi":"10.1186/s13568-024-01733-0","DOIUrl":"https://doi.org/10.1186/s13568-024-01733-0","url":null,"abstract":"<p><p>Rhizopus arrhizus is a saprotrophic, sometimes clinically- and industrially-relevant mold (Mucorales) and distributed worldwide, suggesting it can assimilate a broad spectrum of substrates. Here, 69 strains of R. arrhizus were investigated by using the Biolog FF MicroPlate for the profiles of utilizing 95 carbon and nitrogen substrates. The study showed that most R. arrhizus strains were similar in average well color development (AWCD) and substrate richness (SR). Nevertheless, 13 strains were unique in principal component analyses, heatmap, AWCD, and SR analyses, which may imply a niche differentiation within R. arrhizus. The species R. arrhizus was able to utilize all the 95 carbon and nitrogen substrates, consistent with the hypothesis of a great metabolic diversity. It possessed a substrate preference of alcohols, and seven substrates were most frequently utilized, with N-acetyl-D-galactosamine and L-phenylalanine ranking at the top of the list. Eight substrates, especially L-arabinose and xylitol, were capable of promoting sporulation and being applied for rejuvenating degenerated strains. By phenotyping R. arrhizus strains in carbon and nitrogen assimilation capacity, this study revealed the extent of intra-specific variability and laid a foundation for estimating optimum substrates that may be useful for industrial applications.</p>","PeriodicalId":7537,"journal":{"name":"AMB Express","volume":null,"pages":null},"PeriodicalIF":3.5,"publicationDate":"2024-06-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11213844/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141465486","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Correction to: Enhancement of doxorubicin production in Streptomyces peucetius by genetic engineering and process optimization.","authors":"Songbai Yang, Jiali Gui, Zhengyu Zhang, Jiawei Tang, Shaoxin Chen","doi":"10.1186/s13568-024-01724-1","DOIUrl":"10.1186/s13568-024-01724-1","url":null,"abstract":"","PeriodicalId":7537,"journal":{"name":"AMB Express","volume":null,"pages":null},"PeriodicalIF":3.5,"publicationDate":"2024-06-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11196429/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141441979","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-06-21DOI: 10.1186/s13568-024-01730-3
Seyyed Mohammad Amin Mousavi-Sagharchi, Elina Afrazeh, Seyyedeh Fatemeh Seyyedian-Nikjeh, Maryam Meskini, Delaram Doroud, Seyed Davar Siadat
Mycobacterium tuberculosis, the causative agent of tuberculosis, is a pathogenic bacterium that has claimed millions of lives since the Middle Ages. According to the World Health Organization's report, tuberculosis ranks among the ten deadliest diseases worldwide. The presence of an extensive array of genes and diverse proteins within the cellular structure of this bacterium has provided us with a potent tool for diagnosis. While the culture method remains the gold standard for tuberculosis diagnosis, it is possible that molecular diagnostic methods, emphasis on the identification of mutation genes (e.g., rpoB and gyrA) and single nucleotide polymorphisms, could offer a safe and reliable alternative. Over the past few decades, as our understanding of molecular genetics has expanded, methods have been developed based on gene expansion and detection. These methods typically commence with DNA amplification through nucleic acid targeted techniques such as polymerase chain reaction. Various molecular compounds and diverse approaches have been employed in molecular assays. In this review, we endeavor to provide an overview of molecular assays for the diagnosis of tuberculosis with their properties (utilization, challenges, and functions). The ultimate goal is to explore the potential of replacing traditional bacterial methods with these advanced molecular diagnostic techniques.
结核病的病原体结核分枝杆菌是一种致病细菌,自中世纪以来已夺去了数百万人的生命。根据世界卫生组织的报告,结核病是全球十大致命疾病之一。这种细菌的细胞结构中存在大量基因和多种蛋白质,这为我们提供了一种有效的诊断工具。虽然培养法仍是结核病诊断的黄金标准,但分子诊断方法(侧重于突变基因(如 rpoB 和 gyrA)和单核苷酸多态性的鉴定)有可能提供一种安全可靠的替代方法。在过去的几十年中,随着我们对分子遗传学认识的加深,已经开发出了基于基因扩增和检测的方法。这些方法通常首先通过聚合酶链反应等核酸靶向技术进行 DNA 扩增。分子检测中采用了各种分子化合物和不同的方法。在本综述中,我们将努力概述用于诊断结核病的分子检测方法及其特性(利用、挑战和功能)。最终目的是探讨这些先进的分子诊断技术取代传统细菌方法的潜力。
{"title":"New insight in molecular detection of Mycobacterium tuberculosis.","authors":"Seyyed Mohammad Amin Mousavi-Sagharchi, Elina Afrazeh, Seyyedeh Fatemeh Seyyedian-Nikjeh, Maryam Meskini, Delaram Doroud, Seyed Davar Siadat","doi":"10.1186/s13568-024-01730-3","DOIUrl":"10.1186/s13568-024-01730-3","url":null,"abstract":"<p><p>Mycobacterium tuberculosis, the causative agent of tuberculosis, is a pathogenic bacterium that has claimed millions of lives since the Middle Ages. According to the World Health Organization's report, tuberculosis ranks among the ten deadliest diseases worldwide. The presence of an extensive array of genes and diverse proteins within the cellular structure of this bacterium has provided us with a potent tool for diagnosis. While the culture method remains the gold standard for tuberculosis diagnosis, it is possible that molecular diagnostic methods, emphasis on the identification of mutation genes (e.g., rpoB and gyrA) and single nucleotide polymorphisms, could offer a safe and reliable alternative. Over the past few decades, as our understanding of molecular genetics has expanded, methods have been developed based on gene expansion and detection. These methods typically commence with DNA amplification through nucleic acid targeted techniques such as polymerase chain reaction. Various molecular compounds and diverse approaches have been employed in molecular assays. In this review, we endeavor to provide an overview of molecular assays for the diagnosis of tuberculosis with their properties (utilization, challenges, and functions). The ultimate goal is to explore the potential of replacing traditional bacterial methods with these advanced molecular diagnostic techniques.</p>","PeriodicalId":7537,"journal":{"name":"AMB Express","volume":null,"pages":null},"PeriodicalIF":3.5,"publicationDate":"2024-06-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11192714/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141436577","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-06-15DOI: 10.1186/s13568-024-01698-0
Hailu Gebru, Gezahegn Faye, Tolosa Belete
Functional constituents are the main concern in food production and consumption. Because foods rich in functional constituents have antioxidant capacity and are important in keeping consumers healthy. Pleurotus ostreatus is among foods rich in functional constituents. However, its functional constituents are affected by various factors. This study compared the antioxidant capacity of P. ostreatus grown on different substrates: straws of tef (Trt1), barley (Trt2), and wheat (Trt3), husks of faba bean (Trt4), and field pea (Trt5), sawdust (Trt6), and the mixture of the above with 1:1 w/w (Trt7). Trt7 had significantly higher radical scavenging activity (RSA) (73.27%), vitamin C (10.61 mg/100 g), and vitamin D (4.92 mg/100 g) compared to other treatments. Whereas the lowest values of RSA (44.24%), vitamin C (5.39 mg/100 g), and vitamin D (1.21 mg/100 g) were found in Trt2. The results indicated that mixed substrate may be a good growth substrate for functionally beneficial P. ostreatus and could be a promising source of natural antioxidants.
{"title":"Antioxidant capacity of Pleurotus ostreatus (Jacq.) P. Kumm influenced by growth substrates.","authors":"Hailu Gebru, Gezahegn Faye, Tolosa Belete","doi":"10.1186/s13568-024-01698-0","DOIUrl":"10.1186/s13568-024-01698-0","url":null,"abstract":"<p><p>Functional constituents are the main concern in food production and consumption. Because foods rich in functional constituents have antioxidant capacity and are important in keeping consumers healthy. Pleurotus ostreatus is among foods rich in functional constituents. However, its functional constituents are affected by various factors. This study compared the antioxidant capacity of P. ostreatus grown on different substrates: straws of tef (Trt1), barley (Trt2), and wheat (Trt3), husks of faba bean (Trt4), and field pea (Trt5), sawdust (Trt6), and the mixture of the above with 1:1 w/w (Trt7). Trt7 had significantly higher radical scavenging activity (RSA) (73.27%), vitamin C (10.61 mg/100 g), and vitamin D (4.92 mg/100 g) compared to other treatments. Whereas the lowest values of RSA (44.24%), vitamin C (5.39 mg/100 g), and vitamin D (1.21 mg/100 g) were found in Trt2. The results indicated that mixed substrate may be a good growth substrate for functionally beneficial P. ostreatus and could be a promising source of natural antioxidants.</p>","PeriodicalId":7537,"journal":{"name":"AMB Express","volume":null,"pages":null},"PeriodicalIF":3.7,"publicationDate":"2024-06-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11180080/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141327099","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-06-14DOI: 10.1186/s13568-024-01722-3
Nurfatini Radzlin, Mohd Shukuri Mohamad Ali, Kian Mau Goh, Amira Suriaty Yaakop, Iffah Izzati Zakaria, Ummirul Mukminin Kahar
α-Amylase plays a crucial role in the industrial degradation of starch. The genus Jeotgalibacillus of the underexplored marine bacteria family Caryophanaceae has not been investigated in terms of α-amylase production. Herein, we report the comprehensive analysis of an α-amylase (AmyJM) from Jeotgalibacillus malaysiensis D5T (= DSM28777T = KCTC33550T). Protein phylogenetic analysis indicated that AmyJM belongs to glycoside hydrolase family 13 subfamily 5 (GH13_5) and exhibits low sequence identity with known α-amylases, with its closest counterpart being the GH13_5 α-amylase from Bacillus sp. KSM-K38 (51.05% identity). Purified AmyJM (molecular mass of 70 kDa) is stable at a pH range of 5.5-9.0 and optimally active at pH 7.5. The optimum temperature for AmyJM is 40 °C, where the enzyme is reasonably stable at this temperature. Similar to other α-amylases, the presence of CaCl2 enhanced both the activity and stability of AmyJM. AmyJM exhibited activity toward raw and gelatinized forms of starches and related α-glucans, generating a mixture of reducing sugars, such as glucose, maltose, maltotriose, maltotetraose, and maltopentaose. In raw starch hydrolysis, AmyJM exhibited its highest efficiency (51.10% degradation) in hydrolyzing raw wheat starch after 3-h incubation at 40 °C. Under the same conditions, AmyJM also hydrolyzed tapioca, sago, potato, rice, and corn raw starches, yielding 16.01-30.05%. These findings highlight the potential of AmyJM as a biocatalyst for the saccharification of raw starches, particularly those derived from wheat.
{"title":"Exploring a novel GH13_5 α-amylase from Jeotgalibacillus malaysiensis D5<sup>T</sup> for raw starch hydrolysis.","authors":"Nurfatini Radzlin, Mohd Shukuri Mohamad Ali, Kian Mau Goh, Amira Suriaty Yaakop, Iffah Izzati Zakaria, Ummirul Mukminin Kahar","doi":"10.1186/s13568-024-01722-3","DOIUrl":"10.1186/s13568-024-01722-3","url":null,"abstract":"<p><p>α-Amylase plays a crucial role in the industrial degradation of starch. The genus Jeotgalibacillus of the underexplored marine bacteria family Caryophanaceae has not been investigated in terms of α-amylase production. Herein, we report the comprehensive analysis of an α-amylase (AmyJM) from Jeotgalibacillus malaysiensis D5<sup>T</sup> (= DSM28777<sup>T</sup> = KCTC33550<sup>T</sup>). Protein phylogenetic analysis indicated that AmyJM belongs to glycoside hydrolase family 13 subfamily 5 (GH13_5) and exhibits low sequence identity with known α-amylases, with its closest counterpart being the GH13_5 α-amylase from Bacillus sp. KSM-K38 (51.05% identity). Purified AmyJM (molecular mass of 70 kDa) is stable at a pH range of 5.5-9.0 and optimally active at pH 7.5. The optimum temperature for AmyJM is 40 °C, where the enzyme is reasonably stable at this temperature. Similar to other α-amylases, the presence of CaCl<sub>2</sub> enhanced both the activity and stability of AmyJM. AmyJM exhibited activity toward raw and gelatinized forms of starches and related α-glucans, generating a mixture of reducing sugars, such as glucose, maltose, maltotriose, maltotetraose, and maltopentaose. In raw starch hydrolysis, AmyJM exhibited its highest efficiency (51.10% degradation) in hydrolyzing raw wheat starch after 3-h incubation at 40 °C. Under the same conditions, AmyJM also hydrolyzed tapioca, sago, potato, rice, and corn raw starches, yielding 16.01-30.05%. These findings highlight the potential of AmyJM as a biocatalyst for the saccharification of raw starches, particularly those derived from wheat.</p>","PeriodicalId":7537,"journal":{"name":"AMB Express","volume":null,"pages":null},"PeriodicalIF":3.7,"publicationDate":"2024-06-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11178733/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141316408","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}