Factors associated with COVID-19 presentation in children with asthma are poorly defined. Our study aimed to assess the clinical course of COVID-19 in children with asthma, with particular attention to possible risk factors for severe disease and long-term sequelae in this group of patients. We assessed the occurrence of SARS-CoV-2 infection in children with asthma six months before their regular outpatient visit to the asthma clinic. Characteristics of patients presenting with signs of SARS-CoV-2 upper (URTI) or lower respiratory tract infection (LRTI) were compared. We focused on factors previously associated with COVID-19 severity. Twenty-seven percent of patients (57/210) reported exposure to SARS-CoV-2 infection. In the symptomatic group, 36% (15/42) reported symptoms of LRTI and 64% (27/42) of URTI. Poorer asthma control was observed in patients with LRTI compared to URTI (80% vs. 7%, p < 0.001). In addition, children with poorer asthma control had a higher risk of presenting with SARS-CoV-2 LRTI in a multiple logistic regression analysis. COVID-19 disease course was not associated with regular ICS use and asthma severity. However, patients on regular ICS had better asthma control (p = 0.026). We found no PFT deterioration post-COVID-19 in either group of patients. Our results suggest good asthma control and treatment adherence prior to infection are associated with better COVID-19 outcomes in children with asthma.
{"title":"Better COVID-19 Outcomes in Children with Good Asthma Control","authors":"Jasna Rodman Berlot, Malena Aldeco, Dušanka Lepej, Marina Praprotnik, Saša Šetina Šmid, Aleksandra Zver, Uroš Krivec","doi":"10.3390/applmicrobiol3040083","DOIUrl":"https://doi.org/10.3390/applmicrobiol3040083","url":null,"abstract":"Factors associated with COVID-19 presentation in children with asthma are poorly defined. Our study aimed to assess the clinical course of COVID-19 in children with asthma, with particular attention to possible risk factors for severe disease and long-term sequelae in this group of patients. We assessed the occurrence of SARS-CoV-2 infection in children with asthma six months before their regular outpatient visit to the asthma clinic. Characteristics of patients presenting with signs of SARS-CoV-2 upper (URTI) or lower respiratory tract infection (LRTI) were compared. We focused on factors previously associated with COVID-19 severity. Twenty-seven percent of patients (57/210) reported exposure to SARS-CoV-2 infection. In the symptomatic group, 36% (15/42) reported symptoms of LRTI and 64% (27/42) of URTI. Poorer asthma control was observed in patients with LRTI compared to URTI (80% vs. 7%, p < 0.001). In addition, children with poorer asthma control had a higher risk of presenting with SARS-CoV-2 LRTI in a multiple logistic regression analysis. COVID-19 disease course was not associated with regular ICS use and asthma severity. However, patients on regular ICS had better asthma control (p = 0.026). We found no PFT deterioration post-COVID-19 in either group of patients. Our results suggest good asthma control and treatment adherence prior to infection are associated with better COVID-19 outcomes in children with asthma.","PeriodicalId":8080,"journal":{"name":"Applied microbiology","volume":"32 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-10-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"136033557","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-10-17DOI: 10.3390/applmicrobiol3040084
Lisha K. Poonacha, Rashmi Ramesh, Akshay Ravish, Arunkumar Mohan, Pradeep M. Uppar, Prashant K. Metri, Nanjunda Swamy Shivananju, Santosh L. Gaonkar, Shubha Gopal, Alexey Yu Sukhorukov, Vijay Pandey, Priya Babu Shubha, Basappa Basappa
Heterocyclic compounds can specifically regulate bacterial development by targeting specific bacterial enzymes and metabolic pathways. The ESKAPE pathogens are multidrug-resistant and cause nosocomial infections, which is one of the greatest challenges in clinical practice. The search for novel agents to combat resistant bacteria has become one of the most important areas of antibacterial research today. Heterocyclic compounds offer a valuable strategy in the fight against resistance as they can be designed to interact with bacterial targets that are less prone to developing resistance mechanisms. Bacterial histidine kinases (HKs), which are a component of two-component bacterial systems, are a promising target for new antibacterial compounds. We have designed and synthesized novel indole derivatives as antibacterial agents. Among the series, indole-coumarin (4b) and bisindole (4e) have shown the best inhibitory activity against S. aureus. Further, in silico docking studies show that compounds 4b and 4e could target histidine kinases in bacteria.
{"title":"Development of Novel Indole and Coumarin Derivatives as Antibacterial Agents That Target Histidine Kinase in S. aureus","authors":"Lisha K. Poonacha, Rashmi Ramesh, Akshay Ravish, Arunkumar Mohan, Pradeep M. Uppar, Prashant K. Metri, Nanjunda Swamy Shivananju, Santosh L. Gaonkar, Shubha Gopal, Alexey Yu Sukhorukov, Vijay Pandey, Priya Babu Shubha, Basappa Basappa","doi":"10.3390/applmicrobiol3040084","DOIUrl":"https://doi.org/10.3390/applmicrobiol3040084","url":null,"abstract":"Heterocyclic compounds can specifically regulate bacterial development by targeting specific bacterial enzymes and metabolic pathways. The ESKAPE pathogens are multidrug-resistant and cause nosocomial infections, which is one of the greatest challenges in clinical practice. The search for novel agents to combat resistant bacteria has become one of the most important areas of antibacterial research today. Heterocyclic compounds offer a valuable strategy in the fight against resistance as they can be designed to interact with bacterial targets that are less prone to developing resistance mechanisms. Bacterial histidine kinases (HKs), which are a component of two-component bacterial systems, are a promising target for new antibacterial compounds. We have designed and synthesized novel indole derivatives as antibacterial agents. Among the series, indole-coumarin (4b) and bisindole (4e) have shown the best inhibitory activity against S. aureus. Further, in silico docking studies show that compounds 4b and 4e could target histidine kinases in bacteria.","PeriodicalId":8080,"journal":{"name":"Applied microbiology","volume":"26 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-10-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135993838","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-10-14DOI: 10.3390/applmicrobiol3040082
Diana Neves Sousa, Carlos Gaspar, Joana Rolo, Gilbert G. G. Donders, José Martinez-de-Oliveira, Rita Palmeira-de-Oliveira, Ana Palmeira-de-Oliveira
The interest in the use of probiotics to treat and prevent vaginal infections is known. The new regulation of medical devices by the European Medical Agency (EMA) introduced big changes in Europe regarding probiotic products for vaginal application, as they are no longer considered as medical devices. As the future classification will be as drugs, it will stress the need to define robust and reliable pre-clinical in vitro testing in order to assess the quality, safety and efficacy of probiotics for human use. Before discussing the efficacy in human pathology, it is mandatory to evaluate the survival and multiplication potential of probiotic strains when brought into contact with vaginal fluid. In this work, our objective was to assess the recovery and stability profile of lactobacilli from six vaginal probiotic formulations brought in contact with specific culture media or vaginal fluid simulants (VFS). Overall, the recovery of viable lactobacilli cells from a modified vaginal fluid simulant (MVFS) solution was comparable to the recovery pattern obtained in standard culture medium. Therefore, we conclude that the MVFS seems to better simulate the conditions of the human vaginal fluid, in contrast with other simulants, and may be used to predict the viability of probiotics over time in the normal vaginal milieu. We discovered that each probiotic product has a unique profile that requires stand-alone studies in conditions that mimic the in vivo status in order to assess their preclinical effectiveness and promote their differential use by the medical community.
{"title":"Assessment of Live Lactobacilli Recovery from Probiotic Products for Vaginal Application","authors":"Diana Neves Sousa, Carlos Gaspar, Joana Rolo, Gilbert G. G. Donders, José Martinez-de-Oliveira, Rita Palmeira-de-Oliveira, Ana Palmeira-de-Oliveira","doi":"10.3390/applmicrobiol3040082","DOIUrl":"https://doi.org/10.3390/applmicrobiol3040082","url":null,"abstract":"The interest in the use of probiotics to treat and prevent vaginal infections is known. The new regulation of medical devices by the European Medical Agency (EMA) introduced big changes in Europe regarding probiotic products for vaginal application, as they are no longer considered as medical devices. As the future classification will be as drugs, it will stress the need to define robust and reliable pre-clinical in vitro testing in order to assess the quality, safety and efficacy of probiotics for human use. Before discussing the efficacy in human pathology, it is mandatory to evaluate the survival and multiplication potential of probiotic strains when brought into contact with vaginal fluid. In this work, our objective was to assess the recovery and stability profile of lactobacilli from six vaginal probiotic formulations brought in contact with specific culture media or vaginal fluid simulants (VFS). Overall, the recovery of viable lactobacilli cells from a modified vaginal fluid simulant (MVFS) solution was comparable to the recovery pattern obtained in standard culture medium. Therefore, we conclude that the MVFS seems to better simulate the conditions of the human vaginal fluid, in contrast with other simulants, and may be used to predict the viability of probiotics over time in the normal vaginal milieu. We discovered that each probiotic product has a unique profile that requires stand-alone studies in conditions that mimic the in vivo status in order to assess their preclinical effectiveness and promote their differential use by the medical community.","PeriodicalId":8080,"journal":{"name":"Applied microbiology","volume":"234 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-10-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135803413","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
In the current study, Bacillus coagulants had a role in combating oxidative stress by inhibiting the growth of intestinal pathogens. However, there are few studies on reducing the mechanisms of oxidative stress. Therefore, this study aimed to explore the effects and underlying mechanisms of B. coagulant HYI (BC-HYI) treatment on growth and intestinal functions in laying chickens under LPS-induced oxidative stress. The in vivo experimental group included five groups of laying chicks: normal control, LPS group, B6 group, B7 group and B8 group. The test consisted of six repetitions in each group, with six animals in each repetition. In the in vitro experiment, an LPS-induced oxidative stress model of chicken fibroblast DF-1 cells was established, and the DF-1 cells were divided into control group, LPS-treated group, B5 group, B6 group and B7 group. On the one hand, we found that BC-HYI can inhibit pathological changes in some intestinal tissues. On the other hand, BC-HYI supplementation has a dual effect on the gut microbiota, promoting the proliferation of beneficial microbes such as Barbarella, Lactobacillus, and Antibacterial while maintaining symbiotic balance. The abundance of Barbarella, Bactericide, and Cloistral was significantly different between the LPS group and the BC-HYI group (p < 0.01). Moreover, compared with the LPS group, BC-HYI significantly decreased reactive oxygen species levels and prevented cell apoptosis (p < 0.01). It used to prevent oxidative stress by activating the Nrf2-ARE/HO-1 signaling pathway, enhancing the scavenging of free radicals, and reducing oxidative damage. BC-HYI alleviated oxidative stress in laying chickens by modulating the gut microbiota and activating the Nrf2-ARE/HO-1 signaling pathway. In summary, laying chickens and cell experiments indicate that BC-HYI supplementation can improve the enzyme function of antioxidants, regulate intestinal barrier function and activate the Nrf2-ARE/HO-1 signaling pathway to regulate intestinal barrier function.
{"title":"Bacillus coagulant HYI (BC-HYI) Alleviates LPS-Elicited Oxidative Stress by Engaging the Nrf2/HO-1 Signaling Pathway and Regulates Gut Macrobiotics in Laying Chickens","authors":"Tianhang Lu, Le Wang, Qiong Wu, Hua Zhang, Defeng Cui, Bowen Liu, Jinjin Tong, Yonghong Zhang","doi":"10.3390/applmicrobiol3040081","DOIUrl":"https://doi.org/10.3390/applmicrobiol3040081","url":null,"abstract":"In the current study, Bacillus coagulants had a role in combating oxidative stress by inhibiting the growth of intestinal pathogens. However, there are few studies on reducing the mechanisms of oxidative stress. Therefore, this study aimed to explore the effects and underlying mechanisms of B. coagulant HYI (BC-HYI) treatment on growth and intestinal functions in laying chickens under LPS-induced oxidative stress. The in vivo experimental group included five groups of laying chicks: normal control, LPS group, B6 group, B7 group and B8 group. The test consisted of six repetitions in each group, with six animals in each repetition. In the in vitro experiment, an LPS-induced oxidative stress model of chicken fibroblast DF-1 cells was established, and the DF-1 cells were divided into control group, LPS-treated group, B5 group, B6 group and B7 group. On the one hand, we found that BC-HYI can inhibit pathological changes in some intestinal tissues. On the other hand, BC-HYI supplementation has a dual effect on the gut microbiota, promoting the proliferation of beneficial microbes such as Barbarella, Lactobacillus, and Antibacterial while maintaining symbiotic balance. The abundance of Barbarella, Bactericide, and Cloistral was significantly different between the LPS group and the BC-HYI group (p < 0.01). Moreover, compared with the LPS group, BC-HYI significantly decreased reactive oxygen species levels and prevented cell apoptosis (p < 0.01). It used to prevent oxidative stress by activating the Nrf2-ARE/HO-1 signaling pathway, enhancing the scavenging of free radicals, and reducing oxidative damage. BC-HYI alleviated oxidative stress in laying chickens by modulating the gut microbiota and activating the Nrf2-ARE/HO-1 signaling pathway. In summary, laying chickens and cell experiments indicate that BC-HYI supplementation can improve the enzyme function of antioxidants, regulate intestinal barrier function and activate the Nrf2-ARE/HO-1 signaling pathway to regulate intestinal barrier function.","PeriodicalId":8080,"journal":{"name":"Applied microbiology","volume":"45 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-10-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135093820","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-10-06DOI: 10.3390/applmicrobiol3040079
Rosimeire Floripes Gomes, Glen Jasper Yupanqui García, Joyce da Cruz Ferraz Dutra, Mariana Santos Cardoso, Eduardo Almeida Costa, Vinicius de Abreu Waldow, Claudia Julia Groposo, Rubens Nobumoto Akamine, Maira Paula de Sousa, Henrique Figueiredo, Vasco Ariston de Carvalho Azevedo, Aristóteles Góes-Neto
Characterizing metabolically active microorganisms using RNA-based methods is a crucial tool for monitoring and mitigating operational issues, such as oil biodegradation and biocorrosion of pipelines in the oil and gas industry. Our review, a pioneering study, addresses the main methods used to preserve, isolate, and sequence RNA from oilfield samples and describes the most abundant metabolically active genera studied. Using the MEDLINE/PubMed, PubMed Central, Scopus, and Web of Science databases, 2.561 potentially eligible records were identified. After screening, 20 studies were included in our review, underscoring the scarcity of studies related to the subject. Data were extracted and reported according to the Preferred Reporting Items for Systematic Reviews and Meta-Analysis (PRISMA). These studies evaluated different samples, including produced water (PW), injection water (IW), solid deposits (SD), oil (OIL), and oily sludge (OS) collected from oilfields located in Australia, China, India, Mexico, and the United Arab Emirates. Environmental samples accounted for 55% of the studies, while enriched cultures and microbial consortia represented 35% and 15% of studies, respectively. PW was the most frequently studied sample, comprising 72% of all samples. Filtration and centrifugation were the only processes employed to concentrate the biomass present in samples. For RNA preservation, the most used method was a solution composed of 95:5 v/v ethanol/TRIzol, while for RNA isolation, the TRIzol reagent was the most cited. The Sanger sequencing method was used in all studies evaluating functional genes (alkB, dsrA, aprA, assA, and mcrA), and the Next-Generation Sequencing (NGS) method was employed in studies for sequencing transcripts of the 16S rRNA gene and metatranscriptomes. Pseudomonas (16S rRNA = PW: 2%; IW: 8%; metatranscriptome = PW: 20%) and Acinetobacter (16S rRNA = PW: 1%; IW: 4%; metatranscriptome = PW: 17%) were the most abundant genera. This study outlined the primary methods employed in researching metabolically active microorganisms. These data provide a foundation for future research. However, it is essential to note that we cannot yet determine the most effective method. We hope that this study will inspire further research related to the standardization of RNA preservation, extraction, and sequencing methods and significantly contribute to our understanding of active microbial communities in oilfields.
{"title":"Metabolically Active Microbial Communities in Oilfields: A Systematic Review and Synthesis of RNA Preservation, Extraction, and Sequencing Methods","authors":"Rosimeire Floripes Gomes, Glen Jasper Yupanqui García, Joyce da Cruz Ferraz Dutra, Mariana Santos Cardoso, Eduardo Almeida Costa, Vinicius de Abreu Waldow, Claudia Julia Groposo, Rubens Nobumoto Akamine, Maira Paula de Sousa, Henrique Figueiredo, Vasco Ariston de Carvalho Azevedo, Aristóteles Góes-Neto","doi":"10.3390/applmicrobiol3040079","DOIUrl":"https://doi.org/10.3390/applmicrobiol3040079","url":null,"abstract":"Characterizing metabolically active microorganisms using RNA-based methods is a crucial tool for monitoring and mitigating operational issues, such as oil biodegradation and biocorrosion of pipelines in the oil and gas industry. Our review, a pioneering study, addresses the main methods used to preserve, isolate, and sequence RNA from oilfield samples and describes the most abundant metabolically active genera studied. Using the MEDLINE/PubMed, PubMed Central, Scopus, and Web of Science databases, 2.561 potentially eligible records were identified. After screening, 20 studies were included in our review, underscoring the scarcity of studies related to the subject. Data were extracted and reported according to the Preferred Reporting Items for Systematic Reviews and Meta-Analysis (PRISMA). These studies evaluated different samples, including produced water (PW), injection water (IW), solid deposits (SD), oil (OIL), and oily sludge (OS) collected from oilfields located in Australia, China, India, Mexico, and the United Arab Emirates. Environmental samples accounted for 55% of the studies, while enriched cultures and microbial consortia represented 35% and 15% of studies, respectively. PW was the most frequently studied sample, comprising 72% of all samples. Filtration and centrifugation were the only processes employed to concentrate the biomass present in samples. For RNA preservation, the most used method was a solution composed of 95:5 v/v ethanol/TRIzol, while for RNA isolation, the TRIzol reagent was the most cited. The Sanger sequencing method was used in all studies evaluating functional genes (alkB, dsrA, aprA, assA, and mcrA), and the Next-Generation Sequencing (NGS) method was employed in studies for sequencing transcripts of the 16S rRNA gene and metatranscriptomes. Pseudomonas (16S rRNA = PW: 2%; IW: 8%; metatranscriptome = PW: 20%) and Acinetobacter (16S rRNA = PW: 1%; IW: 4%; metatranscriptome = PW: 17%) were the most abundant genera. This study outlined the primary methods employed in researching metabolically active microorganisms. These data provide a foundation for future research. However, it is essential to note that we cannot yet determine the most effective method. We hope that this study will inspire further research related to the standardization of RNA preservation, extraction, and sequencing methods and significantly contribute to our understanding of active microbial communities in oilfields.","PeriodicalId":8080,"journal":{"name":"Applied microbiology","volume":"213 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-10-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135351348","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-10-06DOI: 10.3390/applmicrobiol3040080
Sazzad Hossen Toushik, Md. Ashrafudoulla
There is no doubt that ruminants have the capability to digest lignocellulosic compounds and to utilize them as an absorbable form of energy by tapping into enzymes produced by the microbial population in their rumens. Among the rumens of various ruminants, this study focused on Korean goat rumens because of their unique digestibility of lignocellulosic biomasses. Therefore, a novel Gene12 gene was screened and unmasked from the constructed rumen metagenomic library of a Korean black goat and expressed in a Bacillus megaterium system. The recombinant protein was distinguished as a novel α-L-arabinofuranosidase enzyme from glycosyl hydrolase family 43 (GH43) for its capability to hydrolyze the non-reducing end of α-1,5-L-arabinofuranose linkages in α-L-arabinofuranosyl groups. The enzyme can also break apart α-L-arabinofuranosidic linkages and act synergistically with other hemicellulolytic enzymes to release α-1,2- and α-1,3-L-arabinofuranosyl groups from L-arabinose-comprising polysaccharides. In silico, phylogenetic, and computational analyses proclaimed that the Gene12 gene encodes a novel carbohydrate-active enzyme possessing a V-shaped indentation of the GH43 catalytic and functional domain (carbohydrate-binding module 6). The recombinant Gene12 protein has shared 81% sequence homology with other members of the GH43 family. Enzymic synopses (optimal pH, temperatures, and stability studies) of the recombinant Gene12 enzyme and its substrate specificity (synthetic and natural substrates) profiling were considered. The recombinant Gene12 α-L-arabinofuranosidase works best at pH 6.0 and 40 °C, and it is stable at pH 4.0 to 7.0 at temperatures of 20 to 50 °C. Additionally, 5-blended β-sheets were identified through a tertiary (3D) structure analysis along with the high substrate specificity against p-nitrophenyl-D-arabinofuranoside (pNPA). The highest substrate specificity of pNPA for Gene12 α-L-arabinofuranosidase indicated its confirmation as an exo-type arabinofuronidase. The results thus propose using the Gene12 protein as an exo-mannered GH43 α-L-arabinofuranosidase (EC 3.2.1.55) enzyme.
毫无疑问，反刍动物有能力消化木质纤维素化合物，并利用它们作为一种可吸收的能量形式，通过利用它们瘤胃中微生物群体产生的酶。在各种反刍动物的瘤胃中，由于韩国山羊具有独特的木质纤维素生物质消化率，因此本研究重点研究了韩国山羊的瘤胃。因此，从构建的韩国黑山羊瘤胃宏基因组文库中筛选出一个新的Gene12基因，并在巨型芽孢杆菌系统中表达。该重组蛋白能够水解α- l -阿拉伯糖醛基上α-1,5- l -阿拉伯糖醛基键的非还原端，被鉴定为来自糖基水解酶家族43 (GH43)的新型α- l -阿拉伯糖醛基酶。该酶还能分解α- l -阿拉伯糖醛基键，并与其他半纤维素水解酶协同作用，从含l -阿拉伯糖的多糖中释放α-1,2-和α-1,3- l -阿拉伯糖醛基。计算机、系统发育和计算分析表明，Gene12基因编码一种新的碳水化合物活性酶，该酶具有GH43催化和功能域的v形凹痕(碳水化合物结合模块6)。重组基因12蛋白与GH43家族的其他成员具有81%的序列同源性。考虑了重组Gene12酶的酶学概要(最佳pH、温度和稳定性研究)及其底物特异性(合成底物和天然底物)分析。重组Gene12 α- l -阿拉伯糖醛酸苷酶在pH 6.0和40℃条件下工作效果最好，在pH 4.0 ~ 7.0、温度20 ~ 50℃条件下稳定。此外，通过三级(3D)结构分析鉴定了5-混合β-薄片，并对对硝基苯基- d -阿拉伯糖醛酸苷(pNPA)具有高底物特异性。pNPA对基因12 α- l -阿拉伯糖醛酸苷酶的最高底物特异性表明其为外显型阿拉伯糖醛酸苷酶。因此，建议将Gene12蛋白作为外显型GH43 α- l -阿拉伯糖醛酸苷酶(EC 3.2.1.55)酶。
{"title":"Recombinant Expression in Bacillus megaterium and Biochemical Characterization of Exo-Mannered Glycosyl Hydrolase Family 43 α-L-Arabinofuranosidase from the Korean Black Goat Rumen Metagenome","authors":"Sazzad Hossen Toushik, Md. Ashrafudoulla","doi":"10.3390/applmicrobiol3040080","DOIUrl":"https://doi.org/10.3390/applmicrobiol3040080","url":null,"abstract":"There is no doubt that ruminants have the capability to digest lignocellulosic compounds and to utilize them as an absorbable form of energy by tapping into enzymes produced by the microbial population in their rumens. Among the rumens of various ruminants, this study focused on Korean goat rumens because of their unique digestibility of lignocellulosic biomasses. Therefore, a novel Gene12 gene was screened and unmasked from the constructed rumen metagenomic library of a Korean black goat and expressed in a Bacillus megaterium system. The recombinant protein was distinguished as a novel α-L-arabinofuranosidase enzyme from glycosyl hydrolase family 43 (GH43) for its capability to hydrolyze the non-reducing end of α-1,5-L-arabinofuranose linkages in α-L-arabinofuranosyl groups. The enzyme can also break apart α-L-arabinofuranosidic linkages and act synergistically with other hemicellulolytic enzymes to release α-1,2- and α-1,3-L-arabinofuranosyl groups from L-arabinose-comprising polysaccharides. In silico, phylogenetic, and computational analyses proclaimed that the Gene12 gene encodes a novel carbohydrate-active enzyme possessing a V-shaped indentation of the GH43 catalytic and functional domain (carbohydrate-binding module 6). The recombinant Gene12 protein has shared 81% sequence homology with other members of the GH43 family. Enzymic synopses (optimal pH, temperatures, and stability studies) of the recombinant Gene12 enzyme and its substrate specificity (synthetic and natural substrates) profiling were considered. The recombinant Gene12 α-L-arabinofuranosidase works best at pH 6.0 and 40 °C, and it is stable at pH 4.0 to 7.0 at temperatures of 20 to 50 °C. Additionally, 5-blended β-sheets were identified through a tertiary (3D) structure analysis along with the high substrate specificity against p-nitrophenyl-D-arabinofuranoside (pNPA). The highest substrate specificity of pNPA for Gene12 α-L-arabinofuranosidase indicated its confirmation as an exo-type arabinofuronidase. The results thus propose using the Gene12 protein as an exo-mannered GH43 α-L-arabinofuranosidase (EC 3.2.1.55) enzyme.","PeriodicalId":8080,"journal":{"name":"Applied microbiology","volume":"40 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-10-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135352121","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-09-28DOI: 10.3390/applmicrobiol3040078
Katrine V. Møller, Jonas Bruhn Wesseltoft, Richelle Malazarte, Sabrina J. Kousgaard, Hans L. Nielsen, Erika Yashiro, Anders Olsen
The role of the microbiota in health and disease is a research area receiving much attention in academia and industry. A person’s microbiota refers to a community of microorganisms found mainly in the gut. It is estimated that around 39 trillion bacteria can be found on and inside the human body and there is increasing evidence that they influence human health. Advances in sequencing techniques are revolutionizing characterization of the human microbiome. However, causality and underlying molecular mechanisms are still largely unknown due to the complexity of the human microbiome and its interaction with the host. Turning towards simpler host organisms and using well-defined microbiomes are two ways to strengthen studies of causality and mechanism. Here, we show that the nematode Caenorhabditis elegans can be used as host to study sub-microbiomes derived from human feces samples prepared for fecal microbiota transplantation following a simple feeding protocol. Approximately 200 amplicon sequence variants were identified in the worm gut following transplantation with human fecal microbiota samples. We find that the gut microbiome does not simply reflect the bacterial community initially fed to the worms. Hence, our experimental setup can be used to identify and characterize host genetic factors shaping the microbiota and improving our understanding of host–human microbiome interactions.
{"title":"Usage of Cultured Human Fecal Microbiota for Colonization of Caenorhabditis elegans to Study Host–Microbe Interaction","authors":"Katrine V. Møller, Jonas Bruhn Wesseltoft, Richelle Malazarte, Sabrina J. Kousgaard, Hans L. Nielsen, Erika Yashiro, Anders Olsen","doi":"10.3390/applmicrobiol3040078","DOIUrl":"https://doi.org/10.3390/applmicrobiol3040078","url":null,"abstract":"The role of the microbiota in health and disease is a research area receiving much attention in academia and industry. A person’s microbiota refers to a community of microorganisms found mainly in the gut. It is estimated that around 39 trillion bacteria can be found on and inside the human body and there is increasing evidence that they influence human health. Advances in sequencing techniques are revolutionizing characterization of the human microbiome. However, causality and underlying molecular mechanisms are still largely unknown due to the complexity of the human microbiome and its interaction with the host. Turning towards simpler host organisms and using well-defined microbiomes are two ways to strengthen studies of causality and mechanism. Here, we show that the nematode Caenorhabditis elegans can be used as host to study sub-microbiomes derived from human feces samples prepared for fecal microbiota transplantation following a simple feeding protocol. Approximately 200 amplicon sequence variants were identified in the worm gut following transplantation with human fecal microbiota samples. We find that the gut microbiome does not simply reflect the bacterial community initially fed to the worms. Hence, our experimental setup can be used to identify and characterize host genetic factors shaping the microbiota and improving our understanding of host–human microbiome interactions.","PeriodicalId":8080,"journal":{"name":"Applied microbiology","volume":"15 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-09-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135387527","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-09-23DOI: 10.3390/applmicrobiol3040077
Jennifer McCabe, Jessika L. Bryant, C. Cristoph Klews, MiCayla Johnson, Ariel N. Atchley, Thomas W. Cousins, Analiska Dominguez, Marie Gabriel, Katie Middleton, Natasha A. Bowles, Heather M. Broughton, Kristina M. Smith, Mark R. Ackermann, Robert Bildfell, Patrick N. Ball, Evan S. Forsythe, Bruce S. Seal
The discovery of novel probiotic bacteria from free-ranging animals for the treatment of inflammatory bowel disease in domestic pets is a unique approach. The chloroform extraction of gastrointestinal (GI) tract material was used to inactivate vegetative cells and select for spore-forming bacteria. A bacterium identified as a novel Paenibacillus sp. strain via small ribosomal RNA (16S) gene sequencing was isolated from the GI tract of a gray wolf (Canis lupus). The bacterium was typed as Gram-variable, both catalase/oxidase-positive and positive via starch hydrolysis and lipase assays. The bacterium inhibited the growth of Staphylococcus aureus, Escherichia coli and Micrococcus luteus. The draft whole genome sequence (WGS) assembly was 7,034,206 bp in length, encoding 6543 genes, and is similar in size and coding capacity to other closely related Paenibacillus spp. The isolate’s genome encodes several germination and sporulation gene products along with antimicrobials such as a bacteriocin system and chitinase. Enzyme genes such as alpha amylase, cellulase, lipases and pectin lyase are also present in the genome. An incomplete lysogenic bacteriophage genome was also present in the isolate’s genome. Phenotypic characteristics combined with a WGS genotype analysis indicate that this bacterium, designated Paenibacillus sp. ClWae2A, could be a potential candidate probiotic for domestic dogs.
{"title":"Phenotypic and Draft Genome Sequence Analyses of a Paenibacillus sp. Isolated from the Gastrointestinal Tract of a North American Gray Wolf (Canis lupus)","authors":"Jennifer McCabe, Jessika L. Bryant, C. Cristoph Klews, MiCayla Johnson, Ariel N. Atchley, Thomas W. Cousins, Analiska Dominguez, Marie Gabriel, Katie Middleton, Natasha A. Bowles, Heather M. Broughton, Kristina M. Smith, Mark R. Ackermann, Robert Bildfell, Patrick N. Ball, Evan S. Forsythe, Bruce S. Seal","doi":"10.3390/applmicrobiol3040077","DOIUrl":"https://doi.org/10.3390/applmicrobiol3040077","url":null,"abstract":"The discovery of novel probiotic bacteria from free-ranging animals for the treatment of inflammatory bowel disease in domestic pets is a unique approach. The chloroform extraction of gastrointestinal (GI) tract material was used to inactivate vegetative cells and select for spore-forming bacteria. A bacterium identified as a novel Paenibacillus sp. strain via small ribosomal RNA (16S) gene sequencing was isolated from the GI tract of a gray wolf (Canis lupus). The bacterium was typed as Gram-variable, both catalase/oxidase-positive and positive via starch hydrolysis and lipase assays. The bacterium inhibited the growth of Staphylococcus aureus, Escherichia coli and Micrococcus luteus. The draft whole genome sequence (WGS) assembly was 7,034,206 bp in length, encoding 6543 genes, and is similar in size and coding capacity to other closely related Paenibacillus spp. The isolate’s genome encodes several germination and sporulation gene products along with antimicrobials such as a bacteriocin system and chitinase. Enzyme genes such as alpha amylase, cellulase, lipases and pectin lyase are also present in the genome. An incomplete lysogenic bacteriophage genome was also present in the isolate’s genome. Phenotypic characteristics combined with a WGS genotype analysis indicate that this bacterium, designated Paenibacillus sp. ClWae2A, could be a potential candidate probiotic for domestic dogs.","PeriodicalId":8080,"journal":{"name":"Applied microbiology","volume":"43 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-09-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135966923","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-09-14DOI: 10.3390/applmicrobiol3030076
Snizhana Olishevska, Arvin Nickzad, Concetta Restieri, Fadi Dagher, Yan Luo, Jie Zheng, Eric Déziel
Gram-negative bacteria belonging to the Xanthomonas genus include plant pathogens representing a major challenge in the field of agriculture for a wide variety of economically important crops, such as tomato, pepper, and lettuce. Due to the massive usage of agrochemicals, Xanthomonas spp. are developing resistance to copper pesticides typically used to control microbial infections. An interesting alternative approach to control bacterial phytopathogens consists of using eco-friendly biocontrol agents, often beneficial microorganisms. Here, following the targeted, broad-spectrum screening of thousands of microorganisms isolated from different environmental locations, we isolated Bacillus velezensis strain 71 and Paenibacillus peoriae strain To99 displaying potent antagonistic activity against Xanthomonas spp. We found that oxydifficidin and polymyxin A secreted by B. velezensis 71 and P. peoriae To99, respectively, are mainly responsible for the anti-Xanthomonas activity. We further evaluated the performance of cell suspensions and cell-free supernatants of these isolates in controlling tomato bacterial spot disease in growth chamber and greenhouse conditions to validate the in vitro results. The overall results demonstrate the potential of treatments based on the secondary metabolites from both isolates and their cells as an alternative to copper-based chemicals to control leaf spot diseases caused by Xanthomonas spp. phytopathogens.
{"title":"Bacillus velezensis and Paenibacillus peoriae Strains Effective as Biocontrol Agents against Xanthomonas Bacterial Spot","authors":"Snizhana Olishevska, Arvin Nickzad, Concetta Restieri, Fadi Dagher, Yan Luo, Jie Zheng, Eric Déziel","doi":"10.3390/applmicrobiol3030076","DOIUrl":"https://doi.org/10.3390/applmicrobiol3030076","url":null,"abstract":"Gram-negative bacteria belonging to the Xanthomonas genus include plant pathogens representing a major challenge in the field of agriculture for a wide variety of economically important crops, such as tomato, pepper, and lettuce. Due to the massive usage of agrochemicals, Xanthomonas spp. are developing resistance to copper pesticides typically used to control microbial infections. An interesting alternative approach to control bacterial phytopathogens consists of using eco-friendly biocontrol agents, often beneficial microorganisms. Here, following the targeted, broad-spectrum screening of thousands of microorganisms isolated from different environmental locations, we isolated Bacillus velezensis strain 71 and Paenibacillus peoriae strain To99 displaying potent antagonistic activity against Xanthomonas spp. We found that oxydifficidin and polymyxin A secreted by B. velezensis 71 and P. peoriae To99, respectively, are mainly responsible for the anti-Xanthomonas activity. We further evaluated the performance of cell suspensions and cell-free supernatants of these isolates in controlling tomato bacterial spot disease in growth chamber and greenhouse conditions to validate the in vitro results. The overall results demonstrate the potential of treatments based on the secondary metabolites from both isolates and their cells as an alternative to copper-based chemicals to control leaf spot diseases caused by Xanthomonas spp. phytopathogens.","PeriodicalId":8080,"journal":{"name":"Applied microbiology","volume":"25 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-09-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"134911395","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-09-12DOI: 10.3390/applmicrobiol3030075
Jan Werner Böhm, Dominik Duckeck, Bojan Duduk, Bernd Schneider, Michael Kube
Phytoplasmas are associated with important bacterial diseases, causing severe symptoms in agricultural and ornamental crops. ‘Candidatus Phytoplasma rubi’, associated with the Rubus stunt in raspberries (Rubus idaeus) and blackberries (Rubus subgenus Rubus), causes shortened internodes, elongated sepals, proliferation, phyllody, and virescence. The recently published genome of ‘Ca. P. rubi’ RS enabled a comprehensive genomic comparison to the complete genomes of 16SrV phytoplasmas, comprising strains of the flavescence dorée-associated phytoplasma CH and two ‘Candidatus Phytoplasma ziziphi’ strains. Besides the typical transporters and metabolic features of phytoplasmas, the phosphorolysis of sucrose and the utilization of the carboxylic acid L-lactate became apparent for the 16SrV-group. With respect to the effector repertoire and the encoded immunodominant membrane proteins involved in host colonization, the group revealed conserved features that comprise the variable membrane proteins A and B. However, SAP11- and SAP54 orthologs were limited to ‘Ca. P. rubi’ RS and ‘Ca. P. ziziphi’. Genome-sequence-based phylogenetic analysis supports the close relationship of these genomes relative to alder yellows phytoplasmas. The analyses supported the impact of the mobilome on phytoplasma evolution but also highlighted that there is the possibility of identifying phytoplasmas with a larger metabolic repertoire in the future.
{"title":"Genome Comparison of ‘Candidatus Phytoplasma rubi’ with Genomes of Other 16SrV Phytoplasmas Highlights Special Group Features","authors":"Jan Werner Böhm, Dominik Duckeck, Bojan Duduk, Bernd Schneider, Michael Kube","doi":"10.3390/applmicrobiol3030075","DOIUrl":"https://doi.org/10.3390/applmicrobiol3030075","url":null,"abstract":"Phytoplasmas are associated with important bacterial diseases, causing severe symptoms in agricultural and ornamental crops. ‘Candidatus Phytoplasma rubi’, associated with the Rubus stunt in raspberries (Rubus idaeus) and blackberries (Rubus subgenus Rubus), causes shortened internodes, elongated sepals, proliferation, phyllody, and virescence. The recently published genome of ‘Ca. P. rubi’ RS enabled a comprehensive genomic comparison to the complete genomes of 16SrV phytoplasmas, comprising strains of the flavescence dorée-associated phytoplasma CH and two ‘Candidatus Phytoplasma ziziphi’ strains. Besides the typical transporters and metabolic features of phytoplasmas, the phosphorolysis of sucrose and the utilization of the carboxylic acid L-lactate became apparent for the 16SrV-group. With respect to the effector repertoire and the encoded immunodominant membrane proteins involved in host colonization, the group revealed conserved features that comprise the variable membrane proteins A and B. However, SAP11- and SAP54 orthologs were limited to ‘Ca. P. rubi’ RS and ‘Ca. P. ziziphi’. Genome-sequence-based phylogenetic analysis supports the close relationship of these genomes relative to alder yellows phytoplasmas. The analyses supported the impact of the mobilome on phytoplasma evolution but also highlighted that there is the possibility of identifying phytoplasmas with a larger metabolic repertoire in the future.","PeriodicalId":8080,"journal":{"name":"Applied microbiology","volume":"30 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-09-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135878625","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
京公网安备 11010802042870号
京ICP备2023020795号-1
扫码关注我们
求助内容：
应助结果提醒方式：