Pub Date : 2024-09-16DOI: 10.1186/s13213-024-01763-w
Daniel Asfaw Kitessa
Fermentation is the oldest biotechnology in which a metabolic process carried out without the involvement of oxygen. It is one of the food processing methods that improve the nutrient contents and sensorial properties with potentially reducing or eliminating pathogenic microorganisms and natural toxins. The aim of this review is to compare, contrast and summarize the scientific data on the effect of fermentation on physicochemical properties, anti-nutritional factors and sensory properties of cereal-based fermented foods and beverages. The results of this review showed that fermentation improves the nutritional value of some proximate composition such as crude protein and fat contents, while decreases the carbohydrate and crude fiber contents. It also improves the bioavailability, antioxidant activities and sensory properties of cereal-based foods and beverages. This review concluded that fermentation improves the nutritional quality of proximate composition, bioavailability of minerals and phytochemicals, and decrease the anti-nutritional factors of cereal-based fermented foods and beverages.
{"title":"Review on effect of fermentation on physicochemical properties, anti-nutritional factors and sensory properties of cereal-based fermented foods and beverages","authors":"Daniel Asfaw Kitessa","doi":"10.1186/s13213-024-01763-w","DOIUrl":"https://doi.org/10.1186/s13213-024-01763-w","url":null,"abstract":"Fermentation is the oldest biotechnology in which a metabolic process carried out without the involvement of oxygen. It is one of the food processing methods that improve the nutrient contents and sensorial properties with potentially reducing or eliminating pathogenic microorganisms and natural toxins. The aim of this review is to compare, contrast and summarize the scientific data on the effect of fermentation on physicochemical properties, anti-nutritional factors and sensory properties of cereal-based fermented foods and beverages. The results of this review showed that fermentation improves the nutritional value of some proximate composition such as crude protein and fat contents, while decreases the carbohydrate and crude fiber contents. It also improves the bioavailability, antioxidant activities and sensory properties of cereal-based foods and beverages. This review concluded that fermentation improves the nutritional quality of proximate composition, bioavailability of minerals and phytochemicals, and decrease the anti-nutritional factors of cereal-based fermented foods and beverages.","PeriodicalId":8069,"journal":{"name":"Annals of Microbiology","volume":"18 1","pages":""},"PeriodicalIF":3.0,"publicationDate":"2024-09-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142261245","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
The incidence of foodborne pathogens in ready- to-eat (RTE) can be attributed to various foodborne diseases. Most of the isolated microorganisms from RTE foods are resistant to common antibiotics and thus, resulted to treatment failure when commercially available antibiotics are administered. However, the secondary metabolites secreted by microorganisms can serve as alternative therapy that are reliable and safe. Secondary metabolites obtained from mono- and co-culture microorganisms can inhibit the growth of antibiotic-resistant microorganisms. Bioactive compounds in the secreted metabolites can be identified and utilized as sources of new antibiotics. In this study, antimicrobial activity of secondary metabolites from Lactobacillus fermentum, Saccharomyces cerevisiae, Pleurotus ostreatus, and their co-cultures were tested against foodborne pathogens isolated from RTE foods using agar well diffusion. The bioactive compounds in the metabolites were identified using gas chromatography-mass spectrometry. From a total of 100 RTE foods examined, Salmonella enterica, Shigella dysenteriae, Escherichia coli, Klebsiella pneumoniae (subsp ozaenae), Pseudomonas fluorescens, Clostridium perfringes, Bacillus cereus, Listeria monocytogens, and Staphylococcus aureus, Penicillium chrysogenum, Aspergillus flavus, and Aspergillus niger were isolated and displayed multiple antibiotic resistance. The secondary metabolites secreted by co-culture of L. fermentum + P. ostreatus + S. cerevisiae, and co-culture of P. ostreatus + S. cerevisiae have the highest (P ≤ 0.05) zones of inhibition (23.70 mm) and (21.10 mm) against E. coli, respectively. Metabolites from mono-cultured L. fermentum, P. ostreatus, and S. cerevisiae showed zones of inhibition against indicator microorganisms with values ranging from 8.80 to 11.70 mm, 9.00 to 14.30 mm, and 9.30 to 13.00 mm, respectively. Some of the bioactive compounds found in the metabolites of co-cultured microorganisms were alpha-linolenic acid (25.71%), acetic acid 3-methylbutyl ester (13.83%), trans-squalene (12.39%), pentadecylic acid (11.68%), 3- phenyllactic acid (30.13%), linolelaidic acid methyl ester (15.63%), and 4-O-methylmannose (53.74%). RTE foods contain multiple antibiotics resistance pathogens. The pronounced antimicrobial activity of the secondary metabolites against microorganisms from RTE foods could be attributed to the presence of bioactive compounds in the metabolites. These metabolites can be exploited as alternative food preservatives, biopharmaceuticals and can be used towards better health delivering systems.
即食食品中的食源性病原体可导致各种食源性疾病。从即食食品中分离出的大多数微生物对普通抗生素具有抗药性，因此，使用市售抗生素治疗时会导致治疗失败。然而，微生物分泌的次级代谢物可作为可靠、安全的替代疗法。从单培养和共培养微生物中获得的次生代谢物可以抑制抗生素耐药微生物的生长。分泌代谢物中的生物活性化合物可被鉴定并用作新抗生素的来源。本研究采用琼脂井扩散法测试了发酵乳杆菌、酿酒酵母、牡蛎及其共培养物的次生代谢物对从即食食品中分离出的食源性致病菌的抗菌活性。代谢物中的生物活性化合物采用气相色谱-质谱法进行鉴定。在检测的 100 种即食性食品中，分离出了肠炎沙门氏菌、痢疾志贺氏菌、大肠埃希氏菌、肺炎克雷伯菌（大肠杆菌亚种）、荧光假单胞菌、产气荚膜梭菌、蜡样芽孢杆菌、单核细胞李斯特菌、金黄色葡萄球菌、金黄色青霉、黄曲霉和黑曲霉，并显示出多种抗生素耐药性。L. fermentum + P. ostreatus + S. cerevisiae 共培养物和 P. ostreatus + S. cerevisiae 共培养物分泌的次生代谢物对大肠杆菌的抑菌作用分别为（23.70 毫米）和（21.10 毫米），抑菌面积最大（P ≤ 0.05）。单培养 L. fermentum、P. ostreatus 和 S. cerevisiae 的代谢物对指示微生物的抑制区分别为 8.80 至 11.70 毫米、9.00 至 14.30 毫米和 9.30 至 13.00 毫米。在共培养微生物的代谢产物中发现的一些生物活性化合物有：α-亚麻酸（25.71%）、乙酸 3-甲基丁酯（13.83%）、反式角鲨烯（12.39%）、十五烷酸（11.68%）、3-苯基乳酸（30.13%）、亚油酸甲酯（15.63%）和 4-O-甲基甘露糖（53.74%）。即食食品中含有多种抗生素耐药性病原体。次生代谢物对来自即食食品的微生物具有明显的抗菌活性，这可能是因为代谢物中含有生物活性化合物。这些代谢物可用作替代食品防腐剂和生物制药，并可用于改善健康服务系统。
{"title":"Antimicrobial metabolites from Probiotics, Pleurotus ostreatus and their co-cultures against foodborne pathogens isolated from ready-to-eat foods","authors":"Oluwaferanmi Esther Bamisi, Clement Olusola Ogidi, Bamidele Juliet Akinyele","doi":"10.1186/s13213-024-01776-5","DOIUrl":"https://doi.org/10.1186/s13213-024-01776-5","url":null,"abstract":"The incidence of foodborne pathogens in ready- to-eat (RTE) can be attributed to various foodborne diseases. Most of the isolated microorganisms from RTE foods are resistant to common antibiotics and thus, resulted to treatment failure when commercially available antibiotics are administered. However, the secondary metabolites secreted by microorganisms can serve as alternative therapy that are reliable and safe. Secondary metabolites obtained from mono- and co-culture microorganisms can inhibit the growth of antibiotic-resistant microorganisms. Bioactive compounds in the secreted metabolites can be identified and utilized as sources of new antibiotics. In this study, antimicrobial activity of secondary metabolites from Lactobacillus fermentum, Saccharomyces cerevisiae, Pleurotus ostreatus, and their co-cultures were tested against foodborne pathogens isolated from RTE foods using agar well diffusion. The bioactive compounds in the metabolites were identified using gas chromatography-mass spectrometry. From a total of 100 RTE foods examined, Salmonella enterica, Shigella dysenteriae, Escherichia coli, Klebsiella pneumoniae (subsp ozaenae), Pseudomonas fluorescens, Clostridium perfringes, Bacillus cereus, Listeria monocytogens, and Staphylococcus aureus, Penicillium chrysogenum, Aspergillus flavus, and Aspergillus niger were isolated and displayed multiple antibiotic resistance. The secondary metabolites secreted by co-culture of L. fermentum + P. ostreatus + S. cerevisiae, and co-culture of P. ostreatus + S. cerevisiae have the highest (P ≤ 0.05) zones of inhibition (23.70 mm) and (21.10 mm) against E. coli, respectively. Metabolites from mono-cultured L. fermentum, P. ostreatus, and S. cerevisiae showed zones of inhibition against indicator microorganisms with values ranging from 8.80 to 11.70 mm, 9.00 to 14.30 mm, and 9.30 to 13.00 mm, respectively. Some of the bioactive compounds found in the metabolites of co-cultured microorganisms were alpha-linolenic acid (25.71%), acetic acid 3-methylbutyl ester (13.83%), trans-squalene (12.39%), pentadecylic acid (11.68%), 3- phenyllactic acid (30.13%), linolelaidic acid methyl ester (15.63%), and 4-O-methylmannose (53.74%). RTE foods contain multiple antibiotics resistance pathogens. The pronounced antimicrobial activity of the secondary metabolites against microorganisms from RTE foods could be attributed to the presence of bioactive compounds in the metabolites. These metabolites can be exploited as alternative food preservatives, biopharmaceuticals and can be used towards better health delivering systems.","PeriodicalId":8069,"journal":{"name":"Annals of Microbiology","volume":"67 1","pages":""},"PeriodicalIF":3.0,"publicationDate":"2024-08-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142221084","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-08-20DOI: 10.1186/s13213-024-01774-7
Aida M. Farag, Hasnaa E-B. Ghonam, Aliaa M. El-Borai
Several antibiotics are partially metabolized by patients after administration and end up in municipal sewage systems. The fate of biodegradation in aquatic environments and the role of biodegradation in the development of bacterial resistance are poorly understood. Thus, as a crucial step in an environmental risk assessment, the biodegradability of many therapeutically significant antibiotics was investigated. A marine halophilic bacteria that degrades penicillin G (PEN-G) was isolated and identified based on morphology, physio-biochemical characteristics, and 16S rDNA sequences as Bacillus pseudomycoides AH1 (accession no. MF037698). The effects of various concentrations of PEN-G and carbon and nitrogen sources on the biotransformation ability at 30°C and pH 7.0 were evaluated. Cells grown in medium supplemented with glucose as an additional carbon source and yeast extract as a nitrogen source exhibited maximal PEN-G biotransformation efficiency and rate (71.678% ±1.28 and 2.99 mg/h, respectively). The culture conditions for B. pseudomycoides AH1 cells were optimized using a Plackett–Burman design (PBD). Six key determinants (p < 0.05) significantly affected the process outcome, as deduced by regression analysis of the PBD data, and modified MSM broth achieved PEN-G biotransformation efficiency (100%) under aerobic shaking conditions at 35°C, irrespective of HPLC analysis. Additionally, the present investigation could strongly support the application of immobilization approaches for the removal of PEN-G-contaminated environmental sites. To the best of the authors’ knowledge, this is the first detailed study on the efficient biotransformation of PEN-G by an alginate-bacteria system as a simple, green, and inexpensive process, as well as a promising method.
{"title":"Eco-friendly biotransformation of penicillin G by free and immobilized marine halophilic Bacillus pseudomycoides AH1","authors":"Aida M. Farag, Hasnaa E-B. Ghonam, Aliaa M. El-Borai","doi":"10.1186/s13213-024-01774-7","DOIUrl":"https://doi.org/10.1186/s13213-024-01774-7","url":null,"abstract":"Several antibiotics are partially metabolized by patients after administration and end up in municipal sewage systems. The fate of biodegradation in aquatic environments and the role of biodegradation in the development of bacterial resistance are poorly understood. Thus, as a crucial step in an environmental risk assessment, the biodegradability of many therapeutically significant antibiotics was investigated. A marine halophilic bacteria that degrades penicillin G (PEN-G) was isolated and identified based on morphology, physio-biochemical characteristics, and 16S rDNA sequences as Bacillus pseudomycoides AH1 (accession no. MF037698). The effects of various concentrations of PEN-G and carbon and nitrogen sources on the biotransformation ability at 30°C and pH 7.0 were evaluated. Cells grown in medium supplemented with glucose as an additional carbon source and yeast extract as a nitrogen source exhibited maximal PEN-G biotransformation efficiency and rate (71.678% ±1.28 and 2.99 mg/h, respectively). The culture conditions for B. pseudomycoides AH1 cells were optimized using a Plackett–Burman design (PBD). Six key determinants (p < 0.05) significantly affected the process outcome, as deduced by regression analysis of the PBD data, and modified MSM broth achieved PEN-G biotransformation efficiency (100%) under aerobic shaking conditions at 35°C, irrespective of HPLC analysis. Additionally, the present investigation could strongly support the application of immobilization approaches for the removal of PEN-G-contaminated environmental sites. To the best of the authors’ knowledge, this is the first detailed study on the efficient biotransformation of PEN-G by an alginate-bacteria system as a simple, green, and inexpensive process, as well as a promising method.","PeriodicalId":8069,"journal":{"name":"Annals of Microbiology","volume":"6 1","pages":""},"PeriodicalIF":3.0,"publicationDate":"2024-08-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142221083","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
In recent years, there has been an increasing interest in the field of research into the isolation and characterization of probiotics in the prevention of diseases and the need to maintain the continuity of healthy microbiota. Therefore, the aim of this study is to isolate and identify bacteria found in maternal colostrum, breast milk, adult and infant feces, analyze possible probiotic potential, and reveal the developmental kinetics of selected strains. We isolated 40 bacterial species from 4 different sources and identified 19 bacteria in the form of bacilli through molecular biology and carried out studies with 11 of them. Five of the selected strains showed the better results considering bile salt resistance and ability to survive at different pH and antimicrobial effect. When the adhesion capacity in cell culture is examined, the better 2 strains are; Lactobacillus pontis ZZ6780 and Lactobacillus reuteri NBC2680 were selected and the growth kinetics of these strains were demonstrated at the 3 L bioreactor scale. Finally, the growth kinetics of selected strains were determined and the maximum specific growth rate of selected Lactobacillus pontis ZZ6780 and Lactobacillus reuteri NBC2680 was calculated as 0.412 h− 1 and 0.481 h− 1, respectively. In addition, the dry cell matter amounts were found to be and 4.45 g/L and 5.23 g/L, respectively. This study established the groundwork for the selection of safety probiotics for the development and application of LAB. It is thought that the two strains obtained as a result of this study can be considered as potential probiotic strains in the food, pharmaceutical and cosmetic industries.
{"title":"Characterization of nuvita biosearch center (NBC) isolated lactic acid bacteria strains from human origin and determination of growth kinetic profiles of selected cultures under bioreactor","authors":"Akif Emre Kavak, İnci Zent, Ezgi Metin Sağır, Gülistan Öncü, Feride İrem Şimşek","doi":"10.1186/s13213-024-01772-9","DOIUrl":"https://doi.org/10.1186/s13213-024-01772-9","url":null,"abstract":"In recent years, there has been an increasing interest in the field of research into the isolation and characterization of probiotics in the prevention of diseases and the need to maintain the continuity of healthy microbiota. Therefore, the aim of this study is to isolate and identify bacteria found in maternal colostrum, breast milk, adult and infant feces, analyze possible probiotic potential, and reveal the developmental kinetics of selected strains. We isolated 40 bacterial species from 4 different sources and identified 19 bacteria in the form of bacilli through molecular biology and carried out studies with 11 of them. Five of the selected strains showed the better results considering bile salt resistance and ability to survive at different pH and antimicrobial effect. When the adhesion capacity in cell culture is examined, the better 2 strains are; Lactobacillus pontis ZZ6780 and Lactobacillus reuteri NBC2680 were selected and the growth kinetics of these strains were demonstrated at the 3 L bioreactor scale. Finally, the growth kinetics of selected strains were determined and the maximum specific growth rate of selected Lactobacillus pontis ZZ6780 and Lactobacillus reuteri NBC2680 was calculated as 0.412 h− 1 and 0.481 h− 1, respectively. In addition, the dry cell matter amounts were found to be and 4.45 g/L and 5.23 g/L, respectively. This study established the groundwork for the selection of safety probiotics for the development and application of LAB. It is thought that the two strains obtained as a result of this study can be considered as potential probiotic strains in the food, pharmaceutical and cosmetic industries.","PeriodicalId":8069,"journal":{"name":"Annals of Microbiology","volume":"50 1","pages":""},"PeriodicalIF":3.0,"publicationDate":"2024-07-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141869851","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
: Lactic acid bacteria (LAB) are a cluster of microbes distributed in a variety of environments and have potential probiotic activity to improve human well-being. This study was aimed at assessing the probiotic potential of LAB isolated from Cheka, an Ethiopian traditionally fermented beverage. Pure isolates obtained from 16 Cheka samples from Konso (n = 8) and Derashe (n = 8) were characterized morphologically, biochemically, and physiologically by considering basic criteria to identify the LAB. The probiotics properties of the LAB were evaluated in vitro at low pH values (2.0 and 3.0), and two bile salt concentrations (0.3 and 0.5%) for 3 and 6 h. The 16 S rRNA gene sequencing was done using an ABI 3730xl sequencer, and the gene sequences were aligned. Of the 27 pure isolates, 11 isolates were proven to be LAB with non-motile, negative for catalase, and non-spore former characteristics. Based on cultural characteristics and sugar fermentation ability, the 11 isolates were assembled into the genera Lactobacillus (55%), Lactococcus (18%), Pediococcus (18%), and Leuconostoc (9%). At pH 3.0 and a bile salt concentration of 0.3%, isolate ChK-11 showed a better survival rate (97 and 94%) than other isolates [ChK-7 (93 and 80%) > ChD-5 (84 and 76%) > ChD-8 (46 and 36%) > ChK-4 (41 and 34%)] for 6 and 3 h, respectively. According to 16 S rRNA sequencing results, isolates ChK-11 and ChK-7 were found to be Weissella paramesenteroides and Leuconostoc pseudomesenteroides with sequence similarity of 99 and 91%, respectively. In the present study, probiotic LAB (Weissella paramesenteroides and Leuconostoc pseudomesenteroides) was successfully isolated and sequenced from Cheka samples. The findings of this in vitro study indicated that fermented beverages like Cheka are a source of the LAB with probiotic functional properties. Overall, Weissella paramesenteroides and Leuconostoc pseudomesenteroides isolates, which showed promising probiotic properties under in vitro conditions, can be used for starter culture development for the Cheka fermentation process.
{"title":"Probiotic potential of lactic acid bacteria isolated from Ethiopian traditional fermented Cheka beverage","authors":"Dawit Albene, Niguse Kelile Lema, Getaneh Tesfaye, Addisu Fekadu Andeta, Kidist Ali, Awoke Guadie","doi":"10.1186/s13213-024-01771-w","DOIUrl":"https://doi.org/10.1186/s13213-024-01771-w","url":null,"abstract":": Lactic acid bacteria (LAB) are a cluster of microbes distributed in a variety of environments and have potential probiotic activity to improve human well-being. This study was aimed at assessing the probiotic potential of LAB isolated from Cheka, an Ethiopian traditionally fermented beverage. Pure isolates obtained from 16 Cheka samples from Konso (n = 8) and Derashe (n = 8) were characterized morphologically, biochemically, and physiologically by considering basic criteria to identify the LAB. The probiotics properties of the LAB were evaluated in vitro at low pH values (2.0 and 3.0), and two bile salt concentrations (0.3 and 0.5%) for 3 and 6 h. The 16 S rRNA gene sequencing was done using an ABI 3730xl sequencer, and the gene sequences were aligned. Of the 27 pure isolates, 11 isolates were proven to be LAB with non-motile, negative for catalase, and non-spore former characteristics. Based on cultural characteristics and sugar fermentation ability, the 11 isolates were assembled into the genera Lactobacillus (55%), Lactococcus (18%), Pediococcus (18%), and Leuconostoc (9%). At pH 3.0 and a bile salt concentration of 0.3%, isolate ChK-11 showed a better survival rate (97 and 94%) than other isolates [ChK-7 (93 and 80%) > ChD-5 (84 and 76%) > ChD-8 (46 and 36%) > ChK-4 (41 and 34%)] for 6 and 3 h, respectively. According to 16 S rRNA sequencing results, isolates ChK-11 and ChK-7 were found to be Weissella paramesenteroides and Leuconostoc pseudomesenteroides with sequence similarity of 99 and 91%, respectively. In the present study, probiotic LAB (Weissella paramesenteroides and Leuconostoc pseudomesenteroides) was successfully isolated and sequenced from Cheka samples. The findings of this in vitro study indicated that fermented beverages like Cheka are a source of the LAB with probiotic functional properties. Overall, Weissella paramesenteroides and Leuconostoc pseudomesenteroides isolates, which showed promising probiotic properties under in vitro conditions, can be used for starter culture development for the Cheka fermentation process.","PeriodicalId":8069,"journal":{"name":"Annals of Microbiology","volume":"49 1","pages":""},"PeriodicalIF":3.0,"publicationDate":"2024-07-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141753940","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Rot disease caused by Fusarium poses a formidable threat to the growth of saffron (Crocus sativus L.), resulting in substantial damage to both yield and quality. It is paramount to delve into the root causes of rot disease in saffron to optimize both yield and quality. Existing preventive and treatment modalities have exerted deleterious effects on corms and the natural environment. Consequently, the quest for efficacious and eco-friendly methods such as biological control agents has become an urgent imperative. The disparate distribution of microbial communities between rhizospheric microorganisms and saffron serves as the foundational exploration for uncovering the underlying causes of rot disease. Samples from various saffron organs and rhizosphere soil were gathered, and the sequencing data from the microbial communities were interpreted using 16S rRNA and ITS gene sequencing methods. This facilitated an in-depth examination of the composition and changes of microorganisms in both healthy and diseased saffron plants. The findings indicated rot disease reduced the abundance and diversity of microorganisms in saffron, and the fungal co-occurrence networks were less stable and their communities were more sensitive to rot disease than the bacterial community. Fusarium was the predominant genus in diseased samples, accounting for 99.19% and 89.77% of the communities in diseased leaves and corms. With corms and leaves displaying heightened susceptibility to infection compared to other plant organs. Some of the beneficial bacterial taxa enriched in the diseased plants were also identified in networks, they showed an antagonistic relationship with Fusarium, suggesting a potential for these bacteria to be used in biologically based control strategies against rot disease. These insights could prove invaluable for the development of biocontrol agents aimed at combating this plant ailment. These findings significantly advance our understanding of saffron-microbiome interactions and could provide fundamental and important data for improving saffron yield and quality in the process of sustainable development.
{"title":"Revealing the microbial composition changes and relationship with Fusarium caused by rot disease in the Crocus sativus L.","authors":"Jia Song, Xiaoyuan Xi, Xiaodong Qian, Jing Li, Yuanyuan Tao, Liqin Li, Guifen Zhou","doi":"10.1186/s13213-024-01770-x","DOIUrl":"https://doi.org/10.1186/s13213-024-01770-x","url":null,"abstract":"Rot disease caused by Fusarium poses a formidable threat to the growth of saffron (Crocus sativus L.), resulting in substantial damage to both yield and quality. It is paramount to delve into the root causes of rot disease in saffron to optimize both yield and quality. Existing preventive and treatment modalities have exerted deleterious effects on corms and the natural environment. Consequently, the quest for efficacious and eco-friendly methods such as biological control agents has become an urgent imperative. The disparate distribution of microbial communities between rhizospheric microorganisms and saffron serves as the foundational exploration for uncovering the underlying causes of rot disease. Samples from various saffron organs and rhizosphere soil were gathered, and the sequencing data from the microbial communities were interpreted using 16S rRNA and ITS gene sequencing methods. This facilitated an in-depth examination of the composition and changes of microorganisms in both healthy and diseased saffron plants. The findings indicated rot disease reduced the abundance and diversity of microorganisms in saffron, and the fungal co-occurrence networks were less stable and their communities were more sensitive to rot disease than the bacterial community. Fusarium was the predominant genus in diseased samples, accounting for 99.19% and 89.77% of the communities in diseased leaves and corms. With corms and leaves displaying heightened susceptibility to infection compared to other plant organs. Some of the beneficial bacterial taxa enriched in the diseased plants were also identified in networks, they showed an antagonistic relationship with Fusarium, suggesting a potential for these bacteria to be used in biologically based control strategies against rot disease. These insights could prove invaluable for the development of biocontrol agents aimed at combating this plant ailment. These findings significantly advance our understanding of saffron-microbiome interactions and could provide fundamental and important data for improving saffron yield and quality in the process of sustainable development.","PeriodicalId":8069,"journal":{"name":"Annals of Microbiology","volume":"64 1","pages":""},"PeriodicalIF":3.0,"publicationDate":"2024-07-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141745850","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-07-20DOI: 10.1186/s13213-024-01764-9
Mohamed M. Gharieb, Aya Rizk, Nora Elfeky
Resistance to antifungal medications poses a significant obstacle in combating fungal infections. The development of novel therapeutics for Candida albicans is necessary due to the increasing resistance of candidiasis to the existing medications. The utilization of biological control is seen as a more advantageous and less hazardous strategy therefore the objective of this study is to identify the antifungal properties of Bacillus subtilis against pathogenic C. albicans. We conducted a study to evaluate the antifungal properties of three bacterial isolates against the human pathogen Candida albicans. One of the bacterial isolates exhibited a potent antifungal activity against this fungal pathogen. This bacterium was identified as Bacillus subtilis based on the 16Sr RNA gene sequence. It exhibited inhibitory efficacy ranging from 33.5 to 44.4% against 15 Candida isolates. The optimal incubation duration for achieving the maximum antifungal activity was determined to be 48 h, resulting in a mean inhibition zone diameter of 29 ± 0.39 mm. The Potato Dextrose agar (PDA) medium was the best medium for the most effective antifungal activity. Incubation temperature of 25oC and medium pH value of 8.0 were the most favorable conditions for maximum antagonistic activity that resulted fungal growth inhibition of 40 ± 0.16 and 36 ± 0.94 mm respectively. Furthermore, the addition of 10.5 mg/ml of bacterial filtrate to C. albicans colonies resulted in 86.51%. decrease in the number of germinated cells. The fungal cell ultrastructural responses due to exposure to B. subtilis filtrate after 48 h were investigated using transmission electron microscopy (TEM). It revealed primary a drastic abnormality that lead to cellular disintegration including folding and lysis of the cell wall, total collapse of the yeast cells, and malformed germ tube following the exposure to the filtrate. However, the control culture treatment had a characteristic morphology of the normal fungal cells featuring a consistently dense central region, a well-organized nucleus, and a cytoplasm containing several components of the endomembrane system. The cells were surrounded by a uniform and intact cell wall. The current study demonstrates a notable antifungal properties of B. subtilis against C. albicans as a result of production of bioactive components of the bacterial exudate. This finding could be a promising natural antifungal agent that could be utilized to combat C. albicans.
{"title":"Anticandidal activity of a wild Bacillus subtilis NAM against clinical isolates of pathogenic Candida albicans","authors":"Mohamed M. Gharieb, Aya Rizk, Nora Elfeky","doi":"10.1186/s13213-024-01764-9","DOIUrl":"https://doi.org/10.1186/s13213-024-01764-9","url":null,"abstract":"Resistance to antifungal medications poses a significant obstacle in combating fungal infections. The development of novel therapeutics for Candida albicans is necessary due to the increasing resistance of candidiasis to the existing medications. The utilization of biological control is seen as a more advantageous and less hazardous strategy therefore the objective of this study is to identify the antifungal properties of Bacillus subtilis against pathogenic C. albicans. We conducted a study to evaluate the antifungal properties of three bacterial isolates against the human pathogen Candida albicans. One of the bacterial isolates exhibited a potent antifungal activity against this fungal pathogen. This bacterium was identified as Bacillus subtilis based on the 16Sr RNA gene sequence. It exhibited inhibitory efficacy ranging from 33.5 to 44.4% against 15 Candida isolates. The optimal incubation duration for achieving the maximum antifungal activity was determined to be 48 h, resulting in a mean inhibition zone diameter of 29 ± 0.39 mm. The Potato Dextrose agar (PDA) medium was the best medium for the most effective antifungal activity. Incubation temperature of 25oC and medium pH value of 8.0 were the most favorable conditions for maximum antagonistic activity that resulted fungal growth inhibition of 40 ± 0.16 and 36 ± 0.94 mm respectively. Furthermore, the addition of 10.5 mg/ml of bacterial filtrate to C. albicans colonies resulted in 86.51%. decrease in the number of germinated cells. The fungal cell ultrastructural responses due to exposure to B. subtilis filtrate after 48 h were investigated using transmission electron microscopy (TEM). It revealed primary a drastic abnormality that lead to cellular disintegration including folding and lysis of the cell wall, total collapse of the yeast cells, and malformed germ tube following the exposure to the filtrate. However, the control culture treatment had a characteristic morphology of the normal fungal cells featuring a consistently dense central region, a well-organized nucleus, and a cytoplasm containing several components of the endomembrane system. The cells were surrounded by a uniform and intact cell wall. The current study demonstrates a notable antifungal properties of B. subtilis against C. albicans as a result of production of bioactive components of the bacterial exudate. This finding could be a promising natural antifungal agent that could be utilized to combat C. albicans.","PeriodicalId":8069,"journal":{"name":"Annals of Microbiology","volume":"81 1","pages":""},"PeriodicalIF":3.0,"publicationDate":"2024-07-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141738350","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-06-29DOI: 10.1186/s13213-024-01765-8
Qifeng Liu
Fenofibrate is a compound with diverse biological properties that can be utilized to lower blood lipids. Understanding the impact of the gut microbiota in hyperlipidemia is vital for controlling systemic inflammation and improving serum lipid control. Nevertheless, the specific effects of fenofibrate on the phenotype and gene expression of resident gut bacteria, as well as its influence on the transformation of microbial metabolism into functional networks, remain unclear. In this study, our aimed to examine the gene and metabolic pathways of the gut microbiota in a hamster fed a high-fat diet (HFD) and administered fenofibrate. In this study, we conducted metagenomic analyses on samples from HFD hamsters treated with fenofibrate. The results indicated that fenofibrate treatments significantly reduce the serum lipid levels in hyperlipidemia hamsters. And the group treated with fenofibrate exhibited higher levels of beneficial bacterial species associated with health, including Bacteroides ovatus, Bifidobacterium animalis, Bacteroides intestinalis, Allobaculum stercoricanis, Lactobacillus reuteri, and Bacteroides acidifaciens, in comparison to the HFD group. Additionally, analysis of metabolic pathways demonstrated that dietary fenofibrate significantly enhanced the biosynthesis of unsaturated fatty acids, glycerophospholipid metabolism, and pyrimidine metabolism, while reducing glyoxylate and dicarboxylate metabolism, tyrosine metabolism, tryptophan metabolism, and nonribosomal peptide structures. Furthermore, these metabolic pathway changes were associated with relative alterations in the abundance of genes from the Kyoto Encyclopedia of Genes and Genomes (KEGG) database, namely K01667, K11358, K13953, K04072, K06131, K00655, K04567, K02864, K06409, K05366, K01867, K21071, and K13292. Moreover, significant changes were observed in related to carbohydrate and antibiotic resistance, such as glycosyltransferase family 51 (GT51) as well as adeC, carA, and MexT. Dietary fenofibrate exerted significant effects on intestinal flora and genes related to lipid, energy, and amino acid metabolism, ultimately promoting a healthier colonic environment for the host. And these findings contribute to a better understanding of the mechanism of action of fenofibrate and provide a valuable foundation for future experimental and clinical studies, aiming to explore its practical applications.
{"title":"Fenofibrate alleviates the composition and metabolic pathways of gut microbiota in high-fat diet treated hamsters","authors":"Qifeng Liu","doi":"10.1186/s13213-024-01765-8","DOIUrl":"https://doi.org/10.1186/s13213-024-01765-8","url":null,"abstract":"Fenofibrate is a compound with diverse biological properties that can be utilized to lower blood lipids. Understanding the impact of the gut microbiota in hyperlipidemia is vital for controlling systemic inflammation and improving serum lipid control. Nevertheless, the specific effects of fenofibrate on the phenotype and gene expression of resident gut bacteria, as well as its influence on the transformation of microbial metabolism into functional networks, remain unclear. In this study, our aimed to examine the gene and metabolic pathways of the gut microbiota in a hamster fed a high-fat diet (HFD) and administered fenofibrate. In this study, we conducted metagenomic analyses on samples from HFD hamsters treated with fenofibrate. The results indicated that fenofibrate treatments significantly reduce the serum lipid levels in hyperlipidemia hamsters. And the group treated with fenofibrate exhibited higher levels of beneficial bacterial species associated with health, including Bacteroides ovatus, Bifidobacterium animalis, Bacteroides intestinalis, Allobaculum stercoricanis, Lactobacillus reuteri, and Bacteroides acidifaciens, in comparison to the HFD group. Additionally, analysis of metabolic pathways demonstrated that dietary fenofibrate significantly enhanced the biosynthesis of unsaturated fatty acids, glycerophospholipid metabolism, and pyrimidine metabolism, while reducing glyoxylate and dicarboxylate metabolism, tyrosine metabolism, tryptophan metabolism, and nonribosomal peptide structures. Furthermore, these metabolic pathway changes were associated with relative alterations in the abundance of genes from the Kyoto Encyclopedia of Genes and Genomes (KEGG) database, namely K01667, K11358, K13953, K04072, K06131, K00655, K04567, K02864, K06409, K05366, K01867, K21071, and K13292. Moreover, significant changes were observed in related to carbohydrate and antibiotic resistance, such as glycosyltransferase family 51 (GT51) as well as adeC, carA, and MexT. Dietary fenofibrate exerted significant effects on intestinal flora and genes related to lipid, energy, and amino acid metabolism, ultimately promoting a healthier colonic environment for the host. And these findings contribute to a better understanding of the mechanism of action of fenofibrate and provide a valuable foundation for future experimental and clinical studies, aiming to explore its practical applications.","PeriodicalId":8069,"journal":{"name":"Annals of Microbiology","volume":"17 1","pages":""},"PeriodicalIF":3.0,"publicationDate":"2024-06-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141506814","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-06-28DOI: 10.1186/s13213-024-01769-4
Huihui Xu, Beiyu Zhang, Pan Yu, Meng Sun, Lu Xie, Lanming Chen
Vibrio parahaemolyticus is a leading seafood borne pathogen worldwide. The aim of this study was to decipher the response mechanism of V. parahaemolyticus isolates of clinical and aquatic animal origins to the hypoxic condition, which challenges the bacterial survival in the host and in the environment. Growth profiles of V. parahaemolyticus isolates (n = 5) of clinical and aquatic animal origins were examined at different stress conditions (osmolality, acid, temperature, and O2 concentrations). Draft genomes of the V. parahaemolyticus isolates were determined using the Illumina sequencing technique. Comparative genomic analysis were performed to identify and validate the hypoxic tolerance-related genes. The V. parahaemolyticus isolates had an oxygen concentration-dependent growth mode, and the 10% O2 condition strongly inhibited the bacterial growth, when incubated in TSB medium (pH 8.5, 3% NaCl) at 37 °C. Unexpectedly, in marked contrast to the normal 21% O2 condition, the 10% O2 treatment for 24 h significantly increased biofilm formation of V. parahaemolyticus isolates (p < 0.05). Draft genome sequences of four V. parahaemolyticus isolates of aquatic animal origins were determined (4.914–5.3530 Mb), which carried mobile genetic elements (n = 12–29). Genome-wide gene expression changes triggered by the hypoxic condition were further examined. Comparative transcriptomic analyses unveiled multiple molecular strategies employed by the bacterium to mitigate the cell damage caused by the hypoxia. Of note, the pathogenic V. parahaemolyticus ATCC17802 down-regulated and/or shut down ten metabolic pathways to reduce cell viability and maintain cell structure under the hypoxic stress. The results of this study fill prior gaps in the response mechanism of V. parahaemolyticus to the hypoxic condition. Different tolerance to hypoxia contributes to the persistence of pathogenic V. parahaemolyticus in the niches.
{"title":"Comparative genomic and transcriptomic analyses reveal distinct response strategies to hypoxia by Vibrio parahaemolyticus isolates of clinical and aquatic animal origins","authors":"Huihui Xu, Beiyu Zhang, Pan Yu, Meng Sun, Lu Xie, Lanming Chen","doi":"10.1186/s13213-024-01769-4","DOIUrl":"https://doi.org/10.1186/s13213-024-01769-4","url":null,"abstract":"Vibrio parahaemolyticus is a leading seafood borne pathogen worldwide. The aim of this study was to decipher the response mechanism of V. parahaemolyticus isolates of clinical and aquatic animal origins to the hypoxic condition, which challenges the bacterial survival in the host and in the environment. Growth profiles of V. parahaemolyticus isolates (n = 5) of clinical and aquatic animal origins were examined at different stress conditions (osmolality, acid, temperature, and O2 concentrations). Draft genomes of the V. parahaemolyticus isolates were determined using the Illumina sequencing technique. Comparative genomic analysis were performed to identify and validate the hypoxic tolerance-related genes. The V. parahaemolyticus isolates had an oxygen concentration-dependent growth mode, and the 10% O2 condition strongly inhibited the bacterial growth, when incubated in TSB medium (pH 8.5, 3% NaCl) at 37 °C. Unexpectedly, in marked contrast to the normal 21% O2 condition, the 10% O2 treatment for 24 h significantly increased biofilm formation of V. parahaemolyticus isolates (p < 0.05). Draft genome sequences of four V. parahaemolyticus isolates of aquatic animal origins were determined (4.914–5.3530 Mb), which carried mobile genetic elements (n = 12–29). Genome-wide gene expression changes triggered by the hypoxic condition were further examined. Comparative transcriptomic analyses unveiled multiple molecular strategies employed by the bacterium to mitigate the cell damage caused by the hypoxia. Of note, the pathogenic V. parahaemolyticus ATCC17802 down-regulated and/or shut down ten metabolic pathways to reduce cell viability and maintain cell structure under the hypoxic stress. The results of this study fill prior gaps in the response mechanism of V. parahaemolyticus to the hypoxic condition. Different tolerance to hypoxia contributes to the persistence of pathogenic V. parahaemolyticus in the niches.","PeriodicalId":8069,"journal":{"name":"Annals of Microbiology","volume":"31 1","pages":""},"PeriodicalIF":3.0,"publicationDate":"2024-06-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141529583","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-05-31DOI: 10.1186/s13213-024-01766-7
Alaric Prins, Siphosethu S. Dyani, Jo-Marie Vreulink, Luis A. Maldonado, Marilize Le Roes-Hill
South Africa is known for its great biodiversity. The Agulhas Plain represents one such unique environment where low-gradient topography has resulted in extensive wetland formation. It is fed by two major river systems, bringing in brackish, alkaline water. It has been exposed to major marine transgression and regression events, and harbours great Fynbos diversity as well as a Mediterranean-type climate, thereby creating unique ecosystems. It is therefore surprising that little is known about the bacterial diversity associated with the Agulhas Plain and associated marine ecosystems. In this study, we focused on the actinobacterial diversity (Phylum Actinomycetota) associated with an emerging peatland on the Agulhas Plain (SF; Areas 1–3) and a marine site (ANP; Ocean, Rocky, Dry) located 10 km away from SF. A combined metataxanomics and isolation approach was taken to evaluate the actinobacterial diversity of the sampling sites and to determine the effect of environmental physicochemical parameters on these populations. Various genome analyses were performed on an Sva0096 marine bin to gain insight into its ecological role. Metataxanomics showed that the two sites shared defined major taxa, including Blastococcus, Geodermatophilus, Microbacterium, Mycobacterium, Nocardioides, Streptomyces, and the Sva0996 marine group. Analysis of the biosynthetic potential of an Sva0996 marine bin134 (obtained from GenBank) provided insights into the potential ecological role of this group of bacteria in both the marine and terrestrial environments. Higher actinobacterial diversity (Shannon index > 5) was observed for Areas 2 and 3 (SF), as well as the ANP Dry samples. The actinobacterial population composition was found to be driven by salinity, pH, Mn, and Ca, with certain areas of SF exhibiting similar (and even higher) salinity (SF: 70–100 Ω vs. ANP: 100–160 Ω) and lower pH levels (SF: 6.3-8.0 vs. ANP: 8.6–8.9) to that of the marine environment. This snapshot study has provided some insights into the actinobacterial diversity of the two sites studied. Analysis of an Sva0096 marine bin134 provided further insights into the potential ability of the Sva0096 marine group to survive in a unique terrestrial environment that is periodically exposed to environmental pressures that mimic the marine environment.
{"title":"Actinobacteria diversity associated with marine sediments and a wetland system, Agulhas-South Africa","authors":"Alaric Prins, Siphosethu S. Dyani, Jo-Marie Vreulink, Luis A. Maldonado, Marilize Le Roes-Hill","doi":"10.1186/s13213-024-01766-7","DOIUrl":"https://doi.org/10.1186/s13213-024-01766-7","url":null,"abstract":"South Africa is known for its great biodiversity. The Agulhas Plain represents one such unique environment where low-gradient topography has resulted in extensive wetland formation. It is fed by two major river systems, bringing in brackish, alkaline water. It has been exposed to major marine transgression and regression events, and harbours great Fynbos diversity as well as a Mediterranean-type climate, thereby creating unique ecosystems. It is therefore surprising that little is known about the bacterial diversity associated with the Agulhas Plain and associated marine ecosystems. In this study, we focused on the actinobacterial diversity (Phylum Actinomycetota) associated with an emerging peatland on the Agulhas Plain (SF; Areas 1–3) and a marine site (ANP; Ocean, Rocky, Dry) located 10 km away from SF. A combined metataxanomics and isolation approach was taken to evaluate the actinobacterial diversity of the sampling sites and to determine the effect of environmental physicochemical parameters on these populations. Various genome analyses were performed on an Sva0096 marine bin to gain insight into its ecological role. Metataxanomics showed that the two sites shared defined major taxa, including Blastococcus, Geodermatophilus, Microbacterium, Mycobacterium, Nocardioides, Streptomyces, and the Sva0996 marine group. Analysis of the biosynthetic potential of an Sva0996 marine bin134 (obtained from GenBank) provided insights into the potential ecological role of this group of bacteria in both the marine and terrestrial environments. Higher actinobacterial diversity (Shannon index > 5) was observed for Areas 2 and 3 (SF), as well as the ANP Dry samples. The actinobacterial population composition was found to be driven by salinity, pH, Mn, and Ca, with certain areas of SF exhibiting similar (and even higher) salinity (SF: 70–100 Ω vs. ANP: 100–160 Ω) and lower pH levels (SF: 6.3-8.0 vs. ANP: 8.6–8.9) to that of the marine environment. This snapshot study has provided some insights into the actinobacterial diversity of the two sites studied. Analysis of an Sva0096 marine bin134 provided further insights into the potential ability of the Sva0096 marine group to survive in a unique terrestrial environment that is periodically exposed to environmental pressures that mimic the marine environment.","PeriodicalId":8069,"journal":{"name":"Annals of Microbiology","volume":"19 1","pages":""},"PeriodicalIF":3.0,"publicationDate":"2024-05-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141197476","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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