1
|
Brink AM, Kremp A, Gorokhova E. Quantitative real-time PCR assays for species-specific detection and quantification of Baltic Sea spring bloom dinoflagellates. Front Microbiol 2024; 15:1421101. [PMID: 39380673 PMCID: PMC11458424 DOI: 10.3389/fmicb.2024.1421101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2024] [Accepted: 09/11/2024] [Indexed: 10/10/2024] Open
Abstract
In the Baltic Sea, the dinoflagellates Apocalathium malmogiense, Biecheleria baltica, and Gymnodinium corollarium are important contributors to the spring bloom. However, their relative contribution to the bloom community cannot be unambiguously determined by conventional light microscopy due to a lack of resolution of distinctive morphological features of the three species. Here, we describe a molecular approach based on a quantitative real-time polymerase chain reaction (qPCR) primer and probe system, targeting the ITS1 and ITS2 regions of the rRNA gene for all three species and enabling their quantification. The specificity of the method was demonstrated using monocultures of A. malmogiense, B. baltica, G. corollarium as well as three other dinoflagellate species co-occurring in the Baltic Sea during spring and validated using field-collected phytoplankton samples.
Collapse
Affiliation(s)
- Annica Marie Brink
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden
| | - Anke Kremp
- Biological Oceanography, Institute for Baltic Sea Research Warnemünde, Rostock, Germany
| | - Elena Gorokhova
- Department of Environmental Science and Analytical Chemistry, Stockholm University, Stockholm, Sweden
| |
Collapse
|
2
|
Kamarinou CS, Papadopoulou OS, Doulgeraki AI, Tassou CC, Galanis A, Chorianopoulos NG, Argyri AA. Application of multi-functional lactic acid bacteria strains in a pilot scale feta cheese production. Front Microbiol 2023; 14:1254598. [PMID: 37886066 PMCID: PMC10598639 DOI: 10.3389/fmicb.2023.1254598] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 09/28/2023] [Indexed: 10/28/2023] Open
Abstract
Feta cheese is the most recognized Greek Protected Designation of Origin (PDO) product in the world. The addition of selected autochthonous lactic acid bacteria (LAB) strains to cheese milk as adjunct cultures is gaining more attention, since they can impact the nutritional, technological and sensory properties of cheeses, as well as improve the safety of the product. The aim of this study was to produce Feta cheese with enhanced quality and safety, and distinctive organoleptic characteristics by applying autochthonous lactic acid bacteria (LAB) with multi-functional properties as adjunct cultures. Feta cheeses were produced with the commercial lactococcal starter culture and the addition of 9 LAB strains (Lactococcus lactis SMX2 and SMX16, Levilactobacillus brevis SRX20, Lacticaseibacillus paracasei SRX10, Lactiplantibacillus plantarum FRX20 and FB1, Leuconostoc mesenteroides FMX3, FMX11, and FRX4, isolated from artisanal Greek cheeses) in different combinations to produce 13 cheese trials (12 Feta trials with the adjunct LAB isolates and the control trial). In addition, Feta cheese manufactured with FMX3 and SMX2 and control Feta cheese were artificially inoculated (4 log CFU/g) with Listeria monocytogenes (a cocktail of 4 acid or non-acid adapted strains). Cheese samples were monitored by microbiological and physicochemical analyses during ripening, and microbiological, physicochemical, molecular and sensory analyses during storage at 4°C. The results showed that after manufacture, the LAB population was ca. 9.0 log CFU/g at all samples, whereas during storage, their population declined to 6.5-7.0 log CFU/g. In the Listeria inoculated samples, Listeria was absent after 60 days (end of ripening) and after 90 days in the adjunct culture, and in the control trials, respectively. Moreover, the addition of selected strains, especially Lcb. paracasei SRX10, led to cheeses with desirable and distinctive organoleptic characteristics. Furthermore, randomly amplified polymorphic PCR (RAPD-PCR) molecular analysis confirmed that the multi-functional LAB strains were viable by the end of storage. Overall, the results of this study are promising for the use of autochthonous strains in various combinations with the commercial starter culture to satisfy industry requirements and consumer demands for traditional and high added value fermented products.
Collapse
Affiliation(s)
- Christina S. Kamarinou
- Institute of Technology of Agricultural Products, Hellenic Agricultural Organization—DIMITRA, Athens, Greece
- Department of Molecular Biology and Genetics, Democritus University of Thrace, Alexandroupolis, Greece
| | - Olga S. Papadopoulou
- Institute of Technology of Agricultural Products, Hellenic Agricultural Organization—DIMITRA, Athens, Greece
| | - Agapi I. Doulgeraki
- Laboratory of Food Microbiology and Hygiene, Department of Food Science and Technology, Faculty of Agriculture, Forestry and Natural Environment, School of Agriculture, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Chrysoula C. Tassou
- Institute of Technology of Agricultural Products, Hellenic Agricultural Organization—DIMITRA, Athens, Greece
| | - Alex Galanis
- Department of Molecular Biology and Genetics, Democritus University of Thrace, Alexandroupolis, Greece
| | - Nikos G. Chorianopoulos
- Laboratory of Microbiology and Biotechnology of Foods, School of Food and Nutritional Sciences, Department of Food Science and Human Nutrition, Agricultural University of Athens, Athens, Greece
| | - Anthoula A. Argyri
- Institute of Technology of Agricultural Products, Hellenic Agricultural Organization—DIMITRA, Athens, Greece
| |
Collapse
|
3
|
ElHadedy DE, Kim C, Yousuf AB, Wang Z, Ndegwa EN. Understanding Age-Related Longitudinal Dynamics in Abundance and Diversity of Dominant Culturable Gut Lactic Acid Bacteria in Pastured Goats. Animals (Basel) 2023; 13:2669. [PMID: 37627460 PMCID: PMC10451344 DOI: 10.3390/ani13162669] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2023] [Revised: 08/01/2023] [Accepted: 08/17/2023] [Indexed: 08/27/2023] Open
Abstract
Understanding gut lactic acid bacteria (LAB) in healthy hosts is an important first step in selecting potential probiotic species. To understand the dynamics of LAB in healthy goats, a cohort of thirty-seven healthy new-born goat kids was studied over a ten-month period. Total LAB was quantified using SYBR green qPCR. Seven hundred LAB isolates were characterized using microscopy, M13 RAPD genotyping and 16S rDNA sequencing. The highest and lowest LAB counts were detected at one week and ten months of age, respectively. Diverse LAB species were detected, whose identity and prevalence varied with age. The main isolates belonged to Limosilactobacillus reuteri, Limosilactibacillus fermentum, Lactobacillus johnsonni, Ligilactobacillus murinus, Ligilactobacillus salivarius, Limosilactobacillus mucosae, Lactiplantibacillus plantarum, Ligilactobacillus agilis, Lactobacillus acidophilus/amyolovolus, Pediococcus spp. and Enterococcus spp. Uniquely, L. reuteri and Pediococcus spp. were most common in pre- and peri-weaned goats, while Lactobacillus mucosae and Enterococcus spp. were predominant in goats one month and older. Based on RAPD genotyping, L. reuteri had the highest genotypic diversity, with age being a factor on the genotypes detected. This data may be relevant in the selection of age-specific probiotics for goats. The findings may also have broader implications by highlighting age as a factor for consideration in probiotic bacteria selection in other animal hosts.
Collapse
Affiliation(s)
- Doaa E. ElHadedy
- Agricultural Research Station, Virginia State University, Petersburg, VA 23806, USA; (D.E.E.); (C.K.); (A.B.Y.); (Z.W.)
- National Centre for Radiation Research and Technology NCRRT, Radiation Microbiology Department, Egyptian Atomic Energy Authority (EAEA), Cairo 11787, Egypt
| | - Chyer Kim
- Agricultural Research Station, Virginia State University, Petersburg, VA 23806, USA; (D.E.E.); (C.K.); (A.B.Y.); (Z.W.)
| | - Adnan B. Yousuf
- Agricultural Research Station, Virginia State University, Petersburg, VA 23806, USA; (D.E.E.); (C.K.); (A.B.Y.); (Z.W.)
| | - Zhenping Wang
- Agricultural Research Station, Virginia State University, Petersburg, VA 23806, USA; (D.E.E.); (C.K.); (A.B.Y.); (Z.W.)
| | - Eunice N. Ndegwa
- Agricultural Research Station, Virginia State University, Petersburg, VA 23806, USA; (D.E.E.); (C.K.); (A.B.Y.); (Z.W.)
| |
Collapse
|
4
|
Luo T, Li L, Wang S, Cheng N. Research Progress of Nucleic Acid Detection Technology for Genetically Modified Maize. Int J Mol Sci 2023; 24:12247. [PMID: 37569623 PMCID: PMC10418336 DOI: 10.3390/ijms241512247] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 07/21/2023] [Accepted: 07/27/2023] [Indexed: 08/13/2023] Open
Abstract
Genetically modified (GM) maize is one of the earliest GM crops to have achieved large-scale commercial cultivation globally, and it is of great significance to excel in the development and implementation of safety policy regarding GM, and in its technical oversight. This article describes the general situation regarding genetically modified maize, including its varieties, applications, relevant laws and regulations, and so on. From a technical point of view, we summarize and critically analyze the existing methods for detecting nucleic acid levels in genetically modified maize. The nucleic acid extraction technology used for maize is explained, and the introduction of traditional detection techniques, which cover variable-temperature and isothermal amplification detection technology and gene chip technology, applications in maize are described. Moreover, new technologies are proposed, with special attention paid to nucleic acid detection methods using sensors. Finally, we review the current limitations and challenges of GM maize nucleic acid testing and share our vision for the future direction of this field.
Collapse
Affiliation(s)
- Tongyun Luo
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China; (T.L.); (L.L.); (S.W.)
| | - Lujing Li
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China; (T.L.); (L.L.); (S.W.)
| | - Shirui Wang
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China; (T.L.); (L.L.); (S.W.)
| | - Nan Cheng
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China; (T.L.); (L.L.); (S.W.)
- Beijing Laboratory for Food Quality and Safety, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| |
Collapse
|
5
|
Tao J, Liu D, Xiong J, Dou L, Zhai W, Zhang R, Wang Y, Shen J, Wen K. Rapid On-Site Detection of Extensively Drug-Resistant Genes in Enterobacteriaceae via Enhanced Recombinase Polymerase Amplification and Lateral Flow Biosensor. Microbiol Spectr 2022; 10:e0334422. [PMID: 36445091 PMCID: PMC9769758 DOI: 10.1128/spectrum.03344-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 11/14/2022] [Indexed: 12/03/2022] Open
Abstract
The widespread emergence of transferable extensively drug-resistant (XDR) genes, including blaNDM and blaKPC for carbapenem resistance, mcr-1 for colistin resistance, and tet(X4) and tet(X6) for tigecycline resistance, in Enterobacteriaceae poses a major threat to public health. Thus, rapid on-site detection of these XDR genes is urgently needed. We developed a cascade system with a unitary polyethylene glycol (PEG) 200-enhanced recombinase polymerase amplification (RPA) as the core, combined with a modified Chelex-100 lysis method and a horseradish peroxidase (HRP)-catalyzed lateral flow immunoassay (LFIA) biosensor, to accurately detect these genes in Enterobacteriaceae. The conventional Chelex-100 lysis method was modified to allow in situ extraction of bacterial DNA in 20 min without requiring bulky high-speed centrifuges. Using PEG 200 increased the amplification efficiency of the RPA by 13%, and the HRP-catalyzed LFIA biosensor intensified the colorimetric signal of the test line. Following optimization, the sensitivity of the cascade system was <10 copies/μL with satisfactory specificity, allowing for highly sensitive detection of these XDR genes in Enterobacteriaceae. The complete detection procedure can be completed in less than 1 h without using large-scale instruments. This assay is conducive to rapid on-site visual detection of these XDR genes in Enterobacteriaceae in practical applications, thus providing better technical support for clinical surveillance of these genes and better treatment of XDR pathogens. IMPORTANCE Carbapenem, colistin, and tigecycline are considered the last resorts for treating severe bacterial infections caused by extensively drug-resistant (XDR) pathogens. A major threat to public health is the emergence and prevalence of transferable XDR genes in Enterobacteriaceae, such as blaNDM and blaKPC for carbapenem resistance, mcr-1 for colistin resistance, and tet(X4) and tet(X6) for tigecycline resistance. Therefore, it is imperative to develop rapid on-site methods to detect these XDR genes. In this study, we constructed a cascade system for detecting these genes based on PEG 200-enhanced recombinase polymerase amplification combined with a modified Chelex-100 lysis method and HRP-catalyzed lateral flow immunoassay. The current method is capable of detecting the above-mentioned XDR genes in situ with satisfactory specificity and sensitivity, which could provide technical support for the surveillance of these genes and provide medication recommendations for the treatment of relevant clinical infections.
Collapse
Affiliation(s)
- Jin Tao
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Veterinary Medicine, China Agricultural University, Beijing, People’s Republic of China
| | - Dejun Liu
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Veterinary Medicine, China Agricultural University, Beijing, People’s Republic of China
| | - Jincheng Xiong
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Veterinary Medicine, China Agricultural University, Beijing, People’s Republic of China
| | - Leina Dou
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Veterinary Medicine, China Agricultural University, Beijing, People’s Republic of China
| | - Weishuai Zhai
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Veterinary Medicine, China Agricultural University, Beijing, People’s Republic of China
| | - Rong Zhang
- Clinical Microbiology Laboratory, 2nd Affiliated Hospital of Zhejiang University, School of Medicine, Zhejiang University, Hangzhou, People’s Republic of China
| | - Yang Wang
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Veterinary Medicine, China Agricultural University, Beijing, People’s Republic of China
| | - Jianzhong Shen
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Veterinary Medicine, China Agricultural University, Beijing, People’s Republic of China
| | - Kai Wen
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Veterinary Medicine, China Agricultural University, Beijing, People’s Republic of China
| |
Collapse
|
6
|
Ranjan A, Arora J, Chauhan A, Basniwal RK, Kumari A, Rajput VD, Prazdnova EV, Ghosh A, Mukerjee N, Mandzhieva SS, Sushkova S, Minkina T, Jindal T. Advances in characterization of probiotics and challenges in industrial application. Biotechnol Genet Eng Rev 2022:1-44. [PMID: 36200338 DOI: 10.1080/02648725.2022.2122287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Accepted: 08/05/2022] [Indexed: 11/02/2022]
Abstract
An unbalanced diet and poor lifestyle are common reasons for numerous health complications in humans. Probiotics are known to provide substantial benefits to human health by producing several bioactive compounds, vitamins, short-chain fatty acids and short peptides. Diets that contain probiotics are limited to curd, yoghurt, kefir, kimchi, etc. However, exploring the identification of more potential probiotics and enhancing their commercial application to improve the nutritional quality would be a significant step to utilizing the maximum benefits. The complex evolution patterns among the probiotics are the hurdles in their characterization and adequate application in the industries and dairy products. This article has mainly discussed the molecular methods of characterization that are based on the analysis of ribosomal RNA, whole genome, and protein markers and profiles. It also has critically emphasized the emerging challenges in industrial applications of probiotics.
Collapse
Affiliation(s)
- Anuj Ranjan
- Academy of Biology and Biotechnology, Southern Federal University, Rostov-on-Don, Russia
| | - Jayati Arora
- Amity Institute of Environmental Sciences, Amity University, Noida, India
| | - Abhishek Chauhan
- Amity Institute of Environmental Toxicology Safety and Management, Amity University, Noida, India
| | - Rupesh Kumar Basniwal
- Amity Institute of Advanced Research and Studies (M&D), Amity University, Noida, India
| | - Arpna Kumari
- Academy of Biology and Biotechnology, Southern Federal University, Rostov-on-Don, Russia
| | - Vishnu D Rajput
- Academy of Biology and Biotechnology, Southern Federal University, Rostov-on-Don, Russia
| | - Evgeniya V Prazdnova
- Academy of Biology and Biotechnology, Southern Federal University, Rostov-on-Don, Russia
| | - Arabinda Ghosh
- Microbiology Division, Department of Botany, Gauhati University, Guwahati, India
| | - Nobendu Mukerjee
- Department of Microbiology, Ramakrishna Mission Vivekananda Centenary College, Kolkata, India
- Department of Health Sciences, Novel Global Community Educational Foundation, New South Wales, Australia
| | - Saglara S Mandzhieva
- Academy of Biology and Biotechnology, Southern Federal University, Rostov-on-Don, Russia
| | - Svetlana Sushkova
- Academy of Biology and Biotechnology, Southern Federal University, Rostov-on-Don, Russia
| | - Tatiana Minkina
- Academy of Biology and Biotechnology, Southern Federal University, Rostov-on-Don, Russia
| | - Tanu Jindal
- Amity Institute of Environmental Toxicology Safety and Management, Amity University, Noida, India
| |
Collapse
|
7
|
Papadopoulou OS, Argyri AA, Bikouli VC, Lambrinea E, Chorianopoulos N. Evaluating the Quality of Cheese Slices Packaged with Na-Alginate Edible Films Supplemented with Functional Lactic Acid Bacteria Cultures after High-Pressure Processing. Foods 2022; 11:foods11182855. [PMID: 36140989 PMCID: PMC9498243 DOI: 10.3390/foods11182855] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 09/02/2022] [Accepted: 09/06/2022] [Indexed: 12/02/2022] Open
Abstract
The aim of the current study was to assess the efficacy of Na-alginate edible films as vehicles for delivering lactic acid bacteria (LAB) with functional properties to sliced cheeses, with or without high-pressure processing (HPP). A three-strain LAB cocktail (Lactococcus lactis Τ4, Leuconostoc mesenteroides Τ25 and Lacticaseibacillus paracasei Τ26) was incorporated into Na-alginate solution in a final population of 9 log CFU/mL. The cheese slices (without or with HPP treatment at 500 MPa for 2 min) were packaged in contact with the LAB edible films (LEFs), and subsequently vacuum packed and stored at 4 °C. Cheese slices without the addition of films, with or without HPP treatment, were used as controls. In all cases, microbiological, pH and sensory analyses were performed, while the presence and the relative abundance of each strain during storage was evaluated using Random Amplified Polymorphic DNA-PCR (RAPD-PCR). In addition, organic acid determination and peptide analysis were performed using high-performance liquid chromatography. The results showed that in cheeses without HPP treatment, the microbiota consisted mostly of mesophilic LAB and lactococci (>7.0 log CFU/g), while HPP caused a reduction in the indigenous microbiota population of approximately 1−1.5 log CFU/g. In the LEF samples, the populations of mesophilic LAB and lactococci were maintained at levels of >6.35 log CFU/g during storage, regardless of the HPP treatment. Sensory evaluation revealed that the LEF samples without HPP had a slightly more acidic taste compared to the control, whereas the HPP-LEF samples exhibited the best organoleptic characteristics. RAPD-PCR confirmed that the recovered strains were attributed to the three strains that had been entrapped in the films, while the strain distribution during storage was random. Overall, the results of the study are promising since the functional LAB strains were successfully delivered to the products by the edible films until the end of storage.
Collapse
|
8
|
Kamarinou CS, Papadopoulou OS, Doulgeraki AI, Tassou CC, Galanis A, Chorianopoulos NG, Argyri AA. Mapping the Key Technological and Functional Characteristics of Indigenous Lactic Acid Bacteria Isolated from Greek Traditional Dairy Products. Microorganisms 2022; 10:246. [PMID: 35208701 PMCID: PMC8875946 DOI: 10.3390/microorganisms10020246] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 01/18/2022] [Accepted: 01/19/2022] [Indexed: 11/25/2022] Open
Abstract
The aim of the current study was to isolate indigenous lactic acid bacteria (LAB) from traditional Greek cheeses and assess their biochemical, technological, and functional characteristics, so as to develop novel cultures with multi-functional properties. Hence, 109 LAB isolates were recovered from traditional fresh cheeses and were evaluated in vitro for their gas production; proteolytic, lipolytic, and haemolytic activity; exopolysaccharide production (EPS); enzymatic potential; and ability to grow at 6.5% NaCl and at different pH, temperature, and anaerobic conditions. Consequently, 48 selected isolates were further evaluated for their survival under simulated gastrointestinal tract conditions, partial bile salt hydrolase activity, antibiotic resistance, and antimicrobial activity against pathogens. These isolates were also incorporated as co-cultures in yogurt production to examine their sensory characteristics and their survival in the product. Some prominent isolates that showed favorable technological and functional characteristics (good survival rates at low pH and bile salts, ability to produce β-galactosidase, and EPS) and attributed desirable sensory characteristics to yogurt were Lactococcuslactis (SRX2, SRX3, SRX5, and SMX16), Lactobacillus paracasei SRX10, and Lactiplantibacillusplantarum (FRX7, FB1), while Leuconostoc mesenteroides FMX3 and L. lactis SMX2 showed an anti-listerial activity in vitro. The results of the present study are promising for the production of novel dairy functional products with an enhanced quality and safety.
Collapse
Affiliation(s)
- Christina S. Kamarinou
- Institute of Technology of Agricultural Products, Hellenic Agricultural Organization—DIMITRA, 14123 Lycovrissi, Greece; (C.S.K.); (O.S.P.); (A.I.D.); (C.C.T.)
- Department of Molecular Biology and Genetics, Democritus University of Thrace, 68100 Alexandroupolis, Greece;
| | - Olga S. Papadopoulou
- Institute of Technology of Agricultural Products, Hellenic Agricultural Organization—DIMITRA, 14123 Lycovrissi, Greece; (C.S.K.); (O.S.P.); (A.I.D.); (C.C.T.)
| | - Agapi I. Doulgeraki
- Institute of Technology of Agricultural Products, Hellenic Agricultural Organization—DIMITRA, 14123 Lycovrissi, Greece; (C.S.K.); (O.S.P.); (A.I.D.); (C.C.T.)
| | - Chrysoula C. Tassou
- Institute of Technology of Agricultural Products, Hellenic Agricultural Organization—DIMITRA, 14123 Lycovrissi, Greece; (C.S.K.); (O.S.P.); (A.I.D.); (C.C.T.)
| | - Alex Galanis
- Department of Molecular Biology and Genetics, Democritus University of Thrace, 68100 Alexandroupolis, Greece;
| | - Nikos G. Chorianopoulos
- Institute of Technology of Agricultural Products, Hellenic Agricultural Organization—DIMITRA, 14123 Lycovrissi, Greece; (C.S.K.); (O.S.P.); (A.I.D.); (C.C.T.)
| | - Anthoula A. Argyri
- Institute of Technology of Agricultural Products, Hellenic Agricultural Organization—DIMITRA, 14123 Lycovrissi, Greece; (C.S.K.); (O.S.P.); (A.I.D.); (C.C.T.)
| |
Collapse
|
9
|
Long-Term Cultivation of a Native Arthrospira platensis (Spirulina) Strain in Pozo Izquierdo (Gran Canaria, Spain): Technical Evidence for a Viable Production of Food-Grade Biomass. Processes (Basel) 2021. [DOI: 10.3390/pr9081333] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Microalgae cultivation is a promising alternative to traditional agriculture in arid—semi-arid areas. The aim of this study is to assess the viability of long-term cultivation of native Arthrospira platensis in Gran Canaria. Maximum culture productivity (0.08 g/L/day) and optimal concentration range (0.6–0.9 g/L) were firstly determined in 8000 L raceway under a greenhouse. Afterwards, a stable productivity of 0.06 g/L/day (6.0 g/m2/day) was obtained by reusing the culture medium during 26 days of cultivation, with consistent biomass biochemical composition. Outdoor temperature and daily solar irradiation ranged between 17.9–30.7 °C and 79.2–274.8 W/m2, while culture pH and salinity were in the range 9.42–10.77 and 11.2–14.9 g/L, respectively. Protein (>60%), potassium (1.8 g/100 g) and C-phycocyanin (7.2%) content is in the high-range of commercial Spirulina, which makes BEA 1257B promising for food and extraction of natural pigments/antioxidants. The dried biomass complies with international standards for human consumption, because of low heavy metal content and no pathogens presence. Product quality can be improved by reducing ash (≃12%) and sodium (1.5%) content through biomass washing optimization and/or further dewatering step. Other microorganisms can be prevented by high alkaline conditions and mild chemical treatments. These results pave the way for a sustainable microalgae-based blue bioeconomy in the Canary Islands.
Collapse
|
10
|
Gorokhova E, El-Shehawy R, Lehtiniemi M, Garbaras A. How Copepods Can Eat Toxins Without Getting Sick: Gut Bacteria Help Zooplankton to Feed in Cyanobacteria Blooms. Front Microbiol 2021; 11:589816. [PMID: 33510717 PMCID: PMC7835405 DOI: 10.3389/fmicb.2020.589816] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 12/17/2020] [Indexed: 11/13/2022] Open
Abstract
Toxin-producing cyanobacteria can be harmful to aquatic biota, although some grazers utilize them with often beneficial effects on their growth and reproduction. It is commonly assumed that gut microbiota facilitates host adaptation to the diet; however, the evidence for adaptation mechanisms is scarce. Here, we investigated the abundance of mlrA genes in the gut of the Baltic copepods Acartia bifilosa and Eurytemora affinis during cyanobacteria bloom season (August) and outside it (February). The mlrA genes are unique to microcystin and nodularin degraders, thus indicating the capacity to break down these toxins by the microbiota. The mlrA genes were expressed in the copepod gut year-round, being >10-fold higher in the summer than in the winter populations. Moreover, they were significantly more abundant in Eurytemora than Acartia. To understand the ecological implications of this variability, we conducted feeding experiments using summer- and winter-collected copepods to examine if/how the mlrA abundance in the microbiota affect: (1) uptake of toxic Nodularia spumigena, (2) uptake of a non-toxic algal food offered in mixtures with N. spumigena, and (3) concomitant growth potential in the copepods. The findings provide empirical evidence that the occurrence of mlrA genes in the copepod microbiome facilitates nutrient uptake and growth when feeding on phytoplankton mixtures containing nodularin-producing cyanobacteria; thus, providing an adaptation mechanism to the cyanobacteria blooms.
Collapse
Affiliation(s)
- Elena Gorokhova
- Department of Environmental Science and Analytical Chemistry, Stockholm University, Stockholm, Sweden
| | - Rehab El-Shehawy
- Department of Environmental Science and Analytical Chemistry, Stockholm University, Stockholm, Sweden
| | - Maiju Lehtiniemi
- Marine Research Centre, Finnish Environment Institute (SYKE), Helsinki, Finland
| | - Andrius Garbaras
- Mass Spectrometry Laboratory, Center for Physical Science and Technology, Vilnius, Lithuania
| |
Collapse
|
11
|
Kanklai J, Somwong TC, Rungsirivanich P, Thongwai N. Screening of GABA-Producing Lactic Acid Bacteria from Thai Fermented Foods and Probiotic Potential of Levilactobacillus brevis F064A for GABA-Fermented Mulberry Juice Production. Microorganisms 2020; 9:microorganisms9010033. [PMID: 33374175 PMCID: PMC7823765 DOI: 10.3390/microorganisms9010033] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Revised: 12/20/2020] [Accepted: 12/21/2020] [Indexed: 12/16/2022] Open
Abstract
Gamma-aminobutyric acid (GABA), the inhibitory neurotransmitter, can be naturally synthesized by a group of lactic acid bacteria (LAB) which is commonly found in rich carbohydrate materials such as fruits and fermented foods. Thirty-six isolates of GABA-producing LAB were obtained from Thai fermented foods. Among these, Levilactobacillus brevis F064A isolated from Thai fermented sausage displayed high GABA content, 2.85 ± 0.10 mg/mL and could tolerate acidic pH and bile salts indicating a promising probiotic. Mulberry (Morus sp.) is widely grown in Thailand. Many mulberry fruits are left to deteriorate during the high season. To increase its value, mulberry juice was prepared and added to monosodium glutamate (MSG), 2% (w/v) prior to inoculation with 5% (v/v) of L. brevis F064A and incubated at 37 °C for 48 h to obtain the GABA-fermented mulberry juice (GABA-FMJ). The GABA-FMJ obtained had 3.31 ± 0.06 mg/mL of GABA content, 5.58 ± 0.52 mg gallic acid equivalent/mL of antioxidant activity, 234.68 ± 15.53 mg cyanidin-3-glucoside/mL of anthocyanin, an ability to inhibit growth of Bacillus cereus TISTR 687, Salmonella Typhi DMST 22842 and Shigella dysenteriae DMST 1511, and 10.54 ± 0.5 log10 colony-forming units (CFU)/mL of viable L. brevis F064A cell count. This GABA-FMJ was considered as a potential naturally functional food for human of all ages.
Collapse
Affiliation(s)
- Jirapat Kanklai
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand; (J.K.); (P.R.)
- Graduate School, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Tasneem Chemama Somwong
- Department of Biology, Faculty of Science and Technology, Princess of Naradhiwas University, Naradhiwas 96000, Thailand;
| | - Patthanasak Rungsirivanich
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand; (J.K.); (P.R.)
- Graduate School, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Narumol Thongwai
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand; (J.K.); (P.R.)
- Research Center in Bioresources for Agriculture, Industry and Medicine, Chiang Mai University, Chiang Mai 50200, Thailand
- Correspondence: ; Tel.: +66-53-941-946-50; Fax: +66-53-892-259
| |
Collapse
|
12
|
Thawornpan P, Thanapongpichat S, Tun AW, Jumpathong W, Jong LD, Buncherd H. Isolation of Nucleic Acids Using Fly Ash as a Low-Cost Adsorbent. ANAL LETT 2020. [DOI: 10.1080/00032719.2020.1835938] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Pongsakorn Thawornpan
- Department of Molecular Biotechnology and Bioinformatics, Faculty of Science, Prince of Songkla University, Songkhla, Thailand
| | | | - Aung Win Tun
- Faculty of Graduate Studies, Mahidol University, Salaya, Thailand
| | - Watthanachai Jumpathong
- Program on Chemical Biology, Chulabhorn Graduate Institute, Center of Excellence on Environmental Health and Toxicology (EHT), Ministry of Education, Bangkok, Thailand
| | - Luitzen de Jong
- Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, Netherlands
| | - Hansuk Buncherd
- Faculty of Medical Technology, Prince of Songkla University, Songkhla, Thailand
- Medical Science Research and Innovation Institute, Prince of Songkla University, Songkhla, Thailand
| |
Collapse
|
13
|
DNA as an in vitro trapping agent for detection of bulky genotoxic metabolites. J Chromatogr B Analyt Technol Biomed Life Sci 2020; 1152:122276. [PMID: 32721860 DOI: 10.1016/j.jchromb.2020.122276] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 06/17/2020] [Accepted: 07/15/2020] [Indexed: 11/20/2022]
Abstract
The instability of electrophilic reactive metabolites in in vitro metabolism studies makes their accurate analysis challenging. To stabilise the reactive compounds prior to their analysis, different trapping agents, such as thiols, amines and cob(I)alamin, have earlier been tested depending on the metabolites to be analysed and the type of study. In the present work, DNA is introduced as a trapping agent for measuring the formation of bulky electrophilic metabolites. Benzo[a]pyrene (B[a]P), a polycyclic aromatic hydrocarbon (PAH), was used as a model compound in a rat liver S9 metabolic system. Under physiological incubation conditions, B[a]P metabolises to diol epoxide (BPDE) metabolites which were trapped by DNA resulting in the formation of covalently bound DNA adducts. The methodology for analysis of these adducts included extraction of the DNA from the metabolic system, digestion of the DNA to yield nucleosides and analysis of the BPDE-adduct to deoxyguanosine (BPDE-dG) by liquid chromatography coupled to high resolution mass spectrometry (HRMS). The chromatographic conditions in combination with the high mass accuracy data (±3 ppm) was useful in resolving BPDE-dG in its protonated form from the complex set of ions present in the metabolic matrix. The method was validated in terms of sensitivity, specificity, accuracy, precision and recovery, and applied to provide a preliminary estimate of BPDE-dG levels from the metabolism of B[a]P in rat S9. The use of DNA as a trapping agent for in vitro metabolites has a potential to aid in cancer risk assessment procedure of PAHs, for instance, in inter-species comparison of metabolism to reactive metabolites and can be adapted for screening of genotoxic metabolites, e.g., from emerging environmental contaminants.
Collapse
|
14
|
Mercury-methylating bacteria are associated with copepods: A proof-of-principle survey in the Baltic Sea. PLoS One 2020; 15:e0230310. [PMID: 32176728 PMCID: PMC7075563 DOI: 10.1371/journal.pone.0230310] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2019] [Accepted: 02/26/2020] [Indexed: 01/08/2023] Open
Abstract
Methylmercury (MeHg) is a potent neurotoxin that biomagnifies in marine food webs. Inorganic mercury (Hg) methylation is conducted by heterotrophic bacteria inhabiting sediment or settling detritus, but endogenous methylation by the gut microbiome of animals in the lower food webs is another possible source. We examined the occurrence of the bacterial gene (hgcA), required for Hg methylation, in the guts of dominant zooplankters in the Northern Baltic Sea. A qPCR assay targeting the hgcA sequence in three main clades (Deltaproteobacteria, Firmicutes and Archaea) was used in the field-collected specimens of copepods (Acartia bifilosa, Eurytemora affinis, Pseudocalanus acuspes and Limnocalanus macrurus) and cladocerans (Bosmina coregoni maritima and Cercopagis pengoi). All copepods were found to carry hgcA genes in their gut microbiome, whereas no amplification was recorded in the cladocerans. In the copepods, hgcA genes belonging to only Deltaproteobacteria and Firmicutes were detected. These findings suggest a possibility that endogenous Hg methylation occurs in zooplankton and may contribute to seasonal, spatial and vertical MeHg variability in the water column and food webs. Additional molecular and metagenomics studies are needed to identify bacteria carrying hgcA genes and improve their quantification in microbiota.
Collapse
|
15
|
Al-hajj EM, Mohamed MS, Abd Alfadil NA, Altayb HN, Idris AB, El-zaki S, Hassan MA. Contamination of Currency Notes with Kanamycin Resistant Shigella flexneri.. [DOI: 10.1101/2020.03.07.982017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
Abstract
AbstractShigella flexneriis the main causative agent of shigellosis commonly distributed in developing countries with high morbidity and mortality rates. This study aimed to examine the presence ofShigellaspecies in Sudanese currency notes using both traditional and molecular techniques. One hundred thirty five currency notes were collected and their contaminants were isolated and identified conventionally and genetically using 16S rRNA gene amplification and sequencing. Eight isolates were identified asShigellaspecies in different notes, and 3 of them were resistant to penicillin, kanamycin and nitrofurantoin. OneS. flexneriisolate has insertion mutation of guanine nucleotide at position 730 of life’s essential gene 16S rRNA which known evolutionarily to be stable gene. Banknotes are highly circulating items and therefore, appropriate measures such as regular replacement of the dirty notes with new papers are necessary to protect peoples from being infected with drug resistant pathogens.
Collapse
|
16
|
Gorokhova E, Martella G, Motwani NH, Tretyakova NY, Sundelin B, Motwani HV. DNA epigenetic marks are linked to embryo aberrations in amphipods. Sci Rep 2020; 10:655. [PMID: 31959811 PMCID: PMC6971077 DOI: 10.1038/s41598-020-57465-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2019] [Accepted: 12/26/2019] [Indexed: 11/22/2022] Open
Abstract
Linking exposure to environmental stress factors with diseases is crucial for proposing preventive and regulatory actions. Upon exposure to anthropogenic chemicals, covalent modifications on the genome can drive developmental and reproductive disorders in wild populations, with subsequent effects on the population persistence. Hence, screening of chemical modifications on DNA can be used to provide information on the probability of such disorders in populations of concern. Using a high-resolution mass spectrometry methodology, we identified DNA nucleoside adducts in gravid females of the Baltic amphipods Monoporeia affinis, and linked the adduct profiles to the frequency of embryo malformations in the broods. Twenty-three putative nucleoside adducts were detected in the females and their embryos, and eight modifications were structurally identified using high-resolution accurate mass data. To identify which adducts were significantly associated with embryo malformations, partial least squares regression (PLSR) modelling was applied. The PLSR model yielded three adducts as the key predictors: methylation at two different positions of the DNA (5-methyl-2'-deoxycytidine and N6-methyl-2'-deoxyadenosine) representing epigenetic marks, and a structurally unidentified nucleoside adduct. These adducts predicted the elevated frequency of the malformations with a high classification accuracy (84%). To the best of our knowledge, this is the first application of DNA adductomics for identification of contaminant-induced malformations in field-collected animals. The method can be adapted for a broad range of species and evolve as a new omics tool in environmental health assessment.
Collapse
Affiliation(s)
- Elena Gorokhova
- Department of Environmental Science and Analytical Chemistry, Stockholm University, Stockholm, SE, 10691, Sweden
| | - Giulia Martella
- Department of Environmental Science and Analytical Chemistry, Stockholm University, Stockholm, SE, 10691, Sweden
| | - Nisha H Motwani
- Department of Environmental Science and Analytical Chemistry, Stockholm University, Stockholm, SE, 10691, Sweden
| | - Natalia Y Tretyakova
- Department of Medicinal Chemistry and Masonic Cancer Center, University of Minnesota, Minneapolis, MN, 55455, United States
| | - Brita Sundelin
- Department of Environmental Science and Analytical Chemistry, Stockholm University, Stockholm, SE, 10691, Sweden
| | - Hitesh V Motwani
- Department of Environmental Science and Analytical Chemistry, Stockholm University, Stockholm, SE, 10691, Sweden.
| |
Collapse
|
17
|
Silva ANBD, Souza RDCMD, Honorato NRM, Martins RR, Câmara ACJD, Galvão LMDC, Chiari E. Comparison of phenol-chloroform and a commercial deoxyribonucleic acid extraction kit for identification of bloodmeal sources from triatomines (Hemiptera: Reduviidae). Rev Soc Bras Med Trop 2020; 53:e20200189. [PMID: 33263682 PMCID: PMC7723369 DOI: 10.1590/0037-8682-0189-2020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Accepted: 09/24/2020] [Indexed: 11/21/2022] Open
|
18
|
Teixeira PD, Silva VS, Tenreiro R. Integrated selection and identification of bacteria from polluted sites for biodegradation of lipids. Int Microbiol 2019; 23:367-380. [PMID: 31828447 DOI: 10.1007/s10123-019-00109-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Revised: 11/21/2019] [Accepted: 11/22/2019] [Indexed: 11/29/2022]
Abstract
Wastewater treatment plants face major social concern towards removal of problematic pollutants such as fat oils and grease (FOG). In this context, the main objective of the present work was to select natural bacterial isolates from different polluted sites and evaluate them comparatively to isolates from commercial products, for improved bioremediation strategies and bioaugmentation. In total, 196 isolates were analysed for genomic diversity by two PCR-fingerprinting methods and screened for biodegradation potential with pollutants as sole carbon source. The net area under curve (NAUC) was used for preliminary evaluation of growth ability in M9 medium supplemented with oleic acid and triolein. A principal component analysis of all NAUC data showed that natural isolates presented higher overall biodegradation ability and enabled the selection of 11 natural isolates for lipid degradation assays. Selected isolates were identified by 16S rRNA gene sequencing as members of genera with previously described degradative strains, namely, Acinetobacter (1), Aeromonas (2), Bacillus (1), Pseudomonas (1) and Staphylococcus (6). Best biodegradation results in 7-days assay of FOG content removal were 37.9% for oleic acid and 19.1% for triolein by an Aeromonas sp. isolate and a Staphylococcus cohnii isolate, respectively. A respirometry approach confirmed their higher oxygen uptake rates, although longer adaptation phases where required by the Aeromonas sp. isolate. Consequently, these isolates showed great potential for future bioaugmentation products, to promote FOG degradation, for both in situ and ex situ approaches.
Collapse
Affiliation(s)
- Pedro D Teixeira
- Faculdade de Ciências, Biosystems & Integrative Sciences Institute (BioISI), Campus da FCUL, Universidade de Lisboa, Campo Grande, 1749-016, Lisbon, Portugal. .,BioTask, Biotecnologia Lda, Av. Jorge MV Pereira, Bloco 4D, Paúl, 2560-232, Torres Vedras, Portugal.
| | - Vitor S Silva
- BioTask, Biotecnologia Lda, Av. Jorge MV Pereira, Bloco 4D, Paúl, 2560-232, Torres Vedras, Portugal
| | - Rogério Tenreiro
- Faculdade de Ciências, Biosystems & Integrative Sciences Institute (BioISI), Campus da FCUL, Universidade de Lisboa, Campo Grande, 1749-016, Lisbon, Portugal
| |
Collapse
|
19
|
Besung INK, Suarjana IGK, Agustina KK, Winaya IBO, Soeharsono H, Suwiti NK, Mahardika GN. Isolation and identification of Streptococcus suis from sick pigs in Bali, Indonesia. BMC Res Notes 2019; 12:795. [PMID: 31806042 PMCID: PMC6896353 DOI: 10.1186/s13104-019-4826-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2019] [Accepted: 11/26/2019] [Indexed: 01/13/2023] Open
Abstract
Objective Streptococcus suis (S. suis) is a causative agent for various syndromes in pigs. It can be transmitted to humans with typical symptoms of meningitis and death. Although human infections have been confirmed at Bali Referral Hospital, Indonesia, since 2014, the bacteria have not been isolated from pigs. Here, we provide confirmation of the presence of the bacteria in sick pigs in the province. Results Streptococcus suis was confirmed in 8 of 30 cases. The final confirmation was made using PCR and sequencing of the glutamate dehydrogenase (GDH) and recombination/repair protein (recN) gene fragments. Upon PCR serotyping, two were confirmed to be serotype 2 or 1/2. Prominent histopathological lesions of confirmed cases were meningitis, endocarditis, pericarditis, bronchopneumonia, enteritis and glomerulonephritis. The dominant inflammatory cells were neutrophils and macrophages. Further research is needed to understand the risk factors for human infection. Community awareness on the risk of contracting S. suis and vaccine development are needed to prevent human infections.
Collapse
Affiliation(s)
- I Nengah Kerta Besung
- Laboratory of Microbiology, Faculty of Veterinary Medicine, Udayana University of Bali, Jl. Sudirman, Denpasar, 80225, Indonesia.
| | - I Gusti Ketut Suarjana
- Laboratory of Microbiology, Faculty of Veterinary Medicine, Udayana University of Bali, Jl. Sudirman, Denpasar, 80225, Indonesia
| | - Kadek Karang Agustina
- Department of Veterinary Public Health, Faculty of Veterinary Medicine, Udayana University of Bali, Jl. Sudirman, Denpasar, 80225, Indonesia
| | - Ida Bagus Oka Winaya
- Laboratory of Pathology, Faculty of Veterinary Medicine, Udayana University of Bali, Jl. Sudirman, Denpasar, 80225, Indonesia
| | - Hamong Soeharsono
- Laboratory of Biochemistry, Faculty of Veterinary Medicine, Udayana University of Bali, Jl. Sudirman, Denpasar, 80225, Indonesia
| | - Ni Ketut Suwiti
- Department of Basic Veterinary Science, Faculty of Veterinary Medicine, Udayana University of Bali, Jl. Sudirman, Denpasar, 80225, Indonesia
| | - Gusti Ngurah Mahardika
- The Animal Biomedical and Molecular Biology Laboratory, Udayana University of Bali, Jl. Sesetan-Markisa #6, Denpasar, 80226, Indonesia
| |
Collapse
|
20
|
Isolation and characterization of spontaneous phage-resistant mutants of Lactobacillus paracasei. Food Control 2019. [DOI: 10.1016/j.foodcont.2018.12.037] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
|
21
|
da Silva RJ, Maciel BG, Medina-Llamas JC, Chávez-Guajardo AE, Alcaraz-Espinoza JJ, Pinto de Melo C. Extraction of plasmid DNA by use of a magnetic maghemite-polyaniline nanocomposite. Anal Biochem 2019; 575:27-35. [PMID: 30917944 DOI: 10.1016/j.ab.2019.03.013] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Revised: 03/21/2019] [Accepted: 03/21/2019] [Indexed: 11/28/2022]
Abstract
We describe the use of a hybrid magnetic nanocomposite (HMNC) for the extraction and purification of plasmid DNA (pDNA) from Escherichia coli aqueous solutions. The HMNC, which was synthesized via emulsion polymerization, was characterized by transmission electron microscopy, scanning electron microscopy, UV-Vis spectroscopy, Fourier transform infrared spectroscopy, dynamic light scattering and magnetic measurements. The results confirmed the incorporation of polyaniline (Pani) in its conducting form onto a core formed by the magnetic iron oxide, with the hybrid particles presenting an average size of (95 ± 30) nm and a saturation magnetization of 30 emu/g. The yield, purity and quality of the pDNA purified by using the Pani HMNC were evaluated by UV-Vis spectroscopy, agarose gel electrophoresis, and Polymerase Chain Reaction (PCR), respectively. An average yield of ~6.9 μg was obtained in the DNA extraction process, with the collected material presenting a good purity (a ₳260/280 ratio in the 1.68-1.82 range) and an excellent quality, as confirmed by subsequent PCR assays. Hence, this HMNC appears as a promising material for use in pDNA purification protocols, and we suggest that this novel HMNC-based methodology can be of general interest and find widespread application in different biomedical procedures.
Collapse
Affiliation(s)
- Romário Justino da Silva
- Pós-Graduação em Ciência de Materiais, Universidade Federal de Pernambuco, 50670-901, Recife, PE, Brazil
| | - Bruna Gomes Maciel
- Pós-Graduação em Ciência de Materiais, Universidade Federal de Pernambuco, 50670-901, Recife, PE, Brazil
| | - Juan Carlos Medina-Llamas
- Centro de Estudios Científicos y Tecnológicos No. 18, Instituto Politécnico Nacional, 98160, Zacatecas, Zac, Mexico
| | | | | | - Celso Pinto de Melo
- Pós-Graduação em Ciência de Materiais, Universidade Federal de Pernambuco, 50670-901, Recife, PE, Brazil; Departamento de Física, Universidade Federal de Pernambuco, 50670-901, Recife, PE, Brazil.
| |
Collapse
|
22
|
Zou Y, Xue W, Luo G, Deng Z, Qin P, Guo R, Sun H, Xia Y, Liang S, Dai Y, Wan D, Jiang R, Su L, Feng Q, Jie Z, Guo T, Xia Z, Liu C, Yu J, Lin Y, Tang S, Huo G, Xu X, Hou Y, Liu X, Wang J, Yang H, Kristiansen K, Li J, Jia H, Xiao L. 1,520 reference genomes from cultivated human gut bacteria enable functional microbiome analyses. Nat Biotechnol 2019; 37:179-185. [PMID: 30718868 PMCID: PMC6784896 DOI: 10.1038/s41587-018-0008-8] [Citation(s) in RCA: 297] [Impact Index Per Article: 59.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Accepted: 12/13/2018] [Indexed: 12/22/2022]
Abstract
Reference genomes are essential for metagenomic analyses and functional characterization of the human gut microbiota. We present the Culturable Genome Reference (CGR), a collection of 1,520 nonredundant, high-quality draft genomes generated from >6,000 bacteria cultivated from fecal samples of healthy humans. Of the 1,520 genomes, which were chosen to cover all major bacterial phyla and genera in the human gut, 264 are not represented in existing reference genome catalogs. We show that this increase in the number of reference bacterial genomes improves the rate of mapping metagenomic sequencing reads from 50% to >70%, enabling higher-resolution descriptions of the human gut microbiome. We use the CGR genomes to annotate functions of 338 bacterial species, showing the utility of this resource for functional studies. We also carry out a pan-genome analysis of 38 important human gut species, which reveals the diversity and specificity of functional enrichment between their core and dispensable genomes. A resource of >1,500 bacterial reference genomes sheds light on the human gut microbiome.
Collapse
Affiliation(s)
- Yuanqiang Zou
- BGI-Shenzhen, Shenzhen, China.,China National Genebank, BGI-Shenzhen, Shenzhen, China.,Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Wenbin Xue
- BGI-Shenzhen, Shenzhen, China.,China National Genebank, BGI-Shenzhen, Shenzhen, China
| | - Guangwen Luo
- BGI-Shenzhen, Shenzhen, China.,China National Genebank, BGI-Shenzhen, Shenzhen, China.,Key Laboratory of Dairy Science, College of Food Sciences, Northeast Agricultural University, Harbin, Heilongjiang, China
| | - Ziqing Deng
- BGI-Shenzhen, Shenzhen, China.,China National Genebank, BGI-Shenzhen, Shenzhen, China
| | - Panpan Qin
- BGI-Shenzhen, Shenzhen, China.,China National Genebank, BGI-Shenzhen, Shenzhen, China.,BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, China
| | - Ruijin Guo
- BGI-Shenzhen, Shenzhen, China.,China National Genebank, BGI-Shenzhen, Shenzhen, China
| | - Haipeng Sun
- BGI-Shenzhen, Shenzhen, China.,China National Genebank, BGI-Shenzhen, Shenzhen, China
| | - Yan Xia
- BGI-Shenzhen, Shenzhen, China.,China National Genebank, BGI-Shenzhen, Shenzhen, China.,BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, China
| | - Suisha Liang
- BGI-Shenzhen, Shenzhen, China.,China National Genebank, BGI-Shenzhen, Shenzhen, China.,Shenzhen Engineering Laboratory of Detection and Intervention of Human Intestinal Microbiome, Shenzhen, China
| | - Ying Dai
- BGI-Shenzhen, Shenzhen, China.,China National Genebank, BGI-Shenzhen, Shenzhen, China
| | - Daiwei Wan
- BGI-Shenzhen, Shenzhen, China.,China National Genebank, BGI-Shenzhen, Shenzhen, China
| | - Rongrong Jiang
- BGI-Shenzhen, Shenzhen, China.,China National Genebank, BGI-Shenzhen, Shenzhen, China
| | - Lili Su
- BGI-Shenzhen, Shenzhen, China.,China National Genebank, BGI-Shenzhen, Shenzhen, China
| | - Qiang Feng
- BGI-Shenzhen, Shenzhen, China.,China National Genebank, BGI-Shenzhen, Shenzhen, China
| | - Zhuye Jie
- BGI-Shenzhen, Shenzhen, China.,China National Genebank, BGI-Shenzhen, Shenzhen, China
| | - Tongkun Guo
- BGI-Shenzhen, Shenzhen, China.,China National Genebank, BGI-Shenzhen, Shenzhen, China
| | - Zhongkui Xia
- BGI-Shenzhen, Shenzhen, China.,China National Genebank, BGI-Shenzhen, Shenzhen, China
| | - Chuan Liu
- BGI-Shenzhen, Shenzhen, China.,China National Genebank, BGI-Shenzhen, Shenzhen, China.,Shenzhen Engineering Laboratory of Detection and Intervention of Human Intestinal Microbiome, Shenzhen, China
| | - Jinghong Yu
- BGI-Shenzhen, Shenzhen, China.,China National Genebank, BGI-Shenzhen, Shenzhen, China
| | - Yuxiang Lin
- BGI-Shenzhen, Shenzhen, China.,China National Genebank, BGI-Shenzhen, Shenzhen, China
| | - Shanmei Tang
- BGI-Shenzhen, Shenzhen, China.,China National Genebank, BGI-Shenzhen, Shenzhen, China
| | - Guicheng Huo
- Key Laboratory of Dairy Science, College of Food Sciences, Northeast Agricultural University, Harbin, Heilongjiang, China
| | - Xun Xu
- BGI-Shenzhen, Shenzhen, China.,China National Genebank, BGI-Shenzhen, Shenzhen, China
| | - Yong Hou
- BGI-Shenzhen, Shenzhen, China.,China National Genebank, BGI-Shenzhen, Shenzhen, China
| | - Xin Liu
- BGI-Shenzhen, Shenzhen, China.,China National Genebank, BGI-Shenzhen, Shenzhen, China.,BGI-Qingdao, BGI-Shenzhen, Qingdao, China
| | - Jian Wang
- BGI-Shenzhen, Shenzhen, China.,James D. Watson Institute of Genome Sciences, Hangzhou, China
| | - Huanming Yang
- BGI-Shenzhen, Shenzhen, China.,James D. Watson Institute of Genome Sciences, Hangzhou, China
| | - Karsten Kristiansen
- BGI-Shenzhen, Shenzhen, China.,China National Genebank, BGI-Shenzhen, Shenzhen, China.,Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Copenhagen, Denmark.,Qingdao-Europe Advanced Institute for Life Sciences, Qingdao, China
| | - Junhua Li
- BGI-Shenzhen, Shenzhen, China. .,China National Genebank, BGI-Shenzhen, Shenzhen, China. .,School of Bioscience and Biotechnology, South China University of Technology, Guangzhou, China.
| | - Huijue Jia
- BGI-Shenzhen, Shenzhen, China. .,China National Genebank, BGI-Shenzhen, Shenzhen, China. .,Macau University of Science and Technology, Taipa, Macau, China.
| | - Liang Xiao
- BGI-Shenzhen, Shenzhen, China. .,China National Genebank, BGI-Shenzhen, Shenzhen, China. .,Shenzhen Engineering Laboratory of Detection and Intervention of Human Intestinal Microbiome, Shenzhen, China. .,Qingdao-Europe Advanced Institute for Life Sciences, Qingdao, China. .,Department of Digestive Diseases, Huashan Hospital of Fudan University, Shanghai, China.
| |
Collapse
|
23
|
Kos Kramar M, Tinta T, Lučić D, Malej A, Turk V. Bacteria associated with moon jellyfish during bloom and post-bloom periods in the Gulf of Trieste (northern Adriatic). PLoS One 2019; 14:e0198056. [PMID: 30645606 PMCID: PMC6333360 DOI: 10.1371/journal.pone.0198056] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Accepted: 12/24/2018] [Indexed: 12/16/2022] Open
Abstract
Jellyfish are a prominent component of the plankton community. They frequently form conspicuous blooms which may interfere with different human enterprises. Among the aspects that remain understudied are jellyfish associations with microorganisms having potentially important implications for organic matter cycling. To the best of our knowledge, this study is the first to investigate the bacterial community associated with live moon jellyfish (Aurelia solida, Scyohozoa) in the Adriatic Sea. Using 16S rRNA clone libraries and culture-based methods, we have analyzed the bacterial community composition of different body parts: the exumbrella surface, oral arms, and gastric cavity, and investigated possible differences in medusa-associated bacterial community structure at the time of the jellyfish population peak, and during the senescent phase at the end of bloom. Microbiota associated with moon jellyfish was different from ambient seawater bacterial assemblage and varied between different body parts. Betaproteobacteria (Burkholderia, Cupriavidus and Achromobacter) dominated community in the gastral cavity of medusa, while Alphaproteobacteria (Phaeobacter, Ruegeria) and Gammaproteobacteria (Stenotrophomonas, Alteromonas, Pseudoalteromonas and Vibrio) prevailed on ‘outer’ body parts. Bacterial community structure changed during senescent phase, at the end of the jellyfish bloom, showing an increased abundance of Gammaproteobacteria, exclusively Vibrio. The results of cultured bacterial isolates showed the dominance of Gammaproeteobacteria, especially Vibrio and Pseudoalteromonas in all body parts. Our results suggest that jellyfish associated bacterial community might have an important role for the host, and that anthropogenic pollution in the Gulf of Trieste might affect their community structure.
Collapse
Affiliation(s)
- Maja Kos Kramar
- Marine Biology Station Piran, National Institute of Biology, Piran, Slovenia
| | - Tinkara Tinta
- Marine Biology Station Piran, National Institute of Biology, Piran, Slovenia
- Department of Limnology and Bio-Oceanography, Center of Functional Ecology, University of Vienna, Vienna, Austria
| | - Davor Lučić
- Institute for Marine and Coastal Research, University of Dubrovnik, Dubrovnik, Croatia
| | - Alenka Malej
- Marine Biology Station Piran, National Institute of Biology, Piran, Slovenia
| | - Valentina Turk
- Marine Biology Station Piran, National Institute of Biology, Piran, Slovenia
- * E-mail:
| |
Collapse
|
24
|
Characterization of Pathogenic Bacteria Isolated from Sudanese Banknotes and Determination of Their Resistance Profile. Int J Microbiol 2018; 2018:4375164. [PMID: 30344610 PMCID: PMC6174782 DOI: 10.1155/2018/4375164] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Revised: 07/16/2018] [Accepted: 08/08/2018] [Indexed: 11/18/2022] Open
Abstract
Background Banknotes are one of the most exchangeable items in communities and always subject to contamination by pathogenic bacteria and hence could serve as vehicle for transmission of infectious diseases. This study was conducted to assess the prevalence of contamination by pathogenic bacteria in Sudanese banknotes, determine the susceptibility of the isolated organisms towards commonly used antibiotics, and detect some antibiotic resistance genes. Methods This study was carried out using 135 samples of Sudanese banknotes of five different denominations (2, 5, 10, 20, and 50 Sudanese pounds), which were collected randomly from hospitals, food sellers, and transporters in all three districts of Khartoum, Bahri, and Omdurman. Bacterial prevalence was determined using culture-based techniques, and their sensitivity patterns were determined using the Kirby–Bauer disk diffusion method. Genotypic identification was carried out using PCR and 16S rDNA sequencing. Antibiotic resistance genes of some isolates were detected using PCR technique. Results All Sudanese banknotes were found to be contaminated with pathogenic bacteria. Klebsiella pneumoniae was found to be the most frequent isolate (23%), whereas Bacillus mycoides (15%) was the most abundant Gram-positive isolate. There was a significant relationship between the number of isolates and the banknote denomination with p value <0.05 (the lower denomination showed higher contamination level). Our study has isolated bacteria that are resistant to penicillins and cephalosporins. Multidrug-resistant strains harboring resistant genes (mecA, blaCTX-M, and blaTEM) were also detected. Conclusion All studied Sudanese banknotes were contaminated with pathogenic bacteria, including multidrug-resistant strains, and may play a significant role in the transmission of bacterial infections.
Collapse
|
25
|
Chen L, Liu B, Xu Z, Liu J. NiO Nanoparticles for Exceptionally Stable DNA Adsorption and Its Extraction from Biological Fluids. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2018; 34:9314-9321. [PMID: 30001142 DOI: 10.1021/acs.langmuir.8b01743] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Selective extraction of a small amount of nucleic acids from complex biological samples containing a high concentration of proteins is critical for bioanalytical chemistry. A number of previously published studies have focused on long, double-stranded DNA such as plasmid DNA. On the other hand, we are interested in short oligonucleotides. Nucleic acids have a negatively charged phosphate backbone that interacts with metal oxides strongly, and this may be used to distinguish them from proteins. In this work, a few metal oxide nanoparticles were screened, including NiO, CoO, ZnO, TiO2, CeO2, and Fe3O4 for DNA recovery. NiO had the highest DNA adsorption efficiency from mixtures containing bovine serum albumin or human blood serum. The adsorption of DNA by NiO was further characterized as a function of the pH, salt concentration, DNA length, and DNA sequence. The adsorption mechanism was studied by adding competing chemicals or denaturing agents. A striking observation was the extremely high adsorption affinity of NiO, much higher than that of the other tested oxides. Polyphosphate was the most effective agent for displacing adsorbed DNA, whereas simple inorganic phosphate was less effective. NiO was able to concentrate DNA from a serum mixture by 33- to 55-fold, depending on the serum concentration. NiO is thus a promising candidate for extracting DNA from biological samples.
Collapse
Affiliation(s)
- Lei Chen
- Research Center for Analytical Sciences , Northeastern University , Shenyang 110004 , China
- Department of Chemistry, Waterloo Institute for Nanotechnology , University of Waterloo , Waterloo , Ontario N2L 3G1 , Canada
| | - Biwu Liu
- Department of Chemistry, Waterloo Institute for Nanotechnology , University of Waterloo , Waterloo , Ontario N2L 3G1 , Canada
| | - Zhangrun Xu
- Research Center for Analytical Sciences , Northeastern University , Shenyang 110004 , China
| | - Juewen Liu
- Department of Chemistry, Waterloo Institute for Nanotechnology , University of Waterloo , Waterloo , Ontario N2L 3G1 , Canada
| |
Collapse
|
26
|
Method for improving the quality of genomic DNA obtained from minute quantities of tissue and blood samples using Chelex 100 resin. Biol Proced Online 2018; 20:12. [PMID: 29881330 PMCID: PMC5984428 DOI: 10.1186/s12575-018-0077-6] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Accepted: 03/19/2018] [Indexed: 11/23/2022] Open
Abstract
Background Although genomic DNA isolation using the Chelex 100 resin is rapid and inexpensive, the DNA obtained by this method has a low concentration in solution and contains suspended impurities. The presence of debris in the DNA solution may result in degradation of DNA on long term storage and inhibition of the polymerase chain reaction. In order to remove impurities and concentrate the DNA in solution, we have introduced modifications in the existing DNA isolation protocol using Chelex-100. We used ammonium acetate to precipitate proteins and a sodium acetate- isopropanol mixture to pellet out DNA which was washed with ethanol. Results A pure DNA pellet that can be dissolved in water or Tris-EDTA buffer and stored for a long time at − 80 °C was obtained. We also observed a 20-fold change in the DNA concentration following precipitation and re-dissolution. Conclusion Our method is different from other extraction methods since it uses non-toxic, easily available and inexpensive reagents as well as minimal amounts of blood or tissue samples for the DNA extraction process. Besides its use in sex determination and genotyping in lab animals as described in this paper, it may also have applications in forensic science and diagnostics such as the easy detection of pathogenic DNA in blood.
Collapse
|
27
|
Dominguez-Moñino I, Jurado V, Gonzalez-Pimentel JL, Miller AZ, Hermosin B, Saiz-Jimenez C. Bacillus onubensis sp. nov., isolated from the air of two Andalusian caves. Syst Appl Microbiol 2018; 41:167-172. [DOI: 10.1016/j.syapm.2018.01.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Revised: 12/29/2017] [Accepted: 01/08/2018] [Indexed: 10/18/2022]
|
28
|
Resende JA, Fontes CO, Ferreira-Machado AB, Nascimento TC, Silva VL, Diniz CG. Antimicrobial-Resistance Genetic Markers in Potentially Pathogenic Gram Positive Cocci Isolated from Brazilian Soft Cheese. J Food Sci 2018; 83:377-385. [DOI: 10.1111/1750-3841.14019] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Accepted: 11/29/2017] [Indexed: 12/22/2022]
Affiliation(s)
- Juliana Alves Resende
- Dept. of Pharmacy and Nutrition; Federal Univ. of Espírito Santo - Campus Alegre; Alegre Brazil
| | - Cláudia Oliveira Fontes
- Dept. of Basic Sciences of Life; Federal Univ. of Juiz de Fora - Campus Governador Valadares; Governador Valadares Brazil
| | | | | | - Vânia Lúcia Silva
- Dept. of Parasitology, Microbiology and Immunology, Inst. of Biological Sciences; Federal Univ. of Juiz de Fora; Juiz de Fora Brazil
| | - Cláudio Galuppo Diniz
- Dept. of Parasitology, Microbiology and Immunology, Inst. of Biological Sciences; Federal Univ. of Juiz de Fora; Juiz de Fora Brazil
| |
Collapse
|
29
|
D'Angelo L, Cicotello J, Zago M, Guglielmotti D, Quiberoni A, Suárez V. Leuconostoc strains isolated from dairy products: Response against food stress conditions. Food Microbiol 2017; 66:28-39. [PMID: 28576370 DOI: 10.1016/j.fm.2017.04.001] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2016] [Revised: 02/24/2017] [Accepted: 04/02/2017] [Indexed: 11/29/2022]
Abstract
A systematic study about the intrinsic resistance of 29 strains (26 autochthonous and 3 commercial ones), belonging to Leuconostoc genus, against diverse stress factors (thermal, acidic, alkaline, osmotic and oxidative) commonly present at industrial or conservation processes were evaluated. Exhaustive result processing was made by applying one-way ANOVA, Student's test (t), multivariate analysis by Principal Component Analysis (PCA) and Matrix Hierarchical Cluster Analysis. In addition, heat adaptation on 4 strains carefully selected based on previous data analysis was assayed. The strains revealed wide diversity of resistance to stress factors and, in general, a clear relationship between resistance and Leuconostoc species was established. In this sense, the highest resistance was shown by Leuconostoc lactis followed by Leuconostoc mesenteroides strains, while Leuconostoc pseudomesenteroides and Leuconostoc citreum strains revealed the lowest resistance to the stress factors applied. Heat adaptation improved thermal cell survival and resulted in a cross-resistance against the acidic factor. However, all adapted cells showed diminished their oxidative resistance. According to our knowledge, this is the first study regarding response of Leuconostoc strains against technological stress factors and could establish the basis for the selection of "more robust" strains and propose the possibility of improving their performance during industrial processes.
Collapse
Affiliation(s)
- Luisa D'Angelo
- Instituto de Lactología Industrial (Universidad Nacional del Litoral - Consejo Nacional de Investigaciones Científicas y Técnicas), Facultad de Ingeniería Química, Santiago del Estero 2829, S3000AOM Santa Fe, Argentina
| | - Joaquín Cicotello
- Instituto de Lactología Industrial (Universidad Nacional del Litoral - Consejo Nacional de Investigaciones Científicas y Técnicas), Facultad de Ingeniería Química, Santiago del Estero 2829, S3000AOM Santa Fe, Argentina
| | - Miriam Zago
- Consiglio per la Ricerca in Agricoltura e l'Analisi dell'Economia Agraria, Centro di Ricerca per le Produzioni Foraggere e Lattiero Casearie (CREA-FLC), Via Lombardo 11, 26900 Lodi, Italy
| | - Daniela Guglielmotti
- Instituto de Lactología Industrial (Universidad Nacional del Litoral - Consejo Nacional de Investigaciones Científicas y Técnicas), Facultad de Ingeniería Química, Santiago del Estero 2829, S3000AOM Santa Fe, Argentina
| | - Andrea Quiberoni
- Instituto de Lactología Industrial (Universidad Nacional del Litoral - Consejo Nacional de Investigaciones Científicas y Técnicas), Facultad de Ingeniería Química, Santiago del Estero 2829, S3000AOM Santa Fe, Argentina
| | - Viviana Suárez
- Instituto de Lactología Industrial (Universidad Nacional del Litoral - Consejo Nacional de Investigaciones Científicas y Técnicas), Facultad de Ingeniería Química, Santiago del Estero 2829, S3000AOM Santa Fe, Argentina.
| |
Collapse
|
30
|
Otaño-Rivera V, Boakye A, Grobe N, Almutairi MM, Kursan S, Mattis LK, Castrop H, Gurley SB, Elased KM, Boivin GP, Di Fulvio M. A highly efficient strategy to determine genotypes of genetically-engineered mice using genomic DNA purified from hair roots. Lab Anim 2017; 51:138-146. [PMID: 27166392 DOI: 10.1177/0023677216646088] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/10/2024]
Abstract
Genotyping of genetically-engineered mice is necessary for the effective design of breeding strategies and identification of mutant mice. This process relies on the identification of DNA markers introduced into genomic sequences of mice, a task usually performed using the polymerase chain reaction (PCR). Clearly, the limiting step in genotyping is isolating pure genomic DNA. Isolation of mouse DNA for genotyping typically involves painful procedures such as tail snip, digit removal, or ear punch. Although the harvesting of hair has previously been proposed as a source of genomic DNA, there has been a perceived complication and reluctance to use this non-painful technique because of low DNA yields and fear of contamination. In this study we developed a simple, economic, and efficient strategy using Chelex® resins to purify genomic DNA from hair roots of mice which are suitable for genotyping. Upon comparison with standard DNA purification methods using a commercially available kit, we demonstrate that Chelex® efficiently and consistently purifies high-quality DNA from hair roots, minimizing pain, shortening time and reducing costs associated with the determination of accurate genotypes. Therefore, the use of hair roots combined with Chelex® is a reliable and more humane alternative for DNA genotyping.
Collapse
Affiliation(s)
- Víctor Otaño-Rivera
- 1 Department of Pharmacology & Toxicology, Wright State University, Boonshoft School of Medicine, Dayton, OH, USA
| | - Amma Boakye
- 1 Department of Pharmacology & Toxicology, Wright State University, Boonshoft School of Medicine, Dayton, OH, USA
| | - Nadja Grobe
- 1 Department of Pharmacology & Toxicology, Wright State University, Boonshoft School of Medicine, Dayton, OH, USA
| | - Mohammed M Almutairi
- 1 Department of Pharmacology & Toxicology, Wright State University, Boonshoft School of Medicine, Dayton, OH, USA
| | - Shams Kursan
- 1 Department of Pharmacology & Toxicology, Wright State University, Boonshoft School of Medicine, Dayton, OH, USA
| | - Lesan K Mattis
- 1 Department of Pharmacology & Toxicology, Wright State University, Boonshoft School of Medicine, Dayton, OH, USA
| | - Hayo Castrop
- 2 Institute of Physiology, University of Regensburg, Regensburg, Germany
| | - Susan B Gurley
- 3 Division of Nephrology, Department of Medicine, Duke O'Brien Center for Kidney Research, Duke University, Durham, NC, USA
| | - Khalid M Elased
- 1 Department of Pharmacology & Toxicology, Wright State University, Boonshoft School of Medicine, Dayton, OH, USA
| | - Gregory P Boivin
- 4 Department of Pathology, Wright State University, Boonshoft School of Medicine, Dayton, OH, USA
- 5 Veterans Affairs Medical Center, Cincinnati, OH, USA
| | - Mauricio Di Fulvio
- 1 Department of Pharmacology & Toxicology, Wright State University, Boonshoft School of Medicine, Dayton, OH, USA
| |
Collapse
|
31
|
Shang Y, Yan Y, Xu W, Tian W, Huang K. Research on Gene Mobility and Gene Flow Between Genetically Modified Mon 15985 Cotton and Pleurotus Ostreatus. J Food Saf 2016. [DOI: 10.1111/jfs.12267] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Ying Shang
- Beijing Laboratory for Food Quality and Safety, College of Food Science and Nutritional Engineering; China Agricultural University; Beijing 100083 China
- Yunnan Food Safety Institute, Kunming University of Science and Technology; Kunming 650500 China
| | - Yan Yan
- Beijing Laboratory for Food Quality and Safety, College of Food Science and Nutritional Engineering; China Agricultural University; Beijing 100083 China
| | - Wentao Xu
- Beijing Laboratory for Food Quality and Safety, College of Food Science and Nutritional Engineering; China Agricultural University; Beijing 100083 China
- The Supervision, Inspection & Testing Center of Genetically Modified Food Safety, Ministry of Agriculture; Beijing 100083 China
| | - Wenying Tian
- The Supervision, Inspection & Testing Center of Genetically Modified Food Safety, Ministry of Agriculture; Beijing 100083 China
| | - Kunlun Huang
- Beijing Laboratory for Food Quality and Safety, College of Food Science and Nutritional Engineering; China Agricultural University; Beijing 100083 China
- The Supervision, Inspection & Testing Center of Genetically Modified Food Safety, Ministry of Agriculture; Beijing 100083 China
| |
Collapse
|
32
|
Carafa I, Nardin T, Larcher R, Viola R, Tuohy K, Franciosi E. Identification and characterization of wild lactobacilli and pediococci from spontaneously fermented Mountain Cheese. Food Microbiol 2015; 48:123-32. [DOI: 10.1016/j.fm.2014.12.003] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2014] [Revised: 12/03/2014] [Accepted: 12/10/2014] [Indexed: 11/26/2022]
|
33
|
Bloom-forming cyanobacteria support copepod reproduction and development in the Baltic Sea. PLoS One 2014; 9:e112692. [PMID: 25409500 PMCID: PMC4237358 DOI: 10.1371/journal.pone.0112692] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2014] [Accepted: 10/11/2014] [Indexed: 01/29/2023] Open
Abstract
It is commonly accepted that summer cyanobacterial blooms cannot be efficiently utilized by grazers due to low nutritional quality and production of toxins; however the evidence for such effects in situ is often contradictory. Using field and experimental observations on Baltic copepods and bloom-forming diazotrophic filamentous cyanobacteria, we show that cyanobacteria may in fact support zooplankton production during summer. To highlight this side of zooplankton-cyanobacteria interactions, we conducted: (1) a field survey investigating linkages between cyanobacteria, reproduction and growth indices in the copepod Acartia tonsa; (2) an experiment testing relationships between ingestion of the cyanobacterium Nodularia spumigena (measured by molecular diet analysis) and organismal responses (oxidative balance, reproduction and development) in the copepod A. bifilosa; and (3) an analysis of long term (1999–2009) data testing relationships between cyanobacteria and growth indices in nauplii of the copepods, Acartia spp. and Eurytemora affinis, in a coastal area of the northern Baltic proper. In the field survey, N. spumigena had positive effects on copepod egg production and egg viability, effectively increasing their viable egg production. By contrast, Aphanizomenon sp. showed a negative relationship with egg viability yet no significant effect on the viable egg production. In the experiment, ingestion of N. spumigena mixed with green algae Brachiomonas submarina had significant positive effects on copepod oxidative balance, egg viability and development of early nauplial stages, whereas egg production was negatively affected. Finally, the long term data analysis identified cyanobacteria as a significant positive predictor for the nauplial growth in Acartia spp. and E. affinis. Taken together, these results suggest that bloom forming diazotrophic cyanobacteria contribute to feeding and reproduction of zooplankton during summer and create a favorable growth environment for the copepod nauplii.
Collapse
|
34
|
Pogačić T, Chuat V, Madec MN, Samaržija D, Lortal S, Valence F. Phenotypic traits of genetically closely related Leuconostoc spp. Int Dairy J 2014. [DOI: 10.1016/j.idairyj.2014.05.014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
|
35
|
Oliveira CFD, Paim TGDS, Reiter KC, Rieger A, D'Azevedo PA. Evaluation of four different DNA extraction methods in coagulase-negative staphylococci clinical isolates. Rev Inst Med Trop Sao Paulo 2014; 56:29-33. [PMID: 24553605 PMCID: PMC4085835 DOI: 10.1590/s0036-46652014000100004] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2013] [Accepted: 04/19/2013] [Indexed: 08/30/2023] Open
Abstract
Currently there are several methods to extract bacterial DNA based on
different principles. However, the amount and the quality of the DNA obtained by each
one of those methods is highly variable and microorganism dependent, as illustrated
by coagulase-negative staphylococci (CoNS) which have a thick cell wall that is
difficult to lyse. This study was designed to compare the quality and the amount of
CoNS DNA, extracted by four different techniques: two in-house protocols and two
commercial kits. DNA amount and quality determination was performed through
spectrophotometry. The extracted DNA was also analyzed using agarose gel
electrophoresis and by PCR. 267 isolates of CoNS were used in this study. The column
method and thermal lyses showed better results with regard to DNA quality (mean ratio
of A260/280 = 1.95) and average concentration of DNA (), respectively. All four methods tested provided appropriate DNA
for PCR amplification, but with different yields. DNA quality is important since it
allows the application of a large number of molecular biology techniques, and also
it's storage for a longer period of time. In this sense the extraction method based
on an extraction column presented the best results for CoNS.
Collapse
Affiliation(s)
- Caio Fernando de Oliveira
- Health Sciences Post-graduate Program, Universidade Federal de Ciências da Saúde de Porto Alegre (UFCSPA), Health Sciences Post-graduate Program, Universidade Federal de Ciências da Saúde de Porto Alegre (UFCSPA)
| | - Thiago Galvão da Silva Paim
- Health Sciences Post-graduate Program, Universidade Federal de Ciências da Saúde de Porto Alegre (UFCSPA), Health Sciences Post-graduate Program, Universidade Federal de Ciências da Saúde de Porto Alegre (UFCSPA)
| | - Keli Cristine Reiter
- Health Sciences Post-graduate Program, Universidade Federal de Ciências da Saúde de Porto Alegre (UFCSPA), Health Sciences Post-graduate Program, Universidade Federal de Ciências da Saúde de Porto Alegre (UFCSPA)
| | - Alexandre Rieger
- Laboratory of Biotechnology and Genetic, Universidade de Santa Cruz do Sul (UNISC), Laboratory of Biotechnology and Genetic, Universidade de Santa Cruz do Sul (UNISC)
| | - Pedro Alves D'Azevedo
- Health Sciences Post-graduate Program, Universidade Federal de Ciências da Saúde de Porto Alegre (UFCSPA), Health Sciences Post-graduate Program, Universidade Federal de Ciências da Saúde de Porto Alegre (UFCSPA)
| |
Collapse
|
36
|
Affiliation(s)
- Duygu Ercan
- Department of Food Engineering; İzmir Institute of Technology; Urla İzmir 35430 Turkey
| | - Figen Korel
- Department of Food Engineering; İzmir Institute of Technology; Urla İzmir 35430 Turkey
| | - Hande Orşahin
- Biotechnology and Bioengineering Program; İzmir Institute of Technology; Urla İzmir 35430 Turkey
| |
Collapse
|
37
|
Motwani NH, Gorokhova E. Mesozooplankton grazing on picocyanobacteria in the Baltic Sea as inferred from molecular diet analysis. PLoS One 2013; 8:e79230. [PMID: 24260175 PMCID: PMC3832457 DOI: 10.1371/journal.pone.0079230] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2013] [Accepted: 09/27/2013] [Indexed: 11/18/2022] Open
Abstract
Our current knowledge on the microbial component of zooplankton diet is limited, and it is generally assumed that bacteria-sized prey is not directly consumed by most mesozooplankton grazers in the marine food webs. We questioned this assumption and conducted field and laboratory studies to examine picocyanobacteria contribution to the diets of Baltic Sea zooplankton, including copepods. First, qPCR targeting ITS-1 rDNA sequence of the picocyanobacteria Synechococcus spp. was used to examine picocyanobacterial DNA occurrence in the guts of Baltic zooplankton (copepods, cladocerans and rotifers). All field-collected zooplankton were found to consume picocyanobacteria in substantial quantities. In terms of Synechococcus quantity, the individual gut content was highest in cladocerans, whereas biomass-specific gut content was highest in rotifers and copepod nauplii. Moreover, the gut content in copepods was positively related to the picocyanobacteria abundance and negatively to the total phytoplankton abundance in the water column at the time of sampling. This indicates that increased availability of picocyanobacteria resulted in the increased intake of this prey and that copepods may rely more on picoplankton when food in the preferred size range declines. Second, a feeding experiments with a laboratory reared copepod Acartia tonsa fed a mixture of the picocyanobacterium Synechococcus bacillaris and microalga Rhodomonas salina confirmed that copepods ingested Synechococcus, even when the alternative food was plentiful. Finally, palatability of the picocyanobacteria for A. tonsa was demonstrated using uptake of 13C by the copepods as a proxy for carbon uptake in feeding experiment with 13C-labeled S. bacillaris. These findings suggest that, if abundant, picoplankton may become an important component of mesozooplankton diet, which needs to be accounted for in food web models and productivity assessments.
Collapse
Affiliation(s)
- Nisha H. Motwani
- Department of Systems Ecology, Stockholm University, Stockholm, Sweden
| | - Elena Gorokhova
- Department of Systems Ecology, Stockholm University, Stockholm, Sweden
- Department of Applied Environmental Sciences, Stockholm University, Stockholm, Sweden
- * E-mail:
| |
Collapse
|
38
|
Rosas S, Bravo J, Gonzalez F, de Moreno N, Sanchez J, Gavilan RG, Goodridge A. High clustering rates of multidrug-resistant Mycobacterium tuberculosis genotypes in Panama. BMC Infect Dis 2013; 13:442. [PMID: 24053690 PMCID: PMC3849774 DOI: 10.1186/1471-2334-13-442] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2013] [Accepted: 09/17/2013] [Indexed: 11/10/2022] Open
Abstract
Background Tuberculosis continues to be one of the leading causes of death worldwide and in the American region. Although multidrug-resistant tuberculosis (MDR-TB) remains a threat to TB control in Panama, few studies have focused in typing MDR-TB strains. The aim of our study was to characterize MDR Mycobacterium tuberculosis clinical isolates using PCR-based genetic markers. Methods From 2002 to 2004, a total of 231 Mycobacterium tuberculosis isolates from TB cases country-wide were screened for antibiotic resistance, and MDR-TB isolates were further genotyped by double repetitive element PCR (DRE-PCR), (GTG)5-PCR and spoligotyping. Results A total of 37 isolates (0.85%) were resistant to both isoniazid (INH) and rifampicin (RIF). Among these 37 isolates, only two (5.4%) were resistant to all five drugs tested. Dual genotyping using DRE-PCR and (GTG)5-PCR of MDR Mycobacterium tuberculosis isolates revealed eight clusters comprising 82.9% of the MDR-TB strain collection, and six isolates (17.1%) showed unique fingerprints. The spoligotyping of MDR-TB clinical isolates identified 68% as members of the 42 (LAM9) family genotype. Conclusion Our findings suggest that MDR Mycobacterium tuberculosis is highly clustered in Panama’s metropolitan area corresponding to Panama City and Colon City, and our study reveals the genotype distribution across the country.
Collapse
Affiliation(s)
- Samantha Rosas
- Centro de Biología Celular y Molecular de Enfermedades, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT-AIP), Ciudad Del Saber, Panama, Panama.
| | | | | | | | | | | | | |
Collapse
|
39
|
Rittich B, Španová A. SPE and purification of DNA using magnetic particles. J Sep Sci 2013; 36:2472-85. [DOI: 10.1002/jssc.201300331] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2013] [Revised: 05/13/2013] [Accepted: 05/13/2013] [Indexed: 12/21/2022]
Affiliation(s)
- Bohuslav Rittich
- Faculty of Chemistry; Brno University of Technology; Brno Czech Republic
| | - Alena Španová
- Faculty of Chemistry; Brno University of Technology; Brno Czech Republic
| |
Collapse
|
40
|
Fontes CO, Silva VL, de Paiva MRB, Garcia RA, Resende JA, Ferreira-Machado AB, Diniz CG. Prevalence, antimicrobial resistance, and virulence characteristics of mecA-encoding coagulase-negative staphylococci isolated from soft cheese in Brazil. J Food Sci 2013; 78:M594-9. [PMID: 23488927 DOI: 10.1111/1750-3841.12088] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2012] [Accepted: 01/23/2013] [Indexed: 12/11/2022]
Abstract
Coagulase-negative staphylococci (CoNS), which are generally neglected as foodborne bacteria, are emerging as significant opportunistic pathogens that may be highly resistant to available antimicrobial drugs. In this study, antimicrobial susceptibility patterns, mecA gene occurrence, and virulence-associated characteristics were evaluated in CoNS isolated from soft cheese in Brazil. A total of 227 bacterial isolates were recovered from 35 cheese samples belonging to 5 batches with 7 different trademarks. The CoNS counts ranged from 10(6) to 10(7) CFU/g. High antimicrobial resistance percentages were observed for oxacillin (76.2%), penicillin (78.5%), erythromycin (67.8%), gentamicin (47.2%), clindamycin (35.7%), rifampicin (26.8%), azithromycin (14.7%), tetracycline (14.7%), levofloxacin (14.2%), and sulfamethoxazole-trimethoprim (11.9%). A low antimicrobial resistance percentage was observed for chloramphenicol (2.3%), and all of the tested bacteria were susceptible to vancomycin and linezolid. In total, a multiple antibiotic resistance (MAR) index of >0.2 was observed for 80.6% of the isolated CoNS. However, the MAR index ranged from 50% to 92.6% when only bacterial cheese isolates belonging to the same trademark were considered. Regarding to the prevalence of CoNS carrying mecA gene, 81.5% of the isolated strains were mecA(+) , and 76.2% of these were phenotypically resistant to oxacillin. Three isolates carried the enterotoxin A gene (sea), 29.5% produced biofilm in a laboratory test, and α- or ß-hemolysis were observed for 3% and 5.2%, respectively. This study highlights the extent of the antimicrobial resistance phenomenon in neglected foodborne microorganisms and the potential public health risks that are related to the consumption of CoNS-contaminated soft cheese.
Collapse
Affiliation(s)
- Cláudia Oliveira Fontes
- Department of Parasitology, Microbiology and Immunology, Federal University of Juiz de Fora, Juiz de Fora, Minas Gerais, Brazil
| | | | | | | | | | | | | |
Collapse
|
41
|
Di Cagno R, De Pasquale I, De Angelis M, Gobbetti M. Accelerated ripening of Caciocavallo Pugliese cheese with attenuated adjuncts of selected nonstarter lactobacilli. J Dairy Sci 2013; 95:4784-4795. [PMID: 22916882 DOI: 10.3168/jds.2011-5283] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2011] [Accepted: 05/10/2012] [Indexed: 11/19/2022]
Abstract
The nonstarter lactic acid bacteria Lactobacillus plantarum CC3M8, Lactobacillus paracasei CC3M35, and Lactobacillus casei LC01, previously isolated from aged Caciocavallo Pugliese cheese or used in cheesemaking, were used as adjunct cultures (AC) or attenuated (by sonication treatment) adjunct cultures (AAC) for the manufacture of Caciocavallo Pugliese cheese on an industrial scale. Preliminary studies on the kinetics of growth and acidification and activities of several enzymes of AAC were characterized in vitro. As shown by the fluorescence determination of live versus dead or damaged cells and other phenotype features, attenuation resulted in a portion of the cells being damaged and a portion of the cells being capable of growing with time. Compared with the control cheese (without adjunct cultures) and the cheese with AAC, the addition of AC resulted in a lower pH after manufacture, which altered the gross composition of the cheese. As shown by plate count and confirmed by random amplification of polymorphic DNA-PCR, the 3 species of nonstarter lactobacilli persisted during ripening but the number of cultivable cells varied between AC and AAC. Slight differences were found between cheeses regarding primary proteolysis. The major differences between cheeses were the accumulation of free amino acids and the activity levels of several enzymes, which were highest in the Caciocavallo Pugliese cheeses made with the addition of AAC. As shown by triangle test, the sensory properties of the cheese made with AAC at 45 d did not differ from those of the control Caciocavallo Pugliese cheese at 60 d of ripening. In contrast, the cheese made with AC at 45 d differed from both the Caciocavallo Pugliese cheese without adjuncts and the cheese made with AAC. Attenuated adjunct cultures are suitable for accelerating the ripening of Caciocavallo Pugliese cheese without modifying the main features of the traditional cheese.
Collapse
Affiliation(s)
- R Di Cagno
- Department of Biologia e Chimica Agro-Forestale ed Ambientale, University of Bari Aldo Moro, 70126 Bari, Italy
| | - I De Pasquale
- Department of Biologia e Chimica Agro-Forestale ed Ambientale, University of Bari Aldo Moro, 70126 Bari, Italy
| | - M De Angelis
- Department of Biologia e Chimica Agro-Forestale ed Ambientale, University of Bari Aldo Moro, 70126 Bari, Italy
| | - M Gobbetti
- Department of Biologia e Chimica Agro-Forestale ed Ambientale, University of Bari Aldo Moro, 70126 Bari, Italy.
| |
Collapse
|
42
|
da Silva VL, Caçador NC, da Silva CDSF, Fontes CO, Garcia GD, Nicoli JR, Diniz CG. Occurrence of multidrug-resistant and toxic-metal tolerant enterococci in fresh feces from urban pigeons in Brazil. Microbes Environ 2012; 27:179-85. [PMID: 22791051 PMCID: PMC4036010 DOI: 10.1264/jsme2.me11296] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Enterococcus are emerging as important putative pathogens resistant to chemicals that are widely released into the environment, and urban pigeons might act as a natural reservoir contributing to the spread of resistant strains. This study aimed to evaluate the occurrence of Enterococcus in pigeon feces and their antimicrobial and toxic metal susceptibility. Bacteria were isolated and identified from 150 fresh feces by phenotypic and genetic techniques. Antimicrobial and toxic metal susceptibility was determined by the agar dilution method, and the multiple antibiotic resistance index (MAR) was calculated. Out of 120 isolates, no resistance was observed against penicillin and vancomycin, but was observed against gentamicin (55.8%), chloramphenicol (21.7%), tetracycline (13.3%), ciprofloxacin (8.4%) and rifampin (2.5%). 18.3% presented a MAR index ≥0.2, ranging between 0.14 to 0.57, indicating resistance to more than one antimicrobial. All samples were tolerant to >1024 μg mL−1 zinc and chromium. Minimal inhibitory concentration (MIC) of 1,024 μg mL−1 was observed for copper (100%) and nickel (71.4%). Mercury inhibited 88.4% at 32 μg mL−1 and the MIC for cadmium ranged from 0.125–128 μg mL−1. Since pigeons were found to harbor drug-resistant Enterococcus, our data support that their presence in the urban environment may contribute to the spread of resistance, with an impact on public health.
Collapse
Affiliation(s)
- Vânia Lúcia da Silva
- Department of Parasitology, Microbiology and Immunology, Institute of Biological Sciences, Federal University of Juiz de Fora, Juiz de Fora, Brazil.
| | | | | | | | | | | | | |
Collapse
|
43
|
Isolation/separation of plasmid DNA using hemoglobin modified magnetic nanocomposites as solid-phase adsorbent. Talanta 2012; 100:107-12. [DOI: 10.1016/j.talanta.2012.07.095] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2012] [Revised: 07/27/2012] [Accepted: 07/31/2012] [Indexed: 11/18/2022]
|
44
|
Lapanje A, Wimmersberger C, Furrer G, Brunner I, Frey B. Pattern of elemental release during the granite dissolution can be changed by aerobic heterotrophic bacterial strains isolated from Damma Glacier (central Alps) deglaciated granite sand. MICROBIAL ECOLOGY 2012; 63:865-882. [PMID: 22105516 DOI: 10.1007/s00248-011-9976-7] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2011] [Accepted: 10/21/2011] [Indexed: 05/31/2023]
Abstract
Colonisation and weathering of freshly deglaciated granite are key processes in initial soil formation and development. We have obtained 438 isolates from granite sand covering glacial toe, 284 isolates at 22°C and 154 at 4°C incubation temperatures, respectively, to obtain cultures for the investigation of their weathering capabilities under laboratory conditions. The isolation of bacteria from granite sand was performed on rich-, intermediate- and low-nutrient-content solid media. Isolates were identified by 16S rRNA gene sequencing. According to the genera-associated weathering capabilities described in the literature and according to their abundance in our culture collection, we selected eight strains to analyse their effects on the weathering dynamics of granite sand during the batch culture experiment. Analysis of culturable bacteria showed higher species richness among isolates from 22°C than from 4°C incubations. In the R2A and 1/100 Ravan media, we observed the highest species richness of isolates obtained at 22°C and 4°C incubation temperatures, respectively. The obtained 16S rRNA sequences revealed the presence of alpha-, beta- and gamma-proteobacteria, Firmicutes, Actinobacteria and Bacteroidetes. The most numerous group of isolates was distantly related to Collimonas representatives, and according to the sequences of the 16S rRNA genes, they can form a new genus. Isolates from this group had the capability of causing increased dissolution rates for Fe, W, Ni and Rb. In general, at each sampling during the 30-day experiment, every strain showed a unique weathering profile resulting from differential rates of the dissolution and the precipitation of different minerals in the batch culture. Consequently, the presence of different strains, their growth stage and changes in proportions of strains in the bacterial community can affect further soil development and the successive colonisation by plants.
Collapse
MESH Headings
- Bacteria, Aerobic/genetics
- Bacteria, Aerobic/growth & development
- Bacteria, Aerobic/isolation & purification
- Bacteria, Aerobic/metabolism
- DNA, Bacterial/analysis
- DNA, Bacterial/genetics
- DNA, Ribosomal/genetics
- Genes, rRNA
- Heterotrophic Processes
- Ice Cover/microbiology
- Minerals/chemistry
- Minerals/metabolism
- Molecular Sequence Data
- RNA, Ribosomal, 16S/genetics
- Sequence Analysis, DNA
- Silicon Dioxide/chemistry
- Soil Microbiology
Collapse
Affiliation(s)
- Aleš Lapanje
- Snow and Landscape Research, Swiss Federal Institute for Forest, Zürcherstrasse 111, Birmensdorf, Switzerland.
| | | | | | | | | |
Collapse
|
45
|
AP-PCR detection of Streptococcus mutans and Streptococcus sobrinus in caries-free and caries-active subjects. Mol Cell Biochem 2012; 365:159-64. [DOI: 10.1007/s11010-012-1255-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2011] [Accepted: 02/07/2012] [Indexed: 10/28/2022]
|
46
|
Günther S, Koch C, Hübschmann T, Röske I, Müller RA, Bley T, Harms H, Müller S. Correlation of community dynamics and process parameters as a tool for the prediction of the stability of wastewater treatment. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2012; 46:84-92. [PMID: 21805973 DOI: 10.1021/es2010682] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Wastewater treatment often suffers from instabilities and the failure of specific functions such as biological phosphorus removal by polyphosphate accumulating organisms. Since most of the microorganisms involved in water clarification are unknown it is challenging to operate the process accounting for the permanent varying abiotic parameters and the complex composition and unrevealed metabolic capacity of a wastewater microbial community. Fulfilling the demands for water quality irrespective of substrate inflow conditions may emit severe problems if the limited management resources of municipal wastewater treatment plants are regarded. We used flow cytometric analyses of cellular DNA and polyphosphate to create patterns mirroring dynamics in community structure. These patterns were resolved in up to 15 subclusters, the presence and abundances of which correlated with abiotic data. The study used biostatistics to determine the kind and strength of the correlation. Samples investigated were obtained from a primary clarifier and two activated sludge basins. The stability of microbial community structure was found to be high in the basins and low in the primary clarifier. Despite major abiotic changes certain subcommunities were dominantly present (up to 80% stability), whereas others emerged only sporadically (down to 3% stability, both according to equivalence testing). Additionally, subcommunities of diagnostic value were detected showing positive correlation with substrate influxes. For instance blackwater (r(s) = 0.5) and brewery inflow (both r(s) = 0.6) were mirrored by increases in cell abundances in subclusters 1 and 6 as well as 4 and 8, respectively. Phosphate accumulation was obviously positively correlated with nitrate (r(s) = 0.4) and the presence of denitrifying organisms (Rhodacyclaceae). Various other correlations between community structure and abiotic parameters were apparent. The bacterial composition of certain subcommunities was determined by cell sorting and phylogenetic tools like T-RFLP. In essence, we developed a monitoring tool which is quick, cheap and causal in its interpretation. It will make laborious PCR based technique less obligatory as it allows reliable process monitoring and control in wastewater treatment plants.
Collapse
Affiliation(s)
- Susanne Günther
- Department of Environmental Microbiology, UFZ-Helmholtz Centre for Environmental Research, Leipzig, Germany
| | | | | | | | | | | | | | | |
Collapse
|
47
|
Patil SA, Harnisch F, Koch C, Hübschmann T, Fetzer I, Carmona-Martínez AA, Müller S, Schröder U. Electroactive mixed culture derived biofilms in microbial bioelectrochemical systems: the role of pH on biofilm formation, performance and composition. BIORESOURCE TECHNOLOGY 2011; 102:9683-9690. [PMID: 21855323 DOI: 10.1016/j.biortech.2011.07.087] [Citation(s) in RCA: 117] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2011] [Revised: 07/21/2011] [Accepted: 07/22/2011] [Indexed: 05/31/2023]
Abstract
The pH-value played a crucial role for the development and current production of anodic microbial electroactive biofilms. It was demonstrated that only a narrow pH-window, ranging from pH 6 to 9, was suitable for growth and operation of biofilms derived from pH-neutral wastewater. Any stronger deviation from pH neutral conditions led to a substantial decrease in the biofilm performance. Thus, average current densities of 151, 821 and 730 μA cm(-2) were measured for anode biofilms grown and operated at pH 6, 7 and 9 respectively. The microbial diversity of the anode chamber community during the biofilm selection process was studied using the low cost method flow-cytometry. Thereby, it was demonstrated that the pH value as well as the microbial inocula had an impact on the resulting anode community structure. As shown by cyclic voltammetry the electron transfer thermodynamics of the biofilms was strongly depending on the solution's pH-value.
Collapse
Affiliation(s)
- Sunil A Patil
- Institute of Environmental and Sustainable Chemistry, Technische Universität Braunschweig, Hagenring 30, 38106 Braunschweig, Germany
| | | | | | | | | | | | | | | |
Collapse
|
48
|
Casquet J, Thebaud C, Gillespie RG. Chelex without boiling, a rapid and easy technique to obtain stable amplifiable DNA from small amounts of ethanol-stored spiders. Mol Ecol Resour 2011; 12:136-41. [PMID: 21943065 DOI: 10.1111/j.1755-0998.2011.03073.x] [Citation(s) in RCA: 143] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
DNA barcoding projects require high-throughput generation of sequence data to assemble the comprehensive reference databases that are required to perform large-scale biodiversity inventories and molecular ecology studies. With the advent of new sequencing technologies, the extraction step, which often requires a considerable amount of time and money, represents a significant bottleneck in many studies. Here, we present a one-step Chelex double-stranded DNA extraction protocol that is quick, cheap, easy and works with a small quantity of ethanol-stored tissue. We developed this protocol by removing the denaturation step appearing in classic methods. This modification reduces the number of handling steps to one, thus simplifying the extraction procedure and reducing the risk of sample contamination, and yields double-stranded DNA instead of the single-stranded form that classical Chelex extraction protocols usually release. DNA obtained through our method is then suitable for long-term conservation (over 1.5 years). We tested our protocol on a highly diverse genus of spiders comprised of mainly very small species. We also apply the method to two other genera of spiders, one with average size species, the other one with giant species, to test the efficacy of the method with varying amounts of input tissue. We also discuss the advantages and limitations of this DNA extraction technique when working with arthropods.
Collapse
Affiliation(s)
- Juliane Casquet
- Laboratoire Evolution et Diversité Biologique - EDB, Université de Toulouse, UPS, 118 route de Narbonne, F-31062, Toulouse, France.
| | | | | |
Collapse
|
49
|
Cressier B, Bissonnette N. Assessment of an extraction protocol to detect the major mastitis-causing pathogens in bovine milk. J Dairy Sci 2011; 94:2171-84. [PMID: 21524507 DOI: 10.3168/jds.2010-3669] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2010] [Accepted: 01/26/2011] [Indexed: 11/19/2022]
Abstract
Despite all efforts to control its spread, mastitis remains the most costly disease for dairy farmers worldwide. One key component of better control of this disease is identification of the causative bacterial agent during udder infections in cows. Mastitis is complex, however, given the diversity of pathogens that must be identified. Development of a rapid and efficient bacterial species identification tool is thus necessary. This study was conducted to demonstrate the feasibility of bacterial DNA extraction for the automated molecular detection of major mastitis-causing pathogens directly in milk samples to complement traditional microbiological identification. Extraction and detection procedures were designed and optimized to achieve detection in a respectable time frame, at a reasonable cost, and with a high throughput capacity. The following species were identified: Staphylococcus aureus, Escherichia coli, Streptococcus uberis, Streptococcus agalactiae, Streptococcus dysgalactiae, and Klebsiella spp. (including Klebsiella oxytoca and Klebsiella pneumoniae). The detection procedure includes specific genomic DNA amplification by multiplex PCR for each species, separation by capillary electrophoresis, and laser-assisted automated detection. The specificity of the primers was assessed with a panel of bacteria representing mastitis-negative control species. The extraction protocol comprised multiple steps, starting with centrifugation for fat removal, followed by heating in the presence of a cation exchange resin to trap divalent ions. The analytical sensitivity was 100 cfu/mL for milk samples spiked with Staph. aureus, Strep. dysgalactiae, and E. coli, with a tendency for K. pneumoniae. The detection limit was 500 cfu/mL for Strep. uberis and Strep. agalactiae. The overall diagnostic sensitivity (95.4%) and specificity (97.3%) were determined in a double-blind randomized assay by processing 172 clinical milk samples with microbiological characterization as the gold standard. When the physical nature of the milk samples was too altered, DNA purification with a magnetic bead-based system was used. Of the apparent false-positive samples, 5 were identified by specific microbiological analysis as true-positive Staph. aureus co-infections, with further confirmation by ribosomal 16S sequencing. The proposed methodology could, therefore, become an interesting tool for automated PCR detection of major mastitis pathogens in dairy cattle.
Collapse
Affiliation(s)
- B Cressier
- Département de Biochimie, Faculté de Médecine et des Sciences de Santé, Université de Sherbrooke, QC, Canada J1H 5N4
| | | |
Collapse
|
50
|
Adventitious dairy Leuconostoc strains with interesting technological and biological properties useful for adjunct starters. ACTA ACUST UNITED AC 2011. [DOI: 10.1007/s13594-011-0022-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
|