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Gilmore BF, White TA, Busetti A, McAteer MI, Maggs CA, Thompson TP. Exiguolysin, a Novel Thermolysin (M4) Peptidase from Exiguobacterium oxidotolerans. Microorganisms 2024; 12:2311. [PMID: 39597700 PMCID: PMC11596557 DOI: 10.3390/microorganisms12112311] [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: 10/10/2024] [Revised: 10/30/2024] [Accepted: 11/01/2024] [Indexed: 11/29/2024] Open
Abstract
This study details a comprehensive biochemical and structural characterization of exiguolysin, a novel thermolysin-like, caseinolytic peptidase secreted by a marine isolate of Exiguobacterium oxidotolerans strain BW26. Exiguolysin demonstrated optimal proteolytic activity at 37 °C and pH 3, retaining 85% activity at 50 °C, highlighting its potential stability under broad reaction conditions. SDS-PAGE and LC-MS analysis identified the enzyme as a 32 kDa M4-family metalloprotease. Exiguolysin activity was inhibited by 1,10-phenanthroline, confirming its dependence on metal ions for activity. Zymographic analysis and substrate specificity assays revealed selective hydrolysis of matrix metalloproteinase (MMP) substrates but no activity against elastase substrates. Analysis of the predicted gene sequence and structural predictions using AlphaFold identified the presence and position of HEXXH and Glu-Xaa-Xaa-Xaa-Asp motifs, crucial for zinc binding and catalytic activity, characteristic of 'Glu-zincins' and members of the M4 peptidase family. High-throughput screening of a 20 × 20 N-alpha mercaptoamide dipeptide inhibitor library against exiguolysin identified SH-CH2-CO-Met-Tyr-NH2 as the most potent inhibitor, with a Ki of 1.95 μM. Notably, exiguolysin selectively inhibited thrombin-induced PAR-1 activation in PC-3 cells, potentially indicating a potential mechanism of virulence in modulating PAR-1 signalling during infection by disarming PARs. This is the first detailed characterization of a peptidase of the M4 (thermolysin) family in the genus Exiguobacterium which may have industrial application potential and relevance as a putative virulence factor.
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Affiliation(s)
- Brendan F. Gilmore
- Biofilm Research Group, School of Pharmacy, Queen’s University Belfast, Medical Biology Centre, 97 Lisburn Road, Belfast BT9 7BL, UK
- School of Medicine, University of Limerick, Limerick V94 T9PX, Ireland
- Institute for Global Food Security, School of Biological Sciences, Queen’s University Belfast, 19 Chlorine Gardens, Belfast BT9 5DL, UK
| | - Tracy A. White
- Biofilm Research Group, School of Pharmacy, Queen’s University Belfast, Medical Biology Centre, 97 Lisburn Road, Belfast BT9 7BL, UK
| | - Alessandro Busetti
- Biofilm Research Group, School of Pharmacy, Queen’s University Belfast, Medical Biology Centre, 97 Lisburn Road, Belfast BT9 7BL, UK
| | - Matthew I. McAteer
- Biofilm Research Group, School of Pharmacy, Queen’s University Belfast, Medical Biology Centre, 97 Lisburn Road, Belfast BT9 7BL, UK
| | - Christine A. Maggs
- Institute for Global Food Security, School of Biological Sciences, Queen’s University Belfast, 19 Chlorine Gardens, Belfast BT9 5DL, UK
| | - Thomas P. Thompson
- Biofilm Research Group, School of Pharmacy, Queen’s University Belfast, Medical Biology Centre, 97 Lisburn Road, Belfast BT9 7BL, UK
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Calderón-Ezquerro MC, Ponce de León A. A, Brunner-Mendoza C, Guerrero-Guerra C. C, Sanchez-Flores A, Salinas-Peralta I, López Jacome LE, Colín Castro C. CA, Martínez Zavaleta MG. Assessment of airborne bacteria from a public health institution in Mexico City. PLOS GLOBAL PUBLIC HEALTH 2024; 4:e0003672. [PMID: 39509382 PMCID: PMC11542838 DOI: 10.1371/journal.pgph.0003672] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2024] [Accepted: 10/12/2024] [Indexed: 11/15/2024]
Abstract
In this work, the composition of the bacterial community in the air of a hospital in Mexico City was evaluated using metabarcoding and proteomics approaches, along with the assessment of environmental factors such as temperature, humidity, and suspended particles. Two types of aerobiological samplers were used: Andersen One-Stage Viable Particle Sampler (AVPS) and Coriolis μ sampler (CμS-Sampler). Sampling was performed in four areas of the hospital: Floor 1 (F1), Floor 2 (F2), and Emergency Unit (EU), as well as outdoors (OH). The use of both samplers showed variations in diversity and composition. Bacterial abundance was 89.55% with the CμS-Sampler and 74.00% with the AVPS. The predominant phyla with the AVPS were Firmicutes, Proteobacteria and Actinobacteria, while with the CμS-Sampler, the main phyla were Proteobacteria, followed by Actinobacteria and Firmicutes. The highest diversity and richness of bacteria was recorded in F1 and F2, with 32 species identified, with a greater number within the hospital. Potentially pathogenic bacteria such as Bacillus spp., B. cereus, B. pumilus, Clostridium spp., Enterococcus gallinarum, Micrococcus luteus and Staphylococcus spp. were detected. Furthermore, a high concentration of particles between 2.5 μm and 10 μm, and Total Particulate Matter (TPM) was observed, with values of TPM, 303 μg/m3 in F1, 195 μg/m3 in F2, 235 μg/m3 in EU and 188 μg/m3 in OH. Temperatures averaged between 26 and 27°C, and relative humidity ranged between 39.8 and 43.5%. These environmental conditions and particulate matter can promote bacterial growth and their dispersion in the air, constituting a continuous risk of exposure to pathogens, mainly in indoor areas of the hospital. This study provides a framework for air monitoring, where the results of different samplers complement the detection of potential pathogens.
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Affiliation(s)
- Maria Carmen Calderón-Ezquerro
- Departamento de Ciencias Ambientales, Instituto de Ciencias de la Atmósfera y Cambio Climático, UNAM, Mexico City, México
| | - Alfredo Ponce de León A.
- Departamento de Infectología, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, México
| | | | - César Guerrero-Guerra C.
- Departamento de Ciencias Ambientales, Instituto de Ciencias de la Atmósfera y Cambio Climático, UNAM, Mexico City, México
| | - Alejandro Sanchez-Flores
- Instituto de Biotecnología, Unidad Universitaria de Secuenciación Masiva y Bioinformática, UNAM, Morelos, México
| | - Ilse Salinas-Peralta
- Instituto de Biotecnología, Unidad Universitaria de Secuenciación Masiva y Bioinformática, UNAM, Morelos, México
| | - Luis Esau López Jacome
- Laboratorio de Microbiología Clínica, Instituto Nacional de Rehabilitación Luis Guillermo Ibarra Ibarra, Mexico City, México
- Facultad de Química, Laboratorio, UNAM, Mexico City, México
| | - Claudia Adriana Colín Castro C.
- Laboratorio de Microbiología Clínica, Instituto Nacional de Rehabilitación Luis Guillermo Ibarra Ibarra, Mexico City, México
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Fang W, Fan T, Wang S, Yu X, Lu A, Wang X, Zhou W, Yuan H, Zhang L. Seasonal changes driving shifts in microbial community assembly and species coexistence in an urban river. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 905:167027. [PMID: 37717779 DOI: 10.1016/j.scitotenv.2023.167027] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 09/05/2023] [Accepted: 09/10/2023] [Indexed: 09/19/2023]
Abstract
Microbial communities play a vital role in urban river biogeochemical cycles. However, the seasonal variations in microbial community characteristics, particularly phylogenetic group-based community assembly and species coexistence, have not been extensively investigated. Here, we systematically explored the microbiome characteristics and assembly mechanisms of urban rivers in different seasons using 16S rRNA gene sequencing and multivariate statistical methods. The results indicated that the microbial community presented significant temporal heterogeneity in different seasons, and the diversity decreased from spring to winter. The phylogenetic group-based microbial community assembly was governed by dispersal limitation and drift in spring, summer, and autumn but was structured by homogeneous selection in winter. Moreover, the main functions of nitrification, denitrification, and methanol oxidation were susceptible to dispersal limitation and drift processes, whereas sulfate respiration and aromatic compound degradation were controlled by dispersal limitation and homogeneous selection. Network analyses indicated that network complexity decreased and then increased with seasonal changes, while network stability showed the opposite trend, suggesting that higher complexity and diversity reduced community stability. Temperature was determined to be the primary driver of microbial community structure and assembly processes in different seasons based on canonical correspondence analysis and linear regression analysis. In conclusion, seasonal variation drives the dynamics of microbial community assembly and species coexistence patterns in urban rivers. This study provides new insights into the generation and maintenance of microbial community diversity in urban rivers under seasonal change conditions.
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Affiliation(s)
- Wangkai Fang
- School of Earth and Environment, Anhui University of Science and Technology, Huainan 232001, China; Anhui Engineering Laboratory for Comprehensive Utilization of Water and Soil Resources & Ecological Protection in Mining Area With High Groundwater Level, Huainan 232001, China
| | - Tingyu Fan
- School of Earth and Environment, Anhui University of Science and Technology, Huainan 232001, China; Anhui Engineering Laboratory for Comprehensive Utilization of Water and Soil Resources & Ecological Protection in Mining Area With High Groundwater Level, Huainan 232001, China.
| | - Shun Wang
- School of Earth and Environment, Anhui University of Science and Technology, Huainan 232001, China; Anhui Engineering Laboratory for Comprehensive Utilization of Water and Soil Resources & Ecological Protection in Mining Area With High Groundwater Level, Huainan 232001, China
| | - Xiaokun Yu
- School of Earth and Environment, Anhui University of Science and Technology, Huainan 232001, China; Anhui Engineering Laboratory for Comprehensive Utilization of Water and Soil Resources & Ecological Protection in Mining Area With High Groundwater Level, Huainan 232001, China
| | - Akang Lu
- School of Earth and Environment, Anhui University of Science and Technology, Huainan 232001, China; Anhui Engineering Laboratory for Comprehensive Utilization of Water and Soil Resources & Ecological Protection in Mining Area With High Groundwater Level, Huainan 232001, China
| | - Xingming Wang
- School of Earth and Environment, Anhui University of Science and Technology, Huainan 232001, China; Anhui Engineering Laboratory for Comprehensive Utilization of Water and Soil Resources & Ecological Protection in Mining Area With High Groundwater Level, Huainan 232001, China
| | - Weimin Zhou
- Anhui Shuiyun Environmental Protection Co., Ltd, Wuhu 241000, China
| | - Hongjun Yuan
- Anhui Shuiyun Environmental Protection Co., Ltd, Wuhu 241000, China
| | - Lei Zhang
- School of Civil Engineering and Architecture, Chuzhou University, Chuzhou 239000, China
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Kati A, Balci G. Study on active capacity and detergent application potential of low-temperature alkaline serine protease produced by new strain Exiguobacterium indicum 1.2.3. BIORESOUR BIOPROCESS 2023; 10:77. [PMID: 38647920 PMCID: PMC10991889 DOI: 10.1186/s40643-023-00701-z] [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: 08/31/2023] [Accepted: 10/23/2023] [Indexed: 04/25/2024] Open
Abstract
Microorganisms have long captivated researchers for their potential to produce enzymes with diverse industrial applications. Efficient production of proteases from new strains is crucial as these enzymes play a vital role in breaking down protein bonds, enabling their use in industrial applications. Therefore, a novel Exiguobacterium indicum 1.2.3 was isolated (Istanbul, Turkiye) and characterized in this study. This strain produced alkaline serine protease, which works in lower temperatures (20-40 °C) with casein as a specific substrate. The protease was utterly stable for 3 h at 30 °C. The enzyme was also highly stable in the pH range of 8-11. The optimum activity was obtained at pH 10. The crude enzyme activity was enhanced by various metal ions and retained 147%, 125%, 124%, and 117% of its activity within 1 mM Ca2+, Mn2+, Cu2+, and Mg2+, respectively. The crude enzyme was inactive with phenylmethylsulfonyl fluoride, indicating a serine residue on the active side. The enzyme exhibited a significant proteolytic effect in the presence of surfactants and oxidizing agents. The addition of Tween 80, Triton X-100, and sodium perborate improved enzymatic activity up to 135%, 109%, and 105%, respectively. According to the washing results, the crude enzyme effectively removed the blood on different types of standard pre-stained textiles at 30 °C. In conclusion, Exiguobacterium indicum 1.2.3 is a promising candidate for protease production, with its diverse applications spanning various industrial sectors, particularly detergents.
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Affiliation(s)
- Ahmet Kati
- Department of Biotechnology, Institute of Health Sciences, University of Health Sciences Turkey, 34668, Istanbul, Türkiye.
- Experimental Medicine Research and Application Center, University of Health Sciences Turkey, 34668, Istanbul, Türkiye.
| | - Gamze Balci
- Department of Biotechnology, Institute of Health Sciences, University of Health Sciences Turkey, 34668, Istanbul, Türkiye
- Experimental Medicine Research and Application Center, University of Health Sciences Turkey, 34668, Istanbul, Türkiye
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Oduro D, Darko S, Blankson ER, Mensah GI. Assessment of Bacteria Contaminants in Different Zones and Point Sources of Sandy Beaches in Accra, Ghana. Microbiol Insights 2023; 16:11786361231195152. [PMID: 37693208 PMCID: PMC10492474 DOI: 10.1177/11786361231195152] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 07/31/2023] [Indexed: 09/12/2023] Open
Abstract
Background Bacteria are ubiquitous in the marine environment. Increasing concern for human health has led to growing interest in contamination on public beaches. The presence of pathogenic microorganisms originating from anthropogenic activities such as defecation and disposal of sewage on beaches are of special concern. In this study, presence of pathogenic bacteria and bacterial load in beach zones and point sources were investigated. Methods Sand core samples from the subtidal zone, intertidal zone, supratidal zone and point sources from 5 beaches in Accra, Ghana, were collected and analysed. Total aerobic, coliform and Escherichia (E. coli) counts were determined for each zone in the respective beaches. Bacteria isolates were presumptively identified using biochemical tests and confirmed with MALDI-TOF MS. Results Mean total aerobic count and total coliform counts ranged from 2.10 to 3.01 log CFU/g and 0.29 to 2.18 log CFU/g respectively while E. coli counts ranged from 0.12 to 1.71 log CFU/g for the beaches. Total aerobic count from point sources was 2.4-folds higher than the subtidal zone while total coliform counts were 5-folds higher in the point sources compared to the supratidal zone. Point sources had 10 times (P = .0016) more E. coli counts as compared to the subtidal zone. Isolates recovered (n = 35) belonged to 10 bacteria genera. These were Bacillus spp. (25.7%), Acinetobacter spp. (14.3%), Aeromonas spp. (14.3%), Klebsiella pneumoniae (14.3%), Aerococcus viridans (8.6%), Staphylococcus spp. (8.6%), Shewanella profunda (5.7%), Rheinheimera soli (2.9%), Pseudomonas aeruginosa (2.9%), and Exiguobacterium aurantiacum (2.9%). Conclusion Point sources are major contributors to contamination on beaches. The presence of potentially pathogenic bacteria in beach sand could be a public health risk. Sensitization on cleanliness in the marine environment including beaches in Ghana is needed to enhance public health and safety.
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Affiliation(s)
- Daniel Oduro
- Department of Animal Biology and Conservation Science, University of Ghana, Legon, Accra, Ghana
| | - Stephanie Darko
- Department of Animal Biology and Conservation Science, University of Ghana, Legon, Accra, Ghana
| | | | - Gloria Ivy Mensah
- Department of Bacteriology, Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Accra, Ghana
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Draft Genome Sequence of Exiguobacterium sp. Strain N5, Isolated from a Recreational Freshwater Kettle Lake in Ontario. Microbiol Resour Announc 2023; 12:e0126122. [PMID: 36880761 PMCID: PMC10112067 DOI: 10.1128/mra.01261-22] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/08/2023] Open
Abstract
Exiguobacterium spp. are facultative anaerobic, Gram-positive, non-spore-forming bacilli, reported to tolerate extreme environments. Here, we report the draft genome sequence of Exiguobacterium sp. strain N5, isolated from a recreational freshwater lake.
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Rahman MM, Al Noman MA, Khatun S, Alam R, Shetu MMH, Talukder EK, Imon RR, Biswas MY, Anis-Ul-Haque K, Uddin MJ, Akhter S. Evaluation of Senna tora (L.) Roxb. leaves as source of bioactive molecules with antioxidant, anti-inflammatory and antibacterial potential. Heliyon 2023; 9:e12855. [PMID: 36747926 PMCID: PMC9898628 DOI: 10.1016/j.heliyon.2023.e12855] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 01/01/2023] [Accepted: 01/04/2023] [Indexed: 01/20/2023] Open
Abstract
Senna tora (L.) Roxb. is an ethno-medicinal herb used by rural and tribal people of the Satpura region of Madhya Pradesh in India and the Phatthalung Province of Thailand for treating rheumatism, bronchitis, ringworm, itches, leprosy, dyspepsia, liver disorders and heart disorders. It is also used in Chinese and Ayurvedic medicine. This study was conducted to investigate the potential of Senna tora (L.) Roxb. as a source of drug candidates against oxidants, inflammation, and bacterial infection. Preliminary phytochemical screening (PPS) and GC-MS were performed to identify the phytochemicals in the ethyl acetate extract of Senna tora (L.) Roxb. leaves (EAESTL). The in vitro antioxidant activity was assessed by 2,2-diphenyl-1-picrylhydrazyl (DPPH)- and H2O2-scavenging tests; the in vitro anti-inflammatory activity was determined by bovine serum albumin (BSA) denaturation and red blood cell (RBC) hemolysis inhibition; and the antibacterial activity was evaluated by agar-well diffusion methods. Cytotoxicity was estimated by Artemia salina larvae lethality, while acute toxicity was evaluated by oral delivery of the extract to mice. In silico antioxidant, anti-inflammatory, and antibacterial activities were predicted by the Prediction of Activity Spectra for Substances (PASS) program. The pharmacokinetics related to ADME and toxicity tests were determined by the admetSAR2 and ADMETlab2 web servers, and drug-able properties were assessed by the SwissADME server. GC-MS detected fifty-nine phytochemicals that support the types of compounds (phenols, flavonoids, tannins, terpenoids, saponins, steroids, alkaloids, glycosides and reducing sugar) identified by phytochemical screening. EAESTL exhibited dose-dependent antioxidant, anti-inflammatory, and antibacterial activities without any adverse effects or fluctuations in body weight. The PASS program predicted that the identified phytochemicals have antioxidant, anti-inflammatory and antibacterial activities. Among 51 phytochemicals, 16 showed good ADME, and 8 fulfilled drug-able properties without toxicity. Altogether, four phytochemicals, viz., benzyl alcohol, 3-(hydroxy-phenyl-methyl)-2,3-dimethyl-octan-4-one, phenylethyl alcohol and 2,6,6-trimethylbicyclo [3.1.1] heptane-3-ol, showed good pharmacokinetics and drug-able properties without toxicity, along with antioxidant, anti-inflammatory, and antibacterial activities. The obtained results suggest that Senna tora (L.) Roxb. leaves contain bioactive phytochemicals that have the potential to fight against oxidants, inflammation, and bacterial infection as potential drug candidates.
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Affiliation(s)
- Md. Mashiar Rahman
- Molecular and Cellular Biology Laboratory, Department of Genetic Engineering and Biotechnology, Jashore University of Science and Technology, Jashore 7408, Bangladesh
| | - Md. Abdullah Al Noman
- Molecular and Cellular Biology Laboratory, Department of Genetic Engineering and Biotechnology, Jashore University of Science and Technology, Jashore 7408, Bangladesh
| | - Shapla Khatun
- Molecular and Cellular Biology Laboratory, Department of Genetic Engineering and Biotechnology, Jashore University of Science and Technology, Jashore 7408, Bangladesh
| | - Rahat Alam
- Molecular and Cellular Biology Laboratory, Department of Genetic Engineering and Biotechnology, Jashore University of Science and Technology, Jashore 7408, Bangladesh
| | - Md. Mahade Hasan Shetu
- Molecular and Cellular Biology Laboratory, Department of Genetic Engineering and Biotechnology, Jashore University of Science and Technology, Jashore 7408, Bangladesh
| | - Enamul Kabir Talukder
- Molecular and Cellular Biology Laboratory, Department of Genetic Engineering and Biotechnology, Jashore University of Science and Technology, Jashore 7408, Bangladesh
| | - Raihan Rahman Imon
- Molecular and Cellular Biology Laboratory, Department of Genetic Engineering and Biotechnology, Jashore University of Science and Technology, Jashore 7408, Bangladesh
| | - Md. Yaman Biswas
- Molecular and Cellular Biology Laboratory, Department of Genetic Engineering and Biotechnology, Jashore University of Science and Technology, Jashore 7408, Bangladesh
| | - K.M. Anis-Ul-Haque
- Department of Chemistry, Jashore University of Science and Technology, Jashore 7408, Bangladesh
| | - Mohammad Jashim Uddin
- Department of Pharmacy, Jashore University of Science and Technology, Jashore 7408, Bangladesh
- Corresponding author.
| | - Shahina Akhter
- Department of Biochemistry and Biotechnology, University of Science and Technology Chittagong, Foy's Lake, Chittagong 4202, Bangladesh
- Corresponding author.
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Qiu Y, Zhou Y, Chang Y, Liang X, Zhang H, Lin X, Qing K, Zhou X, Luo Z. The Effects of Ventilation, Humidity, and Temperature on Bacterial Growth and Bacterial Genera Distribution. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:ijerph192215345. [PMID: 36430064 PMCID: PMC9691097 DOI: 10.3390/ijerph192215345] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2022] [Revised: 11/16/2022] [Accepted: 11/17/2022] [Indexed: 05/16/2023]
Abstract
BACKGROUND Bacteria are readily nourished in airtight environments with high humidity, such as storage cabinets, clothing closets, and corners, where ventilation is normally low and humidity is high. OBJECTIVES We characterized the role of humidity and ventilation in bacterial growth and genus distribution at different temperatures (26 °C and 34 °C). METHODS Fresh pork, which was used as the substrate for bacterial culture, was placed in storage cabinets. Bacterial growth and genera distribution on the surface of pork placed in a storage cabinet under different temperatures (26 °C and 34 °C); relative humidity levels (RH: 50%, 70%, 90%); and ventilation conditions (no ventilation and low, medium, and high levels of ventilation) were assessed by rDNA sequencing. RESULTS Increased ventilation and reduced humidity significantly decreased bacterial growth at 26 °C and 34 °C. The contribution of increased ventilation to the reduction in bacterial growth exceeded that of decreased humidity. Ventilation had the greatest effect on reducing bacterial growth compared to the unventilated conditions at 70% RH. At 34 °C, medium and high levels of ventilation were required to reduce bacterial growth. High temperatures greatly increased bacterial growth, but ventilation could reduce the degree of this increase.
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Affiliation(s)
- Yujia Qiu
- Department of Physiology, The School of Basic Medicine Science, Central South University, Changsha 410000, China
| | - Yan Zhou
- Department of Physiology, The School of Basic Medicine Science, Central South University, Changsha 410000, China
- Correspondence: (Y.Z.); (Z.L.)
| | - Yanfen Chang
- Department of Physiology, The School of Basic Medicine Science, Central South University, Changsha 410000, China
| | - Xinyue Liang
- Department of Physiology, The School of Basic Medicine Science, Central South University, Changsha 410000, China
| | - Hui Zhang
- Center for the Built Environment, University of California at Berkeley, Berkeley, CA 2506, USA
| | - Xiaorui Lin
- China Vanke Co., Ltd., Changsha 410000, China
| | - Ke Qing
- China Vanke Co., Ltd., Changsha 410000, China
| | - Xiaojie Zhou
- School of Environmental and Municipal Engineering, Qingdao University of Technology, Qingdao 266061, China
| | - Ziqiang Luo
- Department of Physiology, The School of Basic Medicine Science, Central South University, Changsha 410000, China
- Correspondence: (Y.Z.); (Z.L.)
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9
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Gill SP, Hunter WR, Coulson LE, Banat IM, Schelker J. Synthetic and biological surfactant effects on freshwater biofilm community composition and metabolic activity. Appl Microbiol Biotechnol 2022; 106:6847-6859. [PMID: 36121483 PMCID: PMC9529700 DOI: 10.1007/s00253-022-12179-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 09/02/2022] [Accepted: 09/08/2022] [Indexed: 11/06/2022]
Abstract
Surfactants are used to control microbial biofilms in industrial and medical settings. Their known toxicity on aquatic biota, and their longevity in the environment, has encouraged research on biodegradable alternatives such as rhamnolipids. While previous research has investigated the effects of biological surfactants on single species biofilms, there remains a lack of information regarding the effects of synthetic and biological surfactants in freshwater ecosystems. We conducted a mesocosm experiment to test how the surfactant sodium dodecyl sulfate (SDS) and the biological surfactant rhamnolipid altered community composition and metabolic activity of freshwater biofilms. Biofilms were cultured in the flumes using lake water from Lake Lunz in Austria, under high (300 ppm) and low (150 ppm) concentrations of either surfactant over a four-week period. Our results show that both surfactants significantly affected microbial diversity. Up to 36% of microbial operational taxonomic units were lost after surfactant exposure. Rhamnolipid exposure also increased the production of the extracellular enzymes, leucine aminopeptidase, and glucosidase, while SDS exposure reduced leucine aminopeptidase and glucosidase. This study demonstrates that exposure of freshwater biofilms to chemical and biological surfactants caused a reduction of microbial diversity and changes in biofilm metabolism, exemplified by shifts in extracellular enzyme activities. KEY POINTS: • Microbial biofilm diversity decreased significantly after surfactant exposure. • Exposure to either surfactant altered extracellular enzyme activity. • Overall metabolic activity was not altered, suggesting functional redundancy.
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Affiliation(s)
- Stephanie P Gill
- Department of Geography and Environmental Studies, Ulster University, Coleraine, BT52 1SA, N. Ireland, UK.
| | - William R Hunter
- Fisheries and Aquatic Ecosystems Branch, Agri-Food and Biosciences Institute, Belfast, N. Ireland, UK
| | - Laura E Coulson
- WasserCluster Lunz, Lunz am See, Austria
- Institute of Hydrobiology and Aquatic Ecosystem Management, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Ibrahim M Banat
- School of Biomedical Sciences, Ulster University, Coleraine, N. Ireland, UK
| | - Jakob Schelker
- WasserCluster Lunz, Lunz am See, Austria
- Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
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10
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Kalkan S. Multimodal analysis of south-eastern Black Sea sediment bacterial population diversity. MARINE POLLUTION BULLETIN 2022; 183:114063. [PMID: 36057154 DOI: 10.1016/j.marpolbul.2022.114063] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 07/15/2022] [Accepted: 08/18/2022] [Indexed: 06/15/2023]
Abstract
This study focused on marine sediments from the Black Sea, mainly due to bacterial diversity-induced public health / biotechnology application value. Sediment samples were gathered from 14 locations at differing depths across Turkish shores on a seasonal basis over 10 months, with bacterial identifications performed through using multimodal analytical platforms. Overall, 26 differing, predominantly Gram-positive (57.5 %) bacterial species were identified for this region, including Bacillaceae (50.0 %) and Pseudomonadaceae (15.0 %). The most dominant classes were identified as Bacilli (52.5 %) and Gammaproteobacteria (40.0 %). Ten isolates (25 %) to the species level and thirty-six isolates (90 %) to the genus level were identified using VITEK® MS and Bruker Microflex® LT/SH, in comparison to 16S rRNA sequencing results. Identified species - particularly, novel reported species - can contribute to the knowledge of microbial life dwelling upon sediments of the south-eastern regions of the Black Sea.
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Affiliation(s)
- Samet Kalkan
- Recep Tayyip Erdogan University, Faculty of Fisheries, Ataturk Street Fener District, 53100 Merkez, Rize, Turkey.
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11
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Parthasarathy A, Miranda RR, Eddingsaas NC, Chu J, Freezman IM, Tyler AC, Hudson AO. Polystyrene Degradation by Exiguobacterium sp. RIT 594: Preliminary Evidence for a Pathway Containing an Atypical Oxygenase. Microorganisms 2022; 10:1619. [PMID: 36014041 PMCID: PMC9416434 DOI: 10.3390/microorganisms10081619] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 08/06/2022] [Accepted: 08/07/2022] [Indexed: 11/16/2022] Open
Abstract
The widespread use of plastics has led to their increasing presence in the environment and subsequent pollution. Some microorganisms degrade plastics in natural ecosystems and the associated metabolic pathways can be studied to understand the degradation mechanisms. Polystyrene (PS) is one of the more recalcitrant plastic polymers that is degraded by only a few bacteria. Exiguobacterium is a genus of Gram-positive poly-extremophilic bacteria known to degrade PS, thus being of biotechnological interest, but its biochemical mechanisms of degradation have not yet been elucidated. Based solely on genome annotation, we initially proposed PS degradation by Exiguobacterium sp. RIT 594 via depolymerization and epoxidation catalyzed by a ring epoxidase. However, Fourier transform infrared (FTIR) spectroscopy analysis revealed an increase of carboxyl and hydroxyl groups with biodegradation, as well as of unconjugated C-C double bonds, both consistent with dearomatization of the styrene ring. This excludes any aerobic pathways involving side chain epoxidation and/or hydroxylation. Subsequent experiments confirmed that molecular oxygen is critical to PS degradation by RIT 594 because degradation ceased under oxygen-deprived conditions. Our studies suggest that styrene breakdown by this bacterium occurs via the sequential action of two enzymes encoded in the genome: an orphan aromatic ring-cleaving dioxygenase and a hydrolase.
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Affiliation(s)
- Anutthaman Parthasarathy
- Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester, NY 14623, USA
- School of Chemistry and Biosciences, University of Bradford, Bradford BD7 1DP, UK
| | - Renata Rezende Miranda
- Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester, NY 14623, USA
| | - Nathan C. Eddingsaas
- School of Chemistry and Materials Science, Rochester Institute of Technology, Rochester, NY 14623, USA
| | - Jonathan Chu
- Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester, NY 14623, USA
| | - Ian M. Freezman
- Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester, NY 14623, USA
| | - Anna C. Tyler
- Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester, NY 14623, USA
| | - André O. Hudson
- Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester, NY 14623, USA
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12
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Akhter S, Hossain MW, Sultana S, Ferdous Jharna J, Sultana Meghla N, Alam R, Anis-Ul-Haque K, Mashiar Rahman M. Ruellia prostrata Poir. activity evaluated by phytoconstituents, antioxidant, anti-inflammatory, antibacterial activity, and in silico molecular functions. JOURNAL OF SAUDI CHEMICAL SOCIETY 2022. [DOI: 10.1016/j.jscs.2021.101401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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13
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Tolpeznikaite E, Ruzauskas M, Pilkaityte R, Bartkevics V, Zavistanaviciute P, Starkute V, Lele V, Zokaityte E, Mozuriene E, Ruibys R, Klupsaite D, Santini A, Bartkiene E. Influence of fermentation on the characteristics of Baltic Sea macroalgae, including microbial profile and trace element content. Food Control 2021. [DOI: 10.1016/j.foodcont.2021.108235] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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14
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Gusman VP, Medić DD, Trudić AD, Banović PZ, Nikolić NM. First Isolation of Exiguobacterium aurantiacum in Serbia. Pol J Microbiol 2021; 70:405-407. [PMID: 34584535 PMCID: PMC8458997 DOI: 10.33073/pjm-2021-037] [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: 06/16/2021] [Revised: 07/16/2021] [Accepted: 07/28/2021] [Indexed: 11/21/2022] Open
Abstract
Exiguobacterium aurantiacum is isolated from a variety of environmental samples but rarely from patients. The aim of the study was to represent isolation of unusual bacterial strains that could cause infection in patients. Final identification was performed using matrix-assisted description/ionization time-of-flight mass spectrometry (MALDI-TOF). Two isolates strains of E. aurantiacum were isolated, one isolate from distilled water used during surgical treatment and the second one from a patient with bacteremia after radical prostatectomy, both sensitive to all tested antimicrobials. Environmental strains could cause infection, especially in immunocompromised patients; therefore, rare bacteria testing is required, in which identification special assistance is provided by an automated system MALDI-TOF.
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Affiliation(s)
- Vera P Gusman
- Department of Microbiology, Faculty of Medicine, University of Novi Sad, Novi Sad, Serbia.,Institute of Public Health of Vojvodina, Novi Sad, Serbia
| | - Deana D Medić
- Department of Microbiology, Faculty of Medicine, University of Novi Sad, Novi Sad, Serbia.,Institute of Public Health of Vojvodina, Novi Sad, Serbia
| | - Anika Dj Trudić
- Department of Microbiology, Faculty of Medicine, University of Novi Sad, Novi Sad, Serbia.,Institute for Pulmonary Diseases of Vojvodina, Sremska Kamenica, Serbia
| | - Pavle Z Banović
- Department of Microbiology, Faculty of Medicine, University of Novi Sad, Novi Sad, Serbia.,Pasteur Institute of Novi Sad, Novi Sad, Serbia
| | - Nataša M Nikolić
- Department of Microbiology, Faculty of Medicine, University of Novi Sad, Novi Sad, Serbia.,Institute of Public Health of Vojvodina, Novi Sad, Serbia
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Selvarajan R, Sibanda T, Pandian J, Mearns K. Taxonomic and Functional Distribution of Bacterial Communities in Domestic and Hospital Wastewater System: Implications for Public and Environmental Health. Antibiotics (Basel) 2021; 10:antibiotics10091059. [PMID: 34572642 PMCID: PMC8470611 DOI: 10.3390/antibiotics10091059] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 08/13/2021] [Accepted: 08/14/2021] [Indexed: 11/17/2022] Open
Abstract
The discharge of untreated hospital and domestic wastewater into receiving water bodies is still a prevalent practice in developing countries. Unfortunately, because of an ever-increasing population of people who are perennially under medication, these wastewaters contain residues of antibiotics and other antimicrobials as well as microbial shedding, the direct and indirect effects of which include the dissemination of antibiotic resistance genes and an increase in the evolution of antibiotic-resistant bacteria that pose a threat to public and environmental health. This study assessed the taxonomic and functional profiles of bacterial communities, as well as the antibiotic concentrations in untreated domestic wastewater (DWW) and hospital wastewater (HWW), using high-throughput sequencing analysis and solid-phase extraction coupled to Ultra-high-performance liquid chromatography Mass Spectrometry (UHPLC–MS/MS) analysis, respectively. The physicochemical qualities of both wastewater systems were also determined. The mean concentration of antibiotics and the concentrations of Cl−, F− and PO43 were higher in HWW samples than in DWW samples. The phylum Firmicutes was dominant in DWW with a sequence coverage of 59.61% while Proteobacteria was dominant in HWW samples with a sequence coverage of 86.32%. At genus level, the genus Exiguobacterium (20.65%) and Roseomonas (67.41%) were predominant in DWW and HWW samples, respectively. Several pathogenic or opportunistic bacterial genera were detected in HWW (Enterococcus, Pseudomonas and Vibrio) and DWW (Clostridium, Klebsiella, Corynebacterium, Bordetella, Staphylocccus and Rhodococcus) samples. Functional prediction analysis indicated the presence of beta-lactam resistance, cationic antimicrobial peptide (CAMP) resistance and vancomycin resistance genes in HWW samples. The presence of these antibiotic resistance genes and cassettes were positively correlated with the presence of pathogens. These findings show the risk posed to public and environmental health by the discharge of untreated domestic and hospital wastewaters into environmental water bodies.
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Affiliation(s)
- Ramganesh Selvarajan
- Department of Environmental Sciences, College of Agricultural and Environmental Sciences, UNISA, Florida 1709, South Africa;
- Correspondence:
| | - Timothy Sibanda
- Department of Biochemistry, Microbiology and Biotechnology, University of Namibia, Mandume Ndemufayo Ave, Pionierspark, Windhoek 13301, Namibia;
| | - Jeevan Pandian
- P.G and Research Department of Microbiology, J.J College of Arts and Science (Autonomous), Pudukkottai 622422, Tamil Nadu, India;
| | - Kevin Mearns
- Department of Environmental Sciences, College of Agricultural and Environmental Sciences, UNISA, Florida 1709, South Africa;
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Chemical, Biological and Morphological Properties of Fine Particles during Local Rice Straw Burning Activities. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2021; 18:ijerph18158192. [PMID: 34360485 PMCID: PMC8346042 DOI: 10.3390/ijerph18158192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/06/2021] [Revised: 07/20/2021] [Accepted: 07/21/2021] [Indexed: 11/20/2022]
Abstract
Rice straw is commonly burned openly after harvesting in Malaysia and many other Asian countries where rice is the main crop. This operation emits a significant amount of air pollution, which can have severe consequences for indoor air quality, public health, and climate change. Therefore, this study focuses on determining the compositions of trace elements and the morphological properties of fine particles. Furthermore, the species of bacteria found in bioaerosol from rice burning activities were discovered in this study. For morphological observation of fine particles, FESEM-EDX was used in this study. Two main categories of particles were found, which were natural particles and anthropogenic particles. The zinc element was found during the morphological observation and was assumed to come from the fertilizer used by the farmers. ICP-OES identifies the concentration of trace elements in the fine particle samples. A cultured method was used in this study by using nutrient agar. From this study, several bacteria were identified: Exiguobavterium indicum, Bacillus amyloliquefaciens, Desulfonema limicola str. Jadabusan, Exiguobacterium acetylicum, Lysinibacillus macrolides, and Bacillus proteolyticus. This study is important, especially for human health, and further research on the biological composition of aerosols should be conducted to understand the effect of microorganisms on human health.
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Liu C, Liu Y, Feng C, Wang P, Yu L, Liu D, Sun S, Wang F. Distribution characteristics and potential risks of heavy metals and antimicrobial resistant Escherichia coli in dairy farm wastewater in Tai'an, China. CHEMOSPHERE 2021; 262:127768. [PMID: 32777611 DOI: 10.1016/j.chemosphere.2020.127768] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 07/17/2020] [Accepted: 07/18/2020] [Indexed: 05/11/2023]
Abstract
Heavy metals and antimicrobial resistant bacteria in livestock and poultry environments can cause declines in production and significant economic losses, leading to potential environmental and public health issues. In this study, the heavy metal pollution status of livestock breeding water bodies in the Dawen river basin of Shandong Province in China was evaluated, and a total of 10 heavy metals were measured. In addition, antimicrobial susceptibility tests were conducted for Escherichia coli strains isolated from the water samples. The results showed that among all the metals, copper, zinc, and iron were detected at each sampling point, followed by nickel (detection rate of 95.74%), arsenic (detection rate of 89.36%), selenium (detection rate of 68.09%), lead (detection rate of 27.66%), and mercury (detection rate of 12.77%). Cadmium and hexavalent chromium were not detected. The contents of nine heavy metals were below the existing water standard values in China, whereas the iron pollution index in the water body in the study area was large and may pose a potential risk. A total of 17 E. coli isolates showed different resistance to β-lactams, aminoglycosides, tetracyclines, quinolone antibiotics and chloramphenicol, but were mainly resistant to β-lactams and tetracyclines. The detection rate of the tetA resistance gene was relatively high, indicating the overuse of cephalosporins and tetracyclines. The results of the present study might provide evidence of metal pollution and theoretical basis on the treatment of colibacillosis in the livestock industries.
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Affiliation(s)
- Cong Liu
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Shandong Agricultural University, Taian, 271018, PR China
| | - Yu Liu
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Shandong Agricultural University, Taian, 271018, PR China
| | - Chenglian Feng
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, 100012, PR China.
| | - Peng Wang
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Shandong Agricultural University, Taian, 271018, PR China
| | - Lanping Yu
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural University, Taian, 271018, PR China
| | - Daqing Liu
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, 100012, PR China
| | - Shuhong Sun
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Shandong Agricultural University, Taian, 271018, PR China; Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural University, Taian, 271018, PR China
| | - Fangkun Wang
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Shandong Agricultural University, Taian, 271018, PR China; Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural University, Taian, 271018, PR China.
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Yasin MT, Ali Y, Ahmad K, Ghani A, Amanat K, Basheir MM, Faheem M, Hussain S, Ahmad B, Hussain A, Bokhari SAI. Alkaline lipase production by novel meso-tolerant psychrophilic Exiguobacterium sp. strain (AMBL-20) isolated from glacier of northeastern Pakistan. Arch Microbiol 2020; 203:1309-1320. [PMID: 33325000 DOI: 10.1007/s00203-020-02133-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Revised: 11/15/2020] [Accepted: 11/19/2020] [Indexed: 11/30/2022]
Abstract
Lipase is an important commercial enzyme with unique and versatile biotechnological applications. This study was conducted to biosynthesize and characterizes alkaliphilic lipase by Exiguobacterium sp. strain AMBL-20T isolated from the glacial water samples of the northeastern (Gilgit-Baltistan) region of Pakistan. The isolated bacterium was identified as Exiguobaterium sp. strain AMBL-20T on the basis of morphological, biochemical, and phylogenetic analysis of 16S rRNA sequences with GenBank accession number MW229267. The bacterial strain was further screened for its lipolytic activity, biosynthesis, and characterization by different parameters with the aim of maximizing lipase activity. Results showed that 2% Olive oil, 0.2% peptone at 25 °C, pH 8, and 24 h of incubation time found optimal for maximum lipase production. The lipase enzyme was partially purified by ammonium sulphate precipitation and its activity was standardized at pH 8 under 30 °C temperature. The enzyme showed functional stability over a range of temperature and pH. Hence, extracellular alkaliphilic lipase from Exiguobacterium sp. is a potential candidate with extraordinary industrial applications, particularly in bio-detergent formulations.
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Affiliation(s)
- Muhammad Talha Yasin
- Department of Biotechnology, Quaid-i-Azam University, Islamabad, 45320, Pakistan.
| | - Yasir Ali
- Department of Biological Sciences, International Islamic University Islamabad, Islamabad, 44000, Pakistan
| | - Khurshid Ahmad
- Department of Biological Sciences, International Islamic University Islamabad, Islamabad, 44000, Pakistan
| | - Abdul Ghani
- Department of Biological Sciences, International Islamic University Islamabad, Islamabad, 44000, Pakistan
| | - Kinza Amanat
- Department of Microbiology, University of Agriculture, Faisalabad, 38000, Pakistan
| | - Muhammad Mudassir Basheir
- Department of Biological Sciences, International Islamic University Islamabad, Islamabad, 44000, Pakistan
| | - Muhammad Faheem
- Department of Biological Sciences, International Islamic University Islamabad, Islamabad, 44000, Pakistan
| | - Saddam Hussain
- Department of Biological Sciences, International Islamic University Islamabad, Islamabad, 44000, Pakistan
| | - Bashir Ahmad
- Department of Biological Sciences, International Islamic University Islamabad, Islamabad, 44000, Pakistan
| | - Adil Hussain
- Department of Biotechnology, University of Okara, Okara, 56130, Pakistan
| | - Syed Ali Imran Bokhari
- Department of Biological Sciences, International Islamic University Islamabad, Islamabad, 44000, Pakistan
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Performance and Application of 16S rRNA Gene Cycle Sequencing for Routine Identification of Bacteria in the Clinical Microbiology Laboratory. Clin Microbiol Rev 2020; 33:33/4/e00053-19. [PMID: 32907806 DOI: 10.1128/cmr.00053-19] [Citation(s) in RCA: 138] [Impact Index Per Article: 27.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
This review provides a state-of-the-art description of the performance of Sanger cycle sequencing of the 16S rRNA gene for routine identification of bacteria in the clinical microbiology laboratory. A detailed description of the technology and current methodology is outlined with a major focus on proper data analyses and interpretation of sequences. The remainder of the article is focused on a comprehensive evaluation of the application of this method for identification of bacterial pathogens based on analyses of 16S multialignment sequences. In particular, the existing limitations of similarity within 16S for genus- and species-level differentiation of clinically relevant pathogens and the lack of sequence data currently available in public databases is highlighted. A multiyear experience is described of a large regional clinical microbiology service with direct 16S broad-range PCR followed by cycle sequencing for direct detection of pathogens in appropriate clinical samples. The ability of proteomics (matrix-assisted desorption ionization-time of flight) versus 16S sequencing for bacterial identification and genotyping is compared. Finally, the potential for whole-genome analysis by next-generation sequencing (NGS) to replace 16S sequencing for routine diagnostic use is presented for several applications, including the barriers that must be overcome to fully implement newer genomic methods in clinical microbiology. A future challenge for large clinical, reference, and research laboratories, as well as for industry, will be the translation of vast amounts of accrued NGS microbial data into convenient algorithm testing schemes for various applications (i.e., microbial identification, genotyping, and metagenomics and microbiome analyses) so that clinically relevant information can be reported to physicians in a format that is understood and actionable. These challenges will not be faced by clinical microbiologists alone but by every scientist involved in a domain where natural diversity of genes and gene sequences plays a critical role in disease, health, pathogenicity, epidemiology, and other aspects of life-forms. Overcoming these challenges will require global multidisciplinary efforts across fields that do not normally interact with the clinical arena to make vast amounts of sequencing data clinically interpretable and actionable at the bedside.
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