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Idrees M, Atiq N, Zahra R, Imran M, Ghazanfar S. Draft genome sequence of Lactiplantibacillus plantarum subsp. plantarum strain HF43, a human gut-associated potential probiotic. Microbiol Resour Announc 2023; 12:e0094522. [PMID: 37466328 PMCID: PMC10508172 DOI: 10.1128/mra.00945-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2023] [Accepted: 06/17/2023] [Indexed: 07/20/2023] Open
Abstract
Lactiplantibacillus plantarum adapts to a wide range of ecological niches, including the human gut. Numerous health-promoting benefits have been associated with L. plantarum strains. Motivated for the development of human-origin target-based probiotics with known genetic markers, we report the draft genome sequence of human gut-associated Lactiplantibacillus plantarum subsp. plantarum HF43.
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Affiliation(s)
- Maryam Idrees
- Department of Microbiology, Quaid-i-Azam University, Islamabad, Pakistan
| | - Naima Atiq
- Department of Microbiology, Quaid-i-Azam University, Islamabad, Pakistan
| | - Rabaab Zahra
- Department of Microbiology, Quaid-i-Azam University, Islamabad, Pakistan
| | - Muhammad Imran
- Department of Microbiology, Quaid-i-Azam University, Islamabad, Pakistan
| | - Shakira Ghazanfar
- National Institute for Genomics and Advanced Biotechnology (NIGAB), National Agricultural Research Centre, Islamabad, Pakistan
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Idrees M, Imran M, Atiq N, Zahra R, Abid R, Alreshidi M, Roberts T, Abdelgadir A, Tipu MK, Farid A, Olawale OA, Ghazanfar S. Probiotics, their action modality and the use of multi-omics in metamorphosis of commensal microbiota into target-based probiotics. Front Nutr 2022; 9:959941. [PMID: 36185680 PMCID: PMC9523698 DOI: 10.3389/fnut.2022.959941] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Accepted: 08/24/2022] [Indexed: 11/13/2022] Open
Abstract
This review article addresses the strategic formulation of human probiotics and allows the reader to walk along the journey that metamorphoses commensal microbiota into target-based probiotics. It recapitulates what are probiotics, their history, and the main mechanisms through which probiotics exert beneficial effects on the host. It articulates how a given probiotic preparation could not be all-encompassing and how each probiotic strain has its unique repertoire of functional genes. It answers what criteria should be met to formulate probiotics intended for human use, and why certain probiotics meet ill-fate in pre-clinical and clinical trials? It communicates the reasons that taint the reputation of probiotics and cause discord between the industry, medical and scientific communities. It revisits the notion of host-adapted strains carrying niche-specific genetic modifications. Lastly, this paper emphasizes the strategic development of target-based probiotics using host-adapted microbial isolates with known molecular effectors that would serve as better candidates for bioprophylactic and biotherapeutic interventions in disease-susceptible individuals.
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Affiliation(s)
- Maryam Idrees
- Department of Microbiology, Quaid-i-Azam University, Islamabad, Pakistan
- National Agricultural Research Centre (NARC), National Institute for Genomics and Advanced Biotechnology (NIGAB), Islamabad, Pakistan
- *Correspondence: Maryam Idrees, ; orcid.org/0000-0001-6948-841X
| | - Muhammad Imran
- Department of Microbiology, Quaid-i-Azam University, Islamabad, Pakistan
| | - Naima Atiq
- Department of Microbiology, Quaid-i-Azam University, Islamabad, Pakistan
| | - Rabaab Zahra
- Department of Microbiology, Quaid-i-Azam University, Islamabad, Pakistan
| | - Rameesha Abid
- National Agricultural Research Centre (NARC), National Institute for Genomics and Advanced Biotechnology (NIGAB), Islamabad, Pakistan
- Department of Biotechnology, University of Sialkot, Sialkot, Pakistan
| | - Mousa Alreshidi
- Department of Biology, College of Science, University of Hail, Hail, Saudi Arabia
- Molecular Diagnostics and Personalized Therapeutics Unit, University of Ha’il, Ha’il, Saudi Arabia
- Mousa Alreshidi,
| | - Tim Roberts
- Metabolic Research Group, Faculty of Science, School of Environmental and Life Sciences, The University of Newcastle, University Drive, Callaghan, NSW, Australia
| | - Abdelmuhsin Abdelgadir
- Department of Biology, College of Science, University of Hail, Hail, Saudi Arabia
- Molecular Diagnostics and Personalized Therapeutics Unit, University of Ha’il, Ha’il, Saudi Arabia
| | | | - Arshad Farid
- Gomal Center of Biochemistry and Biotechnology, Gomal University, Dera Ismail Khan, Pakistan
| | | | - Shakira Ghazanfar
- National Agricultural Research Centre (NARC), National Institute for Genomics and Advanced Biotechnology (NIGAB), Islamabad, Pakistan
- Shakira Ghazanfar,
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Fatima N, Kondratyuk TP, Park EJ, Marler LE, Jadoon M, Qazi MA, Mehboob Mirza H, Khan I, Atiq N, Chang LC, Ahmed S, Pezzuto JM. Endophytic fungi associated with Taxus fuana (West Himalayan Yew) of Pakistan: potential bio-resources for cancer chemopreventive agents. Pharm Biol 2016; 54:2547-2554. [PMID: 27159021 DOI: 10.3109/13880209.2016.1170154] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
CONTEXT Endophytic fungi, being a prolific source of bioactive secondary metabolites, are of great interest for natural product discovery. OBJECTIVE Isolation and partial characterization of endophytic fungi inhabiting the leaves and woody parts of Taxus fuana Nan Li & R.R. Mill. (Taxaceae) and evaluation of biological activity. MATERIALS AND METHODS Endophytic fungal isolates were identified by molecular analysis of internal transcribed spacer (ITS) regions of 18S rDNA. Extracts of the endophytic fungi cultured on potato dextrose agar and modified medium were evaluated using cancer chemoprevention bioassays [inhibition of TNF-α-induced NFκB, aromatase and inducible nitric oxide synthase (iNOS); induction of quinone reductase 1 (QR1)] and growth inhibition with MCF-7 cells. RESULTS Nine of 15 fungal isolates were identified as belonging to Epicoccum, Mucor, Penicillium, Chaetomium, Paraconiothriym, Plectania or Trichoderma. Five of the 15 extracts inhibited NFκB activity (IC50 values ranging between 0.18 and 17 μg/mL) and five inhibited iNOS (IC50 values ranging between 0.32 and 12.9 μg/mL). In the aromatase assay, only two isolates mediated inhibition (IC50 values 12.2 and 10.5 μg/mL). With QR1 induction, three extracts exhibited significant activity (concentrations to double activity values ranging between 0.20 and 5.5 μg/mL), and five extracts inhibited the growth of MCF-7 cells (IC50 values ranging from 0.56 to 17.5 μg/mL). Six active cultures were derived from woody parts of the plant material. CONCLUSION The endophytic fungi studied are capable of producing pharmacologically active natural compounds. In particular, isolates derived from the wood of Taxus fuana should be prioritized for the isolation and characterization of bioactive constituents.
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Affiliation(s)
- Nighat Fatima
- a Department of Biotechnology , Quaid-i-Azam University , Islamabad , Pakistan
- b Department of Microbiology , Quaid-i-Azam University , Islamabad , Pakistan
- c Department of Pharmaceutical Sciences, Daniel K. Inouye College of Pharmacy , University of Hawaii at Hilo , Hilo , HI , USA
| | - Tamara P Kondratyuk
- c Department of Pharmaceutical Sciences, Daniel K. Inouye College of Pharmacy , University of Hawaii at Hilo , Hilo , HI , USA
| | - Eun-Jung Park
- c Department of Pharmaceutical Sciences, Daniel K. Inouye College of Pharmacy , University of Hawaii at Hilo , Hilo , HI , USA
| | - Laura E Marler
- c Department of Pharmaceutical Sciences, Daniel K. Inouye College of Pharmacy , University of Hawaii at Hilo , Hilo , HI , USA
| | - Muniba Jadoon
- b Department of Microbiology , Quaid-i-Azam University , Islamabad , Pakistan
| | - Muneer Ahmed Qazi
- b Department of Microbiology , Quaid-i-Azam University , Islamabad , Pakistan
| | - Hira Mehboob Mirza
- b Department of Microbiology , Quaid-i-Azam University , Islamabad , Pakistan
| | - Ibrar Khan
- b Department of Microbiology , Quaid-i-Azam University , Islamabad , Pakistan
| | - Naima Atiq
- b Department of Microbiology , Quaid-i-Azam University , Islamabad , Pakistan
| | - Leng Chee Chang
- c Department of Pharmaceutical Sciences, Daniel K. Inouye College of Pharmacy , University of Hawaii at Hilo , Hilo , HI , USA
| | - Safia Ahmed
- b Department of Microbiology , Quaid-i-Azam University , Islamabad , Pakistan
| | - John M Pezzuto
- c Department of Pharmaceutical Sciences, Daniel K. Inouye College of Pharmacy , University of Hawaii at Hilo , Hilo , HI , USA
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Atiq N, Kibbelaar RE, de Vries F, Hoogendoorn M. An 88-year-old woman with an ulcerous tumour on the leg. Primary cutaneous diffuse large-B-cell lymphoma, leg type. Neth J Med 2016; 74:93-95. [PMID: 26951356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Affiliation(s)
- N Atiq
- Department of Internal Medicine, Medical Center Leeuwarden, Leeuwarden, the Netherlands
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Ali MI, Ahmed S, Robson G, Javed I, Ali N, Atiq N, Hameed A. Isolation and molecular characterization of polyvinyl chloride (PVC) plastic degrading fungal isolates. J Basic Microbiol 2013; 54:18-27. [DOI: 10.1002/jobm.201200496] [Citation(s) in RCA: 92] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2012] [Accepted: 09/28/2012] [Indexed: 11/09/2022]
Affiliation(s)
| | - Safia Ahmed
- Department of Microbiology; Quaid-i-Azam University; Islamabad Pakistan
| | - Geoff Robson
- Faculty of Life Sciences; University of Manchester; Manchester UK
| | - Imran Javed
- Department of Microbiology; Quaid-i-Azam University; Islamabad Pakistan
| | - Naeem Ali
- Department of Microbiology; Quaid-i-Azam University; Islamabad Pakistan
| | - Naima Atiq
- Department of Microbiology; Quaid-i-Azam University; Islamabad Pakistan
| | - Abdul Hameed
- Department of Microbiology; Quaid-i-Azam University; Islamabad Pakistan
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Tahir L, Ishtiaq Ali M, Zia M, Atiq N, Hasan F, Ahmed S. Production and characterization of esterase in Lantinus tigrinus for degradation of polystyrene. Pol J Microbiol 2013; 62:101-108. [PMID: 23829086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2023] Open
Abstract
Polystyrene is considered stable to biological degradation. Lantinus tigrinus isolated from wood sample produced esterase in growth medium under normal conditions. However, acidic medium, 37 degrees C temperature, presence of tween 80; and urea and yeast extract in mineral salt medium enhance the production of esterase and specific activity. Purified esterase was active at broad pH range and 45 degrees C. FTIR analysis confirmed that esterase produced by Lantinus tigrinus effectively degraded polystyrene film and broke macromolecules down to non-toxic molecules. This study concludes that the presence of Lantinus tigrinus at dumping sites can be exploited for waste management containing high molecular weight synthetic polymers.
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Affiliation(s)
- Lubna Tahir
- Department of Microbiology, Quaid-i-Azam University Islamabad Pakistan 45320
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Andleeb S, Atiq N, Robson GD, Ahmed S. An investigation of anthraquinone dye biodegradation by immobilized Aspergillus flavus in fluidized bed bioreactor. Environ Sci Pollut Res Int 2012; 19:1728-1737. [PMID: 22161118 DOI: 10.1007/s11356-011-0687-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2011] [Accepted: 11/29/2011] [Indexed: 05/31/2023]
Abstract
PURPOSE Biodegradation and biodecolorization of Drimarene blue K(2)RL (anthraquinone) dye by a fungal isolate Aspergillus flavus SA2 was studied in lab-scale immobilized fluidized bed bioreactor (FBR) system. METHOD Fungus was immobilized on 0.2-mm sand particles. The reactor operation was carried out at room temperature and pH 5.0 in continuous flow mode with increasing concentrations (50, 100, 150, 200, 300, 500 mg l(-1)) of dye in simulated textile effluent on the 1st, 2nd, 5th, 8th, 11th, and 14th days. The reactors were run on fill, react, settle, and draw mode, with hydraulic retention time (HRT) of 24-72 h. Total run time for reactor operation was 17 days. RESULTS The average overall biological oxygen demand (BOD), chemical oxygen demand (COD), and color removal in the FBR system were up to 85.57%, 84.70%, and 71.3%, respectively, with 50-mg l(-1) initial dye concentration and HRT of 24 h. Reductions in BOD and COD levels along with color removal proved that the mechanism of biodecolorization and biodegradation occurred simultaneously. HPLC and LC-MS analysis identified phthalic acid, benzoic acid, 1, 4-dihydroxyanthraquinone, 2,3-dihydro-9,10-dihydroxy-1,4-anthracenedione, and catechol as degradation products of Drimarene blue K(2)RL dye. Phytotoxicity analysis of bioreactor treatments provided evidence for the production of less toxic metabolites in comparison to the parent dye. CONCLUSION The present fluidized bed bioreactor setup with indigenously isolated fungal strain in its immobilized form is efficiently able to convert the parent toxic dye into less toxic by-products.
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Affiliation(s)
- Saadia Andleeb
- Department of Microbiology, Quaid-i-Azam University, Islamabad, Pakistan.
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Andleeb S, Atiq N, Parmar A, Robson GD, Ahmed S. An HPLC method development for the assessment of degradation products of anthraquinone dye. Environ Monit Assess 2011; 176:597-604. [PMID: 20680441 DOI: 10.1007/s10661-010-1606-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2010] [Accepted: 07/09/2010] [Indexed: 05/29/2023]
Abstract
This paper describes the development of a simple and sensitive method with reduced run time for the estimation of biodegradation product of an anthraquinone dye, Drimarene blue K(2)RL. The chromatographic analysis was performed using a reversed-phase high performance liquid chromatography (HPLC) with a Lichrospher® RP-18 column, 5 μm particle size, 25 cm × 4.6 mm internal diameter using a 70:20:10 (v/v) mixture of acetonitrile-ammonium acetate buffer (0.02 M) with 0.8% Trifluoroacetic acid (pH 2.5) and methanol as eluent. Flow rate was adjusted to 1.2 mL min(-1). The metabolites (phthalic acid, benzoic acid, 1, 4-dihydroxyanthraquinone, and 2,3-dihydro-9,10-dihydroxy-1,4-anthracenedione) were identified by running HPLC grade standards in defined concentrations. The retention time of the compounds were 2.0, 2.5, 5.2, and 7.2 min for phthalic acid, benzoic acid, 1, 4-dihydroxyanthraquinone, and 2,3-dihydro- 9,10-dihydroxy-1,4-anthracenedione, respectively. The reliability, sensitivity, and validation of the method were checked by calculating recoveries of the individual compounds in the acetonitrile and dye degradation media. The lower limits of detection for anthraquinone metabolites and the separation of acid and anthraquinone metabolites in short time were achieved.
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Affiliation(s)
- Saadia Andleeb
- Department of Microbiology, Quaid-i-Azam University, Islamabad, Pakistan.
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Mutanda LN, Rahman Khan M, Atiq N, Golam Kibriya AK. Antibiotic-resistant enterobacteria in river and pond water in Dhaka. Indian J Med Res 1983; 77:423-6. [PMID: 6874029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
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