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Kalia VC, Patel SKS, Lee JK. Bacterial biofilm inhibitors: An overview. Ecotoxicol Environ Saf 2023; 264:115389. [PMID: 37634478 DOI: 10.1016/j.ecoenv.2023.115389] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 08/05/2023] [Accepted: 08/17/2023] [Indexed: 08/29/2023]
Abstract
Bacteria that cause infectious diseases adopt biofilms as one of their most prevalent lifestyles. Biofilms enable bacteria to tolerate environmental stress and evade antibacterial agents. This bacterial defense mechanism has rendered the use of antibiotics ineffective for the treatment of infectious diseases. However, many highly drug-resistant microbes have rapidly emerged owing to such treatments. Different signaling mechanisms regulate bacterial biofilm formation, including cyclic dinucleotide (c-di-GMP), small non-coding RNAs, and quorum sensing (QS). A cell density-dependent phenomenon, QS is associated with c-di-GMP (a global messenger), which regulates gene expression related to adhesion, extracellular matrix production, the transition from the planktonic to biofilm stage, stability, pathogenicity, virulence, and acquisition of nutrients. The article aims to provide information on inhibiting biofilm formation and disintegrating mature/preformed biofilms. This treatment enables antimicrobials to target the free-living/exposed bacterial cells at lower concentrations than those needed to treat bacteria within the biofilm. Therefore, a complementary action of antibiofilm and antimicrobial agents can be a robust strategic approach to dealing with infectious diseases. Taken together, these molecules have broad implications for human health.
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Affiliation(s)
- Vipin Chandra Kalia
- Department of Chemical Engineering, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, Republic of Korea
| | - Sanjay K S Patel
- Department of Chemical Engineering, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, Republic of Korea
| | - Jung-Kul Lee
- Department of Chemical Engineering, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, Republic of Korea.
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Kalia VC, Patel SKS, Lee JK. Exploiting Polyhydroxyalkanoates for Biomedical Applications. Polymers (Basel) 2023; 15:polym15081937. [PMID: 37112084 PMCID: PMC10144186 DOI: 10.3390/polym15081937] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 04/15/2023] [Accepted: 04/18/2023] [Indexed: 04/29/2023] Open
Abstract
Polyhydroxyalkanoates (PHA) are biodegradable plastic. Numerous bacteria produce PHAs under environmental stress conditions, such as excess carbon-rich organic matter and limitations of other nutritional elements such as potassium, magnesium, oxygen, phosphorus, and nitrogen. In addition to having physicochemical properties similar to fossil-fuel-based plastics, PHAs have unique features that make them ideal for medical devices, such as easy sterilization without damaging the material itself and easy dissolution following use. PHAs can replace traditional plastic materials used in the biomedical sector. PHAs can be used in a variety of biomedical applications, including medical devices, implants, drug delivery devices, wound dressings, artificial ligaments and tendons, and bone grafts. Unlike plastics, PHAs are not manufactured from petroleum products or fossil fuels and are, therefore, environment-friendly. In this review, a recent overview of applications of PHAs with special emphasis on biomedical sectors, including drug delivery, wound healing, tissue engineering, and biocontrols, are discussed.
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Affiliation(s)
- Vipin Chandra Kalia
- Department of Chemical Engineering, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, Republic of Korea
| | - Sanjay K S Patel
- Department of Chemical Engineering, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, Republic of Korea
| | - Jung-Kul Lee
- Department of Chemical Engineering, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, Republic of Korea
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Kalia VC, Gong C, Shanmugam R, Lee JK. Prospecting Microbial Genomes for Biomolecules and Their Applications. Indian J Microbiol 2022; 62:516-523. [PMID: 36458216 PMCID: PMC9705627 DOI: 10.1007/s12088-022-01040-x] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Accepted: 09/04/2022] [Indexed: 11/26/2022] Open
Abstract
Bioactive molecules of microbial origin are finding increasing biotechnological applications. Their sources range from the terrestrial, marine, and endophytic to the human microbiome. These biomolecules have unique chemical structures and related groups, which enable them to improve the efficiency of the bioprocesses. This review focuses on the applications of biomolecules in bioremediation, agriculture, food, pharmaceutical industries, and human health.
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Affiliation(s)
- Vipin Chandra Kalia
- Department of Chemical Engineering, Konkuk University, 1 Hwayang-Dong, Gwangjin-Gu, Seoul, 05029 Republic of Korea
| | - Chunjie Gong
- National “111” Center for Cellular Regulation and Molecular Pharmaceutics, Key Laboratory of Fermentation Engineering (Ministry of Education), Hubei University of Technology, Wuhan, 430068 People’s Republic of China
| | - Ramasamy Shanmugam
- Department of Chemical Engineering, Konkuk University, 1 Hwayang-Dong, Gwangjin-Gu, Seoul, 05029 Republic of Korea
| | - Jung-Kul Lee
- Department of Chemical Engineering, Konkuk University, 1 Hwayang-Dong, Gwangjin-Gu, Seoul, 05029 Republic of Korea
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Kalia VC, Lee JK, Rangappa KS, Gupta VK. Special issue Microbes in Cancer Research in 'Seminar in Cancer Biology' 2021. Semin Cancer Biol 2022; 86:1102-1104. [PMID: 34979275 DOI: 10.1016/j.semcancer.2021.12.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Affiliation(s)
- Vipin Chandra Kalia
- Department of Chemical Engineering, Konkuk University, Seoul, 05029, Republic of Korea.
| | - Jung-Kul Lee
- Department of Chemical Engineering, Konkuk University, Seoul, 05029, Republic of Korea.
| | | | - Vijai Kumar Gupta
- Center for Safe and Improved Food, & Biorefining and Advanced Materials Research Center, SRUC, Kings Buildings, West Mains Road, Edinburgh, EH9 3JG, UK.
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Kumar A, Li J, Kondaveeti S, Singh B, Shanmugam R, Kalia VC, Kim IW, Lee JK. Characterization of a xylitol dehydrogenase from Aspergillus flavus and its application in l-xylulose production. Front Bioeng Biotechnol 2022; 10:1001726. [PMID: 36172018 PMCID: PMC9512048 DOI: 10.3389/fbioe.2022.1001726] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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: 07/23/2022] [Accepted: 08/23/2022] [Indexed: 11/25/2022] Open
Abstract
An NAD+-dependent xylitol dehydrogenase from A. flavus (AfXDH) was cloned and successfully expressed in Escherichia coli. AfXDH gene sequence revealed an open reading frame of 1,110 bp, encoding a polypeptide of 369 amino acids with a calculated molecular mass of 38,893 Da. Among various polyols, sorbitol and xylitol were preferred substrates of AfXDH with Km values of 16.2 and 16.9 mM, respectively. AfXDH showed the highest activity in Tris-glycine-NaOH buffer (pH 9.5) at 50°C; it required Zn2+ or Mn2+ for enzyme activity. The half-life at 40°C and half denaturation temperature (T1/2) was 200 min and 45°C, respectively. Bioinformatic analyses along with biochemical properties confirmed that AfXDH belonged to the medium-chain dehydrogenase/reductase family. AfXDH exhibits higher thermostability and kcat values than those of other XDHs. The feasibility of using AfXDH in l-xylulose production was demonstrated. AfXDH, when coupled with Streptococcus pyogenes NADH oxidase, efficiently converted xylitol to l-xylulose with 97% yield, suggesting its usefulness for the industrial l-xylulose production from xylitol.
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Sood U, Dhingra GG, Anand S, Hira P, Kumar R, Kaur J, Verma M, Singhvi N, Lal S, Rawat CD, Singh VK, Kaur J, Verma H, Tripathi C, Singh P, Dua A, Saxena A, Phartyal R, Jayaraj P, Makhija S, Gupta R, Sahni S, Nayyar N, Abraham JS, Somasundaram S, Lata P, Solanki R, Mahato NK, Prakash O, Bala K, Kumari R, Toteja R, Kalia VC, Lal R. Microbial Journey: Mount Everest to Mars. Indian J Microbiol 2022; 62:323-337. [PMID: 35974919 PMCID: PMC9375815 DOI: 10.1007/s12088-022-01029-6] [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: 01/11/2022] [Accepted: 06/01/2022] [Indexed: 11/05/2022] Open
Abstract
A rigorous exploration of microbial diversity has revealed its presence on Earth, deep oceans, and vast space. The presence of microbial life in diverse environmental conditions, ranging from moderate to extreme temperature, pH, salinity, oxygen, radiations, and altitudes, has provided the necessary impetus to search for them by extending the limits of their habitats. Microbiology started as a distinct science in the mid-nineteenth century and has provided inputs for the betterment of mankind during the last 150 years. As beneficial microbes are assets and pathogens are detrimental, studying both have its own merits. Scientists are nowadays working on illustrating the microbial dynamics in Earth's subsurface, deep sea, and polar regions. In addition to studying the role of microbes in the environment, the microbe-host interactions in humans, animals and plants are also unearthing newer insights that can help us to improve the health of the host by modulating the microbiota. Microbes have the potential to remediate persistent organic pollutants. Antimicrobial resistance which is a serious concern can also be tackled only after monitoring the spread of resistant microbes using disciplines of genomics and metagenomics The cognizance of microbiology has reached the top of the world. Space Missions are now looking for signs of life on the planets (specifically Mars), the Moon and beyond them. Among the most potent pieces of evidence to support the existence of life is to look for microbial, plant, and animal fossils. There is also an urgent need to deliberate and communicate these findings to layman and policymakers that would help them to take an adequate decision for better health and the environment around us. Here, we present a glimpse of recent advancements by scientists from around the world, exploring and exploiting microbial diversity.
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Affiliation(s)
- Utkarsh Sood
- The Energy and Resources Institute, New Delhi, India
| | | | - Shailly Anand
- Deen Dayal Upadhyaya College, University of Delhi, New Delhi, India
| | - Princy Hira
- Maitreyi College, University of Delhi, New Delhi, India
| | - Roshan Kumar
- Post-Graduate Department of Zoology, Magadh University, Bodh Gaya, Bihar India
| | | | - Mansi Verma
- Sri Venkateswara College, University of Delhi, New Delhi, India
| | | | - Sukanya Lal
- Ramjas College, University of Delhi, Delhi, India
| | | | | | - Jaspreet Kaur
- Maitreyi College, University of Delhi, New Delhi, India
| | | | | | - Priya Singh
- Maitreyi College, University of Delhi, New Delhi, India
| | - Ankita Dua
- Shivaji College, University of Delhi, New Delhi, India
| | - Anjali Saxena
- Bhaskaracharya College of Applied Sciences, University of Delhi, New Delhi, India
| | | | - Perumal Jayaraj
- Sri Venkateswara College, University of Delhi, New Delhi, India
| | - Seema Makhija
- Acharya Narendra Dev College, University of Delhi, Delhi, India
| | - Renu Gupta
- Maitreyi College, University of Delhi, New Delhi, India
| | - Sumit Sahni
- Acharya Narendra Dev College, University of Delhi, Delhi, India
| | - Namita Nayyar
- Sri Venkateswara College, University of Delhi, New Delhi, India
| | | | | | - Pushp Lata
- Ramjas College, University of Delhi, Delhi, India
| | - Renu Solanki
- Deen Dayal Upadhyaya College, University of Delhi, New Delhi, India
| | - Nitish Kumar Mahato
- University Department of Zoology, Kolhan University, Chaibasa, Jharkhand India
| | - Om Prakash
- National Centre for Cell Sciences, Pune, Maharashtra India
| | - Kiran Bala
- Deshbandhu College, University of Delhi, New Delhi, India
| | - Rashmi Kumari
- College of Commerce, Arts and Science, Patliputra University, Patna, Bihar India
| | - Ravi Toteja
- Acharya Narendra Dev College, University of Delhi, Delhi, India
| | | | - Rup Lal
- The Energy and Resources Institute, New Delhi, India
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Kalia VC, Shim WY, Patel SKS, Gong C, Lee JK. Recent developments in antimicrobial growth promoters in chicken health: Opportunities and challenges. Sci Total Environ 2022; 834:155300. [PMID: 35447189 DOI: 10.1016/j.scitotenv.2022.155300] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 04/04/2022] [Accepted: 04/11/2022] [Indexed: 06/14/2023]
Abstract
With a continuously increasing human population is an increasing global demand for food. People in countries with a higher socioeconomic status tend to switch their preferences from grains to meat and high-value foods. Their preference for chicken as a source of protein has grown by 70% over the last three decades. Many studies have shown the role of feed in regulating the animal gut microbiome and its impact on host health. The microbiome absorbs nutrients, digests foods, induces a mucosal immune response, maintains homeostasis, and regulates bioactive metabolites. These metabolic activities are influenced by the microbiota and diet. An imbalance in microbiota affects host physiology and progressively causes disorders and diseases. With the use of antibiotics, a shift from dysbiosis with a higher density of pathogens to homeostasis can occur. However, the progressive use of higher doses of antibiotics proved harmful and resulted in the emergence of multidrug-resistant microbes. As a result, the use of antibiotics as feed additives has been banned. Researchers, regulatory authorities, and managers in the poultry industry have assessed the challenges associated with these restrictions. Research has sought to identify alternatives to antibiotic growth promoters for poultry that do not have any adverse effects. Modulating the host intestinal microbiome by regulating dietary factors is much easier than manipulating host genetics. Research efforts have led to the identification of feed additives, including bacteriocins, immunostimulants, organic acids, phytogenics, prebiotics, probiotics, phytoncides, and bacteriophages. In contrast to focusing on one or more of these alternative bioadditives, an improved feed conversion ratio with enhanced poultry products is possible by employing a combination of feed additives. This article may be helpful in future research towards developing a sustainable poultry industry through the use of the proposed alternatives.
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Affiliation(s)
- Vipin Chandra Kalia
- Department of Chemical Engineering, Konkuk University, 1 Hwayang-Dong, Gwangjin-Gu, Seoul 05029, Republic of Korea.
| | - Woo Yong Shim
- Samsung Particulate Matter Research Institute, Samsung Advanced Institute of Technology (SAIT), Samsung Electronics Co., Ltd., 130 Samsung-ro, Yeongtong-gu, Suwon-si, Gyeonggi-do 16678, Republic of Korea
| | - Sanjay Kumar Singh Patel
- Department of Chemical Engineering, Konkuk University, 1 Hwayang-Dong, Gwangjin-Gu, Seoul 05029, Republic of Korea
| | - Chunjie Gong
- National "111" Center for Cellular Regulation and Molecular Pharmaceutics, Key Laboratory of Fermentation Engineering (Ministry of Education), Hubei University of Technology, Wuhan 430068, People's Republic of China
| | - Jung-Kul Lee
- Department of Chemical Engineering, Konkuk University, 1 Hwayang-Dong, Gwangjin-Gu, Seoul 05029, Republic of Korea.
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Otari SV, Kalia VC, Bisht A, Kim IW, Lee JK. Green Synthesis of Silver-Decorated Magnetic Particles for Efficient and Reusable Antimicrobial Activity. Materials (Basel) 2021; 14:ma14247893. [PMID: 34947488 PMCID: PMC8709440 DOI: 10.3390/ma14247893] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 12/11/2021] [Accepted: 12/16/2021] [Indexed: 12/23/2022]
Abstract
Metal and metal hybrid nanostructures have shown tremendous application in the biomedical and catalytic fields because of their plasmonic and catalytic properties. Here, a green and clean method was employed for the synthesis of silver nanoparticle (Ag NP)-SiO2-Fe2O3 hybrid microstructures, and biomolecules from green tea extracts were used for constructing the hybrid structures. The SiO2-Fe2O3 structures were synthesized using an ethanolic green tea leaf extract to form Bio-SiO2-Fe2O3 (BSiO2-Fe2O3) structures. Biochemical studies demonstrated the presence of green tea biomolecules in the BSiO2 layer. Reduction of the silver ions was performed by a BSiO2 layer to form Ag NPs of 5–10 nm in diameter in and on the BSiO2-Fe2O3 microstructure. The reduction process was observed within 600 s, which is faster than that reported elsewhere. The antimicrobial activity of the Ag-BSiO2-Fe2O3 hybrid structure was demonstrated against Staphylococcus aureus and Escherichia coli, and the nanostructures were further visualized using confocal laser scanning microscopy (CLSM). The magnetic properties of the Ag-BSiO2-Fe2O3 hybrid structure were used for studying reusable antimicrobial activity. Thus, in this study, we provide a novel green route for the construction of a biomolecule-entrapped SiO2-Fe2O3 structure and their use for the ultra-fast formation of Ag NPs to form antimicrobial active multifunctional hybrid structures.
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Affiliation(s)
- Sachin V. Otari
- Department of Chemical Engineering, Konkuk University, Seoul 05029, Korea; (S.V.O.); (V.C.K.); (A.B.); (I.-W.K.)
| | - Vipin Chandra Kalia
- Department of Chemical Engineering, Konkuk University, Seoul 05029, Korea; (S.V.O.); (V.C.K.); (A.B.); (I.-W.K.)
| | - Aarti Bisht
- Department of Chemical Engineering, Konkuk University, Seoul 05029, Korea; (S.V.O.); (V.C.K.); (A.B.); (I.-W.K.)
| | - In-Won Kim
- Department of Chemical Engineering, Konkuk University, Seoul 05029, Korea; (S.V.O.); (V.C.K.); (A.B.); (I.-W.K.)
- Institute of SK-KU Biomaterials, Konkuk University, Seoul 05029, Korea
| | - Jung-Kul Lee
- Department of Chemical Engineering, Konkuk University, Seoul 05029, Korea; (S.V.O.); (V.C.K.); (A.B.); (I.-W.K.)
- Correspondence: ; Tel.: +82-2-450-3505
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Abstract
The human gastrointestinal tract (GIT) is a well-recognized hub of microbial activities. The microbiota harboring the mucus layer of the GIT act as a defense against noxious substances, and pathogens including Clostridium difficile, Enterococcus faecium, Escherichia coli, Salmonella Typhimurium. Toxins, pathogens, and antibiotics perturb the commensal floral composition within the GIT. Imbalanced gut microbiota leads to dysbiosis, manifested as diseases ranging from obesity, diabetes, and cancer to reduced lifespan. Among the bacteria present in the gut microbiome, the most beneficial are those representing Firmicutes and Bacteroidetes. Recent studies have revealed the emergence of a novel biotherapeutic agent, Akkermansia, which is instrumental in regaining eubiosis and conferring various health benefits.
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Affiliation(s)
- Vipin Chandra Kalia
- Department of Chemical Engineering, Konkuk University, 1 Hwayang-Dong, Gwangjin-Gu, Seoul, 05029 Republic of Korea
| | - Chunjie Gong
- National “111” Center for Cellular Regulation and Molecular Pharmaceutics, Key Laboratory of Fermentation Engineering (Ministry of Education), Hubei University of Technology, Wuhan, 430068 People’s Republic of China
| | - Ramasamy Shanmugam
- Department of Chemical Engineering, Konkuk University, 1 Hwayang-Dong, Gwangjin-Gu, Seoul, 05029 Republic of Korea
| | - Hui Lin
- College of Life Sciences, Gutian Edible Fungi Research Institute, Fujian Agriculture and Forestry University, Fuzhou, 350002 People’s Republic of China
| | - Liaoyuan Zhang
- College of Life Sciences, Gutian Edible Fungi Research Institute, Fujian Agriculture and Forestry University, Fuzhou, 350002 People’s Republic of China
| | - Jung-Kul Lee
- Department of Chemical Engineering, Konkuk University, 1 Hwayang-Dong, Gwangjin-Gu, Seoul, 05029 Republic of Korea
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Muneeswaran G, Patel SKS, Kondaveeti S, Shanmugam R, Gopinath K, Kumar V, Kim SY, Lee JK, Kalia VC, Kim IW. Biotin and Zn 2+ Increase Xylitol Production by Candida tropicalis. Indian J Microbiol 2021; 61:331-337. [PMID: 34294999 PMCID: PMC8263835 DOI: 10.1007/s12088-021-00960-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Accepted: 06/12/2021] [Indexed: 12/29/2022] Open
Abstract
In this study, the medium requirements to increase the production of xylitol by using Candida tropicalis (CT) have been investigated. The technique of single addition or omission of medium components was applied to determine the nutritional requirements. The addition of amino acids such as Asp, Glu, Gln, Asn, Thr, and Gly had no significant effect on CT growth. However, in the absence of other metal ions, there was a higher concentration of cell growth and xylitol production when only Zn2+ was present in the medium. The analysis of various vitamins unveiled that biotin and thiamine were the only vitamins required for the growth of CT. Surprisingly, when only biotin was present in the medium as a vitamin, there was less growth of CT than when the medium was complete, but the amount of xylitol released was significantly higher. Overall, this study will increase the xylitol production using the single omission or addtion technique.
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Affiliation(s)
- Gurusamy Muneeswaran
- Department of Chemical Engineering, Konkuk University, Seoul, 05029 Republic of Korea
| | - Sanjay K. S. Patel
- Department of Chemical Engineering, Konkuk University, Seoul, 05029 Republic of Korea
| | - Sanath Kondaveeti
- Department of Chemical Engineering, Konkuk University, Seoul, 05029 Republic of Korea
| | - Ramasamy Shanmugam
- Department of Chemical Engineering, Konkuk University, Seoul, 05029 Republic of Korea
| | - Krishnasamy Gopinath
- Department of Chemical Engineering, Konkuk University, Seoul, 05029 Republic of Korea
| | - Virendra Kumar
- Department of Chemical Engineering, Konkuk University, Seoul, 05029 Republic of Korea
| | - Sang-Yong Kim
- Department of Food Science and Biotechnology, Shin-Ansan University, Ansan, 15435 Republic of Korea
| | - Jung-Kul Lee
- Department of Chemical Engineering, Konkuk University, Seoul, 05029 Republic of Korea
| | - Vipin Chandra Kalia
- Department of Chemical Engineering, Konkuk University, Seoul, 05029 Republic of Korea
| | - In-Won Kim
- Department of Chemical Engineering, Konkuk University, Seoul, 05029 Republic of Korea
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Pagolu R, Singh R, Shanmugam R, Kondaveeti S, Patel SKS, Kalia VC, Lee JK. Site-directed lysine modification of xylanase for oriented immobilization onto silicon dioxide nanoparticles. Bioresour Technol 2021; 331:125063. [PMID: 33813167 DOI: 10.1016/j.biortech.2021.125063] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2021] [Revised: 03/21/2021] [Accepted: 03/22/2021] [Indexed: 06/12/2023]
Abstract
Enhanced covalent immobilization of xylanase from Chaetomium globosum (XylCg) onto SiO2 nanoparticles was achieved by the modification of surface residues. The mutation of surface residues to lysine by site-directed mutagenesis increased the immobilization efficiency (IE) and immobilization yield (IY). The immobilized mutant XylCg (N172K-H173K-S176K-K133A-K148A) exhibited an IY of 99.5% and IE of 135%, which were 1.8- and 4.3-fold higher than immobilized wildtype (WT). Regarding the catalytic properties, the kcat and kcat/Km values were 1850 s-1 and 2030 mL mg-1 s-1 for the immobilized mutant, and 331 s-1 and 404 mL mg-1 s-1 for the immobilized WT, respectively. Additionally, the immobilized mutant exhibited four times higher thermal stability than the immobilized WT at 60 °C. These results suggest that surface-mutated lysine residues confer good stability and orientation on the support matrix, thus improving the overall performance of xylanase.
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Affiliation(s)
- Raviteja Pagolu
- Department of Chemical Engineering, Konkuk University, 1 Hwayang-Dong, Gwangjin-Gu, Seoul 05029, Republic of Korea
| | - Raushan Singh
- Department of Chemical Engineering, Konkuk University, 1 Hwayang-Dong, Gwangjin-Gu, Seoul 05029, Republic of Korea
| | - Ramasamy Shanmugam
- Department of Chemical Engineering, Konkuk University, 1 Hwayang-Dong, Gwangjin-Gu, Seoul 05029, Republic of Korea
| | - Sanath Kondaveeti
- Department of Chemical Engineering, Konkuk University, 1 Hwayang-Dong, Gwangjin-Gu, Seoul 05029, Republic of Korea
| | - Sanjay K S Patel
- Department of Chemical Engineering, Konkuk University, 1 Hwayang-Dong, Gwangjin-Gu, Seoul 05029, Republic of Korea
| | - Vipin Chandra Kalia
- Department of Chemical Engineering, Konkuk University, 1 Hwayang-Dong, Gwangjin-Gu, Seoul 05029, Republic of Korea
| | - Jung-Kul Lee
- Department of Chemical Engineering, Konkuk University, 1 Hwayang-Dong, Gwangjin-Gu, Seoul 05029, Republic of Korea.
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Patel SKS, Gupta RK, Kumar V, Kondaveeti S, Kumar A, Das D, Kalia VC, Lee JK. Correction to: Biomethanol Production from Methane by Immobilized Co-cultures of Methanotrophs. Indian J Microbiol 2021; 61:396. [PMID: 34295005 DOI: 10.1007/s12088-021-00946-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
[This corrects the article DOI: 10.1007/s12088-020-00883-6.].
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Affiliation(s)
- Sanjay K S Patel
- Department of Chemical Engineering, Konkuk University, Seoul, 05029 Republic of Korea
| | - Rahul K Gupta
- Department of Chemical Engineering, Konkuk University, Seoul, 05029 Republic of Korea
| | - Virendra Kumar
- Department of Chemical Engineering, Konkuk University, Seoul, 05029 Republic of Korea
| | - Sanath Kondaveeti
- Department of Chemical Engineering, Konkuk University, Seoul, 05029 Republic of Korea
| | - Anurag Kumar
- Department of Chemical Engineering, Konkuk University, Seoul, 05029 Republic of Korea
| | - Devashish Das
- Department of Chemical Engineering, Konkuk University, Seoul, 05029 Republic of Korea
| | - Vipin Chandra Kalia
- Department of Chemical Engineering, Konkuk University, Seoul, 05029 Republic of Korea
| | - Jung-Kul Lee
- Department of Chemical Engineering, Konkuk University, Seoul, 05029 Republic of Korea
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Kalia VC, Gong C, Patel SKS, Lee JK. Regulation of Plant Mineral Nutrition by Signal Molecules. Microorganisms 2021; 9:microorganisms9040774. [PMID: 33917219 PMCID: PMC8068062 DOI: 10.3390/microorganisms9040774] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 03/30/2021] [Accepted: 04/03/2021] [Indexed: 01/15/2023] Open
Abstract
Microbes operate their metabolic activities at a unicellular level. However, it has been revealed that a few metabolic activities only prove beneficial to microbes if operated at high cell densities. These cell density-dependent activities termed quorum sensing (QS) operate through specific chemical signals. In Gram-negative bacteria, the most widely reported QS signals are acylhomoserine lactones. In contrast, a novel QS-like system has been elucidated, regulating communication between microbes and plants through strigolactones. These systems regulate bioprocesses, which affect the health of plants, animals, and human beings. This mini-review presents recent developments in the QS and QS-like signal molecules in promoting plant health.
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Affiliation(s)
- Vipin Chandra Kalia
- Department of Chemical Engineering, Konkuk University, Seoul 05029, Korea; (V.C.K.); (S.K.S.P.)
| | - Chunjie Gong
- National “111” Center for Cellular Regulation and Molecular Pharmaceutics, Key Laboratory of Fermentation Engineering (Ministry of Education), Hubei University of Technology, Wuhan 430068, China;
| | - Sanjay K. S. Patel
- Department of Chemical Engineering, Konkuk University, Seoul 05029, Korea; (V.C.K.); (S.K.S.P.)
| | - Jung-Kul Lee
- Department of Chemical Engineering, Konkuk University, Seoul 05029, Korea; (V.C.K.); (S.K.S.P.)
- Correspondence:
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14
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Kalia VC, Singh Patel SK, Shanmugam R, Lee JK. Polyhydroxyalkanoates: Trends and advances toward biotechnological applications. Bioresour Technol 2021; 326:124737. [PMID: 33515915 DOI: 10.1016/j.biortech.2021.124737] [Citation(s) in RCA: 79] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Revised: 01/10/2021] [Accepted: 01/13/2021] [Indexed: 06/12/2023]
Abstract
Plastics are an integral part of most of the daily requirements. Indiscriminate usage and disposal have led to the accumulation of massive quantities of waste. Their non-biodegradable nature makes it increasingly difficult to manage and dispose them. To counter this impending disaster, biodegradable polymers, especially polyhydroxy-alkanoates (PHAs), have been envisaged as potential alternatives. Owing to their unique physicochemical characteristics, PHAs are gaining importance for versatile applications in the agricultural and medical sectors. Applications in the medical sector are more promising because of their commercial viability and sustainability. Despite such potential, their production and commercialization are significant challenges. The major limitations are their poor mechanical strength, production in small quantities, costly feed, and lack of facilities for industrial production. This article provides an overview of the contemporary progress in the field, to attract researchers and stakeholders to further exploit these renewable resources to produce biodegradable plastics on a commercial scale.
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Affiliation(s)
- Vipin Chandra Kalia
- Department of Chemical Engineering, Konkuk University, Seoul 05029, Republic of Korea
| | | | - Ramasamy Shanmugam
- Department of Chemical Engineering, Konkuk University, Seoul 05029, Republic of Korea
| | - Jung-Kul Lee
- Department of Chemical Engineering, Konkuk University, Seoul 05029, Republic of Korea.
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Dhingra GG, Saxena A, Nigam A, Hira P, Singhvi N, Anand S, Kaur J, Kaur J, Dua A, Negi V, Gupta V, Sood U, Kumar R, Lal S, Verma H, Verma M, Singh P, Rawat CD, Tripathi C, Talwar C, Nagar S, Mahato NK, Prakash O, Singh M, Kuhad RC, Singh Y, Lal B, Pabbi S, Singh N, Kalia VC, Lal R. Microbial World: Recent Developments in Health, Agriculture and Environmental Sciences: An Annual Conference Organized by Association of Microbiologists of India and Indian Network for Soil Contamination Research. Indian J Microbiol 2021; 61:111-115. [PMID: 33814643 PMCID: PMC8006636 DOI: 10.1007/s12088-021-00931-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Affiliation(s)
| | - Anjali Saxena
- Bhaskaracharya College of Applied Sciences, University of Delhi, Delhi, India
| | - Aeshna Nigam
- Shivaji College, University of Delhi, Delhi, India
| | - Princy Hira
- Maitreyi College, University of Delhi, Delhi, India
| | | | - Shailly Anand
- Deen Dyal Upadhyaya College, University of Delhi, Delhi, India
| | - Jasvinder Kaur
- Gargi College, Siri Fort Road, University of Delhi, Delhi, India
| | | | - Ankita Dua
- Shivaji College, University of Delhi, Delhi, India
| | - Vivek Negi
- Sri Aurobindo College, University of Delhi, Delhi, India
| | - Vipin Gupta
- Phixgen Pvt. Ltd, Noida, Uttar Pradesh India
| | - Utkarsh Sood
- The Energy and Resources Institute, Delhi, India
| | - Roshan Kumar
- Department of Zoology, Magadh University, Bodh Gaya, Bihar, India
| | - Sukanya Lal
- Ramjas College, University of Delhi, Delhi, India
| | | | - Mansi Verma
- Sri Venketeshwara College, University of Delhi, Delhi, India
| | - Priya Singh
- Maitreyi College, University of Delhi, Delhi, India
| | | | - Charu Tripathi
- Department of Zoology, CMP College, University of Allahabad, Prayagraj, India
| | - Chandni Talwar
- Department of Zoology, University of Delhi, Delhi, India
| | - Shekhar Nagar
- Department of Zoology, University of Delhi, Delhi, India
| | | | - Om Prakash
- National Centre for Cell Sciences, Pune, Maharashtra India
| | - Mona Singh
- Phixgen Pvt. Ltd, Noida, Uttar Pradesh India
| | - R C Kuhad
- Vice-Chancellor, Central University of Haryana, Mahendragarh, Haryana India
| | - Yogendra Singh
- Department of Zoology, University of Delhi, Delhi, India
| | - Banwari Lal
- The Energy and Resources Institute, Delhi, India
| | - Sunil Pabbi
- ICAR-Indian Agricultural Research Institute, Delhi, India
| | - Namita Singh
- Guru Jambheshwar University of Science and Technology, Hisar, Haryana India
| | - V C Kalia
- Konkuk University, Seoul, Republic of Korea
| | - Rup Lal
- The Energy and Resources Institute, Delhi, India
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Patel SKS, Gupta RK, Kalia VC, Lee JK. Integrating anaerobic digestion of potato peels to methanol production by methanotrophs immobilized on banana leaves. Bioresour Technol 2021; 323:124550. [PMID: 33360718 DOI: 10.1016/j.biortech.2020.124550] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 12/10/2020] [Accepted: 12/11/2020] [Indexed: 06/12/2023]
Abstract
In the present study, potato peels were subjected to anaerobic digestion (AD) to produce biogas (methane [CH4] and carbon dioxide), which was subsequently used as a substrate for methanol production by methanotrophs. AD resulted in high yields of up to 170 L CH4/kg total solids (TS) from 250 mL substrate (2% TS, w/v). Under optimized conditions, maximum methanol production of 4.97 and 3.36 mmol/L from raw biogas was observed in Methylocella tundrae and Methyloferula stellata, respectively. Immobilization of methanotrophs on banana leaves showed loading of up to 156 mg dry cell mass/g support. M. tundrae immobilized on banana leaves retained 31.6-fold higher methanol production stability, compared to non-immobilized cells. To the best of our knowledge, this is the first study on immobilization of methanotrophs on banana leaves for producing methanol from potato peels AD-derived biogas. Such integrative approaches may be improved through process up-scaling to achieve sustainable development.
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Affiliation(s)
- Sanjay K S Patel
- Department of Chemical Engineering, Konkuk University, Seoul 05029, Republic of Korea
| | - Rahul K Gupta
- Department of Chemical Engineering, Konkuk University, Seoul 05029, Republic of Korea
| | - Vipin Chandra Kalia
- Department of Chemical Engineering, Konkuk University, Seoul 05029, Republic of Korea
| | - Jung-Kul Lee
- Department of Chemical Engineering, Konkuk University, Seoul 05029, Republic of Korea.
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Parasuraman P, Devadatha B, Sarma VV, Ranganathan S, Ampasala DR, Reddy D, Kumavath RN, Patel SKS, Kalia VC, Lee JK, Siddhardha B. Corrigendum to: Inhibition of Microbial Quorum Sensing Mediated Virulence Factors by Pestalotiopsis sydowian. J Microbiol Biotechnol 2020. [DOI: 10.4014/jmb.2020.3007.1108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
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Kondaveeti S, Patel SKS, Woo J, Wee JH, Kim SY, Al-Raoush RI, Kim IW, Kalia VC, Lee JK. Characterization of Cellobiohydrolases from Schizophyllum commune KMJ820. Indian J Microbiol 2020; 60:160-166. [PMID: 32255848 PMCID: PMC7105533 DOI: 10.1007/s12088-019-00843-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Accepted: 11/20/2019] [Indexed: 12/18/2022] Open
Abstract
A novel cellobiohydrolase (CBH)-generating fungi have been isolated and categorized as Schizophyllum commune KMJ820 based on morphology and rDNA gene sequence. Cellulose powder was used as carbon source, the total enzyme activity was 11.51 U/ml is noted; which is among the highest amounts of CBH-generating microbes studied. CBH have been purified to homogenize, with pursual of serial chromatography using S. commune supernatants and two different CBHs were found; CBH 1 and 2. The filtered CBHs showed greater activity (V max = 51.4 and 20.8 U/mg) in contrast to CBHs from earlier studies. The MW (molecular weights) of S. commune CBH 1 and 2 were verified to be approximately 50 kDa and 150 kDa, respectively, by size exclusion chromatography. Even though CBHs have been evaluated from other sources, but S. commune CBH is prominent in comparison to other CBHs by its high enzyme activity.
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Affiliation(s)
- Sanath Kondaveeti
- Department of Chemical Engineering, Konkuk University, 1 Hwayang-dong, Gwangjin-gu, Seoul, 05029 Republic of Korea
| | - Sanjay K. S. Patel
- Department of Chemical Engineering, Konkuk University, 1 Hwayang-dong, Gwangjin-gu, Seoul, 05029 Republic of Korea
| | - Janghun Woo
- Department of Chemical Engineering, Konkuk University, 1 Hwayang-dong, Gwangjin-gu, Seoul, 05029 Republic of Korea
| | - Ji Hyang Wee
- Department of Food Science and Biotechnology, Shin-Ansan University, Ansan, 15435 Republic of Korea
| | - Sang-Yong Kim
- Department of Food Science and Biotechnology, Shin-Ansan University, Ansan, 15435 Republic of Korea
| | - Riyadh I. Al-Raoush
- Department of Civil and Architectural Engineering, College of Engineering, Qatar University, P.O. Box 2713, Doha, Qatar
| | - In-Won Kim
- Department of Chemical Engineering, Konkuk University, 1 Hwayang-dong, Gwangjin-gu, Seoul, 05029 Republic of Korea
| | - Vipin Chandra Kalia
- Department of Chemical Engineering, Konkuk University, 1 Hwayang-dong, Gwangjin-gu, Seoul, 05029 Republic of Korea
| | - Jung-Kul Lee
- Department of Chemical Engineering, Konkuk University, 1 Hwayang-dong, Gwangjin-gu, Seoul, 05029 Republic of Korea
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Patel SKS, Gupta RK, Kumar V, Kondaveeti S, Kumar A, Das D, Kalia VC, Lee JK. Biomethanol Production from Methane by Immobilized Co-cultures of Methanotrophs. Indian J Microbiol 2020; 60:318-324. [PMID: 32647392 DOI: 10.1007/s12088-020-00883-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [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: 04/25/2020] [Accepted: 05/06/2020] [Indexed: 11/30/2022] Open
Abstract
Methanol production by co-culture of methanotrophs Methylocystis bryophila and Methyloferula stellata was examined from methane, a greenhouse gas. Co-culture exhibited higher methanol yield of 4.72 mM at optimum ratio of M. bryophila and M. stellata (3:2) compared to individual cultures. The immobilized co-culture within polyvinyl alcohol (PVA) showed relative efficiency of 90.1% for methanol production at polymer concentration of 10% (v/v). The immobilized co-culture cells within PVA resulted in higher bioprocess stability over free cells at different pH, and temperatures. Free and encapsulated co-cultures showed maximum methanol production of 4.81 and 5.37 mM under optimum conditions, respectively. After five cycles of reusage under batch conditions, free and encapsulated co-cultures retained methanol production efficiency of 23.8 and 61.9%, respectively. The present investigation successfully revealed the useful influence of co-culture on the methanol production over pure culture. Further, encapsulation within the polymeric matrix proved to be a better approach for the enhanced stability of the bioprocess.
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Affiliation(s)
- Sanjay K S Patel
- Department of Chemical Engineering, Konkuk University, Seoul, 05029 Republic of Korea
| | - Rahul K Gupta
- Department of Chemical Engineering, Konkuk University, Seoul, 05029 Republic of Korea
| | - Virendra Kumar
- Department of Chemical Engineering, Konkuk University, Seoul, 05029 Republic of Korea
| | - Sanath Kondaveeti
- Department of Chemical Engineering, Konkuk University, Seoul, 05029 Republic of Korea
| | - Anurag Kumar
- Department of Chemical Engineering, Konkuk University, Seoul, 05029 Republic of Korea
| | - Devashish Das
- Department of Chemical Engineering, Konkuk University, Seoul, 05029 Republic of Korea
| | - Vipin Chandra Kalia
- Department of Chemical Engineering, Konkuk University, Seoul, 05029 Republic of Korea
| | - Jung-Kul Lee
- Department of Chemical Engineering, Konkuk University, Seoul, 05029 Republic of Korea
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20
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Patel SKS, Shanmugam R, Kalia VC, Lee JK. Methanol production by polymer-encapsulated methanotrophs from simulated biogas in the presence of methane vector. Bioresour Technol 2020; 304:123022. [PMID: 32070839 DOI: 10.1016/j.biortech.2020.123022] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2019] [Revised: 02/10/2020] [Accepted: 02/10/2020] [Indexed: 06/10/2023]
Abstract
Type I (Methylomicrobium album) and II (Methyloferula stellata) methanotrophs were encapsulated by alginate and polyvinyl alcohol (PVA) to improve methanol production from simulated biogas [methane (CH4) and carbon dioxide (CO2)] in the presence of CH4 vector. Polymeric matrix alginate (2%) and PVA (10%) were found to be optimum for the immobilization of both the methanotrophs, with a relative efficiency of methanol production up to 80.6 and 88.7%, respectively. The stability of methanol production by immobilized cells was improved up to 13.2-fold under repeated batch-culture over free cells. The addition of CH4 vectors showed 1.7-fold higher methanol production on using simulated biogas than in the control. The maximum methanol production of 7.46 and 7.14 mmol/L was noted for PVA-encapsulated M. album and M. stellata, respectively. This study successfully established the beneficial effects of CH4 vectors on methanol production by methanotrophs from greenhouse gases that can be applied for real biogas feedstock.
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Affiliation(s)
- Sanjay K S Patel
- Department of Chemical Engineering, Konkuk University, Seoul 05029, Republic of Korea
| | - Ramasamy Shanmugam
- Department of Chemical Engineering, Konkuk University, Seoul 05029, Republic of Korea
| | - Vipin Chandra Kalia
- Department of Chemical Engineering, Konkuk University, Seoul 05029, Republic of Korea
| | - Jung-Kul Lee
- Department of Chemical Engineering, Konkuk University, Seoul 05029, Republic of Korea.
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21
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Parasuraman P, Devadatha B, Sarma VV, Ranganathan S, Ampasala DR, Reddy D, Kumavath R, Kim IW, Patel SKS, Kalia VC, Lee JK, Siddhardha B. Inhibition of Microbial Quorum Sensing Mediated Virulence Factors by Pestalotiopsis sydowiana. J Microbiol Biotechnol 2020; 30:571-582. [PMID: 31986566 PMCID: PMC9728384 DOI: 10.4014/jmb.1907.07030] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Quorum sensing (QS)-mediated infections cause severe diseases in human beings. The control of infectious diseases by inhibiting QS using antipathogenic drugs is a promising approach as antibiotics are proving inefficient in treating these diseases. Marine fungal (Pestalotiopsis sydowiana PPR) extract was found to possess effective antipathogenic characteristics. The minimum inhibitory concentration (MIC) of the fungal extract against test pathogen Pseudomonas aeruginosa PAO1 was 1,000 μg/ml. Sub-MIC concentrations (250 and 500 μg/ml) of fungal extract reduced QS-regulated virulence phenotypes such as the production of pyocyanin, chitinase, protease, elastase, and staphylolytic activity in P. aeruginosa PAO1 by 84.15%, 73.15%, 67.37%, 62.37%, and 33.65%, respectively. Moreover, it also reduced the production of exopolysaccharides (74.99%), rhamnolipids (68.01%), and alginate (54.98%), and inhibited the biofilm formation of the bacteria by 90.54%. In silico analysis revealed that the metabolite of P. sydowiana PPR binds to the bacterial QS receptor proteins (LasR and RhlR) similar to their respective natural signaling molecules. Cyclo(-Leu-Pro) (CLP) and 4-Hydroxyphenylacetamide (4-HPA) were identified as potent bioactive compounds among the metabolites of P. sydowiana PPR using in silico approaches. The MIC values of CLP and 4-HPA against P. aeruginosa PAO1 were determined as 250 and 125 μg/ml, respectively. All the antivirulence assays were conducted at sub-MIC concentrations of CLP (125 μg/ml) and 4-HPA (62.5 μg/ml), which resulted in marked reduction in all the investigated virulence factors. This was further supported by gene expression studies. The findings suggest that the metabolites of P. sydowiana PPR can be employed as promising QS inhibitors that target pathogenic bacteria.
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Affiliation(s)
- Paramanantham Parasuraman
- Department of Microbiology, School of Life Sciences, Pondicherry University, Puducherry 605014, India
| | - B Devadatha
- Department of Biotechnology, School of Life Sciences, Pondicherry University, Puducherry 605014, India
| | - V. Venkateswara Sarma
- Department of Biotechnology, School of Life Sciences, Pondicherry University, Puducherry 605014, India
| | - Sampathkumar Ranganathan
- Centre for Bioinformatics, School of Life Sciences, Pondicherry University, Puducherry 605014, India
| | - Dinakara Rao Ampasala
- Centre for Bioinformatics, School of Life Sciences, Pondicherry University, Puducherry 605014, India
| | - Dhanasekhar Reddy
- Department of Genomic Science, School of Biological Sciences, Central University of Kerala, Tejaswini Hills, Periya (P.O), Kasaragod, Kerala 671320, India
| | - Ranjith Kumavath
- Department of Genomic Science, School of Biological Sciences, Central University of Kerala, Tejaswini Hills, Periya (P.O), Kasaragod, Kerala 671320, India
| | - In-Won Kim
- Department of Chemical Engineering, Konkuk University, Seoul 05029, Republic of Korea
| | - Sanjay K. S. Patel
- Department of Chemical Engineering, Konkuk University, Seoul 05029, Republic of Korea
| | - Vipin Chandra Kalia
- Department of Chemical Engineering, Konkuk University, Seoul 05029, Republic of Korea,Corresponding authors B.S. Phone: +91-9597761788 E-mail: V.C.K. Phone: +82-2-458-3501 E-mail: J.-K.L. Phone: 82-2-450-3505 Fax: 82-2-458-3504 E-mail:
| | - Jung-Kul Lee
- Department of Chemical Engineering, Konkuk University, Seoul 05029, Republic of Korea,Corresponding authors B.S. Phone: +91-9597761788 E-mail: V.C.K. Phone: +82-2-458-3501 E-mail: J.-K.L. Phone: 82-2-450-3505 Fax: 82-2-458-3504 E-mail:
| | - Busi Siddhardha
- Department of Microbiology, School of Life Sciences, Pondicherry University, Puducherry 605014, India,Corresponding authors B.S. Phone: +91-9597761788 E-mail: V.C.K. Phone: +82-2-458-3501 E-mail: J.-K.L. Phone: 82-2-450-3505 Fax: 82-2-458-3504 E-mail:
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Otari SV, Patel SKS, Kalia VC, Lee JK. One-step hydrothermal synthesis of magnetic rice straw for effective lipase immobilization and its application in esterification reaction. Bioresour Technol 2020; 302:122887. [PMID: 32018086 DOI: 10.1016/j.biortech.2020.122887] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Revised: 01/20/2020] [Accepted: 01/21/2020] [Indexed: 05/22/2023]
Abstract
Immobilization of industrially important enzymes on supports is important to decrease the cost of the overall enzymatic production procedure. Herein, a novel method for synthesizing a new support, magnetic rice straw (MRS) in one step is reported: rice straw (RS) was soaked with Fe2+ ions and these were further reduced to form embedded Fe2O3 nanoparticles on the RS surface, forming MRS. This material presented a magnetic saturation value of 27.32 emu g-1. Lipase immobilization on MRS resulted in 94.3% immobilization efficiency and 91.3 mg g-1 of enzyme loading, which are higher than immobilization on native RS. The lipase stability was increased approximately 8-fold at 70 °C. The lipase-MRS composite was tested in the esterification reaction of biodiesel production, where it showed prominent reusability. Therefore, this novel and rapid synthesis method can provide ecological and economic support for enzyme immobilization and industrially important product formation.
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Affiliation(s)
- Sachin V Otari
- Department of Chemical Engineering, Konkuk University, Seoul 05029, Republic of Korea
| | - Sanjay K S Patel
- Department of Chemical Engineering, Konkuk University, Seoul 05029, Republic of Korea
| | - Vipin Chandra Kalia
- Department of Chemical Engineering, Konkuk University, Seoul 05029, Republic of Korea
| | - Jung-Kul Lee
- Department of Chemical Engineering, Konkuk University, Seoul 05029, Republic of Korea.
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23
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Kondaveeti S, Pagolu R, Patel SKS, Kumar A, Bisht A, Das D, Kalia VC, Kim IW, Lee JK. Bioelectrochemical Detoxification of Phenolic Compounds during Enzymatic Pre-Treatment of Rice Straw. J Microbiol Biotechnol 2020; 29:1760-1768. [PMID: 31693832 DOI: 10.4014/jmb.1909.09042] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Abstract
The use of lignocellulosic biomass such as rice straw can help subsidize the cost of producing value-added chemicals. However, inhibitory compounds, such as phenolics, produced during the pre-treatment of biomass, hamper the saccharification process. Laccase and electrochemical stimuli are both well known to reduce phenolic compounds. Therefore, in this study, we implemented a bioelectrochemical detoxification system (BEDS), a consolidated electrochemical and enzymatic process involving laccase, to enhance the detoxification of phenolics, and thus achieve a higher saccharification efficiency. Saccharification of pretreated rice straw using BEDS at 1.5 V showed 90% phenolic reduction (Phr), thereby resulting in a maximum saccharification yield of 85%. In addition, the specific power consumption when using BEDS (2.2 W/Kg Phr) was noted to be 24% lower than by the electrochemical process alone (2.89 W/kg Phr). To the best of our knowledge, this is the first study to implement BEDS for reduction of phenolic compounds in pretreated biomass.
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Affiliation(s)
- Sanath Kondaveeti
- Department of Chemical Engineering, Konkuk University, Seoul 05029, Republic of Korea
| | - Raviteja Pagolu
- Department of Chemical Engineering, Konkuk University, Seoul 05029, Republic of Korea
| | - Sanjay K S Patel
- Department of Chemical Engineering, Konkuk University, Seoul 05029, Republic of Korea
| | - Ashok Kumar
- Department of Chemical Engineering, Konkuk University, Seoul 05029, Republic of Korea
| | - Aarti Bisht
- Department of Chemical Engineering, Konkuk University, Seoul 05029, Republic of Korea
| | - Devashish Das
- Department of Chemical Engineering, Konkuk University, Seoul 05029, Republic of Korea
| | - Vipin Chandra Kalia
- Department of Chemical Engineering, Konkuk University, Seoul 05029, Republic of Korea
| | - In-Won Kim
- Department of Chemical Engineering, Konkuk University, Seoul 05029, Republic of Korea
| | - Jung-Kul Lee
- Department of Chemical Engineering, Konkuk University, Seoul 05029, Republic of Korea
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Lee JK, Patel SKS, Sung BH, Kalia VC. Biomolecules from municipal and food industry wastes: An overview. Bioresour Technol 2020; 298:122346. [PMID: 31734061 DOI: 10.1016/j.biortech.2019.122346] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Revised: 10/23/2019] [Accepted: 10/25/2019] [Indexed: 06/10/2023]
Abstract
Biological wastes generated from food and fruit processing industries, municipal markets, and water treatment facilities are a major cause of concern for Health Departments and Environmentalists around the world. Conventional means of managing these wastes such as transportation, treatment, and disposal, are proving uneconomical. The need is to develop green and sustainable technologies to circumvent this ever-growing and persistent problem. In this article, the potential of diverse microbes to metabolize complex organic rich biowastes into a variety of bioactive compounds with diverse biotechnological applications have been presented. An integrated strategy has been proposed that can be commercially exploited for the recovery of value-adding products ranging from bioactive compounds, chemical building blocks, energy rich chemicals, biopolymers and materials, which results in a self-sustaining circular bioeconomy with nearly zero waste generation and complete degradation.
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Affiliation(s)
- Jung-Kul Lee
- Department of Chemical Engineering, Konkuk University, 1 Hwayang-Dong, Gwangjin-Gu, Seoul 05029, Republic of Korea
| | - Sanjay Kumar Singh Patel
- Department of Chemical Engineering, Konkuk University, 1 Hwayang-Dong, Gwangjin-Gu, Seoul 05029, Republic of Korea
| | - Bong Hyun Sung
- Bioenergy and Biochemical Research Center, Korea Research Institute of Bioscience and Biotechnology, 125 Gwahak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Vipin Chandra Kalia
- Department of Chemical Engineering, Konkuk University, 1 Hwayang-Dong, Gwangjin-Gu, Seoul 05029, Republic of Korea.
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Patel SKS, Kalia VC, Joo JB, Kang YC, Lee JK. Biotransformation of methane into methanol by methanotrophs immobilized on coconut coir. Bioresour Technol 2020; 297:122433. [PMID: 31761623 DOI: 10.1016/j.biortech.2019.122433] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2019] [Revised: 11/09/2019] [Accepted: 11/12/2019] [Indexed: 06/10/2023]
Abstract
This study aimed to establish a unique approach for the production of methanol from methane (CH4) in the presence of paraffin oil mediated by methanotrophs immobilized on coconut coir (CC). Immobilization of different methanotrophs through covalent method increased the immobilization yield and relative efficiency for methanol production to 48.6% and 96.8%, respectively. In the presence of paraffin oil, methanol production was 1.6-fold higher by Methylocystis bryophila than by control. Compared to free cells, whole cells immobilized on CC showed higher stability for methanol production. Under repeated batch conditions, cumulative methanol production by immobilized cells and free cells, after eight cycles of reuse, was 52.9 and 30.9 mmol/L, respectively. This study effectively demonstrated the beneficial influence of lignocellulosic biowaste CC as support for immobilization of methanotrophs and paraffin oil on bioconversion of CH4 to methanol.
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Affiliation(s)
- Sanjay K S Patel
- Department of Chemical Engineering, Konkuk University, Seoul 05029, Republic of Korea
| | - Vipin Chandra Kalia
- Department of Chemical Engineering, Konkuk University, Seoul 05029, Republic of Korea
| | - Ji Bong Joo
- Department of Chemical Engineering, Konkuk University, Seoul 05029, Republic of Korea
| | - Yun Chan Kang
- Department of Materials Science and Engineering, Korea University, Seoul 02841, Republic of Korea
| | - Jung-Kul Lee
- Department of Chemical Engineering, Konkuk University, Seoul 05029, Republic of Korea.
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Affiliation(s)
- Vipin Gupta
- 1Department of Zoology, University of Delhi, Delhi, India
| | - Utkarsh Sood
- 2The Energy and Resources Institute Darbari Seth Block, IHC Complex, Lodhi Road, New Delhi, 110003 India
| | - Roshan Kumar
- 3P.G. Department of Zoology, Magadh University, Bodh-Gaya, Bihar 824234 India
| | - Rup Lal
- 2The Energy and Resources Institute Darbari Seth Block, IHC Complex, Lodhi Road, New Delhi, 110003 India
| | - Vipin Chandra Kalia
- 4Department of Chemical Engineering, Konkuk University, 1 Hwayang-Dong, Gwangjin-Gu, Seoul, 05029 Republic of Korea
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Sood U, Singh DN, Hira P, Lee JK, Kalia VC, Lal R, Shakarad M. Rapid and solitary production of mono-rhamnolipid biosurfactant and biofilm inhibiting pyocyanin by a taxonomic outlier Pseudomonas aeruginosa strain CR1. J Biotechnol 2020; 307:98-106. [DOI: 10.1016/j.jbiotec.2019.11.004] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2019] [Revised: 10/15/2019] [Accepted: 11/04/2019] [Indexed: 01/20/2023]
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Gaur M, Vasudeva A, Singh A, Sharma V, Khurana H, Negi RK, Lee JK, Kalia VC, Misra R, Singh Y. Comparison of DNA Extraction Methods for Optimal Recovery of Metagenomic DNA from Human and Environmental Samples. Indian J Microbiol 2019; 59:482-489. [PMID: 31762512 DOI: 10.1007/s12088-019-00832-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [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: 08/31/2019] [Accepted: 10/04/2019] [Indexed: 12/19/2022] Open
Abstract
Metagenomics is the study of gene pool of an entire community in a particular niche. This provides valuable information about the functionality of host-microbe interaction in a biological ecosystem. Efficient metagenomic DNA extraction is a critical pre-requisite for a successful sequencing run in a metagenomic study. Although isolation of human stool metagenomic DNA is fairly standardized, the same protocol does not work as efficiently in fecal DNA from other organisms. In this study, we report a comparison of manual and commercial DNA extraction methods for diverse samples such as human stool, fish gut and soil. Fishes are known to have variable microbial diversity based on their food habits, so the study included two different varieties of fishes. A modified protocol for effective isolation of metagenomic DNA from human milk samples is also reported, highlighting critical precautions. Recent studies have emphasized the importance of studying functionality of human milk metagenome to understand its influence on infants' health. While manual method works well with most samples and therefore can be a method of choice for testing new samples, broad-range commercial kit offers advantage of high purity and quality. DNA extraction of different samples would go a long way in unraveling the unexplored association between microbes and host in a biological system.
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Affiliation(s)
- Mohita Gaur
- 1Department of Zoology, University of Delhi, Delhi, India
| | | | - Anoop Singh
- 1Department of Zoology, University of Delhi, Delhi, India
| | - Vishal Sharma
- 1Department of Zoology, University of Delhi, Delhi, India
| | - Himani Khurana
- 1Department of Zoology, University of Delhi, Delhi, India
| | | | - Jung-Kul Lee
- 2Department of Chemical Engineering, Konkuk University, Seoul, 05029 Republic of Korea
| | - Vipin Chandra Kalia
- 2Department of Chemical Engineering, Konkuk University, Seoul, 05029 Republic of Korea
| | - Richa Misra
- 3Department of Zoology, Sri Venkateswara College, University of Delhi, Delhi, India
| | - Yogendra Singh
- 1Department of Zoology, University of Delhi, Delhi, India
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Kalia VC. Advances in Environmental Biotechnology in India: Status Report. PINSA 2019. [DOI: 10.16943/ptinsa/2019/49721] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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Patel SKS, Jeon MS, Gupta RK, Jeon Y, Kalia VC, Kim SC, Cho BK, Kim DR, Lee JK. Hierarchical Macroporous Particles for Efficient Whole-Cell Immobilization: Application in Bioconversion of Greenhouse Gases to Methanol. ACS Appl Mater Interfaces 2019; 11:18968-18977. [PMID: 31046215 DOI: 10.1021/acsami.9b03420] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [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: 06/09/2023]
Abstract
A viable approach for methanol production under ambient physiological conditions is to use greenhouse gases, methane (CH4) and carbon dioxide (CO2), as feed for immobilized methanotrophs. In the present study, unique macroporous carbon particles with pore sizes in the range of ∼1-6 μm were synthesized and used as support for the immobilization of Methylocella tundrae. Immobilization was accomplished covalently on hierarchical macroporous carbon particles. Maximal cell loading of covalently immobilized M. tundrae was 205 mgDCM g-1 of particles. Among these particles, the cells immobilized on 3.6 μm pore size particles showed the highest reusability with the least leaching and were chosen for further study. After immobilization, M. tundrae showed up to 2.4-fold higher methanol production stability at various pH and temperature values because of higher stability and metabolic activity than free cells. After eight cycles of reuse, the immobilized cells retained 18.1-fold higher relative production stability compared to free cells. Free and immobilized cells exhibited cumulative methanol production of 5.2 and 9.5 μmol mgDCM-1 under repeated batch conditions using simulated biogas [CH4 and CO2, 4:1 (v/v)] as feed, respectively. The appropriate pore size of macroporous particles favors the efficient M. tundrae immobilization to retain better biocatalytic properties. This is the first report concerning the covalent immobilization of methanotrophs on the newly synthesized macroporous carbon particles and its subsequent application in repeated methanol production using simulated biogas as a feed.
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Affiliation(s)
- Sanjay K S Patel
- Department of Chemical Engineering , Konkuk University , 1 Hwayang-Dong , Gwangjin-Gu, Seoul 05029 , Republic of Korea
| | | | - Rahul K Gupta
- Department of Chemical Engineering , Konkuk University , 1 Hwayang-Dong , Gwangjin-Gu, Seoul 05029 , Republic of Korea
| | | | - Vipin Chandra Kalia
- Department of Chemical Engineering , Konkuk University , 1 Hwayang-Dong , Gwangjin-Gu, Seoul 05029 , Republic of Korea
| | - Sun Chang Kim
- Intelligent Synthetic Biology Center , Daejeon 34141 , Republic of Korea
| | - Byung Kwan Cho
- Intelligent Synthetic Biology Center , Daejeon 34141 , Republic of Korea
| | | | - Jung-Kul Lee
- Department of Chemical Engineering , Konkuk University , 1 Hwayang-Dong , Gwangjin-Gu, Seoul 05029 , Republic of Korea
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Dudeja SS, Shukla P, Kalia VC. Obituary to an Eminent Member of AMI, Dr Dadarwal. Indian J Microbiol 2019. [DOI: 10.1007/s12088-018-0771-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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Patel SKS, Ray S, Prakash J, Wee JH, Kim SY, Lee JK, Kalia VC. Co-digestion of Biowastes to Enhance Biological Hydrogen Process by Defined Mixed Bacterial Cultures. Indian J Microbiol 2019; 59:154-160. [PMID: 31031429 DOI: 10.1007/s12088-018-00777-8] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [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: 12/10/2018] [Accepted: 12/24/2018] [Indexed: 01/29/2023] Open
Abstract
Co-digestion of biowastes for hydrogen (H2) production using defined mixed cultures can overcome the high risk of failure due to contamination and imbalanced nutrient status. H2 production from biowastes-pea-shells, potato peels (PP), onion peels (OP) and apple pomace, either individually or in various combinations was evaluated by hydrolyzing with defined hydrolytic mixed bacterial culture (MHC5) and subjecting the hydrolysate to mixture of defined H2 producers (MMC6). Co-digestion of OP and PP hydrolysate supplemented at H2 production stage with GM-2 and M-9 media resulted in 95 and 102 l H2/kg of Total solids (TS), respectively compared to 84 l H2/kg of TS in control. Upscaling the process by digesting 4.0 l slurry (16-fold) resulted in 88.5 and 95 l H2/kg of TS, respectively compared to 72 l H2/kg of TS in control. Thus, H2 production by co-digestion of biowastes could be improved through the supplementation with very dilute medium (0.1 ×) and selection of suitable biowastes under unsterile conditions. The overall efficiency can be further enhanced by integrating it with bioprocesses for biopolymers such as polyhydroxyalkanoates and or biofuels like methane production.
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Affiliation(s)
- Sanjay K S Patel
- 1Department of Chemical Engineering, Konkuk University, 1 Hwayang-Dong, Gwangjin-Gu, Seoul, 05029 Republic of Korea
| | - Subhasree Ray
- 2Department of Microbial Biotechnology and Genomics, CSIR-Institute of Genomics and Integrative Biology, Mall Road, Delhi University Campus, Delhi, 110007 India
| | - Jyotsana Prakash
- 2Department of Microbial Biotechnology and Genomics, CSIR-Institute of Genomics and Integrative Biology, Mall Road, Delhi University Campus, Delhi, 110007 India
| | - Ji Hyang Wee
- 3Department of Food Science and Biotechnology, Shin-Ansan University, Ansan, 15435 Republic of Korea
| | - Sang-Yong Kim
- 3Department of Food Science and Biotechnology, Shin-Ansan University, Ansan, 15435 Republic of Korea
| | - Jung-Kul Lee
- 1Department of Chemical Engineering, Konkuk University, 1 Hwayang-Dong, Gwangjin-Gu, Seoul, 05029 Republic of Korea
| | - Vipin Chandra Kalia
- 1Department of Chemical Engineering, Konkuk University, 1 Hwayang-Dong, Gwangjin-Gu, Seoul, 05029 Republic of Korea
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Kalia VC, Patel SKS, Kang YC, Lee JK. Quorum sensing inhibitors as antipathogens: biotechnological applications. Biotechnol Adv 2018; 37:68-90. [PMID: 30471318 DOI: 10.1016/j.biotechadv.2018.11.006] [Citation(s) in RCA: 167] [Impact Index Per Article: 27.8] [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: 05/10/2018] [Revised: 10/19/2018] [Accepted: 11/18/2018] [Indexed: 12/20/2022]
Abstract
The mechanisms through which microbes communicate using signal molecules has inspired a great deal of research. Microbes use this exchange of information, known as quorum sensing (QS), to initiate and perpetuate infectious diseases in eukaryotic organisms, evading the eukaryotic defense system by multiplying and expressing their pathogenicity through QS regulation. The major issue to arise from such networks is increased bacterial resistance to antibiotics, resulting from QS-dependent mediation of the formation of biofilm, the induction of efflux pumps, and the production of antibiotics. QS inhibitors (QSIs) of diverse origins have been shown to act as potential antipathogens. In this review, we focus on the use of QSIs to counter diseases in humans as well as plants and animals of economic importance. We also discuss the challenges encountered in the potential applications of QSIs.
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Affiliation(s)
- Vipin Chandra Kalia
- Department of Chemical Engineering, Konkuk University, Seoul 05029, Republic of Korea.
| | - Sanjay K S Patel
- Department of Chemical Engineering, Konkuk University, Seoul 05029, Republic of Korea
| | - Yun Chan Kang
- Department of Materials Science and Engineering, Korea University, Anam-Dong, Seongbuk-Gu, Seoul 02841, Republic of Korea
| | - Jung-Kul Lee
- Department of Chemical Engineering, Konkuk University, Seoul 05029, Republic of Korea.
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Prakash J, Sharma R, Patel SKS, Kim IW, Kalia VC. Bio-hydrogen production by co-digestion of domestic wastewater and biodiesel industry effluent. PLoS One 2018; 13:e0199059. [PMID: 29995877 PMCID: PMC6040696 DOI: 10.1371/journal.pone.0199059] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Accepted: 05/30/2018] [Indexed: 11/18/2022] Open
Abstract
The increasing water crisis makes fresh water a valuable resource, which must be used wisely. However, with growing population and inefficient waste treatment systems, the amount of wastewater dispelled in rivers is increasing abominably. Utilizing this freely available waste-water along with biodiesel industry waste- crude glycerol for bio-hydrogen production is being reported here. The bacterial cultures of Bacillus thuringiensis strain EGU45 and Bacillus amyloliquefaciens strain CD16 produced2.4-3.0 L H2/day/L feed during a 60 days continuous culture system at hydraulic retention time of 2 days. An average H2 yield of 100-120 L/L CG was reported by the two strains. Recycling of the effluent by up to 25% resulted in up to 94% H2 production compared to control.
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Affiliation(s)
- Jyotsana Prakash
- Department of Chemical Engineering, Konkuk University, Seoul, Republic of Korea
- CSIR–Institute of Genomics and Integrative Biology (IGIB), Delhi University Campus, Delhi, India
- Academy of Scientific & Innovative Research (AcSIR), Anusandhan Bhawan, New Delhi, India
| | - Rakesh Sharma
- CSIR–Institute of Genomics and Integrative Biology (IGIB), Delhi University Campus, Delhi, India
| | - Sanjay K. S. Patel
- Department of Chemical Engineering, Konkuk University, Seoul, Republic of Korea
| | - In-Won Kim
- Department of Chemical Engineering, Konkuk University, Seoul, Republic of Korea
- * E-mail: (VCK); (IWK)
| | - Vipin Chandra Kalia
- Department of Chemical Engineering, Konkuk University, Seoul, Republic of Korea
- CSIR–Institute of Genomics and Integrative Biology (IGIB), Delhi University Campus, Delhi, India
- Academy of Scientific & Innovative Research (AcSIR), Anusandhan Bhawan, New Delhi, India
- * E-mail: (VCK); (IWK)
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Sood U, Bajaj A, Kumar R, Khurana S, Kalia VC. Infection and Microbiome: Impact of Tuberculosis on Human Gut Microbiome of Indian Cohort. Indian J Microbiol 2018; 58:123-125. [PMID: 29434408 PMCID: PMC5801191 DOI: 10.1007/s12088-018-0706-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Affiliation(s)
- Utkarsh Sood
- Department of Zoology, University of Delhi, Delhi, 110007 India
| | - Abhay Bajaj
- Department of Zoology, University of Delhi, Delhi, 110007 India
| | - Roshan Kumar
- Department of Zoology, University of Delhi, Delhi, 110007 India
| | - Sachin Khurana
- Department of Zoology, University of Delhi, Delhi, 110007 India
| | - Vipin Chandra Kalia
- Microbial Biotechnology and Genomics, CSIR - Institute of Genomics and Integrative Biology (IGIB), Delhi University Campus, Mall Road, Delhi, 110007 India
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Prakash J, Sharma R, Ray S, Koul S, Kalia VC. Wastewater: A Potential Bioenergy Resource. Indian J Microbiol 2017; 58:127-137. [PMID: 29651171 DOI: 10.1007/s12088-017-0703-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [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: 12/15/2017] [Accepted: 12/26/2017] [Indexed: 12/29/2022] Open
Abstract
Wastewaters are a rich source of nutrients for microorganisms. However, if left unattended the biodegradation may lead to severe environmental hazards. The wastewaters can thus be utilized for the production of various value added products including bioenergy (H2 and CH4). A number of studies have reported utilization of various wastewaters for energy production. Depending on the nature of the wastewater, different reactor configurations, wastewater and inoculum pretreatments, co-substrate utilizations along with other process parameters have been studied for efficient product formation. Only a few studies have reported sequential utilization of wastewaters for H2 and CH4 production despite its huge potential for complete waste degradation.
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Affiliation(s)
- Jyotsana Prakash
- 1Microbial Biotechnology and Genomics, CSIR - Institute of Genomics and Integrative Biology (IGIB), Delhi University Campus, Mall Road, New Delhi, Delhi 110007 India
- 2Academy of Scientific and Innovative Research (AcSIR), 2, Rafi Marg, Anusandhan Bhawan, New Delhi, 110001 India
| | - Rakesh Sharma
- 1Microbial Biotechnology and Genomics, CSIR - Institute of Genomics and Integrative Biology (IGIB), Delhi University Campus, Mall Road, New Delhi, Delhi 110007 India
- 2Academy of Scientific and Innovative Research (AcSIR), 2, Rafi Marg, Anusandhan Bhawan, New Delhi, 110001 India
| | - Subhasree Ray
- 1Microbial Biotechnology and Genomics, CSIR - Institute of Genomics and Integrative Biology (IGIB), Delhi University Campus, Mall Road, New Delhi, Delhi 110007 India
- 2Academy of Scientific and Innovative Research (AcSIR), 2, Rafi Marg, Anusandhan Bhawan, New Delhi, 110001 India
| | - Shikha Koul
- 1Microbial Biotechnology and Genomics, CSIR - Institute of Genomics and Integrative Biology (IGIB), Delhi University Campus, Mall Road, New Delhi, Delhi 110007 India
- 2Academy of Scientific and Innovative Research (AcSIR), 2, Rafi Marg, Anusandhan Bhawan, New Delhi, 110001 India
| | - Vipin Chandra Kalia
- 1Microbial Biotechnology and Genomics, CSIR - Institute of Genomics and Integrative Biology (IGIB), Delhi University Campus, Mall Road, New Delhi, Delhi 110007 India
- 2Academy of Scientific and Innovative Research (AcSIR), 2, Rafi Marg, Anusandhan Bhawan, New Delhi, 110001 India
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Ray S, Sharma R, Kalia VC. Co-utilization of Crude Glycerol and Biowastes for Producing Polyhydroxyalkanoates. Indian J Microbiol 2017; 58:33-38. [PMID: 29434395 DOI: 10.1007/s12088-017-0702-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [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: 12/12/2017] [Accepted: 12/26/2017] [Indexed: 02/01/2023] Open
Abstract
Polyhydroxyalkanoate (PHA) production by Bacillus thuringiensis EGU45 and defined mixed culture of Bacillus spp. were studied by using crude glycerol (CG) and hydrolyzed biowastes as feed material. Hydrolysates from onion peels (OP), potato peels, pea-shells (PS), apple pomace 2% total solids obtained with defined mixed hydrolytic cultures (MHC2) were inoculated with B. thuringiensis EGU45 and defined mixed bacterial cultures (5MC1), which produced PHA at the rate of 40-350 and 65-450 mg/L, respectively. Addition of CG (1%, v/v) to these hydrolysates resulted in 1.8-fold and 4.5-fold enhancement in PHA production from OP by B. thuringiensis EGU45 and 5MC1, respectively. Co-utilization of OP and PS (in 2:1 ratio) supplemented with CG (1%, v/v) by B. thuringiensis EGU45 resulted in 2-fold increase in PHA production in comparison to OP + CG. This co-metabolism of OP and PS also enabled PHA co-polymer production (1300 mg/L), having an enhanced HV content of 21.2% (w/w).
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Affiliation(s)
- Subhasree Ray
- 1Microbial Biotechnology and Genomics, CSIR - Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi University Campus, Mall Road, New Delhi, Delhi 110007 India.,2Academy of Scientific and Innovative Research (AcSIR), 2, Rafi Marg, Anusandhan Bhawan, New Delhi, 110001 India
| | - Rakesh Sharma
- 1Microbial Biotechnology and Genomics, CSIR - Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi University Campus, Mall Road, New Delhi, Delhi 110007 India.,2Academy of Scientific and Innovative Research (AcSIR), 2, Rafi Marg, Anusandhan Bhawan, New Delhi, 110001 India
| | - Vipin Chandra Kalia
- 1Microbial Biotechnology and Genomics, CSIR - Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi University Campus, Mall Road, New Delhi, Delhi 110007 India.,2Academy of Scientific and Innovative Research (AcSIR), 2, Rafi Marg, Anusandhan Bhawan, New Delhi, 110001 India
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Prakash J, Gupta RK, Xx P, Kalia VC. Bioprocessing of Biodiesel Industry Effluent by Immobilized Bacteria to Produce Value-Added Products. Appl Biochem Biotechnol 2017; 185:179-190. [PMID: 29101733 DOI: 10.1007/s12010-017-2637-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [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: 06/27/2017] [Accepted: 10/16/2017] [Indexed: 12/28/2022]
Abstract
Biodiesel industrial effluent rich in crude glycerol (CG) was processed to produce value-added product. Under continuous culture system, Bacillus amyloliquefaciens strain CD16 immobilized within its biofilm, produced 3.2 L H2/day/L feed, over a period of 60 days at a hydraulic retention time of 2 days. The effective H2 yield by B. amyloliquefaciens strain CD16 was 165 L/L CG. This H2 yield was 1.18-fold higher than that observed with non-biofilm forming Bacillus thuringiensis strain EGU45. Bioprocessing of the effluent released after this stage, by recycling it up to 25% did not have any adverse effect on H2 production by strain EGU45; however, a 25% reduction in yield was recorded with strain CD16. Biofilm forming H2 producers thus proved effective as self-immobilizing system leading to enhanced process efficiency.
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Affiliation(s)
- Jyotsana Prakash
- Microbial Biotechnology and Genomics, CSIR - Institute of Genomics and Integrative Biology (IGIB), Delhi University Campus, Mall Road, New Delhi, 110007, India. .,Academy of Scientific and Innovative Research (AcSIR), 2, Rafi Marg, Anusandhan Bhawan, New Delhi, 110001, India.
| | - Rahul Kumar Gupta
- Microbial Biotechnology and Genomics, CSIR - Institute of Genomics and Integrative Biology (IGIB), Delhi University Campus, Mall Road, New Delhi, 110007, India
| | - Priyanka Xx
- Microbial Biotechnology and Genomics, CSIR - Institute of Genomics and Integrative Biology (IGIB), Delhi University Campus, Mall Road, New Delhi, 110007, India.,Academy of Scientific and Innovative Research (AcSIR), 2, Rafi Marg, Anusandhan Bhawan, New Delhi, 110001, India
| | - Vipin Chandra Kalia
- Microbial Biotechnology and Genomics, CSIR - Institute of Genomics and Integrative Biology (IGIB), Delhi University Campus, Mall Road, New Delhi, 110007, India.,Academy of Scientific and Innovative Research (AcSIR), 2, Rafi Marg, Anusandhan Bhawan, New Delhi, 110001, India
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Abstract
Polyhydroxyalkanoates (PHA) are produced by a large number of microbes under stress conditions such as high carbon (C) availability and limitations of nutrients such as nitrogen, potassium, phosphorus, magnesium, and oxygen. Here, microbes store C as granules of PHAs-energy reservoir. PHAs have properties, which are quite similar to those of synthetic plastics. The unique properties, which make them desirable materials for biomedical applications is their biodegradability, biocompatibility, and non-toxicity. PHAs have been found suitable for various medical applications: biocontrol agents, drug carriers, biodegradable implants, tissue engineering, memory enhancers, and anticancer agents.
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Affiliation(s)
- Subhasree Ray
- Microbial Biotechnology and Genomics, CSIR - Institute of Genomics and Integrative Biology (IGIB), Delhi University Campus, Mall Road, Delhi, 110007 India
- Academy of Scientific and Innovative Research (AcSIR), 2, Rafi Marg, Anusandhan Bhawan, New Delhi, 110001 India
| | - Vipin Chandra Kalia
- Microbial Biotechnology and Genomics, CSIR - Institute of Genomics and Integrative Biology (IGIB), Delhi University Campus, Mall Road, Delhi, 110007 India
- Academy of Scientific and Innovative Research (AcSIR), 2, Rafi Marg, Anusandhan Bhawan, New Delhi, 110001 India
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Ray S, Kalia VC. Co-metabolism of substrates by Bacillus thuringiensis regulates polyhydroxyalkanoate co-polymer composition. Bioresour Technol 2017; 224:743-747. [PMID: 27914782 DOI: 10.1016/j.biortech.2016.11.089] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Revised: 11/19/2016] [Accepted: 11/21/2016] [Indexed: 06/06/2023]
Abstract
Polyhydroxyalkanoate (PHA) production by Bacillus thuringiensis EGU45 was studied by co-metabolism of crude glycerol (CG) (1%, v/v), glucose (0.05-0.5%, w/v) and propionic acid (0.05-0.5%, v/v) under batch (shake flask) culture conditions. Glycerol+PA combination resulted in 15-100mg/L PHA co-polymers with a HV content of 33-81mol%. The addition of NH4Cl (0.5%, w/v) to CG+PA enhanced PHA production by 1.55-fold, with a HV content of 58-70mol%. The time period of incubation of PA to the feed: CG+glucose was optimized to be 3h after initiation of fermentation. The PHA contents were found to be stable at 1900-2050mg/L up scaling from 0.4 to 2.0L feed material. Biochemical characterization through GC-MS of PHA co-polymer revealed the presence of 3-hydroxydecanoate (3-HDD), 3-hydroxyoctadecanoate (3HOD), 3-hydroxyhexadecanoate (3HHD).
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Affiliation(s)
- Subhasree Ray
- Microbial Biotechnology and Genomics, CSIR - Institute of Genomics and Integrative Biology (IGIB), Delhi University Campus, Mall Road, Delhi 110007, India; Academy of Scientific & Innovative Research (AcSIR), 2, Rafi Marg, Anusandhan Bhawan, New Delhi 110001, India.
| | - Vipin Chandra Kalia
- Microbial Biotechnology and Genomics, CSIR - Institute of Genomics and Integrative Biology (IGIB), Delhi University Campus, Mall Road, Delhi 110007, India; Academy of Scientific & Innovative Research (AcSIR), 2, Rafi Marg, Anusandhan Bhawan, New Delhi 110001, India
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41
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Koul S, Kalia VC. Multiplicity of Quorum Quenching Enzymes: A Potential Mechanism to Limit Quorum Sensing Bacterial Population. Indian J Microbiol 2016; 57:100-108. [PMID: 28148985 DOI: 10.1007/s12088-016-0633-1] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [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: 11/01/2016] [Accepted: 11/17/2016] [Indexed: 11/28/2022] Open
Abstract
Bacteria express certain of their characteristics especially, pathogenicity factors at high cell densities. The process is termed as quorum sensing (QS). QS operates via signal molecules such as acylhomoserine lactones (AHLs). Other bacteria inhibit QS through the inactivation of AHL signals by producing enzymes like AHL-lactonases and -acylases. Comparative genomic analysis has revealed the multiplicity of genes for AHL lactonases (up to 12 copies per genome) among Bacillus spp. and that of AHL-acylases (up to 5 copies per genome) among Pseudomonas spp. This genetic evolution can be envisaged to enable host to withstand the attacks from bacterial population, which regulates its functioning through QS.
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Affiliation(s)
- Shikha Koul
- Microbial Biotechnology and Genomics, CSIR - Institute of Genomics and Integrative Biology (IGIB), Delhi University Campus, Mall Road, Delhi, 110007 India.,Academy of Scientific and Innovative Research (AcSIR), 2, Rafi Marg, Anusandhan Bhawan, New Delhi, 110001 India
| | - Vipin Chandra Kalia
- Microbial Biotechnology and Genomics, CSIR - Institute of Genomics and Integrative Biology (IGIB), Delhi University Campus, Mall Road, Delhi, 110007 India.,Academy of Scientific and Innovative Research (AcSIR), 2, Rafi Marg, Anusandhan Bhawan, New Delhi, 110001 India
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42
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Abstract
Polyhydroxyalkanoate (PHAs) are natural, biodegradable biopolymers, which can be produced from renewable materials. PHAs have potential to replace petroleum derived plastics. Quite a few bacteria can produce PHA under nutritional stress. They generally produce homopolymers of butyrate i.e., polyhydroxybutyrate (PHB), as a storage material. The biochemical characteristics of PHB such as brittleness, low strength, low elasticity, etc. make these unsuitable for commercial applications. Co-polymers of PHA, have high commercial value as they overcome the limitations of PHBs. Co-polymers can be produced by supplementing the feed with volatile fatty acids or through hydrolysates of different biowastes. In this review, we have listed the potential bacterial candidates and the substrates, which can be co-metabolized to produce PHA co-polymers.
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Affiliation(s)
- Subhasree Ray
- Microbial Biotechnology and Genomics, CSIR - Institute of Genomics and Integrative Biology (IGIB), Delhi University Campus, Mall Road, Delhi, 110007 India.,Academy of Scientific and Innovative Research (AcSIR), 2, Rafi Marg, Anusandhan Bhawan, New Delhi, 110001 India
| | - Vipin Chandra Kalia
- Microbial Biotechnology and Genomics, CSIR - Institute of Genomics and Integrative Biology (IGIB), Delhi University Campus, Mall Road, Delhi, 110007 India.,Academy of Scientific and Innovative Research (AcSIR), 2, Rafi Marg, Anusandhan Bhawan, New Delhi, 110001 India
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43
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Kalia VC, Prakash J, Koul S, Ray S. Simple and Rapid Method for Detecting Biofilm Forming Bacteria. Indian J Microbiol 2016; 57:109-111. [PMID: 28148986 DOI: 10.1007/s12088-016-0616-2] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [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: 07/23/2016] [Accepted: 08/10/2016] [Indexed: 12/28/2022] Open
Abstract
Biofilm forming bacteria play a vital role in causing infectious diseases and for enhancing the efficiency of the bioremediation process through immobilization. Different media and conditions have been reported for detecting biofilm forming bacteria, however, they are not quite rapid. Here, we propose the use of a simple medium which can be used for detecting biofilm former, and also provide a mechanism to regulate the expression of biofilm formation process.
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Affiliation(s)
- Vipin Chandra Kalia
- Microbial Biotechnology and Genomics, CSIR - Institute of Genomics and Integrative Biology (IGIB), Delhi University Campus, Mall Road, Delhi, 110007 India
- Academy of Scientific and Innovative Research (AcSIR), 2, Rafi Marg, Anusandhan Bhawan, New Delhi, 110001 India
| | - Jyotsana Prakash
- Microbial Biotechnology and Genomics, CSIR - Institute of Genomics and Integrative Biology (IGIB), Delhi University Campus, Mall Road, Delhi, 110007 India
- Academy of Scientific and Innovative Research (AcSIR), 2, Rafi Marg, Anusandhan Bhawan, New Delhi, 110001 India
| | - Shikha Koul
- Microbial Biotechnology and Genomics, CSIR - Institute of Genomics and Integrative Biology (IGIB), Delhi University Campus, Mall Road, Delhi, 110007 India
- Academy of Scientific and Innovative Research (AcSIR), 2, Rafi Marg, Anusandhan Bhawan, New Delhi, 110001 India
| | - Subhasree Ray
- Microbial Biotechnology and Genomics, CSIR - Institute of Genomics and Integrative Biology (IGIB), Delhi University Campus, Mall Road, Delhi, 110007 India
- Academy of Scientific and Innovative Research (AcSIR), 2, Rafi Marg, Anusandhan Bhawan, New Delhi, 110001 India
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Abstract
The biodiesel industry has the potential to meet the fuel requirements in the future. A few inherent lacunae of this bioprocess are the effluent, which is 10 % of the actual product, and the fact that it is 85 % glycerol along with a few impurities. Biological treatments of wastes have been known as a dependable and economical direction of overseeing them and bring some value added products as well. A novel eco-biotechnological strategy employs metabolically diverse bacteria, which ensures higher reproducibility and economics. In this article, we have opined, which organisms and what bioproducts should be the focus, while exploiting glycerol as feed.
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Affiliation(s)
- Vipin Chandra Kalia
- Microbial Biotechnology and Genomics, CSIR - Institute of Genomics and Integrative Biology (IGIB), Delhi University Campus, Mall Road, Delhi, 110007 India ; Academy for Scientific and Innovative Research (AcSIR), 2 Rafi Marg, New Delhi, 110001 India
| | - Jyotsana Prakash
- Microbial Biotechnology and Genomics, CSIR - Institute of Genomics and Integrative Biology (IGIB), Delhi University Campus, Mall Road, Delhi, 110007 India ; Academy for Scientific and Innovative Research (AcSIR), 2 Rafi Marg, New Delhi, 110001 India
| | - Shikha Koul
- Microbial Biotechnology and Genomics, CSIR - Institute of Genomics and Integrative Biology (IGIB), Delhi University Campus, Mall Road, Delhi, 110007 India ; Academy for Scientific and Innovative Research (AcSIR), 2 Rafi Marg, New Delhi, 110001 India
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45
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Kumar R, Koul S, Kumar P, Kalia VC. Searching Biomarkers in the Sequenced Genomes of Staphylococcus for their Rapid Identification. Indian J Microbiol 2016; 56:64-71. [PMID: 26843698 DOI: 10.1007/s12088-016-0565-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [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: 12/31/2015] [Accepted: 01/11/2016] [Indexed: 12/19/2022] Open
Abstract
Bacterial identification using rrs (16S rRNA) gene is widely reported. Bacteria possessing multiple copies of rrs lead to overestimation of its diversity. Staphylococcus genomes carries 5-6 copies of rrs showing high similarity in their nucleotide sequences, which lead to ambiguous results. The genomes of 31 strains of Staphylococcus representing 7 species were searched for the presence of common genes. In silico digestion of 34 common genes using 10 restriction endonucleases (REs) lead to select gene-RE combinations, which could be used as biomarkers. RE digestion of recA allowed unambiguous identification of 13 genomes representing all the 7 species. In addition, a few more genes (argH, argR, cysS, gyrB, purH, and pyrE) and RE combinations permitted further identification of 12 strains. By employing additional RE and genes unique to a particular strain, it was possible to identify the rest 6 Staphylococcus aureus strains. This approach has the potential to be utilized for rapid detection of Staphylococcus strains.
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Affiliation(s)
- Ravi Kumar
- Microbial Biotechnology and Genomics, CSIR - Institute of Genomics and Integrative Biology (IGIB), Delhi University Campus, Mall Road, New Delhi, 110007 India
| | - Shikha Koul
- Microbial Biotechnology and Genomics, CSIR - Institute of Genomics and Integrative Biology (IGIB), Delhi University Campus, Mall Road, New Delhi, 110007 India ; Academy for Scientific and Innovative Research (AcSIR), 2 Rafi Marg, New Delhi, 110001 India
| | - Prasun Kumar
- Microbial Biotechnology and Genomics, CSIR - Institute of Genomics and Integrative Biology (IGIB), Delhi University Campus, Mall Road, New Delhi, 110007 India
| | - Vipin Chandra Kalia
- Microbial Biotechnology and Genomics, CSIR - Institute of Genomics and Integrative Biology (IGIB), Delhi University Campus, Mall Road, New Delhi, 110007 India ; Academy for Scientific and Innovative Research (AcSIR), 2 Rafi Marg, New Delhi, 110001 India
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Kalia VC, Kumar R, Kumar P, Koul S. A Genome-Wide Profiling Strategy as an Aid for Searching Unique Identification Biomarkers for Streptococcus. Indian J Microbiol 2015; 56:46-58. [PMID: 26843696 DOI: 10.1007/s12088-015-0561-5] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [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: 10/27/2015] [Accepted: 11/13/2015] [Indexed: 12/19/2022] Open
Abstract
The use of rrs (16S rRNA) gene is widely regarded as the "gold standard" for identifying bacteria and determining their phylogenetic relationships. Nevertheless, multiple copies of this gene in a genome is likely to give an overestimation of the bacterial diversity. In each of the 50 Streptococcus genomes (16 species, 50 strains), 4-7 copies of rrs are present. The nucleotide sequences of these rrs genes show high similarity within and among genomes, which did not allow unambiguous identification. A genome-wide search revealed the presence of 27 gene sequences common to all the Streptococcus species. Digestion of these 27 gene sequences with 10 type II restriction endonucleases (REs) showed that unique RE digestion in purH gene is sufficient for clear cut identification of 30 genomes belonging to 16 species. Additional gene-RE combinations allowed identification of another 15 strains belonging to S. pneumoniae, S. pyogenes, and S. suis. For the rest 5 strains, a combination of 2 genes was required for identifying them. The proposed strategy is likely to prove helpful in proper detection of pathogens like Streptococcus.
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Affiliation(s)
- Vipin Chandra Kalia
- Microbial Biotechnology and Genomics, CSIR - Institute of Genomics and Integrative Biology (IGIB), Delhi University Campus, Mall Road, Delhi, 110007 India ; Academy of Scientific and Innovative Research (AcSIR), 2, Rafi Marg, Anusandhan Bhawan, New Delhi, 110001 India
| | - Ravi Kumar
- Microbial Biotechnology and Genomics, CSIR - Institute of Genomics and Integrative Biology (IGIB), Delhi University Campus, Mall Road, Delhi, 110007 India
| | - Prasun Kumar
- Microbial Biotechnology and Genomics, CSIR - Institute of Genomics and Integrative Biology (IGIB), Delhi University Campus, Mall Road, Delhi, 110007 India
| | - Shikha Koul
- Microbial Biotechnology and Genomics, CSIR - Institute of Genomics and Integrative Biology (IGIB), Delhi University Campus, Mall Road, Delhi, 110007 India ; Academy of Scientific and Innovative Research (AcSIR), 2, Rafi Marg, Anusandhan Bhawan, New Delhi, 110001 India
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Koul S, Prakash J, Mishra A, Kalia VC. Potential Emergence of Multi-quorum Sensing Inhibitor Resistant (MQSIR) Bacteria. Indian J Microbiol 2015; 56:1-18. [PMID: 26843692 DOI: 10.1007/s12088-015-0558-0] [Citation(s) in RCA: 75] [Impact Index Per Article: 8.3] [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: 10/17/2015] [Accepted: 10/28/2015] [Indexed: 12/15/2022] Open
Abstract
Expression of certain bacterial genes only at a high bacterial cell density is termed as quorum-sensing (QS). Here bacteria use signaling molecules to communicate among themselves. QS mediated genes are generally involved in the expression of phenotypes such as bioluminescence, biofilm formation, competence, nodulation, and virulence. QS systems (QSS) vary from a single in Vibrio spp. to multiple in Pseudomonas and Sinorhizobium species. The complexity of QSS is further enhanced by the multiplicity of signals: (1) peptides, (2) acyl-homoserine lactones, (3) diketopiperazines. To counteract this pathogenic behaviour, a wide range of bioactive molecules acting as QS inhibitors (QSIs) have been elucidated. Unlike antibiotics, QSIs don't kill bacteria and act at much lower concentration than those of antibiotics. Bacterial ability to evolve resistance against multiple drugs has cautioned researchers to develop QSIs which may not generate undue pressure on bacteria to develop resistance against them. In this paper, we have discussed the implications of the diversity and multiplicity of QSS, in acting as an arsenal to withstand attack from QSIs and may use these as reservoirs to develop multi-QSI resistance.
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Affiliation(s)
- Shikha Koul
- Microbial Biotechnology and Genomics, CSIR - Institute of Genomics and Integrative Biology (IGIB), Delhi University Campus, Mall Road, Delhi, 110007 India ; Academy for Scientific and Innovative Research (AcSIR), 2 Rafi Marg, New Delhi, 110001 India
| | - Jyotsana Prakash
- Microbial Biotechnology and Genomics, CSIR - Institute of Genomics and Integrative Biology (IGIB), Delhi University Campus, Mall Road, Delhi, 110007 India ; Academy for Scientific and Innovative Research (AcSIR), 2 Rafi Marg, New Delhi, 110001 India
| | - Anjali Mishra
- Microbial Biotechnology and Genomics, CSIR - Institute of Genomics and Integrative Biology (IGIB), Delhi University Campus, Mall Road, Delhi, 110007 India
| | - Vipin Chandra Kalia
- Microbial Biotechnology and Genomics, CSIR - Institute of Genomics and Integrative Biology (IGIB), Delhi University Campus, Mall Road, Delhi, 110007 India ; Academy for Scientific and Innovative Research (AcSIR), 2 Rafi Marg, New Delhi, 110001 India
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48
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Abstract
Bacterial identification on the basis of the highly conserved 16S rRNA (rrs) gene is limited by its presence in multiple copies and a very high level of similarity among them. The need is to look for other genes with unique characteristics to be used as biomarkers. Fifty-one sequenced genomes belonging to 10 different Yersinia species were used for searching genes common to all the genomes. Out of 304 common genes, 34 genes of sizes varying from 0.11 to 4.42 kb, were selected and subjected to in silico digestion with 10 different Restriction endonucleases (RE) (4-6 base cutters). Yersinia species have 6-7 copies of rrs per genome, which are difficult to distinguish by multiple sequence alignments or their RE digestion patterns. However, certain unique combinations of other common gene sequences-carB, fadJ, gluM, gltX, ileS, malE, nusA, ribD, and rlmL and their RE digestion patterns can be used as markers for identifying 21 strains belonging to 10 Yersinia species: Y. aldovae, Y. enterocolitica, Y. frederiksenii, Y. intermedia, Y. kristensenii, Y. pestis, Y. pseudotuberculosis, Y. rohdei, Y. ruckeri, and Y. similis. This approach can be applied for rapid diagnostic applications.
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Affiliation(s)
- Vipin Chandra Kalia
- Microbial Biotechnology and Genomics, CSIR - Institute of Genomics and Integrative Biology (IGIB), Delhi University Campus, Mall Road, Delhi, 110007 India
| | - Prasun Kumar
- Microbial Biotechnology and Genomics, CSIR - Institute of Genomics and Integrative Biology (IGIB), Delhi University Campus, Mall Road, Delhi, 110007 India
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Kalia VC, Kumar P, Kumar R, Mishra A, Koul S. Genome Wide Analysis for Rapid Identification of Vibrio Species. Indian J Microbiol 2015; 55:375-83. [PMID: 26543262 DOI: 10.1007/s12088-015-0553-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [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: 08/26/2015] [Accepted: 09/01/2015] [Indexed: 12/17/2022] Open
Abstract
The highly conserved 16S rRNA (rrs) gene is generally used for bacterial identification. In organisms possessing multiple copies of rrs, high intra-genomic heterogeneity does not allow easy distinction among different species. In order to identify Vibrio species, a wide range of genes have been employed. There is an urgent requirement of a consensus gene, which can be used as biomarker for rapid identification. Eight sequenced genomes of Vibrio species were screened for selecting genes which were common among all the genomes. Out of 108 common genes, 24 genes of sizes varying from 0.11 to 3.94 kb were subjected to in silico digestion with 10 type II restriction endonucleases (RE). A few unique genes-dapF, fadA, hisD, ilvH, lpxC, recF, recR, rph and ruvB in combination with certain REs provided unique digestion patterns, which can be used as biomarkers. This protocol can be exploited for rapid diagnosis of Vibrio species.
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Affiliation(s)
- Vipin Chandra Kalia
- Microbial Biotechnology and Genomics, CSIR - Institute of Genomics and Integrative Biology (IGIB), Delhi University Campus, Mall Road, New Delhi, 110007 India ; Academy of Scientific and Innovative Research (AcSIR), 2, Rafi Marg, Anusandhan Bhawan, New Delhi, 110001 India
| | - Prasun Kumar
- Microbial Biotechnology and Genomics, CSIR - Institute of Genomics and Integrative Biology (IGIB), Delhi University Campus, Mall Road, New Delhi, 110007 India
| | - Ravi Kumar
- Microbial Biotechnology and Genomics, CSIR - Institute of Genomics and Integrative Biology (IGIB), Delhi University Campus, Mall Road, New Delhi, 110007 India
| | - Anjali Mishra
- Microbial Biotechnology and Genomics, CSIR - Institute of Genomics and Integrative Biology (IGIB), Delhi University Campus, Mall Road, New Delhi, 110007 India
| | - Shikha Koul
- Microbial Biotechnology and Genomics, CSIR - Institute of Genomics and Integrative Biology (IGIB), Delhi University Campus, Mall Road, New Delhi, 110007 India ; Academy of Scientific and Innovative Research (AcSIR), 2, Rafi Marg, Anusandhan Bhawan, New Delhi, 110001 India
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Bhushan A, Mukherjee T, Joshi J, Shankar P, Kalia VC. Insights into the Origin of Clostridium botulinum Strains: Evolution of Distinct Restriction Endonuclease Sites in rrs (16S rRNA gene). Indian J Microbiol 2015; 55:140-50. [PMID: 25805900 DOI: 10.1007/s12088-015-0514-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [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: 01/02/2015] [Accepted: 01/12/2015] [Indexed: 11/26/2022] Open
Abstract
Diversity analysis of Clostridium botulinum strains is complicated by high microheterogeneity caused by the presence of 9-22 copies of rrs (16S rRNA gene). The need is to mine genetic markers to identify very closely related strains. Multiple alignments of the nucleotide sequences of the 212 rrs of 13 C. botulinum strains revealed intra- and inter-genomic heterogeneity. Low intragenomic heterogeneity in rrs was evident in strains 230613, Alaska E43, Okra, Eklund 17B, Langeland, 657, Kyoto, BKT015925, and Loch Maree. The most heterogenous rrs sequences were those of C. botulinum strains ATCC 19397, Hall, H04402065, and ATCC 3502. In silico restriction mapping of these rrs sequences was observable with 137 type II Restriction endonucleases (REs). Nucleotide changes (NC) at these RE sites resulted in appearance of distinct and additional sites, and loss in certain others. De novo appearances of RE sites due to NC were recorded at different positions in rrs gene. A nucleotide transition A>G in rrs of C. botulinum Loch Maree and 657 resulted in the generation of 4 and 10 distinct RE sites, respectively. Transitions A>G, G>A, and T>C led to the loss of RE sites. A perusal of the entire NC and in silico RE mapping of rrs of C. botulinum strains provided insights into their evolution. Segregation of strains on the basis of RE digestion patterns of rrs was validated by the cladistic analysis involving six house keeping genes: dnaN, gyrB, metG, prfA, pyrG, and Rho.
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Affiliation(s)
- Ashish Bhushan
- Microbial Biotechnology and Genomics, CSIR-Institute of Genomics and Integrative Biology (IGIB), Delhi University Campus, Mall Road, Delhi, 110007 India
| | - Tanmoy Mukherjee
- Microbial Biotechnology and Genomics, CSIR-Institute of Genomics and Integrative Biology (IGIB), Delhi University Campus, Mall Road, Delhi, 110007 India
| | - Jayadev Joshi
- Microbial Biotechnology and Genomics, CSIR-Institute of Genomics and Integrative Biology (IGIB), Delhi University Campus, Mall Road, Delhi, 110007 India
| | - Pratap Shankar
- Microbial Biotechnology and Genomics, CSIR-Institute of Genomics and Integrative Biology (IGIB), Delhi University Campus, Mall Road, Delhi, 110007 India
| | - Vipin Chandra Kalia
- Microbial Biotechnology and Genomics, CSIR-Institute of Genomics and Integrative Biology (IGIB), Delhi University Campus, Mall Road, Delhi, 110007 India
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