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Choksket S, Sharma S, Harshvardhan, Pal V, Jain A, Patil PB, Korpole S, Grover V. Evaluation of Human Dental Plaque Lactic Acid Bacilli for Probiotic Potential and Functional Analysis in Relevance to Oral Health. Indian J Microbiol 2023; 63:520-532. [PMID: 38031619 PMCID: PMC10682319 DOI: 10.1007/s12088-023-01108-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Accepted: 10/07/2023] [Indexed: 12/01/2023] Open
Abstract
Members of the lactic acid bacillus group are well-known probiotics and primarily isolated from fermented food, dairy products, intestinal and gut environment of human. Since probiotics from the human source are preferred, there exists a huge repertoire of lactobacilli in the human oral cavity which could prove a much better niche to be exploited for these beneficial microorganisms. Therefore, in this study, four lactobacilli strains, including strain DISK7, reported earlier, isolated from dental plaque samples of a healthy humans were evaluated for their probiotic potential. Strains displayed 99.9% of 16S rRNA gene sequence identity with species of the genera Lactobacillus and Limosilactobacillus. All strains showed lactic acid production, tolerance to low pH and antibiotic sensitivity. Variations were observed among strains in their aggregation ability, biofilm formation, bile salt resistance and cholesterol degradation. Further, we analyzed the interaction of strains with other oral commensals and opportunistic pathogens in co-culture experiments. Isolates DISK7 and DISK26 exhibited high co-aggregation (> 70%) with secondary colonizers, Streptococcus pyogenes and Veillonella parvula, respectively, but their aggregation ability was decreased with opportunistic pathogens. Furthermore, strains showed a substantial increase in biofilm in co-culture with other Lactobacillus isolates, indicating their ability to proliferate commensal bacteria in the oral environment. These microbes continually evolve in terms of niche adaptation as evidenced in genome analysis. The highlight of the investigation is the isolation and evaluation of the probiotic lactobacilli from the human oral cavity, which could prove a much better niche to be exploited for the effective commercialization of these beneficial microbes. Taken together, probiotic properties and interaction with commensal bacteria, these isolates exhibit the huge potential to be developed as alternative bioresource agents for maintenance of oral health. Supplementary Information The online version contains supplementary material available at 10.1007/s12088-023-01108-2.
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Affiliation(s)
- Stanzin Choksket
- CSIR-Institute of Microbial Technology, Sector 39A, Chandigarh, India
| | - Shikha Sharma
- CSIR-Institute of Microbial Technology, Sector 39A, Chandigarh, India
| | - Harshvardhan
- CSIR-Institute of Microbial Technology, Sector 39A, Chandigarh, India
| | - Vijay Pal
- CSIR-Institute of Microbial Technology, Sector 39A, Chandigarh, India
| | - Ashish Jain
- Dr. Harvansh Singh Judge Institute of Dental Sciences and Hospital, Panjab University, Chandigarh, India
| | - Prabhu B. Patil
- CSIR-Institute of Microbial Technology, Sector 39A, Chandigarh, India
| | - Suresh Korpole
- CSIR-Institute of Microbial Technology, Sector 39A, Chandigarh, India
| | - Vishakha Grover
- Dr. Harvansh Singh Judge Institute of Dental Sciences and Hospital, Panjab University, Chandigarh, India
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The Alphabet of the Elementary Microbiology: Revisited. Indian J Microbiol 2021; 61:397-400. [PMID: 34629565 PMCID: PMC8492822 DOI: 10.1007/s12088-021-00987-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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Khurana H, Sharma M, Verma H, Lopes BS, Lal R, Negi RK. Genomic insights into the phylogeny of Bacillus strains and elucidation of their secondary metabolic potential. Genomics 2020; 112:3191-3200. [PMID: 32512145 DOI: 10.1016/j.ygeno.2020.06.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2019] [Revised: 05/17/2020] [Accepted: 06/02/2020] [Indexed: 12/16/2022]
Abstract
The genus Bacillus constitutes a plethora of species that have medical, environmental, and industrial applications. While genus Bacillus has been the focus of several studies where genomic data have been used to resolve many taxonomic issues, there still exist several ambiguities. Through the use of in-silico genome-based methods, we tried to resolve the taxonomic anomalies of a large set of Bacillus genomes (n = 178). We also proposed species names for uncharacterized strains and reported genome sequence of a novel isolate Bacillus sp. RL. In the hierarchical clustering on genome-to-genome distances, we observed 11 distinct monophyletic clusters and investigated the functional pathways annotated as the property of these clusters and core-gene content of the entire dataset. Thus, we were able to assert the possible outlier strains (n = 17) for this genus. Analyses of secondary metabolite potential of each strain helped us unravel still unexplored diversity for various biosynthetic genes.
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Affiliation(s)
- Himani Khurana
- Fish Molecular Biology Laboratory, Department of Zoology, University of Delhi, Delhi 110007, India
| | - Monika Sharma
- Fish Molecular Biology Laboratory, Department of Zoology, University of Delhi, Delhi 110007, India
| | - Helianthous Verma
- Molecular Biology and Genomics Research Laboratory, Ramjas College, University of Delhi, Delhi 110007, India
| | - Bruno Silvester Lopes
- School of Medicine, Medical Sciences and Nutrition, Medical Microbiology, 0:025 Polwarth Building, Aberdeen AB25 2ZD, UK
| | - Rup Lal
- The Energy and Resources Institute, Darbari Seth Block, IHC Complex, Lodhi Road, New Delhi 110003, India.
| | - Ram Krishan Negi
- Fish Molecular Biology Laboratory, Department of Zoology, University of Delhi, Delhi 110007, India.
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Yoon HM, Song SJ, Ko JS, Yoon HK, Kim SJ, Kim SJ, Kim JW, Yoo M. PCR Screening of Enterococcus faecalis from Mixture of Lactic Acid Bacteria Using Bile Salt Hydrolase Gene as a Selective Marker. Indian J Microbiol 2020; 60:251-253. [PMID: 32255858 DOI: 10.1007/s12088-019-00851-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Accepted: 12/19/2019] [Indexed: 10/25/2022] Open
Abstract
It is very important to rapidly detect the contamination of Enterococcus faecalis in fermented foods such as Korean Kimchi to maintain its freshness since Kimchi is exported to all over the world. However, gene sequence of E. faecalis is very similar among various Lactobacillus. So, there have been difficulties in its screening. We have designed primers based on Bile salt hydrolase gene of E. faecalis and applied them to PCR test. PCR band was identified only from E. faecalis and only from the mixture contaminated with E. faecalis. It means that the primers we designed are highly specific for distinguishing contamination of E. faecalis. It will be possible to precisely screen within 1 h, which will greatly contribute to the prevention of food poisoning and quick quarantine.
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Affiliation(s)
- Hye Min Yoon
- Department of Biological Sciences, Keimyung University, Daegu, 42601 Korea
| | - Su Jin Song
- Department of Biological Sciences, Keimyung University, Daegu, 42601 Korea
| | - Ji Su Ko
- Department of Biological Sciences, Keimyung University, Daegu, 42601 Korea
| | - Hye Kyoung Yoon
- Department of Biological Sciences, Keimyung University, Daegu, 42601 Korea
| | - Su Jeong Kim
- Department of Biological Sciences, Keimyung University, Daegu, 42601 Korea
| | - So Jin Kim
- Department of Biological Sciences, Keimyung University, Daegu, 42601 Korea
| | - Ji Woon Kim
- Department of Biological Sciences, Keimyung University, Daegu, 42601 Korea
| | - Min Yoo
- Department of Biological Sciences, Keimyung University, Daegu, 42601 Korea
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Urvashi, Sharma D, Sharma S, Pal V, Lal R, Patil P, Grover V, Korpole S. Bacterial Populations in Subgingival Plaque Under Healthy and Diseased Conditions: Genomic Insights into Oral Adaptation Strategies by Lactobacillus sp. Strain DISK7. Indian J Microbiol 2020; 60:78-86. [PMID: 32089577 PMCID: PMC7000561 DOI: 10.1007/s12088-019-00828-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2019] [Accepted: 09/30/2019] [Indexed: 12/23/2022] Open
Abstract
Human oral cavity is a complex habitat comprising about 700 microbial species and represents the most complex microbiota after gastrointestinal tract. In fact, oral microbiota directly influences health, metabolism and immune responses of the host. Metagenomic studies based on 16S rDNA profiling has reported the inhabitant bacteria mainly belonging to phyla Firmicutes, Proteobacteria, Actinobacteria, Fusobacteria, Spirochaetes and Bacteroidetes. Therefore, it is essential to isolate these strains and characterize in detail to understand their interaction. We have isolated strains from subgingival plaque from healthy to diseased individuals and the molecular characterization based on 16S rRNA gene sequence analysis showed predominance of Firmicutes, specifically members of the genus Streptococcus. Species of Lactobacillus and Veillonella were also found in significant number, which are considered as secondary colonizers. However, the population of Lactobacillus was decreased in diseased conditions with the increase in opportunistic pathogenic strains pertaining to genera like Campylobacter, Neisseria, Enterobacter, Pseudomonas and Morococcus. Further, we have also made an attempt to gain genomic insights on adaptation features and interactions of an isolate, Lactobacillus sp. strain DISK7 by performing whole genome sequencing and analysis, subsequently biochemical characterization to explore its functional and metabolic properties for the development as probiotic agent.
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Affiliation(s)
- Urvashi
- MTCC and Gene Bank, CSIR-Institute of Microbial Technology, Sector 39A, Chandigarh, 160036 India
| | - Deepika Sharma
- MTCC and Gene Bank, CSIR-Institute of Microbial Technology, Sector 39A, Chandigarh, 160036 India
| | - Shikha Sharma
- MTCC and Gene Bank, CSIR-Institute of Microbial Technology, Sector 39A, Chandigarh, 160036 India
| | - Vijay Pal
- MTCC and Gene Bank, CSIR-Institute of Microbial Technology, Sector 39A, Chandigarh, 160036 India
| | - Rup Lal
- The Energy and Resources Institute, New Delhi, India
| | - Prabhu Patil
- MTCC and Gene Bank, CSIR-Institute of Microbial Technology, Sector 39A, Chandigarh, 160036 India
| | - Vishakha Grover
- Dr. HS Singh Judge Institute of Dental Sciences and Hospital, Panjab University, Chandigarh, India
| | - Suresh Korpole
- MTCC and Gene Bank, CSIR-Institute of Microbial Technology, Sector 39A, Chandigarh, 160036 India
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Mapping Microbial Capacities for Bioremediation: Genes to Genomics. Indian J Microbiol 2019; 60:45-53. [PMID: 32089573 DOI: 10.1007/s12088-019-00842-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Accepted: 11/12/2019] [Indexed: 12/15/2022] Open
Abstract
Bioremediation is a process wherein the decontamination strategies are designed so that a site could achieve the environmental abiotic and biotic parameters close to its baseline. In the process, the driving force is the available microbial genetic degradative capabilities, which are supported by required nutrients so that the desired expression of these capabilities could be exploited in favour of removal of pollutants. With genomics tools not only the available abilities could be estimated but their dynamic performance could also be established. These tools are now playing important role in bioprocess optimization, which not only derive the bio-stimulation plans but also could suggest possible genetic bio-augmentation options.
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Purohit HJ. Aligning Microbial Biodiversity for Valorization of Biowastes: Conception to Perception. Indian J Microbiol 2019; 59:391-400. [PMID: 31762500 DOI: 10.1007/s12088-019-00826-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Accepted: 09/12/2019] [Indexed: 12/16/2022] Open
Abstract
Generation of biowastes is increasing rapidly and its uncontrolled, slow and persistent fermentation leads to the release of Green-house gases (GHGs) into the environment. Exploration and exploitation of microbial diversity for degrading biowastes can result in producing diverse range of bioactive molecules, which can act as a source of bioenergy, biopolymers, nutraceuticals and antimicrobials. The whole process is envisaged to manage biowastes, and reduce their pollution causing capacity, and lead to a sustainable society. A strategy has been proposed for: (1) producing bioactive molecules, and (2) achieving a zero-pollution emission by recycling of the GHGs through biological routes.
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Affiliation(s)
- Hemant J Purohit
- Environmental Biotechnology and Genomics Division, CSIR-National Environmental and Engineering Research Institute (CSIR-NEERI), Nehru Marg, Nagpur, Maharashtra 440020 India
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Talwar C, Nagar S, Lal R, Negi RK. Fish Gut Microbiome: Current Approaches and Future Perspectives. Indian J Microbiol 2018; 58:397-414. [PMID: 30262950 DOI: 10.1007/s12088-018-0760-y] [Citation(s) in RCA: 78] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Accepted: 08/17/2018] [Indexed: 12/13/2022] Open
Abstract
In recent years, investigations of microbial flora associated with fish gut have deepened our knowledge of the complex interactions occurring between microbes and host fish. The gut microbiome not only reinforces the digestive and immune systems in fish but is itself shaped by several host-associated factors. Unfortunately, in the past, majority of studies have focused upon the structure of fish gut microbiome providing little knowledge of effects of these factors distinctively and the immense functional potential of the gut microbiome. In this review, we have highlighted the recently gained insights into the diversity and functions of the fish gut microbiome. We have also delved on the current approaches that are being employed to study the fish gut microbiome with an aim to collate all the knowledge gained and make accurate conclusions for their application based perspectives. The literature reviewed indicated that the future research should shift towards functional microbiomics to improve the maximum sustainable yield in aquaculture.
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Affiliation(s)
- Chandni Talwar
- Department of Zoology, University of Delhi, Delhi, 110007 India
| | - Shekhar Nagar
- Department of Zoology, University of Delhi, Delhi, 110007 India
| | - Rup Lal
- Department of Zoology, University of Delhi, Delhi, 110007 India
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Parmar KM, Hathi ZJ, Dafale NA. Control of Multidrug-Resistant Gene Flow in the Environment Through Bacteriophage Intervention. Appl Biochem Biotechnol 2016; 181:1007-1029. [PMID: 27723009 DOI: 10.1007/s12010-016-2265-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2016] [Accepted: 09/23/2016] [Indexed: 02/06/2023]
Abstract
The spread of multidrug-resistant (MDR) bacteria is an emerging threat to the environment and public wellness. Inappropriate use and indiscriminate release of antibiotics in the environment through un-metabolized form create a scenario for the emergence of virulent pathogens and MDR bugs in the surroundings. Mechanisms underlying the spread of resistance include horizontal and vertical gene transfers causing the transmittance of MDR genes packed in different host, which pass across different food webs. Several controlling agents have been used for combating pathogens; however, the use of lytic bacteriophages proves to be one of the most eco-friendly due to their specificity, killing only target bacteria without damaging the indigenous beneficial flora of the habitat. Phages are part of the natural microflora present in different environmental niches and are remarkably stable in the environment. Diverse range of phage products, such as phage enzymes, phage peptides having antimicrobial properties, and phage cocktails also have been used to eradicate pathogens along with whole phages. Recently, the ability of phages to control pathogens has extended from the different areas of medicine, agriculture, aquaculture, food industry, and into the environment. To avoid the arrival of pre-antibiotic epoch, phage intervention proves to be a potential option to eradicate harmful pathogens generated by the MDR gene flow which are uneasy to cure by conventional treatments.
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Affiliation(s)
- Krupa M Parmar
- Environmental Biotechnology and Genomics Division, CSIR-National Environmental Engineering Research Institute, Nagpur, 440020, India
| | - Zubeen J Hathi
- Environmental Biotechnology and Genomics Division, CSIR-National Environmental Engineering Research Institute, Nagpur, 440020, India
| | - Nishant A Dafale
- Environmental Biotechnology and Genomics Division, CSIR-National Environmental Engineering Research Institute, Nagpur, 440020, India.
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Gene Specific Impedimetric Bacterial DNA Sensor for Rheumatic Heart Disease. Indian J Microbiol 2016; 57:112-115. [PMID: 28148987 DOI: 10.1007/s12088-016-0620-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Accepted: 09/14/2016] [Indexed: 12/19/2022] Open
Abstract
An impedimetric mga gene specific DNA sensor was developed by immobilization of single stranded DNA probe onto the screen printed modified gold-dendrimer nanohybrid composite electrode for early and rapid detection of S. pyogenes in human throat swab samples causing rheumatic heart disease. Electrochemical impedance response was measured after hybridization with bacterial single stranded genomic DNA (ssG-DNA) with probe. The sensor was found highly specific to S. pyogenes and can detect as low as 0.01 ng ssDNA in 6 µL sample only in 30 min. The nanohybrid sensor was also tested with non-specific pathogens and characterized by FTIR. An early detection of the pathogen S. pyogenes in human can save damage of mitral and aortic heart valves (rheumatic heart disease) by proper medical care.
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