Papers by Yogesh Nimonkar
iScience
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Microbes and Infection, Nov 1, 2021
Facultative anaerobes are the most common cause of infections in anoxic parts of the human body, ... more Facultative anaerobes are the most common cause of infections in anoxic parts of the human body, including deep wound, vagina, periodontal pockets, gastrointestinal tract, genitourinary tract and lungs. Generally, antibiotic susceptibility tests (AST) for facultative anaerobes are performed under aerobic conditions due to ease of handling and rapid growth. However, variation in susceptibility of facultative anaerobes to antibiotics under aerobic and anaerobic conditions can lead to failure of antibiotic treatment. Our study evaluated the susceptibility of facultative anaerobic microorganisms to antibiotics during growth under anaerobic or aerobic conditions. We compared the resistance patterns of representatives from 15 bacterial genera isolated from the human-gastrointestinal tract against 22 different antibiotics from six classes under aerobic and anaerobic conditions. Preliminary results obtained by a disc diffusion method were verified using minimum inhibitory concentration (MIC) testing. The results demonstrated that 7-strains had a similar pattern of drug resistance under both conditions, while the remaining ten strains had significant differences in resistance patterns between aerobic and anaerobic conditions for at least one antibiotic. We conclude that successful antibiotic therapy for host-associated pathogens requires proper assessment of the oxygen condition of the growth environment and MIC testing of each pathogen under anaerobic and aerobic conditions.
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Journal of Basic Microbiology
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Frontiers in Microbiology
We reported our comparative observations on oligotrophs vs. copiotrophs from a hyper-alkaline and... more We reported our comparative observations on oligotrophs vs. copiotrophs from a hyper-alkaline and hypersaline habitat, Lonar Lake, situated in the Buldhana district of Maharashtra, India. Cell numbers of oligotrophic and copiotrophic microbes from the sediment were enumerated by the three-tube most probable number (MPN) method using an array of nutrient-rich and oligotrophic (≈10–20 mg carbon L−1) media offering simulated natural conditions of pH and salinity. A total of 50 strains from 15 different genera and 30 different species were isolated from the highest positive dilutions of MPN to identify the taxa of oligotrophs and copiotrophic microorganisms dominating in Lonar Lake. We did not get any true oligotrophs due to their adaptation to higher carbon levels during the isolation procedure. On the contrary, several true copiotrophs, which could not adapt and survive on a low-carbon medium, were isolated. It is also observed that changes in medium composition and nutrient level alt...
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Microbiology resource announcements, Jul 18, 2023
The genome of Ignatzschineria sp. strain RMDPL8A was sequenced and analyzed. This draft genome se... more The genome of Ignatzschineria sp. strain RMDPL8A was sequenced and analyzed. This draft genome sequence was 2,175,527 bp long, with a GC content of 45.12% and 1,890 protein coding genes.
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Journal of Biosciences
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Anaerobe
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ABSTRACTConcerning the biological interactions within the gut microbiome, the specialized small m... more ABSTRACTConcerning the biological interactions within the gut microbiome, the specialized small molecules encoded by commensal microbes mediate distinct functional aspects. However, the landscape of antagonistic interactions mediated by specialized strains and their small molecules broadly remains. Here, we sought to evaluate antimicrobial interactions as a defensive contributor to gain new insights into structure-related functions or to bring the therapeutic potential of derived molecules. We elucidated the antagonistic landscape within a collection of 330 human-gut-derived commensal microbial strains cultivated from healthy human subjects. We characterized potential antagonistic strains and found a strain-specific selective inhibition contrary to common antimicrobial drugs that wipe out a broad range of species usually found in environmental microbes. Using functional and genomic approaches for accessing biologically active natural product molecules, we identified significant bios...
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Microbiology Spectrum
In the manuscript, we have developed a novel yet simple and innovative approach to improving the ... more In the manuscript, we have developed a novel yet simple and innovative approach to improving the cultivability of natural microorganisms without sophisticated instrumentation. The method used gradient centrifugation combined with serial dilution (two-dimensional cell separation) to improve taxum recovery from samples.
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Detailed information on genes present in genomic islands in all the strains. (XLSX 137Â kb)
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Detailed information on the unique genes present in the strains under study. (XLSX 29Â kb)
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Detailed information on the accessory genes present in the strains under study. (XLSX 115Â kb)
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Detailed information on the core genes present in the genomes under study (XLSX 57Â kb)
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Figure S1 Features assigned to subsystems from RAST present in all ten Enterococcus strains. Figu... more Figure S1 Features assigned to subsystems from RAST present in all ten Enterococcus strains. Figure S2. (A) Proportion of known, hypothetical and unknown proteins in the group of core, accessory and unique genes (B) Venn Diagram for accessory genome between probiotic, non-pathogenic and pathogenic group. Figure S3. Functional analysis of the accessory genes in COG categories. Table S1. IS elements found in Enterococcus genomes by ISfinder tool. + Present, â Absent. Table S2. Number of Phage elements present in Enterococcus genomes as intact, questionable and incomplete. Table S3. Number of Genomic Islands in Enterococcus genomes. Table S4. Antibiotic Resistance genes found in Enterococcus plasmids as performed by CARD analysis, where + Present and - Absent. Table S5. IS elements found in Enterococcus plasmids by ISfinder tool. + Present, â Absent. Table S6. Table showing the various genes used in the study for generating PCA plot. (DOCX 351Â kb)
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International journal of systematic and evolutionary microbiology, 2014
A yellow Gram-stain-positive, non-motile, non-endospore -forming, spherical endophytic actinobact... more A yellow Gram-stain-positive, non-motile, non-endospore -forming, spherical endophytic actinobacterium, designated strain AE-6(T), was isolated from the inner fleshy leaf tissues of Aloe barbadensis (Aloe vera) collected from Pune, Maharashtra, India. Strain AE-6(T) grew at high salt concentrations [10% (w/v) NaCl], temperatures of 15-41 °C and a pH range of 5-12. It showed highest (99.7%) 16S rRNA gene sequence similarity with Micrococcus yunnanensis YIM 65004(T) followed by Micrococcus luteus NCTC 2665(T) (99.6%) and Micrococcus endophyticus YIM 56238(T) (99.0%). Ribosomal protein profiling by MALDI-TOF/MS also showed it was most closely related to M. yunnanensis YIM 65004(T) and M. luteus NCTC 2665(T). Like other members of the genus Micrococcus, strain AE-6(T) had a high content of branched chain fatty acids (iso-C15:0 and anteiso-C15:0). MK-8(H2) and MK-8 were the predominant isoprenoid quinones. Cell wall analysis showed an 'A2 L-Lys-peptide subunit' type of peptidogly...
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Indian Journal of Microbiology
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Probiotics are live microbial cells or cultures which promote host growth and vigour. The study o... more Probiotics are live microbial cells or cultures which promote host growth and vigour. The study of the role of microorganisms in soil and plant health and plant-microbe interactions has been the area of interest for plant pathologists and soil microbiologists since beginning of microbiology. Plant probiotics have garnered a considerable amount of attention due to success of human probiotics in improved human health. Plant probiotics are microorganisms or group of microorganisms which by virtue of their potential role in improved nutrient acquisition and/or biocontrol activities can promote soil health, plant growth and enhance plant tolernace or immunity against various abiotic and biotic stresses. Plant growth-promoting bacteria (PGPBs) are good examples of plant probiotics which augment crop production by different activities like nitrogen fixation, growth hormones production, and phosphorus- and mineral- solubilization, enhancing water and nutrient use efficiency, and act as bioc...
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Microbes are the provider of ecosystem services and act as a key component for environmental sust... more Microbes are the provider of ecosystem services and act as a key component for environmental sustainability and human health. It is believed that the cultivation and preservation of new taxa with innovative traits is essential for biotechnological growth even in the era of omics-driven science. Cultivation and preservation of entire microbial diversity is impossible even with extra efforts and use of novel high-throughput cultivation approaches. Therefore, development of protocols for community and habitat preservation should be priorities. In current article, we discussed about importance of microbes for biotechnological growth and their preservation for future reference research and application. In addition we also incorporated the loopholes of current preservation research and tried to incorporate the suggestion to fill the existing gaps. We tried to give a brief overview of different preservation methods used for preservation of bacteria and fungi and also incorporated the conce...
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Facultative anaerobes are the most common cause of infections in anoxic parts of the human body, ... more Facultative anaerobes are the most common cause of infections in anoxic parts of the human body, including deep wound, vagina, periodontal pockets, gastrointestinal tract, genitourinary tract and lungs. Generally, antibiotic susceptibility tests (AST) for facultative anaerobes are performed under aerobic conditions due to ease of handling and rapid growth. However, variation in susceptibility of facultative anaerobes to antibiotics under aerobic and anaerobic conditions can lead to failure of antibiotic treatment. Our study evaluated the susceptibility of facultative anaerobic microorganisms to antibiotics during growth under anaerobic or aerobic conditions. We compared the resistance patterns of representatives from 15 bacterial genera isolated from the human-gastrointestinal tract against 22 different antibiotics from six classes under aerobic and anaerobic conditions. Preliminary results obtained by a disc diffusion method were verified using minimum inhibitory concentration (MIC...
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Papers by Yogesh Nimonkar