Publications by authors named "Diptaraj Chaudhari"

10 Publications

  • Page 1 of 1

Benchmarking of 16S rRNA gene databases using known strain sequences.

Bioinformation 2021 31;17(3):377-391. Epub 2021 Mar 31.

Symbiosis School of Biological Sciences (SSBS), Symbiosis International (Deemed University), Pune, India.

16S rRNA gene analysis is the most convenient and robust method for microbiome studies. Inaccurate taxonomic assignment of bacterial strains could have deleterious effects as all downstream analyses rely heavily on the accurate assessment of microbial taxonomy. The use of mock communities to check the reliability of the results has been suggested. However, often the mock communities used in most of the studies represent only a small fraction of taxa and are used mostly as validation of sequencing run to estimate sequencing artifacts. Moreover, a large number of databases and tools available for classification and taxonomic assignment of the 16S rRNA gene make it challenging to select the best-suited method for a particular dataset. In the present study, we used authentic and validly published 16S rRNA gene type strain sequences (full length, V3-V4 region) and analyzed them using a widely used QIIME pipeline along with different parameters of OTU clustering and QIIME compatible databases. Data Analysis Measures (DAM) revealed a high discrepancy in ratifying the taxonomy at different taxonomic hierarchies. Beta diversity analysis showed clear segregation of different DAMs. Limited differences were observed in reference data set analysis using partial (V3-V4) and full-length 16S rRNA gene sequences, which signify the reliability of partial 16S rRNA gene sequences in microbiome studies. Our analysis also highlights common discrepancies observed at various taxonomic levels using various methods and databases.
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http://dx.doi.org/10.6026/97320630017377DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8131573PMC
March 2021

Restoration of dysbiotic human gut microbiome for homeostasis.

Life Sci 2021 Aug 17;278:119622. Epub 2021 May 17.

Symbiosis School of Biological Sciences (SSBS), Symbiosis International (Deemed University), Pune, India. Electronic address:

The human microbiome is a complex and dynamic ecosystem, and the imbalance of its microbial community structure from the normal state is termed dysbiosis. The dysbiotic gut microbiome has been proved to be related to several pathological conditions like Inflammatory Bowel Disease (IBD), Irritable Bowel Syndrome (IBS), Colorectal Cancer (CRC), etc., and several other extra-intestinal conditions like Type 1 & 2 diabetes, obesity, etc. The complex gut microbial ecosystem starts to build before the birth of an individual. It is known to get affected by several factors such as birth mode, individual lifestyle, dietary practices, medications, and antibiotics. A dysbiotic microbiome can potentially hamper host homeostasis due to its role in immune modulation, metabolism, nutrient synthesis, etc. Restoration of the dysbiotic gut microbiome has emerged as a promising aid and a better therapeutic approach. Several approaches have been investigated to achieve this goal, including prebiotics and probiotics, Fecal Microbiota Transplantation (FMT), extracellular vesicles, immune modulation, microbial metabolites, dietary interventions, and phages. This review discusses the various factors that influence the human microbiome with respect to their cause-effect relationship and the effect of gut microbiome compositional changes on the brain through the gut-brain axis. We also discuss the practices used globally for gut microbiome restoration purposes, along with their effectiveness.
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http://dx.doi.org/10.1016/j.lfs.2021.119622DOI Listing
August 2021

Contrasting Composition, Diversity and Predictive Metabolic Potential of the Rhizobacterial Microbiomes Associated with Native and Invasive Prosopis Congeners.

Curr Microbiol 2021 May 10;78(5):2051-2060. Epub 2021 Apr 10.

National Centre for Cell Sciences, Pune University Campus, Ganeskhind, Pune, 411007, India.

Invasive plants are known to alter the soil microbial communities; however, the effects of co-occurring native and invasive congeners on the soil bacterial diversity and their predictive metabolic profiles are not known. Here, we compared the rhizosphere bacterial communities of invasive Prosopis juliflora and its native congener Prosopis cineraria using high-throughput sequencing of the 16S rRNA gene. Unweighted Pair Group Method with Arithmetic mean (UPGMA) based dendrogram revealed significant variation in the communities of these co-occurring Prosopis species. Additionally, Canonical Correspondence Analysis (CCA) based on microbial communities in addition to the soil physiochemical parameters viz. soil pH, electrical conductivity, moisture content and sampling depth showed ~ 80% of the variation in bacterial communities of the rhizosphere and control soil. We observed that Proteobacteria was the predominant phylum of P. juliflora rhizosphere and the control soil, while P. cineraria rhizosphere was dominated by Cyanobacteria. Notably, the invasive P. juliflora rhizosphere showed an enhanced abundance of bacterial phyla like Actinobacteria, Chloroflexi, Firmicutes and Acidobacteria compared to the native P. cineraria as well as the control soil. Predictive metagenomics revealed that the bacterial communities of the P. juliflora rhizosphere had a higher abundance of pathways involved in antimicrobial biosynthesis and degradation, suggesting probable exposure to enemy attack and an active response mechanism to counter it as compared to native P. cineraria. Interestingly, the higher antimicrobial biosynthesis predicted in the invasive rhizosphere microbiome is further corroborated by the fact that the bacterial isolates purified from the rhizosphere of P. juliflora belonged to genera like Streptomyces, Isoptericola and Brevibacterium from the phylum Actinobacteria, which are widely reported for their antibiotic production ability. In conclusion, our results demonstrate that the co-occurring native and invasive Prosopis species have significantly different rhizosphere bacterial communities in terms of composition, diversity and their predictive metabolic potentials. In addition, the rhizosphere microbiome of invasive Prosopis proffers it a fitness advantage and influences invasion success of the species.
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http://dx.doi.org/10.1007/s00284-021-02473-1DOI Listing
May 2021

Bacterial Communities Associated with the Biofilms Formed in High-Altitude Brackish Water Pangong Tso Located in the Himalayan Plateau.

Curr Microbiol 2020 Dec 20;77(12):4072-4084. Epub 2020 Oct 20.

National Center for Microbial Resource-National Center for Cell Science, Pune, 411021, India.

Pangong Tso is a long and narrow lake situated at an altitude of ~ 4266 m amsl in the Himalayan Plateau on the side of the India/China border. Biofilm has been observed in a small area near the shore of Pangong Tso. Bacterial communities of the lake sediment, water and biofilms were studied using amplicon sequencing of V3-V4 region of the 16S rRNA gene. The standard QIIME pipeline was used for analysis. The metabolic potential of the community was predicted using functional prediction tool Tax4Fun. Bacterial phyla Proteobacteria, followed by Bacteroidetes, Acidobacteria, Planctomycetes, Actinobacteria, and Firmicutes, were found to be dominant across these samples. Shannon's and Simpson's alpha diversity analysis revealed that sediment communities are the most diverse, and water communities are the least diverse. Principal Coordinates based beta diversity analysis showed significant variation in the bacterial communities of the water, sediment and biofilm samples. Bacterial phyla Verrucomicrobia, Deinococcus-Thermus and Cyanobacteria were explicitly enriched in the biofilm samples. Predictive functional profiling of these bacterial communities showed a higher abundance of genes involved in photosynthesis, biosynthesis of secondary metabolites, carbon fixation in photosynthetic organisms and glyoxylate and dicarboxylate metabolism in the biofilm sample. In conclusion, the Pangong Tso bacterial communities are quite similar to other saline and low-temperature lakes in the Tibetan Plateau. Bacterial community structure of the biofilm samples was significantly different from that of the water and sediment samples and enrichment of saprophytic communities was observed in the biofilm samples, indicating an important succession event in this high-altitude lake.
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http://dx.doi.org/10.1007/s00284-020-02244-4DOI Listing
December 2020

Rhizobium indicum sp. nov., isolated from root nodules of pea (Pisum sativum) cultivated in the Indian trans-Himalayas.

Syst Appl Microbiol 2020 Sep 30;43(5):126127. Epub 2020 Jul 30.

National Centre for Microbial Resource, National Centre for Cell Science, Pune, Maharashtra 411007, India.

Three strains of rhizobia isolated from effective root nodules of pea (Pisum sativum L.) collected from the Indian trans-Himalayas were characterized using 16S rRNA, atpD and recA genes. Phylogeny of the 16S rRNA genes revealed that the newly isolated strains were members of the genus Rhizobium with ≥99.9% sequence similarity to the members within the "Rhizobium leguminosarum" group. Phylogenetic analyses based on the concatenated sequences of atpD and recA gene, and 92 core genes extracted from the genome sequences indicated that strains JKLM 12A2 and JKLM 13E are grouped as a separate clade closely related to R. laguerreae FB206. In contrast, the strain JKLM 19E was placed with "R. hidalgonense" FH14. Whole-genome average nucleotide identity (ANI) values were 97.6% within strains JKLM 12A2 and JKLM 13E, and less than 94% with closely related species. The digital DNA-DNA hybridization (dDDH) values were 81.45 within the two strains and less than 54.8% to closely related species. The major cellular fatty acids were C in summed feature 8, C/C in summed feature 2, and C. The DNA G+C content of JKLM 12A2 and JKLM 13E was 60.8mol%. The data on genomic, chemotaxonomic, and phenotypic characteristics indicates that the strains JKLM 12A2 and JKLM 13E represent a novel species, Rhizobium indicum sp. nov. The type strain is JKLM 12A2 (= MCC 3961=KACC 21380=JCM 33658). However, the strain JKLM 19E represents a member of "R. hidalgonense" and the symbiovar viciae.
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http://dx.doi.org/10.1016/j.syapm.2020.126127DOI Listing
September 2020

Pea ( l.) Plant Shapes Its Rhizosphere Microbiome for Nutrient Uptake and Stress Amelioration in Acidic Soils of the North-East Region of India.

Front Microbiol 2020 3;11:968. Epub 2020 Jun 3.

National Center for Microbial Resource, National Center for Cell Science, Pune, India.

Rhizosphere microbiome significantly influences plant growth and productivity. Legume crops such as pea have often been used as a rotation crop along with rice cultivation in long-term conservation agriculture experiments in the acidic soils of the northeast region of India. It is essential to understand how the pea plant influences the soil communities and shapes its rhizosphere microbiome. It is also expected that the long-term application of nutrients and tillage practices may also have a lasting effect on the rhizosphere and soil communities. In this study, we estimated the bacterial communities by 16S rRNA gene amplicon sequencing of pea rhizosphere and bulk soils from a long-term experiment with multiple nutrient management practices and different tillage history. We also used Tax4Fun to predict the functions of bacterial communities. Quantitative polymerase chain reaction (qPCR) was used to estimate the abundance of total bacterial and members of Firmicutes in the rhizosphere and bulk soils. The results showed that bacterial diversity was significantly higher in the rhizosphere in comparison to bulk soils. A higher abundance of Proteobacteria was recorded in the rhizosphere, whereas the bulk soils have higher proportions of Firmicutes. At the genus level, proportions of , , , , , and were significantly higher in the rhizosphere. At the same time, , , and were more abundant in the bulk soils. Higher abundance of genes reported for plant growth promotion and several other genes, including iron complex outer membrane receptor, cobalt-zinc-cadmium resistance, sigma-70 factor, and ribonuclease E, was predicted in the rhizosphere samples in comparison to bulk soils, indicating that the pea plants shape their rhizosphere microbiome, plausibly to meet its requirements for nutrient uptake and stress amelioration.
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http://dx.doi.org/10.3389/fmicb.2020.00968DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7283456PMC
June 2020

sp. nov., isolated from the surface of a tomato.

Int J Syst Evol Microbiol 2020 May;70(5):3278-3286

National Centre for Microbial Resource, National Centre for Cell Science, Pune 411007, India.

A novel bacterial strain, designated TOUT106, was isolated from the surface of a tomato. The cells were rod-shaped, Gram-negative, encapsulated and non-motile. Strain TOUT106 grows best at 28 °C and pH 7.0 and can tolerate up to 2 % (w/v) NaCl. Based on 16S rRNA gene phylogeny, strain TOUT106 was placed close to the clade, with close similarity to subsp. strain NCTC 8297 (98.42 %). Results of genome-based phylogenetic analysis revealed that strain TOUT106 is placed well in the clade, by forming a distinct branch with DSM25444, NCTC132727, 06D021 and SB6412. The genomic DNA G+C content of strain TOUT106 is 53.53 mol%. The average nucleotide identity values of TOUT106 were less than 86.5 % with closely related members of the family . The major fatty acids of strain TOUT106 were C, C cyclo, C 3OH/C iso, C, C cyclo ω8, C ω6/C ω7, C and C ω7/C ω6. Strain TOUT106 showed differences in physiological, phenotypic and protein profiles by MALDI-TOF MS compared to its closest relatives. Based on the results of phenotypic, chemotaxonomic and phylogenetic analyses, strain TOUT106 could be distinguished from the recognized species of the genus . It is suggested to represent a novel species of this genus, for which the name sp. nov. is proposed. The type strain is TOUT106 (=MCC 2901=KACC 21384=JCM 33718).
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http://dx.doi.org/10.1099/ijsem.0.004168DOI Listing
May 2020

Gut, oral and skin microbiome of Indian patrilineal families reveal perceptible association with age.

Sci Rep 2020 03 30;10(1):5685. Epub 2020 Mar 30.

National Centre for Microbial Resource, National Centre for Cell Science, Central Tower, Sai Trinity Building Garware Circle, Sutarwadi, Pashan, Pune, India.

The human microbiome plays a key role in maintaining host homeostasis and is influenced by age, geography, diet, and other factors. Traditionally, India has an established convention of extended family arrangements wherein three or more generations, bound by genetic relatedness, stay in the same household. In the present study, we have utilized this unique family arrangement to understand the association of age with the microbiome. We characterized stool, oral and skin microbiome of 54 healthy individuals from six joint families by 16S rRNA gene-based metagenomics. In total, 69 (1.03%), 293 (2.68%) and 190 (8.66%) differentially abundant OTUs were detected across three generations in the gut, skin and oral microbiome, respectively. Age-associated changes in the gut and oral microbiome of patrilineal families showed positive correlations in the abundance of phyla Proteobacteria and Fusobacteria, respectively. Genera Treponema and Fusobacterium showed a positive correlation with age while Granulicatella and Streptococcus showed a negative correlation with age in the oral microbiome. Members of genus Prevotella illustrated high abundance and prevalence as a core OTUs in the gut and oral microbiome. In conclusion, this study highlights that precise and perceptible association of age with microbiome can be drawn when other causal factors are kept constant.
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http://dx.doi.org/10.1038/s41598-020-62195-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7105498PMC
March 2020

Understanding the association between the human gut, oral and skin microbiome and the Ayurvedic concept of prakriti.

J Biosci 2019 Oct;44(5)

National Centre for Microbial Resource, National Centre for Cell Science, Central Tower, Sai Trinity Building Garware Circle, Sutarwadi, Pashan, Pune, India.

Ayurveda is one of the ancient systems of medicine which is widely practised as a personalized scientific approach towards the general wellness. Ayurvedic prakriti is broadly defined as the phenotypes which are determined on the basis of physical, psychological and physiological traits irrespective of their social, ethnic, dietary and geographical stature. Prakriti is the constitution of a person, which comprises vata, pitta, and kapha and is a key determinant of how one individual is different from the other. Human microbiome is considered the 'latest discovered' human organ and microbiome research reiterates the fundamental principles of Ayurveda for creating a healthy gut environment by maintaining the individual-specific microbiome. Hence, it is important to understand the association of human microbiome with the Ayurvedic prakriti of an individual. Here, we provide a comprehensive analysis of human microbiome from the gut, oral and skin samples of healthy individuals (n=18) by 16S rRNA gene-based metagenomics using standard QIIME pipeline. In the three different prakriti samples differential abundance of Bacteroides, Desulfovibrio, Parabacteroides, Slackia, and Succinivibrio was observed in the gut microbiome. Analysis also revealed prakriti-specific presence of Mogibacterium, Propionibacterium, Pyramidobacter, Rhodococcus in the kapha prakriti individuals Planomicrobium, Hyphomicrobium, Novosphingobium in the pitta prakriti individuals and Carnobacterium, Robiginitalea, Cetobacterium, Psychrobacter in the vata prakriti individuals. Similarly, the oral and skin microbiome also revealed presence of prakriti-specific differential abundance of diverse bacterial genera. Prakriti-specific presence of bacterial taxa was recorded and only 42% microbiome in the oral samples and 52% microbiome in the skin samples were shared. Bacteria known for preventing gut inflammation by digesting the resistant starch were abundant in the pitta prakriti individuals, who are more prone to develop gut-inflammation-related disorders. In summary, human gut, oral and skin microbiome showed presence or high abundance of few bacterial taxa across three prakriti types, suggesting their specific physiological importance.
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October 2019

Cultivable Microbial Diversity Associated With Cellular Phones.

Front Microbiol 2018 7;9:1229. Epub 2018 Jun 7.

National Centre for Microbial Resource, National Centre for Cell Science, Pune, India.

A substantial majority of global population owns cellular phones independently to demographic factors like age, economic status, and educational attainment. In this study, we investigated the diversity of microorganisms associated with cellular phones of 27 individuals using cultivation-based methods. Cellular phones were sampled using cotton swabs and a total of 554 isolates representing different morphotypes were obtained on four growth media. Matrix-assisted laser desorption ionization time of flight (MALDI-TOF) mass spectrometry could generate protein profiles for 527 isolates and species-level identification was obtained for 415 isolates. A dendrogram was constructed based on the protein profiles of the remaining isolates, to group 112 isolates under 39 different proteotypes. The representative strains of each group were selected for 16S rRNA gene and ITS region sequencing based identification. , , , and were the most frequently encountered bacteria, and , , , and were in case of fungi. At species-level the prevalence of , , , , , and was observed, most of these species are commensal microorganisms of human skin. UPGMA dendrogram and PCoA biplot generated based on the microbial communities associated with all cellular phones exhibited build-up of specific communities on cellular phones and the prevalence of objectionable microorganisms in some of the cellular phones can be attributed to the poor hygiene and sanitary practices. The study also revealed the impact of MALDI-TOF MS spectral quality on the identification results. Overall MALDI-TOF appears a powerful tool for routine microbial identification and de-replication of microorganisms. Quality filtering of MALDI-TOF MS spectrum, development of better sample processing methods and enriching the spectral database will improve the role of MALDI-TOF MS in microbial identifications.
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http://dx.doi.org/10.3389/fmicb.2018.01229DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6000418PMC
June 2018
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