10 results on '"Prachi Karodi"'
Search Results
2. Alkalihalobacterium elongatum gen. nov. sp. nov.: An Antibiotic-Producing Bacterium Isolated From Lonar Lake and Reclassification of the Genus Alkalihalobacillus Into Seven Novel Genera
- Author
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Amaraja Joshi, Sonia Thite, Prachi Karodi, Neetha Joseph, and Tushar Lodha
- Subjects
alkaliphilic bacteria ,Alkalihalobacterium ,Alkalihalobacillus ,taxogenomic ,Lonar lake ,Shouchella ,Microbiology ,QR1-502 - Abstract
A Gram-stain positive, long, rod-shaped, motile, and spore-forming bacterium (MEB199T) was isolated from a sediment sample collected from Lonar Lake, India. The strain was oxidase and catalase positive. The strain grew optimally at pH 10, NaCl concentration of 3.5% at 37°C. The major fatty acids were iso-C15:0, iso-C16:0, anteiso-C15:0, and iso-C17:0. The peptidoglycan contained meso-diaminopimelic acid (meso-DAP). Phosphatidylethanolamine, diphosphatidylglycerol, and phosphatidylglycerol were the major polar lipids of MEB199T. Phylogenetic analysis based on 16S rRNA gene sequence showed that strain MEB199T belonged to the family Bacillaceae and exhibited a distinctive position among the members of the genus Alkalihalobacillus (Ahb.). Strain MEB199T shared the highest 16S rRNA gene sequence similarity with Alkalihalobacillus alkalinitrilicus ANL-iso4T (98.36%), whereas with type species Ahb. alcalophilus DSM 485T, it is 94.91%, indicating that strain MEB199T is distinctly related to the genus Alkalihalobacillus. The G + C content of genomic DNA was 36.47 mol%. The digital DNA–DNA hybridization (dDDH) (23.6%) and average nucleotide identity (ANI) (81%) values between strain MEB199T and Ahb. alkalinitrilicus ANL-iso4T confirmed the novelty of this new species. The pairwise identity based on the 16S rRNA gene sequence between the species of genus Alkalihalobacillus ranges from 87.4 to 99.81% indicating the heterogeneity in the genus. The different phylogenetic analysis based on the genome showed that the members of the genus Alkalihalobacillus separated into eight distinct clades. The intra-clade average amino acid identity (AAI) and percentage of conserved proteins (POCP) range from 52 to 68% and 37 to 59%, respectively, which are interspersed on the intra-genera cutoff values; therefore, we reassess the taxonomy of genus Alkalihalobacillus. The phenotypic analysis also corroborated the differentiation between these clades. Based on the phylogenetic analysis, genomic indices, and phenotypic traits, we propose the reclassification of the genus Alkalihalobacillus into seven new genera for which the names Alkalihalobacterium gen. nov., Halalkalibacterium gen. nov., Halalkalibacter gen. nov., Shouchella gen. nov., Pseudalkalibacillus gen. nov., Alkalicoccobacillus gen. nov., and Alkalihalophilus gen. nov. are proposed and provide an emended description of Alkalihalobacillus sensu stricto. Also, we propose the Ahb. okuhidensis as a heterotypic synonym of Alkalihalobacillus halodurans. Based on the polyphasic taxonomic analysis, strain MEB199T represents a novel species of newly proposed genus for which the name Alkalihalobacterium elongatum gen. nov. sp. nov. is proposed. The type strain is MEB199T (= MCC 2982T, = JCM 33704T, = NBRC 114256T, = CGMCC 1.17254T).
- Published
- 2021
- Full Text
- View/download PDF
3. Correction to: Paenibacillus albicereus sp. nov. and Niallia alba sp. nov., isolated from digestive syrup
- Author
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Vipool Thorat, Kiran Kirdat, Bhavesh Tiwarekar, Priyanka Dhanavade, Prachi Karodi, Yogesh Shouche, Shivaji Sathe, Tushar Lodha, and Amit Yadav
- Subjects
Genetics ,General Medicine ,Molecular Biology ,Biochemistry ,Microbiology - Published
- 2023
- Full Text
- View/download PDF
4. Description and genomic insights into a multidrug resistant novel bacterium Savagea serpentis sp. nov., isolated from the scats of a vine snake (Ahaetulla nasuta)
- Author
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Yogita Lugani, Pramod C. Mane, Vikas S. Patil, Shrikant Pawar, Venkata Ramana Vemuluri, Prachi Karodi, Yogesh S. Shouche, Priyam Mehrotra, and Ravindra D. Chaudhari
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0303 health sciences ,Strain (chemistry) ,Phylogenetic tree ,030306 microbiology ,Virulence ,Ahaetulla nasuta ,General Medicine ,Biology ,16S ribosomal RNA ,biology.organism_classification ,Microbiology ,03 medical and health sciences ,chemistry.chemical_compound ,chemistry ,Peptidoglycan ,Molecular Biology ,Gene ,Bacteria ,030304 developmental biology - Abstract
Two Gram-stain positive, endospore forming, non-motile, rod shaped bacterial strains SN6T and SN6b were isolated from scats of a mildly venomous vine snake (Ahaetulla nasuta). Strains were phenotypically resistant to multiple antibiotics of four different classes i.e. aminoglycosides, β-lactams, fluoroquinolones and sulphonamides. Cells of both the strains were catalase positive and oxidase negative. Phylogenetic analysis based on 16S rRNA gene sequence analysis of these two strains showed closest similarity (99.2% and 99.3%) with Savagea faecisuis Con12T, the only species of the genus Savagea and ≤ 94.9% with the species of other closest genera of the family Planococcaceae. The 16S rRNA gene sequence similarity (99%), DNA-DNA relatedness (95%) and similar phenotypic characteristics between the strains SN6T and SN6b revealed their phylogenetic affiliation to the same species. Hence, strain SN6b is an additional strain of the type strain SN6T. DNA-DNA relatedness of strain SN6T with S. faecisuis Con12T was 32.8%. Predominant fatty acids were iso-C15:0 (32.0%), iso-C16:1 ω11c (19.2%) and iso-C17:1 ω10c (12.1%). MK-6 (100%) was the only respiratory quinone of strain SN6T. Diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine were the major polar lipids. Cell wall peptidoglycan was A4α; L-Lys-Gly-D-Glu type. The DNA G + C content (mol%) of SN6T was 40.8. Whole genome sequence of SN6T consisted of 26,37,389 base pairs in length with 2667 annotated genes, out of which 1021 corresponds to hypothetical proteins and 1646 with functional assignments including antibiotic resistance, multidrug resistance efflux pumps, invasion and virulence factors. Comparative polyphasic study of the strains SN6T, SN6b and S. faecisuis Con12T elucidated the differentiating characteristics which led to describing strain SN6T and SN6b as a novel species of the genus Savagea for which the name Savagea serpentis sp. nov is proposed. The type strain of Savagea serpentis is SN6T (= KCTC 33546T = CCUG 6786T).
- Published
- 2021
- Full Text
- View/download PDF
5. Alkalihalobacterium elongatum gen. nov. sp. nov.: An Antibiotic-Producing Bacterium Isolated From Lonar Lake and Reclassification of the Genus Alkalihalobacillus Into Seven Novel Genera
- Author
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Sonia Thite, Amaraja Joshi, Tushar Lodha, Prachi Karodi, and Neetha Joseph
- Subjects
Microbiology (medical) ,Phylogenetic tree ,taxogenomic ,Strain (biology) ,Shouchella ,Halalkalibacter ,Biology ,Alkalihalobacillus ,16S ribosomal RNA ,Lonar lake ,Microbiology ,QR1-502 ,alkaliphilic bacteria ,Type species ,genomic DNA ,Synonym (taxonomy) ,Halalkalibacterium ,Genus ,Botany ,Taxonomy (biology) ,Alkalihalobacterium ,Original Research - Abstract
A Gram-stain positive, long, rod-shaped, motile, and spore-forming bacterium (MEB199T) was isolated from a sediment sample collected from Lonar Lake, India. The strain was oxidase and catalase positive. The strain grew optimally at pH 10, NaCl concentration of 3.5% at 37°C. The major fatty acids were iso-C15:0, iso-C16:0, anteiso-C15:0, and iso-C17:0. The peptidoglycan contained meso-diaminopimelic acid (meso-DAP). Phosphatidylethanolamine, diphosphatidylglycerol, and phosphatidylglycerol were the major polar lipids of MEB199T. Phylogenetic analysis based on 16S rRNA gene sequence showed that strain MEB199T belonged to the family Bacillaceae and exhibited a distinctive position among the members of the genus Alkalihalobacillus (Ahb.). Strain MEB199T shared the highest 16S rRNA gene sequence similarity with Alkalihalobacillus alkalinitrilicus ANL-iso4T (98.36%), whereas with type species Ahb. alcalophilus DSM 485T, it is 94.91%, indicating that strain MEB199T is distinctly related to the genus Alkalihalobacillus. The G + C content of genomic DNA was 36.47 mol%. The digital DNA–DNA hybridization (dDDH) (23.6%) and average nucleotide identity (ANI) (81%) values between strain MEB199T and Ahb. alkalinitrilicus ANL-iso4T confirmed the novelty of this new species. The pairwise identity based on the 16S rRNA gene sequence between the species of genus Alkalihalobacillus ranges from 87.4 to 99.81% indicating the heterogeneity in the genus. The different phylogenetic analysis based on the genome showed that the members of the genus Alkalihalobacillus separated into eight distinct clades. The intra-clade average amino acid identity (AAI) and percentage of conserved proteins (POCP) range from 52 to 68% and 37 to 59%, respectively, which are interspersed on the intra-genera cutoff values; therefore, we reassess the taxonomy of genus Alkalihalobacillus. The phenotypic analysis also corroborated the differentiation between these clades. Based on the phylogenetic analysis, genomic indices, and phenotypic traits, we propose the reclassification of the genus Alkalihalobacillus into seven new genera for which the names Alkalihalobacterium gen. nov., Halalkalibacterium gen. nov., Halalkalibacter gen. nov., Shouchella gen. nov., Pseudalkalibacillus gen. nov., Alkalicoccobacillus gen. nov., and Alkalihalophilus gen. nov. are proposed and provide an emended description of Alkalihalobacillus sensu stricto. Also, we propose the Ahb. okuhidensis as a heterotypic synonym of Alkalihalobacillus halodurans. Based on the polyphasic taxonomic analysis, strain MEB199T represents a novel species of newly proposed genus for which the name Alkalihalobacterium elongatum gen. nov. sp. nov. is proposed. The type strain is MEB199T (= MCC 2982T, = JCM 33704T, = NBRC 114256T, = CGMCC 1.17254T).
- Published
- 2021
6. Description of Paenibacillus albicerus sp. nov. and Niallia alba sp. nov., isolated from digestive syrup
- Author
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Priyanka Dhanavade, Prachi Karodi, Yogesh S. Shouche, Kiran Kirdat, Shivaji Sathe, Tushar Lodha, Amit Yadav, Bhavesh Tiwarekar, and Vipool Thorat
- Subjects
Paenibacillus ,biology ,Botany ,biology.organism_classification - Abstract
Two aerobic, Gram-stain variable, catalase and oxidase-positive, spore-forming, motile rods of strain UniB2T and UniB3T, were isolated from digestive syrup containing fungal diastase (10 mg/ml), pepsin (2 mg/ml) and sugar base containing polyethene glycol. Based on 16S rRNA gene sequence analysis, strain UniB2T has the highest sequence similarity with Paenibacillus humicus NBRC 102415T (98.30 %) and strain UniB3T showed the highest sequence similarity with Niallia circulans DSM 11T (98.95 %). The DNA G+C content of UniB2T was 63.74 mol %. The dDDH and ANI values between the strain UniB2T and its phylogenetically close relative were T were C16:00 (13.9 %), C15:0 anteiso (39.7 %), C17:0 anteiso (15.5 %). The DNA G+C content of UniB3T was 35.6 mol%. The dDDH and ANI values between the strain UniB3T and its close relatives were T were C16:0 (13.54 %), C15:0 anteiso (40.09 %) and C17:0 anteiso (16.03 %). Major polar lipids for both strains were Diphosphotidylglycerol and Phosphatidylethanolamine. Additionally, both the strains showed unique carbon utilization and assimilation pattern that differentiated them from their phylogenetically related neighbours. These phenotypic, genotypic and chemotaxonomic characters indicated the strains UniB2T and UniB3T represent two novel species for which the names Paenibacillus albicerus sp. nov. (Type strain UniB2T =MCC 3997T =KCTC 43095T =JCM34513T) and Niallia alba sp. nov. (Type strain UniB3T = MCC 3998T =KCTC 43235T =JCM 34492T) are proposed.
- Published
- 2021
- Full Text
- View/download PDF
7. Paenibacillus albicereus sp. nov. and Niallia alba sp. nov., isolated from digestive syrup
- Author
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Vipool Thorat, Kiran Kirdat, Bhavesh Tiwarekar, Priyanka Dhanavade, Prachi Karodi, Yogesh Shouche, Shivaji Sathe, Tushar Lodha, and Amit Yadav
- Subjects
DNA, Bacterial ,RNA, Ribosomal, 16S ,Fatty Acids ,Genetics ,Vitamin K 2 ,General Medicine ,Sequence Analysis, DNA ,Molecular Biology ,Biochemistry ,Microbiology ,Paenibacillus ,Phylogeny ,Bacterial Typing Techniques - Abstract
Two aerobic, Gram-stain variable, catalase-positive and oxidase-negative rods named strain UniB2
- Published
- 2021
8. Classification of uncultivated anammox bacteria and Candidatus Uabimicrobium into new classes and provisional nomenclature as Candidatus Brocadiia classis nov. and Candidatus Uabimicrobiia classis nov. of the phylum Planctomycetes and novel family Candidatus Scalinduaceae fam. nov to accommodate the genus Candidatus Scalindua
- Author
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Tushar Lodha, Prachi Karodi, and Simran Narvekar
- Subjects
DNA, Bacterial ,Phylogenetic tree ,Bacteria ,Biology ,biology.organism_classification ,Applied Microbiology and Biotechnology ,Microbiology ,Genus ,Anammox ,Evolutionary biology ,RNA, Ribosomal, 16S ,Candidatus ,Scalindua ,Clade ,Nomenclature ,Oxidation-Reduction ,Ecology, Evolution, Behavior and Systematics ,Phylogeny - Abstract
The phylum Planctomycetes is metabolically unique group of bacteria divided in two classes Planctomycetia and Phycisphaerae. Anaerobic ammonia-oxidizing (anammox) bacteria are the uncultured representatives of the phylum Planctomycetes. Anammox bacterial genera are placed in the family Candidatus (Ca.) Brocadiaceae of the order Ca. Brocadiales, assigned to the class Planctomycetia. Phylogenetic analysis, showed that the anammox bacteria and Ca. Uabimicrobium form a divergent clade from the rest of the cultured representatives of the phylum Planctomycetes. The phylogenetic study, pairwise distance and Average Amino acid Identity (AAI) showed that anammox bacteria don’t belong to the classes Planctomycetia and Phycisphaerae. Anammox bacteria and Ca. Uabimicrobium form a deep-branching third clade in the phylogenetic analysis indicating that it is the most ancient third class within the phylum Planctomycetes. Phenotypic characters also separate anammox bacteria from classes Planctomycetia and Phycisphaerae. Therefore, based on phenotypic, phylogenetic, pairwise distance, AAI and phylogenomic analysis we propose a novel class Ca. Brocadiia to accommodate the order Ca. Brocadiales of anammox bacteria except Ca. Anammoximicrobium. Genera Ca. Jettenia, Ca. Anammoxoglobus, Ca. Kuenenia and Ca. Brocadia show their phylogenetic affiliation to the family Ca. Brocadiaceae. However, Ca. Scalindua showed a distant relationship with the family Ca. Brocadiaceae. Therefore, we suggest the exclusion of the genus Ca. Scalindua from the family Ca. Brocadiaceae; and propose its inclusion under a novel family with a provisional name as Ca. Scalinduaceae fam. nov. Similarly, Ca. Uabimicrobium amporphum showed distinct phylogenetic affiliation, therefore we propose a novel class Ca. Uabimicrobiia classis nov. to accommodate the genus Ca. Uabimicrobium.
- Published
- 2021
9. Subsaxibacter sediminis sp. nov., isolated from Arctic glacial sediment and emended description of the genus Subsaxibacter
- Author
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Swapnil Kajale, Sisinthy Shivaji, Praveen Rahi, Prachi Karodi, Guang-Da Feng, Yogesh S. Shouche, Vishal Thite, Kunal Jani, Venkata Ramana Vemuluri, Hong-Hui Zhu, and Avinash Sharma
- Subjects
DNA, Bacterial ,0301 basic medicine ,Geologic Sediments ,Spermidine ,Microbiology ,Svalbard ,03 medical and health sciences ,Genus ,RNA, Ribosomal, 16S ,Botany ,Extremophile ,Ice Cover ,Psychrophile ,Phylogeny ,Ecology, Evolution, Behavior and Systematics ,Base Composition ,Phylogenetic tree ,biology ,Strain (chemistry) ,Arctic Regions ,Pigmentation ,Phosphatidylethanolamines ,Fatty Acids ,Nucleic Acid Hybridization ,Vitamin K 2 ,Sequence Analysis, DNA ,General Medicine ,biology.organism_classification ,16S ribosomal RNA ,Bacterial Typing Techniques ,030104 developmental biology ,Arctic ,Flavobacteriaceae ,Bacteria - Abstract
A Gram-stain-negative, yellowish-orange pigmented, rod-shaped, motile bacterium, designated strain ARC111T, was isolated from sediment of Arctic permafrost at Midtre Lovenbreen glacier, Svalbard. 16S rRNA gene based identification of strain ARC111T demonstrated highest sequence similarities to Subsaxibacter broadyi P7T (97.8 %) and Subsaxibacter arcticus JCM30334T (97.5 %) and ≤95.2 % with all other members of the family Flavobacteriaceae . Phylogenetic analysis revealed the distinct positioning of strain ARC111T within the genus Subsaxibacter . The G+C content of ARC111T was 37.8±0.5 mol% while DNA–DNA hybridization depicted 35.6 % relatedness with S. arcticus JCM30334T. Strain ARC111T had C15 : 0iso, C16 : 0iso 3-OH, C15 : 1iso G, C15 : 0anteiso, C16 : 1iso H and C17 : 0iso 3-OH as major (>5 % of the total) cellular fatty acids and MK-6 was the predominant respiratory quinone. The polar lipid profile of strain ARC111T consisted of phosphatidylethanolamine, aminolipid and an unidentified lipid. Strain ARC111T harboured sym-homospermidine as the major polyamine. Characteristic differences obtained using polyphasic analysis of strain ARC111T and its closest relatives suggested that strain ARC111T is a novel species of genus Subsaxibacter , for which the name Subsaxibacter sediminis sp. nov. has been proposed. The type strain is ARC111T (=MCC 3191T=KCTC 42965T=LMG 29783T=GDMCC 1.1201T).
- Published
- 2018
- Full Text
- View/download PDF
10. Corynebacterium godavarianum sp. nov., isolated from the Godavari river, India
- Author
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Yogesh S. Shouche, Venkata Ramana Vemuluri, Kaustubh Khare, Prachi Karodi, Vinay Rale, Kunal Jani, S. V. Senik, Avinash Sharma, and Jayashree Bandal
- Subjects
0301 basic medicine ,DNA, Bacterial ,Corynebacterium ,India ,Microbiology ,03 medical and health sciences ,Corynebacterium imitans ,Rivers ,RNA, Ribosomal, 16S ,Humans ,Ecology, Evolution, Behavior and Systematics ,Phospholipids ,Phylogeny ,Base Composition ,biology ,Phylogenetic tree ,Strain (chemistry) ,Fatty Acids ,Nucleic Acid Hybridization ,General Medicine ,Sequence Analysis, DNA ,biology.organism_classification ,Corynebacterium appendicis ,Molecular analysis ,Bacterial Typing Techniques ,Religion ,030104 developmental biology ,16s rrna gene sequencing ,Water Microbiology ,Bacteria - Abstract
A Gram-stain-positive, rod-shaped, non-motile bacterium, strain PRD07T, was isolated from Godavari river, India during the world's largest spiritual and religious mass bathing event 'Kumbh Mela'. Molecular analysis using 16S rRNA gene sequencing and phylogenetic analysis reveals the distinct phylogenetic positioning of strain PRD07T within the genus Corynebacterium. The strain demonstrated highest sequence similarity to Corynebacterium imitans DSM 44264T (97.9 %), Corynebacterium appendicis DSM 44531T (97.1 %) and
- Published
- 2017
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