18 research outputs found
An Approach to In Silico Dissection of Bacterial Intelligence Through Selective Genomic Tools
All the genetic potential and the intelligence a
bacteria can showcase in a given environment are embedded
in its genome. In this study, we have presented systematic
guidelines to understand a bacterial genome with
the relevant set of in silico tools using a novel bacteria as
an example. This study presents a multi-dimensional
approach from genome annotation to tracing genes and
their network of metabolism operating in an organism. It
also shows how the sequence can be used to mine the
enzymes and construction of its 3-dimensional structure so
that its functional behavior can be predicted and compared.
The discriminating algorithm allows analysis of the promoter
region and provides the insight in the regulation of
genes in spite of the similarity in its sequences. The ecological
niche specific bacterial behavior and adapted
altered physiology can be understood through the presence
of secondary metabolite, antibiotic resistance genes, and
viral genes; and it helps in the valorization of genetic
information for developing new biological application/
processes. This study provides an in silico work plan and
necessary steps for genome analysis of novel bacteria
without any rigorous wet lab experiments
An Approach to In Silico Dissection of Bacterial Intelligence Through Selective Genomic Tools
All the genetic potential and the intelligence a
bacteria can showcase in a given environment are embedded in its genome. In this study, we have presented systematic guidelines to understand a bacterial genome with
the relevant set of in silico tools using a novel bacteria as
an example. This study presents a multi-dimensional
approach from genome annotation to tracing genes and
their network of metabolism operating in an organism. It
also shows how the sequence can be used to mine the
enzymes and construction of its 3-dimensional structure so
that its functional behavior can be predicted and compared.
The discriminating algorithm allows analysis of the promoter region and provides the insight in the regulation of
genes in spite of the similarity in its sequences. The ecological niche specific bacterial behavior and adapted
altered physiology can be understood through the presence
of secondary metabolite, antibiotic resistance genes, and
viral genes; and it helps in the valorization of genetic
information for developing new biological application/
processes. This study provides an in silico work plan and
necessary steps for genome analysis of novel bacteria
without any rigorous wet lab experiments
Exploring the rearrangement of sensory intelligence in proteobacteria: insight of Pho regulon
Pho regulon is a highly evolved and conserved mechanism across the microbes to fulfil their phosphate need. In this study,
52 proteobacteria genomes were analyzed for the presence of phosphorus acquisition genes, their pattern of arrangement
and copy numbers. The diverse genetic architecture of the Pho regulon genes indicates the evolutionary challenge of nutrient
limitation, particularly phosphorus, faced by bacteria in their environment. The incongruence between the Pho regulon
proteins phylogeny and species phylogeny along with the presence of additional copies of pstS and pstB genes, having cross
similarity with other genera, suggest the possibility of horizontal gene transfer event. The substitution rate analysis and
multiple sequence alignment of the Pho regulon proteins were analyzed to gain additional insight into the evolution of the
Pho regulon system. This comprehensive study confirms that genes perform the regulatory function (phoBR) were vertically
inherited, whereas interestingly, genes whose product involved in direct interaction with the environment (pstS) acquired by
horizontal gene transfer. The substantial amino acid substitutions in PstS most likely contribute to the successful adaptation of
bacteria in different ecological condition dealing with different phosphorus availability. The findings decipher the intelligence
of the bacteria which enable them to carry out the targeted alteration of genes to cope up with the environmental condition
An Insight into Phage Diversity at Environmental Habitats using Comparative Metagenomics Approach
Bacteriophages play significant role in driving
microbial diversity; however, little is known about the
diversity of phages in different ecosystems. A dynamic
predator–prey mechanism called ‘‘kill the winner’’ suggests
the elimination of most active bacterial populations
through phages. Thus, interaction between phage and host
has an effect on the composition of microbial communities
in ecosystems. In this study, secondary phage metagenome
data from aquatic habitats: wastewater treatment plant
(WWTP), fresh, marine, and hot water spring habitat were
analyzed using MG-RAST and STAMP tools to explore the
diversity of the viruses. Differential relative abundance of
phage families—Siphoviridae (34%) and Myoviridae
(26%) in WWTP, Myoviridae (30%) and Podoviridae
(23%) in fresh water, and Myoviridae (41%) and
Podoviridae (8%) in marine—was found to be a discriminating
factor among four habitats while Rudiviridae (9%),
Globuloviridae (8%), and Lipothrixviridae (1%) were
exclusively observed in hot water spring. Subsequently, at
genera level, Bpp-1-like virus, Chlorovirus, and T4-like
virus were found abundant in WWTP, fresh, and marine
habitat, respectively. PCA analysis revealed completely
disparate composition of phage in hot water spring from
other three ecosystems. Similar analysis of relative abundance
of functional features corroborated observations
from taxa analysis. Functional features corresponding to
phage packaging machinery, replication, integration and
excision, and gene transfer discriminated among four
habitats. The comparative metagenomics approach exhibited
genetically distinct phage communities among four
habitats. Results revealed that selective distribution of
phage communities would help in understanding the role of
phages in food chains, nutrient cycling, and microbial
ecology. Study of specific phages would also help in controlling
environmental pathogens including MDR bacterial
populations using phage therapy approach by selective
mining and isolation of phages against specific pathogens
persisting in a given environment