Human gut microbiome studies are increasing at a rapid pace to understand contributions of the prokaryotic life to the innate workings of their eukaryotic host. Majority of studies focus on the ...pattern of gut microbial diversity in various diseases, however, understanding the core microbiota of healthy individuals presents a unique opportunity to study the microbial fingerprint in population specific studies. Present study was undertaken to determine the core microbiome of a healthy population and its imputed metabolic role. A total of 8990, clone library sequences (> 900 bp) of 16S rRNA gene from fecal samples of 43 individuals were used. The core gut microbiota was computed using QIIME pipeline. Our results show the distinctive predominance of genus
Prevotella
and the core composition of genera
Prevotella, Bacteroides, Roseburia
and
Megasphaera
in the Indian gut. PICRUSt analysis for functional imputation of the microbiome indicates a higher potential of the microbiota for carbohydrate metabolism. The presence of core microbiota may indicate key functions played by these microbes for the human host.
Despite high vaccination coverage using acellular (ACV) and whole-cell pertussis (WCV) vaccines, the resurgence of pertussis is observed globally. Genetic divergence in circulating strains of ...Bordetella pertussis has been reported as one of the contributing factors for the resurgence of the disease. Our current knowledge of B. pertussis genetic evolution in circulating strains is mostly based on studies conducted in countries using ACVs targeting only a few antigens used in the production of ACVs. To better understand the adaptation to vaccine-induced selection pressure, it will be essential to study B. pertussis populations in developing countries which are using WCVs. India is a significant user and global supplier of WCVs. We report here comparative genome analyses of vaccine and clinical isolates reported from India. Whole-genome sequences obtained from vaccine strains: WCV (J445, J446, J447 and J448), ACV (BP165) were compared with Tohama-I reference strain and recently reported clinical isolates from India (BPD1, BPD2). Core genome-based phylogenetic analysis was also performed using 166 isolates reported from countries using ACV.
Whole-genome analysis of vaccine and clinical isolates reported from India revealed high genetic similarity and conserved genome among strains. Phylogenetic analysis showed that clinical and vaccine strains share genetic closeness with reference strain Tohama-I. The allelic profile of vaccine strains (J445:ptxP1/ptxA2/prn1/fim2-1/fim3-1; J446: ptxP2/ptxA4/prn7/fim2-2/fim3-1; J447 and J448: ptxP1/ptxA1/ prn1/fim2-1/fim3-1), which matched entirely with clinical isolates (BPD1:ptxP1/ptxA1/prn1/fim2-1 and BPD2: ptxP1/ptxA1/prn1/fim2-1) reported from India. Multi-locus sequence typing (MLST) demonstrated the presence of dominant sequence types ST2 and primitive ST1 in vaccine strains which will allow better coverage against circulating strains of B. pertussis.
The study provides a detailed characterization of vaccine and clinical strains reported from India, which will further facilitate epidemiological studies on genetic shifts in countries which are using WCVs in their immunization programs.
Obesity is a consequence of a complex interplay between the host genome and the prevalent obesogenic factors among the modern communities. The role of gut microbiota in the pathogenesis of the ...disorder was recently discovered; however, 16S-rRNA-based surveys revealed compelling but community-specific data. Considering this, despite unique diets, dietary habits and an uprising trend in obesity, the Indian counterparts are poorly studied. Here, we report a comparative analysis and quantification of dominant gut microbiota of lean, normal, obese and surgically treated obese individuals of Indian origin. Representative gut microbial diversity was assessed by sequencing fecal 16S rRNA libraries for each group (n = 5) with a total of over 3000 sequences. We detected no evident trend in the distribution of the predominant bacterial phyla, Bacteroidetes and Firmicutes. At the genus level, the bacteria of genus Bacteroides were prominent among the obese individuals, which was further confirmed by qPCR (P < 0.05). In addition, a remarkably high archaeal density with elevated fecal SCFA levels was also noted in the obese group. On the contrary, the treated-obese individuals exhibited comparatively reduced Bacteroides and archaeal counts along with reduced fecal SCFAs. In conclusion, the study successfully identified a representative microbial diversity in the Indian subjects and demonstrated the prominence of certain bacterial groups in obese individuals; nevertheless, further studies are essential to understand their role in obesity.
We performed whole-genome sequencing of two phytoplasmas associated with sugarcane grassy shoot (SCGS) and Bermuda grass white leaf diseases. These are the first draft genomes of SCGS phytoplasma ...(strain SCGS) and '
Phytoplasma cynodontis' (strain LW01) and may help to delineate these phytoplasmas at a finer taxonomic level.
Chronic exposures to tobacco and biomass smoke are the most prevalent risk factors for COPD development. Although microbial diversity in tobacco smoke-associated COPD (TSCOPD) has been investigated, ...microbiota in biomass smoke-associated COPD (BMSCOPD) is still unexplored. We aimed to compare the nasal and oral microbiota between healthy, TSCOPD, and BMSCOPD subjects from a rural population in India. Nasal swabs and oral washings were collected from healthy (
n
= 10), TSCOPD (
n
= 11), and BMSCOPD (
n
= 10) subjects. The downstream analysis was performed using QIIME pipeline (v1.9). In nasal and oral microbiota no overall differences were noted, but there were key taxa that had differential abundance in either Healthy vs COPD and/or TSCOPD vs. BMSCOPD. Genera such as
Actinomyces, Actinobacillus, Megasphaera
,
Selenomonas,
and
Corynebacterium
were significantly higher in COPD subjects. This study suggests that microbial community undergoes dysbiosis which may further contribute to the progression of disease. Thus, it is important to identify etiological agents for such a polymicrobial alterations which contribute highly to the disease manifestation.
The frequency of infections associated with multidrug resistant
has risen substantially in India. The use of next-generation sequencing (NGS) techniques combined with comparative genomics has great ...potential for tracking, monitoring, and ultimately controlling the spread of this troublesome pathogen. Here, we investigated the whole genome sequences of 47 A
from India.
In brief,
genomes were analyzed for the presence of antibiotic resistance genes (ARGs), virulence factors genes (VFGs), and mobile genetic elements (MGEs) using various in silico tools. The AbaR-type resistance islands (AbaRIs) were detected by examining the genetic environment of the chromosomal
gene. Multilocus sequence types were determined using the Pasteur scheme. The eBURST and whole genome SNPs-based phylogenetic analysis were performed to analyze genetic diversity between
genomes.
A larger number of
isolates belonging to the ST2 genotype was observed. The SNPs-based phylogenetic analysis showed a diversity between compared genomes. The predicted resistome showed the presence of intrinsic and acquired ARGs. The presence of plasmids, insertion sequences, and resistance islands carrying putative ARGs conferring resistance to antibiotics, quaternary ammonium compounds, and heavy metals was predicted in 43 (91%) genomes. The presence of putative VFGs related to adherence, biofilm formation and iron uptake was observed in the study. Overall, the comprehensive genome analysis in this study provides an essential insight into the resistome, virulome and mobilome of
isolates from 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.
The landfill is an inexpensive way of municipal solid waste (MSW) management and contributes extensively to the total carbon budget and global climate change. Three landfills from two geographically ...distinct metro- cities of India were taken as model systems to create microcosms and study their physiochemistry, microbiology, and carbon emission. The microcosm experiments revealed that facultative anaerobic bacterial community showing the dominance in the beginning but with the progression of anoxia and anaerobic conditions, methanogenesis prevailed, resulting in a clear shift towards the abundance of methanogens especially the members of
Methanosarcina, Methanocorpusculum
, and
Methanoculleus
(70–90% of the total microbial population). Geochemical data showed a wide range of heterogeneity in landfills’ composition located even in the same city. In past, greenhouse gas emission from landfills is mainly estimated using different models which lack accuracy. As limited information is available as of now, this study can elicit researcher interest for in-depth characterization of microbial diversity and carbon emission from landfills. The microcosm model presented in the current study is a robust and straightforward method of accurate estimation of amounts of different types of gases release from landfill. It can also be extrapolate for estimation of different gases release from actual landfill sites by setting the on-site experiments.
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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