Jay Siddharth

House of Lab Science

The gut microbiome and lipid metabolism are both recognized as essential components in the maintenance of metabolic health. The mechanisms involved are multifactorial and (especially for microbiome) poorly defined. A strategic approach to investigate the complexity of the microbial influence on lipid metabolism would facilitate determination of rel...

The microbiome has been demonstrated to play an integral role in the maintenance of many aspects of health that are also associated with aging. In order to identify areas of potential exploration and intervention, we simultaneously characterized age-related alterations in gut microbiome, muscle physiology and serum proteomic and lipidomic profiles...

The importance of gut microbes to metabolic health is becoming more evident and nutrition-based therapies to alter the composition of bacterial communities to manage metabolic disease are an attractive avenue to ameliorate some effects of Western diets. While the composition of gut microbial communities can vary significantly across disease states,...

Escherichia coli is one of the common inhabitants of the mammalian gastrointestinal track. We isolated a strain from an ob/ob mouse and performed whole-genome sequencing, which yielded a chromosome of ~5.1 Mb and three plasmids of ~160 kb, ~6 kb, and ~4 kb.

The gut microbiota is involved in many aspects of host physiology but its role in body weight and glucose metabolism remains unclear. Here we studied the compositional changes of gut microbiota in diet-induced obesity mice that were conventionally raised or received microbiota transplantation. In conventional mice, the diversity of the faecal micro...

Development of NGS has revolutionized the analysis in microbial ecology contributing to our deeper understanding of microbiota in health and disease. However, the quality, quantity and confidence of summarized taxonomic abundances are in need of further scrutiny due to sample dependent and independent effects. In this article we introduce 'AVIT (Ab...

Longitudinal studies aim typically at following populations of subjects over time and are important to understand the global evolution of biological processes. When it comes to longitudinal Omics data, it will often depend on the overall objective of the study, and constraints imposed by the data, to define the appropriate modeling tools. Here, we...

The interplay between diet and the microbiota has been implicated in the growing frequency of chronic diseases associated with the Western lifestyle. However, the complexity and variability of microbial ecology in humans and preclinical models has hampered identification of the molecular mechanisms underlying the association of the microbiota in th...

The micro-eukaryotic diversity from the human gut was investigated using universal primers directed towards 18S rRNA gene, fecal samples being the source of DNA. The subjects in this study included two breast-fed and two formula-milk-fed infants and their mothers. The study revealed that the infants did not seem to harbour any microeukaryotes in th...

The integration of host genetics, environmental triggers and the microbiota is a recognised factor in the pathogenesis of barrier function diseases such as IBD. In order to determine how these factors interact to regulate the host immune response and ecological succession of the colon tissue-associated microbiota, we investigated the temporal inter...

Bacterial FISH probe validation. Formalin-fixed paraffin-embedded colon samples were processed and probed with EUB338 FISH probest for 16S rRNA as described in Experimental Procedures. Left panels: Cy5 probes only. Right panels: Cy5 probes in the presence of 100× excess ‘cold’ EUB338 probes to assess non-specific binding. (TIF)

Validation of FACS-based bacterial quantitation. A. Gate selection (forward/side scatter: yellow) for bacterial quantitfication using cultured bacteria and overlap with fecal bacteria (in blue). B: Validation of quantification by comparison with EUB338 FISH probe. Both methods gave comparable statistical significance (*p≤0.05: Students T test) usin...

Cytokines WT vs Nod2 KO littermates. Colon tissue homogenates were prepared and the indicated cytokine concentrations determined by ELISA as outlined in Materials and Methods. *p<0.05, **p<0.01, ***p<0.001: 1 way ANOVA with Bonferroni's multiple comparison test. Means +/− SEM, n = 5–11. (TIF)

Phylum and Genus classification of full length 16S rRNA sequences from WT and Nod2 KO mouse colon tissue 42 days post DSS or control as indicated. Full length 16S rRNA sequence libraries were generated from DNA extracted from colon tissue and analysed in the bioinformatics pipeline as described in Materials and Methods. The sequences were classifie...

Both antibiotics and steroid treatment significantly impact damage and bacterial tissue penetration. Top left: time line for antibiotic/dexamethasone experiment. Top right: Histological score following therapeutic treatment. *p≤0.05 Students T test vs Vehicle. Bottom left: colon tissue-associated bacterial counts by FACS. *p≤0.05, ***p≤0.001 vs Veh...

Histology and bacterial load assessment of WT and Nod2 KO littermates following DSS damage. Histology score summary (left) and colon tissue-associated bacterial loads (right) assessed by FACS 42 days following DSS damage. * = p≤0.05 by Students T test. See Figure 4 for additional independent experimental data. (TIF)

Sequence distribution and rarefaction plots for 16S rRNA microbiota analysis. WT and Nod2 KO littermates were treated with or without DSS in the drinking water as indicated. 16S rRNA libraries were prepared as indicated in Materials and Methods, sequenced and classified using Mothur and a reference Silva alignment. Rarefaction curves were determine...

Classification of 16S rRNA sequences derived from WT and Nod2 KO littermates. Mice were treated or not with DSS and the colon removed on day 42 post-DSS. The sequences were classified using Mothur using the RDP classification scheme, the confidence values for genus assignment are shown. These are based on the output from Mothur using the latest rel...

Serum antibody levels in WT vs Nod2 KO littermates. Serum was taken from WT and Nod2 KO mice treated or not with DSS in the drinking water. IgA, IgG1, and IgG2a levels in the serum were quantified by ELISA. Bars are mean +/− SEM, n = 7–9. *p≤0.05, 1 way ANOVA with Bonferroni's multiple comparison test. (TIF)

Bioinformatic pipeline used for analysis of 16S rRNA sequences. See Materials and Methods for details. (TIF)

The prokaryotic diversity associated with an Indian soda lake (Lonar Crater Lake) located in a basaltic soil area was investigated using a culture-independent approach. Community DNA was extracted directly from four sediment samples obtained by coring to depths of 10-20 cm. Small subunit rRNA genes (16S rDNA) were amplified by PCR using primers spe...

Ravenelia esculenta Naras. and Thium. is a rust fungus, which infects mostly thorns, flowers and fruits of Acacia eburnea Willd. The dominant stage is aeciospores which forms hypertrophy on host plant. The present study was undertaken to sequence 18S rDNA of Ravenelia esculenta and to establish its phylogeny. Aeciospores were scraped and DNA was is...

Seventy-five marine bacterial strains associated with four species of sponges (Echinodictyum sp., Spongia sp., Sigmadocia fibulatus and Mycale mannarensis) were isolated from the Tuticorin coast, Gulf of Mannar region. The agar-overlay method was used to screen for antibiotic production by these strains against four bacteria, viz., Bacillus subtili...