In silico functional and evolutionary analyses of rubber oxygenases (RoxA and RoxB).

The study presents an in silico identification of poly (cis-1,4-isoprene) cleaving enzymes, viz., RoxA and RoxB in bacteria, followed by their functional and evolutionary exploration using comparative genomics. The orthologs of these proteins were found to be restricted to Gram-negative beta-, gamma-, and delta-proteobacteria. Toward the evolutionary propagation, the RoxA and RoxB genes were predicted to have evolved via a common interclass route of horizontal gene transfer in the phylum Proteobacteria (delta → gamma → beta). Besides, recombination, mutation, and gene conversion were also detected in both the genes leading to their diversification. Further, the differential selective pressure is predicted to be operating on entire RoxA and RoxB genes such that the former is diversifying further, whereas the latter is evolving to reduce its genetic diversity. However, the structurally and functionally important sites/residues of these genes were found to be preventing changes implying their evolutionary conservation. Further, the phylogenetic analysis demonstrated a sharp split between the RoxA and RoxB orthologs and indicated the emergence of their variant as another type of putative rubber oxygenase (RoxC) in the class Gammaproteobacteria. A detailed in silico analysis of the signature motifs and residues of Rox sequences exhibited important differences as well as similarities among the RoxA, RoxB, and putative RoxC sequences. Although RoxC appears to be a hybrid of RoxA and RoxB, the signature motifs and residues of RoxC are more similar to RoxB.

Comparative gut microbiome analysis of the Prakriti and Sasang systems reveals functional level similarities in constitutionally similar classes.

The traditional medicinal systems (TMS) of India (Prakriti) and Korea (Sasang) classify human individuals based on their constitution determined by the physiological and psychological traits of individuals. Similarities in the constitutions are already found between the classes of Prakriti (Vata, Pitta, and Kapha) and Sasang (TE: Taeeumin, SE: Soeumin, and SY: Soyangin) systems. Gut health is an important aspect of this constitution based classification in TMS. To determine the role of gut microbes in such classifications, we have analyzed the gut microbiome (taxa and imputed functions) in the constitutionally similar Prakriti and Sasang classes. An enrichment of Bacteroides and Prevotella enterotypes is observed in the Sasang and Prakriti samples, respectively. The impact of the constitution is found to be more prominent with respect to the taxa and predicted-functions within the Prakriti classes. Gut microbiome functional-level similarities are found to correlate well with the host phenotypes of the constitutionally similar Prakriti and Sasang classes. An enrichment of carbohydrate and amino-acid metabolism is observed in the Vata and SE classes which may be responsible for meeting with their high energy demands and lean phenotype. The Pitta and SY classes exhibit the high capacity to metabolize toxins. An enrichment of functions responsible for predisposition to obesity and high drug metabolism is observed in the Kapha and TE classes. The contribution of gut adaptive functions is found to correlate with the constitution-based classification in both Prakriti and Sasang systems. The TE class harboured the highest number of biofilm-forming and stress-tolerant microbes thus exhibiting the maximum tolerance of environmental stress. Similarities in the gut microbiota and the resulting disease predisposition patterns are found to exist between the constitutionally matching Prakriti and Sasang classes.

Functional signature analysis of extreme Prakriti endophenotypes in gut microbiome of western Indian rural population.

Ayurveda is practiced in India from ancient times and stratifies the individuals based on their Prakriti constitution. Advancements in modern science have led to the association of Prakriti with molecular, biochemical, genomic and other entities. We have recently explored the gut microbiome composition and microbial signatures in healthy extreme Prakriti endo-phenotypes. However, their functional potentials are still lacking. The present study includes 63 females (29 Vata, 11 Pitta, and 23 Kapha) and 50 males (13 Vata, 18 Pitta, and 19 Kapha) samples. The predictive functional profiling and organism level functional traits of the human gut microbiome have been carried out in Prakriti groups using imputed metagenomic approach. A higher functional level redundancy is found than the taxonomy across the Prakriti groups, however the dominant taxa contributing to the functional profiles are found to be different. A high number of functional signatures specific to the Prakriti groups were identified in female datasets. Some of the functional signatures were found to be gender specific. For example, a higher abundance of microbes contributing potential pathogenic and stress tolerance related functions was found in Kapha in female and Pitta in male. The functional signatures correlated well with phenotypes and disease predisposition of Prakriti groups.

Exploration of Survival Traits, Probiotic Determinants, Host Interactions, and Functional Evolution of Bifidobacterial Genomes Using Comparative Genomics.

Members of the genus Bifidobacterium are found in a wide-range of habitats and are used as important probiotics. Thus, exploration of their functional traits at the genus level is of utmost significance. Besides, this genus has been demonstrated to exhibit an open pan-genome based on the limited number of genomes used in earlier studies. However, the number of genomes is a crucial factor for pan-genome calculations. We have analyzed the pan-genome of a comparatively larger dataset of 215 members of the genus Bifidobacterium belonging to different habitats, which revealed an open nature. The pan-genome for the 56 probiotic and human-gut strains of this genus, was also found to be open. The accessory- and unique-components of this pan-genome were found to be under the operation of Darwinian selection pressure. Further, their genome-size variation was predicted to be attributed to the abundance of certain functions carried by genomic islands, which are facilitated by insertion elements and prophages. In silico functional and host-microbe interaction analyses of their core-genome revealed significant genomic factors for niche-specific adaptations and probiotic traits. The core survival traits include stress tolerance, biofilm formation, nutrient transport, and Sec-secretion system, whereas the core probiotic traits are imparted by the factors involved in carbohydrate- and protein-metabolism and host-immunomodulations.

Correction: Metabolic and taxonomic insights into the Gram-negative natural rubber degrading bacterium Steroidobacter cummioxidans sp. nov., strain 35Y.

[This corrects the article DOI: 10.1371/journal.pone.0197448.].

Metabolic and taxonomic insights into the Gram-negative natural rubber degrading bacterium Steroidobacter cummioxidans sp. nov., strain 35Y.

The pathway of rubber (poly [cis-1,4-isoprene]) catabolism is well documented for Gram-positive rubber degraders but only little information exists for Gram-negative species. The first documented potent rubber degrading Gram-negative strain is Xanthomonas sp. strain 35Y that uses extracellular rubber oxygenases for the initial cleavage of the polyisoprene molecule. However, neither the exact phylogenetic position of Xanthomonas sp. strain 35Y nor the catabolic pathway of the primary polyisoprene cleavage products have been investigated. In this contribution, we started to address both these issues by a comprehensive taxonomic characterization and by the analysis of the draft genome sequence of strain 35Y. Evaluation of the 16S rRNA gene sequence pointed to a borderline taxonomic position of strain 35Y as a novel species of the genus Steroidobacter. Further, substantial differences in the genotypic properties of strain 35Y and the members of the genus Steroidobacter, including average nucleotide identity (ANI) and in silico DNA-DNA hybridization (DDH), resolved the taxonomic position of strain 35Y and suggested its positioning as a novel species of the genus Steroidobacter. This was further confirmed by comparative analysis of physiological and biochemical features of strain 35Y with other members of the genus Steroidobacter. Thus, we conclude that strain 35Y represents a novel species of the genus Steroidobacter, for which we propose the designation Steroidobacter cummioxidans sp. nov., strain 35YT. A comprehensive analysis of the draft genome of S. cummioxidans strain 35Y revealed similarities but also substantial differences to rubber degrading Gram-positive counterparts. In particular, the putative transporters for the uptake of polyisoprene cleavage products differ from Gram-positive rubber degrading species. The draft genome sequence of S. cummioxidans strain 35Y will be useful for researchers to experimentally verify the predicted similarities and differences in the pathways of polyisoprene catabolism in Gram-positive and Gram-negative rubber degrading species.

Western Indian Rural Gut Microbial Diversity in Extreme Prakriti Endo-Phenotypes Reveals Signature Microbes.

Heterogeneity amidst healthy individuals at genomic level is being widely acknowledged. This, in turn, is modulated by differential response to environmental cues and treatment regimens, necessitating the need for stratified/personalized therapy. We intend to understand the molecular determinants of Ayurvedic way (ancient Indian system of medicine) of endo-phenotyping individuals into distinct constitution types termed "Prakriti," which forms the basis of personalized treatment. In this study, we explored and analyzed the healthy human gut microbiome structure within three predominant Prakriti groups from a genetically homogenous cohort to discover differentially abundant taxa, using 16S rRNA gene based microbial community profiling. We found Bacteroidetes and Firmicutes as major gut microbial components in varying composition, albeit with similar trend across Prakriti. Multiple species of the core microbiome showed differential abundance within Prakriti types, with gender specific signature taxons. Our study reveals that despite overall uniform composition of gut microbial community, healthy individuals belonging to different Prakriti groups have enrichment of specific bacteria. It highlights the importance of Prakriti based endo-phenotypes to explain the variability amongst healthy individuals in gut microbial flora that have important consequences for an individual's health, disease and treatment.

Enterotype Variations of the Healthy Human Gut Microbiome in Different Geographical Regions.

Enterotypes are used for classifying individuals based on the gut microbiome. A number of studies are available to find the Enterotypes in healthy individuals; however, most of them lack comparisons at the world level. We analyzed the healthy human gut microbiomes of 495 datasets available in the European Nucleotide Archive (ENA) database derived from fifteen countries from four continents. Firmicutes and Bacteroidetes were the two most abundant phyla in the healthy human gut, worldwide. A high ratio of Proteobacteriato Actinobacteria and a low abundance of Prevotella were identified as the indicators of IBD. Prevotella, Bacteroides, and Bifidobacterium were identified as the Enterotypes in the inter-continental comparisons. At the intra-continental level, two (Bacteroides and Ruminococcaceae), four (Faecalibacterium, Bacteroides, Prevotella, and Clostridiales), and two (Prevotella, Bacteroides/Bifidobacterium) Enterotypes were identified in the American, European, and Asian continents, respectively. In addition, a high abundance of the unknown genus of Ruminococcaeae was observed in the Colombian human gut microbiome. A substantial impact of the geographical distance was observed on human gut microbiome variations, demonstrating a cumulative effect of factors, including dietary habits, genetics, lifestyle, environment, and climate, etc.

Comparative Genomics of Herpesviridae Family to Look for Potential Signatures of Human Infecting Strains.

Herpesviridae family is one of the significant viral families which comprises major pathogens of a wide range of hosts. This family includes at least eight species of viruses which are known to infect humans. This family has evolved 180-220 million years ago and the present study highlights that it is still evolving and more genes can be added to the repertoire of this family. In addition, its core-genome includes important viral proteins including glycoprotein B and helicase. Most of the infections caused by human herpesviruses have no definitive cure; thus, search for new therapeutic strategies is necessary. The present study finds core-genome of human herpesviruses that differs from that of Herpesviridae family and nonhuman herpes strains of this family and might be a putative target for vaccine development. The phylogenetic reconstruction based upon the protein sequences of core gene set of Herpesviridae family reveals the sharp splits of its different subfamilies and supports the hypothesis of coevolution of viruses with their hosts. In addition, data mining for cis-elements in the genomes of human herpesviruses results in the prediction of numerous regulatory elements which can be used for regulating the expression of viral based vectors implicated in gene therapies.