Ramesh Kothari

Effect of roughage on rumen microbiota composition in the efficient feed converter and sturdy Indian Jaffrabadi buffalo ( Bubalus bubalis )

BackgroundThe rumen microbiota functions as an effective system for conversion of dietary feed to microbial proteins and volatile fatty acids. In the present study, metagenomic approach was applied to elucidate the buffalo rumen microbiome of Jaffrabadi buffalo adapted to varied dietary treatments with the hypothesis that the microbial diversity and subsequent in the functional capacity will alter with diet change and enhance our knowledge of effect of microbe on host physiology. Eight adult animals were gradually adapted to an increasing roughage diet (4 animals each with green and dry roughage) containing 50:50 (J1), 75:25 (J2) and 100:0 (J3) roughage to concentrate proportion for 6xa0weeks. Metagenomic sequences of solid (fiber adherent microbiota) and liquid (fiber free microbiota) fractions obtained using Ion Torrent PGM platform were analyzed using MG-RAST server and CAZymes approach.ResultsTaxonomic analysis revealed that Bacteroidetes was the most abundant phylum followed by Firmicutes, Fibrobacter and Proteobacteria. Functional analysis revealed protein (25-30xa0%) and carbohydrate (15-20xa0%) metabolism as the dominant categories. Principal component analysis demonstrated that roughage proportion, fraction of rumen and type of forage affected rumen microbiome at taxonomic as well as functional level. Rumen metabolite study revealed that rumen fluid nitrogen content reduced in high roughage diet fed animals and pathway analysis showed reduction in the genes coding enzymes involved in methanogenesis pathway. CAZyme annotation revealed the abundance of genes encoding glycoside hydrolases (GH), with the GH3 family most abundant followed by GH2 and GH13 in all samples.ConclusionsResults reveals that high roughage diet feed improved microbial protein synthesis and reduces methane emission. CAZyme analysis indicated the importance of microbiome in feed component digestion for fulfilling energy requirements of the host. The findings help determine the role of rumen microbes in plant polysaccharide breakdown and in developing strategies to maximize productivity in ruminants.

Correlation between genomic analyses with metatranscriptomic study reveals various functional pathways of Clostridium sartagoforme AAU1, a buffalo rumen isolate

ABSTRACT The present study describes the isolation and pheno-genotypic analysis of anaerobic Clostridium sartagoforme strain AAU1 from buffalo rumen, having major role in cellulose and chitin degradation. The isolate was cultured between 37°C and 42°C (optimum 40°C) temperature with an optimum pH of 7.5 in Hungates medium supplemented with cellulose. Whole genome sequencing was performed using ion torrent PGM platforms. Local BLAST showed highest phylogenetic relation with C. sartagoforme DSM 1292 strain based on comparison of the 16S rDNA sequences. Comparison of sequences coding for housekeeping genes phosphoglycerate kinase (pgk) and gyrase B (gyrB) confirmed its taxonomic position within Clostridium genus. The fermentation ability analysed biochemically using AN-Biolog plate showed that the strain utilized more than 30 different substrates as metabolite precursors. Pathway analysis based on Rapid Annotation using Subsystem Technology reveals the organism to be highly active in the production of volatile fatty acids (VFAs). Genomic analysis confirmed the role of bacteria in determining ruminant host physiology. VFAs produced by the isolate play a prominent role in animal health maintenance by contributing a major proportion of the ruminants’ daily energy requirement. A deeper understanding of enzymes encoded allows further industrial applications and modulation of the rumen for enhanced farming applications.

Intriguing Interaction of Bacteriophage-Host Association: An Understanding in the Era of Omics

Innovations in next-generation sequencing technology have introduced new avenues in microbial studies through “omics” approaches. This technology has considerably augmented the knowledge of the microbial world without isolation prior to their identification. With an enormous volume of bacterial “omics” data, considerable attempts have been recently invested to improve an insight into virosphere. The interplay between bacteriophages and their host has created a significant influence on the biogeochemical cycles, microbial diversity, and bacterial population regulation. This review highlights various concepts such as genomics, transcriptomics, proteomics, and metabolomics to infer the phylogenetic affiliation and function of bacteriophages and their impact on diverse microbial communities. Omics technologies illuminate the role of bacteriophage in an environment, the influences of phage proteins on the bacterial host and provide information about the genes important for interaction with bacteria. These investigations will reveal some of bio-molecules and biomarkers of the novel phage which demand to be unveiled.

Isolation of chitinolytic Clostridium sp. NCR from Mehsani buffalo rumen, its genomic analysis and potential role in rumen.

Genomic analysis of Clostridium sp. NCR, an anaerobic Gram positive bacterium which was isolated from rumen fluid of Mehsani breed of buffalo revealed presence of various environmental gene tags (EGTs) involved in pathways for utilizing a wide range of substrates. Here we report the sequence of this rumen isolate, its whole genome sequence has been deposited in DDBJ/EMBL/GenBank under the accession number JQHY00000000. The genome comprises of a 3.62-Mb draft genome with a G + C content of 28.10%, which encodes a total of 3126 proteins. Functional analysis provides information about the microbes role in maintaining host homeostasis and its fiber degradation potential.

Draft Genome Sequence of Commercial Textile Dye-Decolorizing and -Degrading Bacillus subtilis Strain C3 Isolated in India

ABSTRACT Bacillus subtilis C3, a commercial textile dye-decolorizing and -degrading bacterium, was isolated from the common effluent treatment plant (CEPT) of the Jetpur textile dyeing and printing industrial sector situated in the district of Rajkot, Gujarat, India. Here, we present the annotated 4.18-Mb draft genome sequence of B. subtilis C3, providing information about the metabolic pathways involved in decolorization and degradation of several commercial textile azo dyes. Thus, we confirm B. subtilis C3 as a potential candidate for bioremediation of textile effluents.

Chapter 11 – Comprehensive Exploration of the Rumen Microbial Ecosystem With Advancements in Metagenomics

Abstract Ruminant farming and its environmental impact has long remained an economic concern. Metagenomics unravel the vast structural and functional diversity of the rumen microbial community that plays a major role in animal nutrition. Hereby, we summarize rumen metagenomic studies that have enhanced the knowledge of rumen microbe dynamics subsequently leading to development of better feed strategies to improve livestock production and reduce methane emissions.

Prospects and Progress in Extreme Biosphere Microbiome

There is a considerable market potential of extremophiles and their biomolecules; however, their high evolutionary rates and culturability limitations restrict their industrial exploration. The impressive development of “omics” technologies has allowed the culture-free technique, i.e., metagenomics as a valuable tool for mining the hidden information of the extremophiles and their biospheres. At present, environmental microbiomes are being studied using functional-based and sequence-based approaches. The growth of the extreme environmental metagenomics literature and projects is increased nearly tenfold in the last decade due to the advancement in the sequencing technologies. Here, in the context, we summarize all the aspects of extreme biosphere metagenomics with recent prospects and progress.

Metatranscriptomic Studies of the Plant Rhizosphere for Finding Biological Agents

Soilborne diseases are accountable for most important crop losses globally. There are two ways to control this ailment. The judicious use of synthetic agrochemicals harms ecosystem and beneficial soil microbes and alternatively promotes the use of biological agents to control plant pathogens. Rhizospheric beneficial microbes play a crucial role in disease suppression process in the soil ecosystems by guarding plants from infections that they likely get from soilborne pathogens. The microorganisms and mechanisms involved in the disease suppression in soils are poorly known till date. Therefore, development of meta-omics techniques would provide deeper understanding of this association. Metatranscriptomics, a study of the total content of gene transcripts (RNA copies of the genes) in a microbial community, is a right approach to unveil the role of genes responsible for the disease suppression mechanism at molecular level as this technique is considered as a unique entity at a specific moment of sampling. This technique is applied to obtain the whole expression profile in a community and to follow the dynamics of gene expression patterns over time and/or various environmental parameters. The microbial communities in several environments have been extensively studied to reveal their roles in plant-microbes interaction and disease suppression in rhizospheric soils.

Advancements in Molecular Techniques and Bioinformatics for Understanding the Rumen Microbiome

Microbial diversity in the forestomach is of major importance to the ruminants. Rumen microbiome diversity and gene tag predictions are important areas of scientific interests due to their global impacts including methane emission control and ruminant health. Earlier the knowledge of rumen biodiversity was entirely dependent on the anaerobic culturing approach. However, advancements in molecular techniques have revealed hitherto uncovered features of the rumen microbiome. Next-generation sequencing in combination with conventional techniques has provided significant opportunities to understand animal performance in context to rumen ecology and subsequent nutrient manipulation. Metagenomic sequencing generates enormous data making its informatics handling and analysis intricate due to the immense complexity of the data. Bioinformatic resources are rapidly emerging to outwit the intricacies. In this book chapter, we highlight the advances in the metagenomic analysis that help to improve the genomic aspect of the tree of life by getting an in-depth understanding of the Candidatus uncultured population of the rumen microbiome focusing on correlation between the microbial functioning and animal efficiency. It also describes the strategies and specific bioinformatic approaches that can be applied to metagenomic sequences for accurate and in-depth metagenomic analysis, data binning, and genome reconstruction of individual microbes.

Exploring the Complexity of Macroalgal-Bacterial Interactions Through Interkingdom Signalling System

Macroalgae belong to a diverse group of photosynthetic organisms that play an essential role in marine ecosystems. These ecosystem engineers contribute significantly to global primary production and are the major habitat formers on rocky shores in temperate waters, providing food and shelter for marine life. Macroalgae harbour a rich diversity of associated microorganisms with varied functions related to host performance and defence. In particular, epiphytic bacterial communities have been reported as essential for normal morphological development of the algal host. Moreover, bacteria with antifouling properties are thought to protect chemically undefended macroalgae from detrimental, secondary colonization by other microscopic and macroscopic epibiota. This tight relationship suggests that macroalgae and epiphytic bacteria interact as an integrated functional entity or “holobiont”. Many of these interactions are controlled via chemical signalling systems in a type of interkingdom communication. Indeed recent studies have demonstrated that chemical signalling molecules from bacteria regulate important functions in green algae such as reproduction and host defence.