GiAN Program report: GIAN (GLOBAL INITIATIVES OF ACADEMIC NETWORK) SHORT-TERM COURSE ON ‘METAGENOMICS & MICROBIOMES
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The GIAN short-term course on 'Metagenomics & Microbiomes' was held from February 20-25, 2017, at Saurashtra University, featuring lectures and hands-on training from various experts in the field. Topics included next-generation sequencing, bioinformatics tools, applications of the QIIME software, and metagenomics project design. The course concluded with a multiple-choice assessment to evaluate participants' knowledge, engaging faculty, researchers, and students nationwide.
GiAN Program report: GIAN (GLOBAL INITIATIVES OF ACADEMIC NETWORK) SHORT-TERM COURSE ON ‘METAGENOMICS & MICROBIOMES
- 1. GIAN (GLOBAL INITIATIVES OF ACADEMIC NETWORK) SHORT-TERM COURSE ON ‘METAGENOMICS & MICROBIOMES’20-25 FEBRUARY 2017 UGC-CAS DEPARTMENT OF BIOSCIENCES, SAURASHTRA UNIVERSITY, RAJKOT February 20, Monday The GIAN-short term course on the Metagenomics and Microbiome was inaugurated on 20 February 2017 at 9.30 AM. Prof. Partapsinh Chauhan, Vice- Chancellor, Saurashtra University, Prof. G. C. Bhimani, Dean, Faculty of Science, Dr. Mehul Rupani, Other than Dean, Dr. Dan Knights, USA, Prof. Satya P. Singh, Coordinator of the Short-Term Course and Prof. Ramesh K. Kothari, Co-cordinator of the Short-Term Course were present in this event of inaugural session. Prof. Partapsinh Chauhan expressed his happiness on the organization of such event in Saurashtra University. Other speakers highlighted the significance of this course programme and the available opportunities to the young researchers. Dr. Knights briefly outlined the fast emerging field of the Metagenomics and Computational Biology and the significance of such courses. After the inaugural session the technical sessions began. Dr. Dan Knights, Assistant Professor in the Department of Computer Science and Engineering and the Biotechnology Institute at the University of Minnesota delivered the talk and highlighted the importance of Next Generation Sequencing
- 2. in the exploration of the Metagenomics. As a computational microbiologist, he taught the delegates about the applications of the QIIME software in quantifying and visualizing microbial diversity. Dr. Knights personated a detailed account on predictive modelling of the microbial communities using machine learning. The delegates had a good interaction with Dr. Dan Knights regarding the use of QIIME software and explored the possibilities of this tool in their research work. Dr. Prakash Koringa, Assistant Professor, Department of Animal Biotechnology, College of Veterinary Science, Anand Agricultural University, Anand, Gujrat, India was another resource person. He gave informative lecture on NGS in metagenomics and discussed the history and evolution of metagenomics. He also presented a view of the instruments used for NGS and explained how it functions. He explained and discussed different types of software used in metagenomics, such as MG-RAST, EBI metagenomics, QIIME and img/M, MEGAN. His lecture was very informative and useful as also evident by the discussions and interactions it followed. February 21, Tuesday Dr. Dan Knights continued his lectures on the methods for precise taxonomic annotation of microbiome data and hands on training. Mr. Ankit Hinsu from the Department of Animal Biotechnology, College of Veterinary Science, Anand Agricultural University, Anand, Gujarat, India was involved in the hand-on training of the participants on the applications and analysis using QIIME. QIIME is a popular software pipeline for metagenomics data analysis and it consists of a number of scripts written in the Python programming language. This allows multiple scripts to be combined into an analysis pipeline that can be invoked with a
- 3. single command. It is useful for the analyse 16S rRNA for prokaryotes and 18S rRNA for eukaryotes (Other markers are ITS, rpoB) February 22, Wednesday Dr. Rajesh Patel, Assistant Professor (Microbiology) at Department of Life Science, Hemchandracharya North Gujarat University, Patan, Gujarat, India delivered his talk on the use of various bioinformatics tools for the analysis of metagenomics data. He explained the BI driven analysis of the metagenomics data. Dr. Patel also discussed various tools, such as METAGENassist, Metaphylan, PICRUST, which generate information on the metagenomics data. Dr. Neelam Nathani, National Post-Doctoral Fellow & PI (DST-SERB) at Deparment of Life Sciences, Maharaja Krishnakumarsinhji Bhavnagar University, Bhavnagar, Gujarat, India presentated on the “Metagenomics: Public resources, applications and future”. She provided Hands on-training on the processing of raw data for metagenomics using softwares, such as Glimmer, Frag Gene Scan, MG- RAST etc. She also provided insight into the designing of a research project based on Metagenomics. Ms. Jalpa Thakkar from the Department of Animal biotechnology, College of Veterinary Science, Anand Agricultural University, Anand, Gujarat, India provided hands-on training on the MG-RAST, Metagenome Rapid Annotation using Subsystem Technology Server for the taxonomic and functional analysis of the metagenomes. It offers automated quality control, annotation, comparative analysis, and archiving services. It works best in Firefox browser. By using this software one can perform QC analysis and diversity of bacteria, Archaea and fungi. This software is freely available on internet.
- 4. February 23, Thursday Dr. K. M. Singh, Laboratory Manager at Eurofins Clinical Genetics Laboratory, Bangalore, India enlightened the participants on the RumenOmics, ie, Rumen metagenomics. He gave an informative talk on the analysis of the microbiota found in the rumen of different breeds of buffalo and made them aware of amplicon sequencing and shotgun sequencing. He gave information on how to discover novel and useful enzymes after the bioinformatics analysis of the metagenomics data. On February 23, another talk was by Dr. Subrata K. Das, Scientist at Institute of Life Sciences, a DBT Institute, Bhubaneswar, India. He delivered talk on the genome scale reconstruction of metabolic model and functional analysis of the microbiome of the corals. Dr. Das discussed phylogenetic and functional characterization of microbes and microbiome using various bioinformatics tools. Dr. Mithil J. Parekh, Research Associate at Department of Animal biotechnology, College of Veterinary Science, Anand Agricultural University, Anand, Gujarat, discussed and provided information on EBI (European Bioinformatics Institute) Metagenomics. He provided awareness on the applications of the EBI Metagenomics software for the analysis of metagenomic data to obtain different types of graphs and figures for the comparison of different metagenomic data February 24, Friday Prof. C. G. Joshi (Professor & Head, Department of Animal Biotechnology, College of Veterinary Science, Anand Agricultural University, Anand, Gujrat, India) delivered lectures on designing a metagenomics project. He provided valuable information on variable regions in 16S rRNA bacterial gene. He then
- 5. discussed various steps involved in sequencing of metagenomic DNA and explained in detail how Illumine Technology works. He also discussed contigs generation and trimming of reads. Prof. S.K.Khare, Professor (Biochemistry), Enzyme and Microbial Biochemistry Laboratory, Department of Chemistry, Indian Institute of Technology, New Delhi, India delivered a detailed talk on the analytical techniques employed in metabolomics. He emphasized that metabolomics is an emerging field of research and quite interesting and useful for discovering unknown metabolites in different organisms. He gave instruction about “OMICS” Research, Metabolism, Reduction and oxidation, Glycolytic and Fermentation pathway, Protemics. Proteomics can be studied by using 2-Gel electrophoresis, peptide fragmentations by tryptic digestion. He further described how to analyze peptide mixture by 2D LC-MS/MS with ProteomeX. Further, Peptide and proteins identification by TurboSEQUEST software was also discussed. Dr. Ramesh Pandit, Research Associate at Department of Animal biotechnology, College of Veterinary Science, Anand Agricultural University, Anand, Gujrat, discussed STAMP. He provided hands-on training to the participants of this software. Statistical analysis of metagenomic profiles is a software package for identifying number of marker genes assigned to different taxonomic units or a functional profile indicating the number of sequences assigned to different biological subsystems or pathways. Dr. Jakhesara, Assistant Professor at Department of Animal biotechnology, College of Veterinary Science, Anand Agricultural University, Anand, Gujrat, delivered a lecture on the challenges one faces during the analysis of the metagenomics data. He provided detailed information on the coverage of the
- 6. maximum data during the metagenomics analysis using various bioinformatics softwares. Finally on February 25, Saturday, Dr. Ramesh K. Kothari, Professor at the UGC – CAS Department of Biosciences, Saurashtra University, Rajkot, Gujarat, India delivered a lecture on the Environmental metagenomics. He discussed the idea of the exploration of extreme habitats and designing various metagenomics projects for the discovery of novel genes. He also enriched the participants with the knowledge of the current metagenomic projects currently being pursued around the globe. At the end of the technical sessions, a Multiple Choice Questions (MCQ) based examination was conducted for the participants to assess the knowledge and awareness gained by them during the Short Term course. The participants enthusiastically participated in this examination and over all their performance were very good. In this GIAN-Short Term Course programme, the spectrum of the participants included, faculty members, scientists from National Research Institutes, Post- doctoral scientist and Ph. D. students from various parts of the country.