12 BioMed Research International Table 6: Continued. Database Feature description Web/open source Availability MetaCyc MetaCyc Metabolic Pathway Database Yes/yes http://metacyc.org/ MetaBioMe Metabolome Searcher ProCyc MEMOSys EAWAG-BBD Datamining engine for known Commercially Useful Enzymes (CUEs) in metagenomic datasets and genomes HTS tool for metabolite identification and metabolic pathway mapping directly from mass spectrometry and metabolites An open resource for the study of metabolic capabilities in microorganisms from food, environment, and specific pathogens from these sources. Bioinformatics platform for genome-scale metabolic models Microbial biocatalytic reactions and biodegradation pathways Yes/yes http://metasystems.riken.jp/metabiome/ http://procyc.westcent.usu.edu/cgi-bin/MetaboSearcher.cgi Yes/yes http://procyc.westcent.usu.edu:1555/ Yes/yes http://icbi.at/software/memosys/memosys.shtml Yes/yes http://eawag-bbd.ethz.ch/ Desharky Microbial biodegradation to host metabolites. http://soft.synth-bio.org/desharky.html PathPred Microbial biodegradation Yes/yes http://www.genome.jp/tools-bin/pathpred/pathpred.cgi CRAFT EAWAG-BBD/PPS/BPT Chemical Reactivity and Fate tool Biodegradation of aerobic bacteria Biodegradation information of aerobic/anaerobic bacteria https://www.mn-am.com/products/craft Yes/yes http://eawag-bbd.ethz.ch/ MetaboleExpert Biodegradation by plants and animals http://www.compudrug.com/metabolexpert ModelSEED Microbial and plant metabolic modelling Yes/yes http://modelseed.org/ Constraint-based modelling; MATLAB and Python COBRAToolBox Yes/yes http://opencobra.github.io/cobratoolbox/ OptFlux Tool for metabolic engineering Yes/yes http://www.optflux.org/
BioMed Research International 13 published such as 16S rRNA-based taxonomic microarray for Proteobacteria  and Alphaproteobacteria , Actinomycetes microarray , Bacillus-PhyloChip , Burkholderia-PhyloChip , ECC-PhyloChip , Compost Community-Microarray , Freshwater Sediment- Microarray , Soil microbial community PhyloChip , SRP-PhyloChip , and Nitrifier-Microarray . Recent advancement in sequencing and molecular technologies has opened the doors for metagenomic studies. Captured metagenomics is one example for high resolution study for soil metagenomes [152, 164]. 11.2. Next-Generation Sequencing. The high-throughput next-generation sequencing (HT-NGS) technologies produce a lot more data compared to capillary sequencing based method. Sequencing technology revolution started with Roche 454 GS FLX+ and currently it can produce relatively long read length (approx. 700 bp) and low number of reads (approx. 1 million reads/run) and is used for different applications such as examining 16S variable regions, targeted amplicon sequences, microbial genomes, BACs, and plastids. Illumina is one of the biggest players in the sequencing market with their versatile range of instruments and is ideal for genome sequencing and resequencing, transcriptome sequencing, SNP detection, and metagenomic studies. Illumina read length (50–300 bp) and read number (25 Million–6 billion per run) vary from platform to platform . Ion Torrent technology (Ion PGM and Ion proton) is relatively new and semiconductor based sequencing platform. Potential of the platform varies with respect to the semiconductor chip that is used, that is, Ion 314 Chip v2, Ion 316 Chip v2, and Ion 318 Chip v2 (read length: 200–400 bp, reads/run: 500K– 5 million). It is used for various sequencing applications such as amplicons, small genomes, and targeted genomic sequencing. Automated workflow from sample preparation to analysis makes it ideal for smaller sized studies and routine practices . PacBio RS have been developed for long read lengths through single molecule real-time sequencing technology, which can generate reads from 1 kb up to 60 Kb. Each SMRT cell can generate approx. 50,000 reads. Longer read length feature makes it ideal for sequencing small genomes such as bacteria or viruses, regions of high G/C content and DNA with modified bases (methylation, hydroxymethylation), resequencing projects and so forth . 11.3. Bioinformatics Resources. In 1970, Paulien Hogeweg and Ben Hesper coined the term “bioinformatics” for the study of information processes in biological systems as technique. Currently, bioinformatics is enormously integrated in almost all biological fields. The success of bioinformatics is mainly due to the recent advancements in computational resources andinfrastructureacrosstheglobewhichhasfacilitated bioinformatics research on complex biological systems . Molecular insight in the diversity of the microbial communities is a relatively young field as not much was knownaboutitpriorto1975duetotheunavailabilityof advancemethods,tool,andtechniques.Theadvancement of sequencing and computational technology promoted metagenomics researches which increased the bioinformatics outreach in microbial informatics and experimentation. Further development of the bioinformatics methods resulted in a large number of databases, tools, and data formats for the analysis of microorganism and microbiome related studies which enhanced our knowledge and understanding of microbial populations . In recent years, the advancement of high-throughput next-generation sequencing (NGS) platforms has enabled large scale sequencing efforts for the exploration of microbial ecosystems. Consequently, the microbial ecological analysis in the near future will need a paradigm shift from data generation to data management and sharing and hypothesis driven and targeted data generation , in silico generated knowledge coding, mining, and networking to improve our encoded models for new knowledge discovery [172, 173]. Here (Table 6) we have reviewed major microbial databases and tools that can be useful for microbial research application in emerging applied fields like food waste management and applications. 12. Conclusions Proper disposal of food waste has posed a stern pecuniary and environmental concern. It appears that conversion of food waste into energy via anaerobic processes in terms of methane is economically viable. However, difficulties accompanying the collection as well as transportation of food waste should also be considered. Nevertheless, the stumpy or no cost of food waste along with the environmental aids considering the waste discarding would balance the initial high investment costs of the biorefineries. Moreover, the efficacy and cost base of the generation could be upgraded by intensifying research and optimization studies on assimilating different value-added product manufacturing processes. Competing Interests The authors declare that they have no conflict of interests. Acknowledgments The authors would like to thank Department of Biotechnology and Department of Sciences and Technology, Government of India. References  FAO, Towards the Future we Want: End Hunger and Make the Transition to Sustainable Agricultural and Food Systems, Food and Agriculture Organization of the United Nations Rome, 2012.  M.Melikoglu,C.S.K.Lin,andC.Webb,“Analysingglobalfood waste problem: pinpointing the facts and estimating the energy content,” CentralEuropeanJournalofEngineering,vol.3,no.2, pp.157–164,2013. A.Agarwal,A.Singhmar,M.Kulshrestha,andA.K.Mittal, “Municipal solid waste recycling and associated markets in Delhi, India,” Resources, Conservation and Recycling,vol.44,no. 1,pp.73–90,2005.