Food Waste to Energy: An Overview of Sustainable Approaches for Food Waste Management and Nutrient Recycling

Table 6

Bioinformatics tools and data bases used for microbial community analysis.

Database	Feature description	Web/open source	Availability
Microbial genome and metagenomic data resource
IMG	Integrated Microbial Genomes and Microbiome. Repository of 33,116 genome datasets and 4,615 microbiome dataset	Yes/yes	https://img.jgi.doe.gov/
MGDB	Microbial genome database with 4742 genomes	Yes/yes	http://mbgd.genome.ad.jp/
ENSEMBL	Access to over 40,000 Bacterial Genomes	Yes/yes	http://bacteria.ensembl.org/index.html
RefSeq (microbial)	Archaeal and bacterial repository at NCBI Reference Sequence	Yes/yes	https://www.ncbi.nlm.nih.gov/refseq/
Microarrays and gene expression database
(M3D)	Many Microbe Microarrays Database	Yes/yes	http://m3d.mssm.edu/
BG@Sbase	Microarray datasets for microbial gene expression	Yes/yes	http://bugs.sgul.ac.uk/bugsbase/tabs/experiment.php
COLOMBOS	Collection of bacterial gene expression compendium.	Yes/yes	http://www.colombos.net/
Microbeonline	Repository of 3707 genomes, gene expression data for 113 organisms	Yes/yes	http://www.microbesonline.org/
Taxonomic, Functional Annotation and Comparative Genomics
POGO	Database of Pairwise-Comparisons Of Genomes and Orthologous genes	Yes/yes	http://pogo.ece.drexel.edu/about.php
MicroScope	Microbial Genome Annotation & Analysis Platform	Yes/yes	https://www.genoscope.cns.fr/agc/microscope/home/
AGeS:	A Software System for Microbial Genome Sequence Annotation	Yes/yes	http://www.bhsai.org/ages.html
NMPDR	National Microbial Pathogen Data Resource for annotation, comparative genomics with an emphasis on the food-borne pathogens	Yes/yes	http://www.nmpdr.org/FIG/wiki/view.cgi
MetaPathways:	A pipeline for taxonomic and functional annotation from environmental sequence information.	Yes/yes	http://hallam.microbiology.ubc.ca/MetaPathways/
ShotgunFunctionalizeR	an R-package for functional comparison of metagenomes.	Yes/yes	http://shotgun.math.chalmers.se/
MG-RAST	automated analysis platform for metagenomes based on sequence data	Yes/yes	http://metagenomics.anl.gov/
MEGAN	A comprehensive toolbox for interactively analyzing microbiome data	No/yes	http://ab.inf.uni-tuebingen.de/software/megan6/welcome/
Metabolic analysis and modelling tool and databases
CellDesigner	Metabolic pathway reconstruction and simulation	Yes/yes	http://www.celldesigner.org/
E-zyme	Prediction of EC numbers from chemical transformation pattern	Yes/yes	http://www.genome.jp/tools/e-zyme/
Triton	Tool for Enzyme Engineering	Yes/yes	www.ncbr.muni.cz/triton/
ECMDB	E. coli Metabolme database	Yes/yes	http://ecmdb.ca/
MicrobesFlux:	A web platform for genome reconstruction and constraint-based modelling	Yes/yes	http://www.microbesflux.org/
MetaCyc	MetaCyc Metabolic Pathway Database	Yes/yes	http://metacyc.org/
MetaBioMe	Datamining engine for known Commercially Useful Enzymes (CUEs) in metagenomic datasets and genomes	Yes/yes	http://metasystems.riken.jp/metabiome/
Metabolome Searcher	HTS tool for metabolite identification and metabolic pathway mapping directly from mass spectrometry and metabolites		http://procyc.westcent.usu.edu/cgi-bin/MetaboSearcher.cgi
ProCyc	An open resource for the study of metabolic capabilities in microorganisms from food, environment, and specific pathogens from these sources.	Yes/yes	http://procyc.westcent.usu.edu:1555/
MEMOSys	Bioinformatics platform for genome-scale metabolic models	Yes/yes	http://icbi.at/software/memosys/memosys.shtml
EAWAG-BBD	Microbial biocatalytic reactions and biodegradation pathways	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	Chemical Reactivity and Fate tool; Biodegradation of aerobic bacteria		https://www.mn-am.com/products/craft
EAWAG-BBD/PPS/BPT	Biodegradation information of aerobic/anaerobic bacteria	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/
COBRAToolBox	Constraint-based modelling; MATLAB and Python	Yes/yes	http://opencobra.github.io/cobratoolbox/
OptFlux	Tool for metabolic engineering	Yes/yes	http://www.optflux.org/