Abstract
The term microbe refers to the diverse spectrum of microscopic archaea, bacteria, protist, fungi, and algae, of which some are beneficial, whereas others might be harmful. Being omnipresent, these microbes impact the entire biosphere with the human body being no exception. All the microbiota that reside within and outside the human body constitute the human microbiome, the study of which in recent times has garnered much importance due to the advancement in the understanding of the role of microbes in normal human physiology as well as pathology. This has led to a notable surge in the available sequenced genome data generated from various microbial genomics and metagenomic studies. This big data being heterogenous in nature makes it difficult for the researchers to analyze and interpret them. As such, databases and bioinformatic tools, both existing ones and newly emerging, aim to curate this data for easy access and analysis by the people. This chapter thus summarizes various microbe-related databases, specifies the information stored and retrievable from them, and attempts to shed light on various bioinformatic tools and their application in microbial genomic and human microbiome studies.
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Abbreviations
- AIDS:
-
Acquired immunodeficiency syndrome
- AMDB:
-
Animal microbiome database
- BV-BRC:
-
Bacterial and Viral Bioinformatics Resource Center
- CGED:
-
Cancer gene expression database
- DB:
-
Database
- DDBJ:
-
DNA Data Bank of Japan
- DNA:
-
Deoxyribonucleic acid
- EBI:
-
European Bioinformatics Institute
- eHOMD:
-
Expanded Human Oral Microbiome Database
- EMBL:
-
European Molecular Biology Laboratory
- GEO:
-
Gene Expression Omnibus
- GOLD:
-
Genomes OnLine Database
- GTDB:
-
Genome Taxonomy Database
- HGD:
-
Human Genome Database
- HGFs:
-
Host genetic factors
- HGMA:
-
Human Gut Microbiome Atlas
- HIFs:
-
Host immune factors
- HIV:
-
Human immunodeficiency viruses
- HPC:
-
High-performance computing
- IMG/M:
-
Integrated Microbial Genomes/Microbiome
- IMG/VR:
-
Integrated Microbial Genomes/Viral
- INSDC:
-
International Nucleotide Sequence Database
- IRD:
-
Influenza Research Database
- JGI:
-
Joint Genome Institute
- KEGG:
-
Kyoto Encyclopedia of Genes and Genomes
- MADET:
-
Microbiomics of Anticancer Drug Efficacy and Toxicity
- MASI:
-
Microbiota-Active Substance Interactions database
- MBGB:
-
Microbial Genome Database
- MiST:
-
Microbial Signal Transduction Database
- MLST:
-
Multilocus sequence typing
- NCBI:
-
National Center for Biotechnology Information
- NGS:
-
Next-generation sequencing
- NIH:
-
National Institute of Health
- NMDC:
-
National Microbiome Data Collaborative
- OMIM:
-
Online Mendelian Inheritance in Man
- PaVE:
-
Papillomavirus Episteme
- PDB:
-
Protein Data Bank
- RNA:
-
Ribonucleic acid
- RVDB:
-
Reference Viral Database
- SGD:
-
Saccharomyces Genome Database
- UCSC:
-
University of California-Santa Cruz
- VEP:
-
Variant Effect Predictor
- VEuPathDB:
-
Eukaryotic Pathogen, Vector and Host Informatics Process
- ViPR:
-
Virus Pathogen Database and Analysis Resource
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We would like to acknowledge the Department of MBBT, Tezpur Central University, for providing computational facilities.
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Hojaisa, S., Jha, A.N. (2023). Databases and Tools for Microbial Genome and Human Microbiome Studies. In: Verma, P. (eds) Industrial Microbiology and Biotechnology. Springer, Singapore. https://doi.org/10.1007/978-981-99-2816-3_3
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