Ecosystem-specific microbiota and microbiome databases in the era of big data

Abstract

The rapid development of sequencing methods over the past decades has accelerated both the potential scope and depth of microbiota and microbiome studies. Recent developments in the field have been marked by an expansion away from purely categorical studies towards a greater investigation of community functionality. As in-depth genomic and environmental coverage is often distributed unequally across major taxa and ecosystems, it can be difficult to identify or substantiate relationships within microbial communities. Generic databases containing datasets from diverse ecosystems have opened a new era of data accessibility despite costs in terms of data quality and heterogeneity. This challenge is readily embodied in the integration of meta-omics data alongside habitat-specific standards which help contextualise datasets both in terms of sample processing and background within the ecosystem. A special case of large genomic repositories, ecosystem-specific databases (ES-DB’s), have emerged to consolidate and better standardise sample processing and analysis protocols around individual ecosystems under study, allowing independent studies to produce comparable datasets. Here, we provide a comprehensive review of this emerging tool for microbial community analysis in relation to current trends in the field. We focus on the factors leading to the formation of ES-DB’s, their comparison to traditional microbial databases, the potential for ES-DB integration with meta-omics platforms, as well as inherent limitations in the applicability of ES-DB’s.

Big Data for a Small World: A Review on Databases and Resources for Studying Microbiomes

“…Identified small molecules from these environments show the extreme metabolic capacity of the extremophiles 28 . Despite having many microbiome databases capturing the meta-omics of the environmental microbiome from different environments, they lack meta-information from the environments, which are very crucial factors in exploring the context-specific variation in altering the composition and functionality of the community 69 .…”

Fish disease prevention via microbial dysbiosis‐associated biomarkers in aquaculture

“…Results may be biased due to methodological differences in sampling, preservation, sequencing methods, reference databases, or subsequent bioinformatic analysis. It is therefore of paramount importance to develop standardized guidelines to ensure the reliability of different assays and facilitate comparison between studies, as we have recently described elsewhere 116 . Much of the current research in this field has instead focused on human medical applications, though the field of aquaculture can clearly benefit from similar efforts to develop more specific tools and databases to address coverage and reference shortcomings.…”

“…between studies, as we have recently described elsewhere. 116 Much of the current research in this field has instead focused on human medical applications, though the field of aquaculture can clearly benefit from similar efforts to develop more specific tools and databases to address coverage and reference shortcomings.…”

Microbiota shaping and bioburden monitoring of indoor antimicrobial surfaces

“…Metagenomics can be used to detect known species as well as unknown microbes (Ko et al, 2022). In addition, multiomics approaches that can help identify connections between the microbiome of an antimicrobial surface and human gene expression can be beneficial for studies on AMC health risks (Lobanov et al, 2022;Park et al, 2022) The microbial metabolomics-based approach can provide an additional methodological repertoire for surface hygiene studies, complementing metagenomic, metatranscriptomic, and proteomic analyses (Tang, 2011;Vernocchi et al, 2016;Ahn and Hayes, 2021). Although metagenomic mappings of interior surfaces have been carried out for a decade, genetic real-life studies of AMCs are scarce.…”