TerrestrialMetagenomeDB: a public repository of curated and standardized metadata for terrestrial metagenomes

Corrêa, Felipe Borim; Saraiva, J.; Stadler, Peter F.; Rocha, Ulisses Nunes da

doi:10.1101/796441

Cited by 11 publications

(16 citation statements)

References 19 publications

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“…Example of database developed for different biomes is the TerrestrialMetagenomeDB for terrestrial metagenomes (Corrêa et al . 2020 ), while similar products have not yet been developed for metagenomic studies from food microbiomes.…”

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confidence: 99%

The food-gut axis: lactic acid bacteria and their link to food, the gut microbiome and human health

Filippis

Pasolli

2020

FEMS Microbiology Reviews

166

108

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Abstract Lactic acid bacteria (LAB) are present in foods, the environment and the animal gut, although fermented foods (FFs) are recognized as the primary niche of LAB activity. Several LAB strains have been studied for their health-promoting properties and are employed as probiotics. FFs are recognized for their potential beneficial effects, which we review in this article. They are also an important source of LAB, which are ingested daily upon FF consumption. In this review, we describe the diversity of LAB and their occurrence in food as well as the gut microbiome. We discuss the opportunities to study LAB diversity and functional properties by considering the availability of both genomic and metagenomic data in public repositories, as well as the different latest computational tools for data analysis. In addition, we discuss the role of LAB as potential probiotics by reporting the prevalence of key genomic features in public genomes and by surveying the outcomes of LAB use in clinical trials involving human subjects. Finally, we highlight the need for further studies aimed at improving our knowledge of the link between LAB-fermented foods and the human gut from the perspective of health promotion.

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confidence: 99%

The food-gut axis: lactic acid bacteria and their link to food, the gut microbiome and human health

Filippis

Pasolli

2020

FEMS Microbiology Reviews

166

108

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“…Currently, numerous research teams around the world have put efforts in trying to collect and harmonize data from different microbiome fields and various curated collections of microbiome datasets have been published, like the TerrestrialMetagenomeDB ( 77 ), the HumanMetagenomeDB ( 40 ), or the Planet Microbe ( 78 ). Each one of these collections is focused on a specific topic and sometimes on a specific type of data and aims at providing each microbiome research sub-field with a valuable resource to perform data-driven meta-analyses.…”

Section: Discussionmentioning

confidence: 99%

SKIOME Project: a curated collection of skin microbiome datasets enriched with study-related metadata

Agostinetto¹,

Bozzi²,

Porro

et al. 2021

Preprint

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Large amounts of data from microbiome-related studies have been (and are currently being) deposited on international public databases. These datasets represent a valuable resource for the microbiome research community and could serve future researchers interested in integrating multiple datasets into powerful meta-analyses. However, this huge amount of data lacks harmonization and is far from being completely exploited in its full potential to build a foundation that places microbiome research at the nexus of many subdisciplines within and beyond biology. Thus, urges the need for data accessibility and reusability, according to FAIR (Findable, Accessible, Interoperable, and Reusable) principles, as supported by National Microbiome Data Collaborative and FAIR Microbiome. To tackle the challenge of accelerating discovery and advances in skin microbiome research, we collected, integrated and organized existing microbiome data resources from human skin 16S rRNA amplicon sequencing experiments. We generated a comprehensive collection of datasets, enriched in metadata, and organized this information into data frames ready to be integrated into microbiome research projects and advanced post-processing analysis, such as data science applications (e.g. machine learning). Furthermore, we have created a data retrieval and curation framework built on three different stages to maximize the retrieval of datasets and metadata associated with them. Lastly, we highlighted some caveats regarding metadata retrieval and suggested ways to improve future metadata submissions. Overall, our work resulted in a curated skin microbiome datasets collection accompanied by a state-of-the-art analysis of the last 10 years of the skin microbiome field.

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“…In 2013, differential coverage binning was used in the first open-source tool for genome-resolved metagenomics [10]. Since then, the bioinformatics community has developed different frameworks specific for genome recovery in Prokaryotes [11–13], Eukaryotes [13–15], and viruses [13,16–19]. Genome-centric metagenomics allows the simultaneous exploration of individual species’ functional potential and phylogeny in a microbial community [20–23].…”

Section: Introductionmentioning

confidence: 99%

MuDoGeR: Multi-Domain Genome Recovery from metagenomes made easy

Rocha

Kasmanas

Kallies

et al. 2022

Preprint

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Several frameworks that recover genomes from Prokaryotes, Eukaryotes, and viruses from metagenomes exist. For those with little bioinformatics experience, it is difficult to evaluate quality, annotate genes, dereplicate, assign taxonomy and calculate relative abundance and coverage from genomes belonging to different domains. MuDoGeR is a user-friendly tool accessible for non-bioinformaticians that make genome recovery from metagenomes of Prokaryotes, Eukaryotes, and viruses alone or in combination easy. By testing MuDoGeR using 574 metagenomes and 24 genomes, we demonstrated users could run it in a few samples or high-throughput. MuDoGeR is an open-source software available at https://github.com/mdsufz/MuDoGeR.

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TerrestrialMetagenomeDB: a public repository of curated and standardized metadata for terrestrial metagenomes

Cited by 11 publications

References 19 publications

The food-gut axis: lactic acid bacteria and their link to food, the gut microbiome and human health

The food-gut axis: lactic acid bacteria and their link to food, the gut microbiome and human health

SKIOME Project: a curated collection of skin microbiome datasets enriched with study-related metadata

MuDoGeR: Multi-Domain Genome Recovery from metagenomes made easy

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