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Comprehensive reference data is essential for accurate taxonomic and functional characterization of the human gut microbiome. Here we present the Unified Human Gastrointestinal Genome (UHGG) collection, a resource combining 286,997 genomes representing 4,644 prokaryotic species from the human gut. These genomes contain over 625 million protein sequences used to generate the Unified Human Gastrointestinal Protein (UHGP) catalogue, a collection that more than doubles the number of gut protein clusters over the Integrated Gene Catalogue. We find that a large portion of the human gut microbiome remains to be fully explored, with over 70% of the UHGG species lacking cultured representatives, and 40% of the UHGP missing meaningful functional annotations. Intra-species genomic variation analyses revealed a large reservoir of accessory genes and single-nucleotide variants, many of which were specific to individual human populations. These freely available genomic resources should greatly facilitate investigations into the human gut microbiome.

Background Genomic Observatories (GOs) are sites of long-term scientific study that undertake regular assessments of the genomic biodiversity. The European Marine Omics Biodiversity Observation Network (EMO BON) is a network of GOs that conduct regular biological community samplings to generate environmental and metagenomic data of microbial communities from designated marine stations around Europe. The development of an effective workflow is essential for the analysis of the EMO BON metagenomic data in a timely and reproducible manner. Findings Based on the established MGnify resource, we developed metaGOflow. metaGOflow supports the fast inference of taxonomic profiles from GO-derived data based on ribosomal RNA genes and their functional annotation using the raw reads. Thanks to the Research Object Crate packaging, relevant metadata about the sample under study, and the details of the bioinformatics analysis it has been subjected to, are inherited to the data product while its modular implementation allows running the workflow partially. The analysis of 2 EMO BON samples and 1 Tara Oceans sample was performed as a use case. Conclusions metaGOflow is an efficient and robust workflow that scales to the needs of projects producing big metagenomic data such as EMO BON. It highlights how containerization technologies along with modern workflow languages and metadata package approaches can support the needs of researchers when dealing with ever-increasing volumes of biological data. Despite being initially oriented to address the needs of EMO BON, metaGOflow is a flexible and easy-to-use workflow that can be broadly used for one-sample-at-a-time analysis of shotgun metagenomics data. [ABSTRACT FROM AUTHOR]

The aims of this study were to isolate, characterize and identify the native culturable putative endophytic bacterial community associated with tall fescue ( Festuca arundinacea) cv. SFRO Don Tomás, cultivated in Uruguay, and to study the effects of inoculation on cv. SFRO Don Tomás and the commercial cv. Tacuabé. A total of 342 isolates were collected from surface-sterilized roots, stems and seeds of healthy cv. SFRO Don Tomás. The functional ability of the isolates to produce indole, to solubilize minerals (P, Fe, K) and to biologically fix molecular nitrogen (N) was determined. Several infection traits, such as the ability to produce proteases, peroxidases, cellulases and hemicellulases, were identified in the isolates. Selected bacterial isolates were identified by 16S rRNA sequencing and shown to belong to a broad spectrum of genera, including Bacillus, Microbacterium, Curtobacterium, Streptomyces, Acidovorax, Variovorax, Acinetobacter, Pseudomonas, Pantoea, Rhanella and Xanthomonas. Plant growth promotion assays shown that ten isolates were able to promote the growth of cv. SFRO Don Tomás under gnotobiotic conditions, thereby highlighting the potential of these isolates in biotechnological applications as inoculant for this cultivar which is highly adapted to dry and cold seasons. [ABSTRACT FROM AUTHOR]

Ensembl (www.ensembl.org) is an open platform integrating publicly available genomics data across the tree of life with a focus on eukaryotic species related to human health, agriculture and biodiversity. This year has seen a continued expansion in the number of species represented, with >4800 eukaryotic and >31 300 prokaryotic genomes available. The new Ensembl site, currently in beta, has continued to develop, currently holding >2700 eukaryotic genome assemblies. The new site provides genome, gene, transcript, homology and variation views, and will replace the current Rapid Release site; this represents a key step towards provision of a single integrated Ensembl site. Additional activities have included developing improved regulatory annotation for human, mouse and agricultural species, and expanding the Ensembl Variant Effect Predictor tool. To learn more about Ensembl, help and documentation are available along with an extensive training program that can be accessed via our training pages., (© The Author(s) 2024. Published by Oxford University Press on behalf of Nucleic Acids Research.)