Because of its outstanding biological and industrial importance, many efforts have been made to characterize the mycobiota of new environments and their biochemical and biotechnological potentials. Gut mycobiota can be a source of novel yeasts with the potential to be used as probiotics or have industrial applications. In this work, we characterized two as-yet unexplored yeast communities from the intestinal content of the cultured marine Chilean fishes Genypterus chilensis (G. chilensis) and Seriolella violacea (S. violacea). Yeasts were isolated through culture, identified by sequencing their ITS region, and characterized their enzymatic profile with API^®ZYM. Rhodotorula mucilaginosa was identified in both fish species. For the first time, Candida palmioleophila, Candida pseudorugosa, Cystobasidium slooffiae, and a member of the Yamadazyma genus were also identified and described as part of the normal fish gut–microbiota. Furthermore, the diverse enzymatic profile exhibited by some of these isolates suggests that it may be possible to develop novel applications for them, such as new probiotics and other biotechnological applications.

The human gut microbiome is associated with numerous health outcomes, often in a region-specific manner. Unfortunately, global microbiome research remains profoundly imbalanced: over 70% of sequenced human microbiomes originate from Europe and North America, which together represent only 15% of the world’s population. To address this disparity, we developed saMBA—the largest archive of gut microbiomes from South America, one of the world’s most microbiome-diverse regions but also among the least studied. The archive comprises 33 studies, ~73% of which had not been included in any previous compendium. A total of 3382 samples were reanalysed, of which 2913 were successfully included after applying quality filters. By leveraging this resource, we reveal both high within-population diversity and between-population uniqueness in the continent, expanding our current understanding of the gut microbiome to be more globally representative. Additionally, saMBA reveals that much of the region’s gut microbiome diversity remains undercharacterised, and provides guidance for future sampling efforts to more accurately capture regional biodiversity. The framework used to build saMBA is compatible with existing global resources and is openly available, thus promoting the inclusion of other underrepresented populations to accelerate microbiome research globally.

The expansion of microbiome research has led to the accumulation of interlinked datasets encompassing versatile taxonomic and functional assays. The analysis of increasingly large and heterogeneous multi-modal microbiome data would benefit from unified approaches supporting the design of modular data science workflows through interoperable methods. The Bioconductor project has recently developed an optimized statistical programming framework for multi-assay data integration. Building on this foundation, we introduce a community-developed open source ecosystem for microbiome data science. In contrast to the previous alternatives, the methodology is specifically designed to support joint analysis of hierarchical, interlinked, and heterogeneous multi-table datasets that are increasingly common in modern microbiome research. This data science ecosystem encompasses open data, methods, tutorials, and an active online community. These resources support standardized and reproducible data wrangling, joint analysis, and reporting. We have detailed the functionality and usage in the online book https://microbiome.github.io/OMA , which offers guidance for prospective users and contributors.

Lactiplantibacillus plantarum is a commensal bacterial species often found within the human gut. To expand our knowledge about this human-associated taxon with potential probiotic properties, here we present the draft genome sequence of Lactiplantibacillus plantarum strain APC2688, isolated from a human fecal sample.

The composition and function of the human gut microbiome has been linked to multiple health outcomes across all world regions, often with region-specific associations. Unfortunately, the extent to which microbiomes from different populations are characterised is limited by their economic resources. Over 70% of the sequenced human microbiomes come from analyses of European and North American populations, skewing our understanding by focusing excessively on just 15% of the global population. Thus, entire continents rely on results from research conducted in wealthier countries whose main findings are unlikely to generalize across other world regions. Moreover, statistical models perform poorly when applied to minorities, a blind spot with serious consequences in biomedicine, and which can only be addressed by analysing microbiome data from currently neglected areas. To address this problem, we created saMBA— the largest archive of gut microbiomes from South America, one of the world’s most biodiverse regions in terms of the gut microbiome of its inhabitants, yet the one with the fewest samples. ‘saMBA’ includes 33 gut microbiome studies, ∼73% of which were incorporated in a microbiome archive for the first time. By leveraging this resource, we uncovered a high biodiversity within —and uniqueness between— gut microbiomes across the continent, expanding the concept of the healthy microbiome to be more globally representative. Additionally, our results highlight that the gut microbiome biodiversity of this region remains far from fully characterized. We demonstrate how saMBA can guide new sampling efforts to better capture this diversity. Finally, the code deployed to build saMBA is compatible with that of a previous global compendium and is openly available to researchers from other underrepresented regions, fostering the inclusion of other neglected populations to accelerate microbiome research globally.