Biology subjects

Ribeiro, T. G.

Publications and source records attributed to Ribeiro, T. G..

6 recordsLinked to original sources

bioRxiv2026

Gardnerella fastidiominuta sp. nov. isolated from the female urinary microbiome

The genus Gardnerella comprises a group of fastidious bacteria associated with the female urogenital tract and has undergone extensive taxonomic revision in recent years. In this study, a bacterial strain, designated CCPDSM, was isolated from the female urinary microbiome and subjected to a comprehensive polyphasic taxonomic characterization. The 16S rRNA gene sequence confirmed that this strain is a member of the genus Gardnerella, and phylogenetic analyses based on cpn60 sequences, together with phylogenomic reconstruction placed strain CCPDSM within the genus Gardnerella as a distinct and well-supported lineage. Genome-based relatedness indices (ANIb, ANIm, TETRA and dDDH), demonstrated clear separation of CCPDSM from all validly published Gardnerella species. In contrast, comparisons with two publicly available closely related genomes yielded values above accepted species delineation thresholds, supporting their assignment to the same taxon. Phenotypic characterization, together with genome-based functional predictions, revealed a fastidious, fermentative metabolic profile that further differentiated CCPDSM from its closest relatives, while remaining consistent with traits characteristic of the genus. On the basis of combined phylogenetic, genomic and phenotypic evidence, strain CCPDSM is proposed as representing a novel species within the genus Gardnerella, for which the name Gardnerella fastidiominuta sp. nov. is proposed, with strain CCPDSM (=CECT 31324=CCP 588) designated as the type strain. This study expands the recognized diversity of Gardnerella and highlights the female urinary tract as a reservoir of previously uncharacterized species within this genus.

microbiology↗

bioRxiv2025

Unraveling the Gardnerella Pangenome: Insights into Genetic Diversity, Virulence, and Antibiotic Resistance

In recent years, the development of user-friendly and accessible bioinformatic tools has significantly advanced Gardnerella genome analysis. Despite the taxonomic reclassification of the genus in 2019, many studies continue to rely on subgroups/ clades for species identification. This leads to frequent misidentifications, hindering accurate assessments of species-specific features, such as antimicrobial resistance and pathogenic potential. This study aims to address these gaps by employing precise species-level identification to improve our understanding on Gardnerella and its clinical implications. We performed the most extensive pangenome analysis of Gardnerella to date, analyzing 153 genomes (120 from NCBI and 33 newly sequenced). G. vaginalis, G. leopoldii, G. swidsinskii, and G. pickettii species exhibited open pangenomes. The Gardnerella pangenome is highly diverse, with 90% of its genes belonging to the accessory genome. Carbohydrate transport and metabolism contributed the most for the primary genomic differences observed among Gardnerella species. Additionally, the search for antibiotic resistance genes (ARGs) revealed lsaC gene as the most prevalent ARG, potentially conferring resistance to clindamycin, a commonly prescribed antibiotic for treating bacterial vaginosis (BV). The clustering of Gardnerella genomes mimics the core genome phylogeny, pointing to species specific virulence-associated factors, highlighting important factors such as vaginolysin and sialidases. Our comprehensive pangenome analysis shows that Gardnerella species are well-adapted within the urogenital tract, with identified virulence factors and metabolic capabilities potentially enhancing the pathogenicity of some strains. Future studies should explore Gardnerellas ecological interactions and pathogenic mechanisms within the urogenital microbiome. ImportanceIn recent years, the availability of user-friendly and accessible bioinformatics tools has led to a surge in studies analyzing the Gardnerella genome. Despite the redefinition of the genus in 2019, many researchers continue to rely on subgroups or clades for Gardnerella identification. Our study builds upon the updated taxonomy of Gardnerella, offering a more comprehensive understanding of its genetic diversity. By conducting a pangenome analysis of 153 Gardnerella genomes, we uncover significant genetic variability, species-specific virulence factors, and the widespread presence of antibiotic resistance genes, highlighting the urgent need for precise species-level identification. The identification of novel genomic features and antibiotic resistance profiles not only enhances our understanding of Gardnerellas clinical implications but also sheds light on its metabolic and virulence potential. These insights help clarify the pathogenic mechanisms of Gardnerella and provide a more refined understanding of its role in the urogenital microbiome.

microbiology↗

bioRxiv2023

Litter Matters: The Importance of Decomposition Products for Soil Bacterial Diversity and abundance of key groups of the N cycle in Tropical Areas

This study investigated the contribution of soil organic layers to bacterial diversity evaluations. We used a forest in the eastern Amazon and an adjacent pasture as model systems. Distinct organic and organo-mineral layers were identified in the forest and pasture floors, including the litter, partially and wholly decomposed organic material, and the mineral and rhizospheric soils. DNA was extracted, and 16S rRNA gene sequencing and qPCR were performed to assess bacterial community structure and the abundance of critical groups of the N cycle. We observed a clear vertical gradient in bacterial community composition. Species followed a log-normal distribution, with the highest richness and diversity observed in transitional organic layers of both land uses. Generally, critical groups of the N cycle were more abundant in these transitional layers, especially in the pastures fragmented litter and in the forests partially decomposed organic material. Considering the organic layers increased diversity estimates significantly, with the highest alpha and gamma bacterial diversity observed on the pasture floor and the highest beta diversity on the forest floor. The results show that organic layers harbor significant bacterial diversity in natural and anthropized systems and suggest that they can be crucial for maintaining the N cycle in these ecosystems, highlighting the need to consider them when studying soil bacterial diversity.

microbiology↗

bioRxiv2020

Land-use and forest floor explain prokaryotic metacommunity structuring and spatial turnover in Amazonian forest-to-pasture conversion areas

Advancing extensive cattle production shifts the forest landscape and is considered one of the main drivers against biodiversity conservation in the Brazilian Amazonia. Considering soil as an ecosystem it becomes vital to identify the effects of land-use changes on soil microbial communities, structure, as well as its ecological functions and services. Herein, we explored relationships between land-use, soil types and forest floor (i.e., association between litter, root layer and bulk soil) on the prokaryotic metacommunity structuring in the Western Amazonia. Sites under high anthropogenic pressure were evaluated along a gradient of {+/-} 800 km. Prokaryotic metacommunity are synergistically affected by soil types and land-use systems. Especially, the gradient of soil fertility and land-use shapes the structuring of the metacommunity and determines its composition. Forest-to-pasture conversion increases alpha, beta, and gamma diversities when considering only the prokaryotes from the bulk soil. Beta diversity was significantly higher in all forests when the litter and root layer were taken into account with the bulk soil. Our argumentation is that the forest floor harbors a prokaryotic metacommunity that adds at the regional scale of diversity a spatial turnover hitherto underestimated. Our findings highlight the risks of biodiversity loss and, consequently, the soil microbial diversity maintenance in tropical forests.

microbiology↗

bioRxiv2020

Humic acids enrich the plant microbiota with bacterial candidates for the suppression of pathogens

Humic acids (HAs) stimulate the growth of several plant species by regulating their hormonal and redox metabolisms. Nevertheless, studies on the relationship of these substances with the plant-associated microbiota are almost nonexistent. Here, we hypothesized that the effect of HAs occurs in parallel with the regulation of the plant-associated bacterial community. Our results show the positive influence of HAs on the growth of rice and its stimulation of the root system. Metataxonomics revealed that the structure and composition of root bacterial communities were affected upon the application of HAs. Chitinophaga and Mucilaginibacter were the predominant genera in HA-treated roots. These bacteria produce enzymes that degrade compounds like those present in the wall of fungi, oomycetes, and nematode eggs. Pseudomonas and the Gp 1 group of Acidobacteria, both siderophore-producers and plant-growth promoters were also enriched, although with lower abundances. Given these results, we suggest that plants recruit these microorganisms in response to the stress caused by the HA-root interaction. For the first time, our findings indicate that HA-stimulated plants adopt the ecological strategy of recruiting members of the bacterial community that are candidates for the suppression of pathogens and, therefore, involved in plant defense.

microbiology↗

bioRxiv2019

Significant temporal shifts on clonal and plasmid backgrounds of Enterobacteriaceae producing acquired AmpC in Portuguese clinical settings

OBJECTIVESTo provide detailed molecular data on clinical acquired AmpC (qAmpC)-producing Enterobacteriaceae from two different periods (2002-2008 and 2010-2013) in order to clarify the contribution of clonal and plasmid genetic platforms for the current epidemiological scenario concerning extended-spectrum beta-lactams resistance. METHODSWe analysed 1246 Enterobacteriaceae non-susceptible to third-generation cephalosporins from 2 hospitals and 1 community laboratory between 2010 and 2013. Bacterial identification, antibiotic susceptibility, identification of qAmpC and plasmid-mediated quinolone resistance genes, clonal (PFGE, MLST) and plasmid (S1-/I-CeuI-PFGE, replicon typing, hybridization) analysis were performed by standard methods. WGS was performed in two ST11-K. pneumoniae isolates harbouring DHA-1. RESULTSThe occurrence of qAmpC was lower (2.6%) than that observed in a previous survey (7.4%), and varied slightly over time. Isolates produced DHA-1 (53%), CMY-2 (44%) or DHA-6 (3%), but significant epidemiological changes were observed in the two surveys. While DHA-1 persisted in different institutions by selection of a worldwide epidemic IncR plasmid in a ST11 harbouring KL105, CMY-2 rates increased over time linked to IncI1 plasmids (instead of IncK or IncA/C2) in multiple E. coli clones. CONCLUSIONSThe higher frequency of DHA-1 qAmpC in these species contrasts with the scenario of most European countries. Furthermore, the different genetic backgrounds associated with either ESBL or qAmpC in our country might have contributed to their differential expansion.

epidemiology↗