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Background Metagenomes can be analysed using different approaches and tools. One of the most important distinctions is the way to perform taxonomic and functional assignment, choosing between the use of assembly algorithms or the direct analysis of raw sequence reads instead by homology searching, k-mer analysys, or detection of marker genes. Many instances of each approach can be found in the literature, but to the best of our knowledge no evaluation of their different performances has been carried on, and we question if their results are comparable. Results We have analysed several real and mock metagenomes using different methodologies and tools, and compared the resulting taxonomic and functional profiles. Our results show that database completeness (the representation of diverse organisms and taxa in it) is the main factor determining the performance of the methods relying on direct read assignment either by homology, k-mer composition or similarity to marker genes, while methods relying on assembly and assignment of predicted genes are most influenced by metagenomic size, that in turn determines the completeness of the assembly (the percentage of read that were assembled). Conclusions Although differences exist, taxonomic profiles are rather similar between raw read assignment and assembly assignment methods, while they are more divergent for methods based on k-mers and marker genes. Regarding functional annotation, analysis of raw reads retrieves more functions, but it also makes a substantial number of over-predictions. Assembly methods are more advantageous as the size of the metagenome grows bigger.

Background Despite the important role that microorganisms play in environmental processes, the low percentage of cultured microbes (5%) has limited, until now, our knowledge of their ecological strategies. However, the development of high-throughput sequencing has generated a huge amount of genomic and metagenomic data without the need of culturing that can be used to study ecological questions. This study aims to estimate the functional capabilities, genomic sizes and 16S copy number of different taxa in relation to their ubiquity and their environmental preferences. Results To achieve this goal, we compiled data regarding the presence of each prokaryotic genera in diverse environments. Then, genomic characteristics such as genome size, 16S rRNA gene copy number, and functional content of the genomes were related to their ubiquity and different environmental preferences of the corresponding taxa. The results showed clear correlations between genomic characteristics and environmental conditions. Conclusions Ubiquity and adaptation were linked to genome size, while 16S copy number was not directly related to ubiquity. We observed that different combinations of these two characteristics delineate the different environments. Besides, the analysis of functional classes showed some clear signatures linked to particular environments.

Nematodes typically comprise the most abundant phylum in meiofaunal communities. We aim to characterize the specific ecological conditions that influence Nematoda communities in Posidonia oceanica grasslands focusing on three habitats: leaves, matte, and unvegetated adjacent sediment. We hypothesized that the constant flux of nutrients under the canopy would result in a higher concentration of metazoans compared to the unvegetated sediment outside; however, the hypothesis was not confirmed by the obtained results. The habitat heterogeneity played an important role in shaping the community, yielding a greater richness in the matte. The resource specificity of the leaves (microepiphytes) was also expected to shape the community by favoring nematodes capable of exploiting this resource (epistratum feeders with scraping-like structures), such as the family Chromadoridae that dominated this habitat. In addition, the high light exposure of the leaves explains the higher concentration of ocellated nematodes in this habitat. Organic carbon and nitrogen contents had an impact on the Nematoda community composition, meanwhile average grain size only affected the abundance of nematodes with elongated/filiform tails.

Patients’ quality of life is a key consideration of chronic kidney disease care. Nonetheless, qualitative research on patients’ experience, quality of life, and frequent associated comorbidities remains limited. This study identifies aspects of the disease experience, healthcare journey, and caregiver experience contributing to quality of life for early-stage (stage 3 CKD) and advanced chronic kidney disease (stages 4–5) patients and their caregivers. In this cross-sectional, observational, multicenter study based on qualitative methodology, participants completed a general (Short Form-36) and disease-specific (Kidney Disease Quality of Life Short Form−36) quality of life assessment and semi-structured interviews. Quota and convenience sampling were used to enroll 36 patients selected by clinicians based on chronic kidney disease stage and the presence of key comorbidities (heart failure, hyperkalemia). Twelve caregivers were also invited to participate in patient interviews. All data were examined thematically. Three themes emerged: (1) Impact of chronic kidney disease on quality of life throughout the patient journey (physical, social, and emotional); (2) attitudes toward the disease (characterized by ‘acceptance’ or ‘powerlessness’); and (3) caregivers’ role and burden. Patients’ characteristics and caregiver support must be considered for designing medical interventions and improvement of patient-doctor communication. Family caregivers are pillars clinicians should rely on to raise awareness about chronic kidney disease’s relevance among patients and families.

The genus Salmonella comprises two species, Salmonella bongori and Salmonella enterica , which are infectious to a wide variety of animal hosts. The diversity within S. enterica has been further partitioned into 6–10 subspecies based on such features as host range, geography, and most recently, genetic relatedness and phylogenetic affiliation. Although Salmonella pathogenicity is attributable to large numbers of acquired virulence factors, the extent of homologous exchange in the species at large is apparently constrained such that the species and subspecies form distinct clusters of strains. To explore the extent of gene flow within and among subspecies, and to ultimately define true biological species, we evaluated patterns of recombination in over 1,000 genomes currently assigned to the genus. Those Salmonella subspecies containing sufficient numbers of sequenced genomes to allow meaningful analysis — i.e., subsp. enterica and diarizonae —were found to be reproductively isolated from one another and from all other subspecies. Based on the configuration of genomic sequence divergence among subspecies, it is expected that each of the other Salmonella subspecies will also represent a biological species. Our findings argue against the application of prescribed nucleotide-identity thresholds to delineate bacterial species and contend that the Biological Species Concept should not be disregarded for bacteria, even those, like Salmonella , that demonstrate complex patterns of species and subspecies divergence. The Biological Species Concept (BSC), which defines species boundaries based on the capacity for gene exchange, is widely used to classify sexually reproducing eukaryotes but is generally thought to be inapplicable to bacteria due to their completely asexual mode of reproduction. We show that the genus Salmonella , whose thousands of described serovars were formerly considered to be strictly clonal, undergoes sufficient levels of homologous recombination to be assigned to species according to the BSC. Aside from the two recognized species, Salmonella enterica and Salmonella bongori , several (and likely all) of the subspecies within S. enterica are reproductively isolated from one another and should each be considered a separate biological species. These findings demonstrate that species barriers in bacteria can form despite high levels of nucleotide identity and that commonly applied thresholds of genomic sequence identity are not reliable indicators of bacterial species status.

The population with concomitant heart and kidney disease (often termed ‘cardiorenal’ disease) is expected to grow, significantly impacting public health and healthcare utilization. Moreover, the cardiorenal nexus encompasses a bidirectional relationship that worsens prognosis and may complicate pharmacological management in often elderly and frail patients. Therefore, a more cohesive multidisciplinary team approach aiming to provide holistic, coordinated and specialized care would be a positive shift towards improving patient outcomes and optimizing healthcare resources. This article aims to define the organizational aspects and key elements for setting up a multidisciplinary cardiorenal clinical program as a potential healthcare model adapted to the particular characteristics of patients with cardiorenal disease. Graphical Abstract Graphical Abstract

Abstract Escherichia coli have served as important model organisms for over a century—used to elucidate key aspects of genetics, evolution, molecular biology, and pathogenesis. However, defining which strains actually belong to this species is erratic and unstable due to shifts in the characters and criteria used to distinguish bacterial species. Additionally, many isolates designated as E. coli are genetically more closely related to strains of Shigella than to other E. coli, creating a situation in which the entire genus of Shigella and its four species are encompassed within the single species E. coli. We evaluated all complete genomes assigned to E. coli and its closest relatives according to the biological species concept (BSC), using evidence of reproductive isolation and gene flow (i.e., homologous recombination in the case of asexual bacteria) to ascertain species boundaries. The BSC establishes a uniform, consistent, and objective principle that allows species-level classification across all domains of life and does not rely on either phenotypic or genotypic similarity to a defined type-specimen for species membership. Analyzing a total of 1,887 sequenced genomes and comparing our results to other genome-based classification methods, we found few barriers to gene flow among the strains, clades, phylogroups, or species within E. coli and Shigella. Due to the utility in recognizing which strains constitute a true biological species, we designate genomes that form a genetic cohesive group as members of E. coliBIO.

Heart failure (HF), particularly of an ischemic etiology, is steadily increasing worldwide. Non-anemic iron deficiency (ID) is highly prevalent among HF patients, and it has been related to worse outcomes. Growth differentiation factor 15 (GDF15) has been related to atherosclerotic cardiovascular (CV) disease, HF and iron pathophysiology. Nevertheless, the specific potential role of GDF15 in HF patients with ID has not been fully explored. In this cross-sectional study we determined serum GDF15 levels in 60 HF patients with ID from the IRON-PATH II study. The discriminative capacity of GDF15 in logistic regression models for classifying these patients according to ischemic etiology was defined as the primary endpoint. Additionally, relationships between GDF15 levels and impaired right ventricle function, impaired functional capacity and HF were included as secondary endpoints. GDF15 was inversely related to tricuspid annular plane systolic excursion (TAPSE) and the six-minute walking test (6MWT), and positively related to hallmarks of HF [i.e., N-terminal prohormone of brain natriuretic peptide (NT-proBNP)] and other molecules influenced by HF progression [i.e., creatinine and ferritin]. Moreover, GDF15 was inversely related to hemoglobin, suggesting a potential link to iron homeostasis. Furthermore, GDF15 showed good classification capacity and improved the accuracy of a logistic regression model for ischemic HF classification in patients with ID. Overall, the findings of this study propose serum GDF15 levels as a potential tool for the classification of HF patients with ID according to the ischemic etiology.

Worsening kidney function (WKF) is common in patients with acute heart failure (AHF) syndromes. Although WKF has traditionally been associated with worse outcomes on a population level, serum creatinine concentrations vary greatly during episodes of worsening heart failure, with substantial individual heterogeneity in terms of their clinical meaning. Consequently, interpreting such changes within the appropriate clinical context is essential to unravel the pathophysiology of kidney function changes and appropriately interpret their clinical meaning. This article aims to provide a critical overview of WKF in AHF, aiming to provide physicians with some tips and tricks to appropriately interpret kidney function changes in the context of AHF. Lay Summary In this article we thoroughly review the literature on a debatable topic in cardiorenal medicine. We aimed to provide physicians with some tips and tricks for interpreting kidney function changes in patients with acute heart failure syndromes.

Cystic fibrosis (CF) lung microbiota composition has recently been redefined by the application of next-generation sequencing (NGS) tools, identifying, among others, previously undescribed anaerobic and uncultivable bacteria. In the present study, we monitored the fluctuations of this ecosystem in 15 CF patients during a 1-year follow-up period, describing for the first time, as far as we know, the presence of predator bacteria in the CF lung microbiome. In addition, a new computational model was developed to ascertain the hypothetical ecological repercussions of a prey-predator interaction in CF lung microbial communities. Fifteen adult CF patients, stratified according to their pulmonary function into mild ( n = 5), moderate ( n = 9), and severe ( n = 1) disease, were recruited at the CF unit of the Ramón y Cajal University Hospital (Madrid, Spain). Each patient contributed three or four induced sputum samples during a 1-year follow-up period. Lung microbiota composition was determined by both cultivation and NGS techniques and was compared with the patients’ clinical variables. Results revealed a particular microbiota composition for each patient that was maintained during the study period, although some fluctuations were detected without any clinical correlation. For the first time, Bdellovibrio and Vampirovibrio predator bacteria were shown in CF lung microbiota and reduced-genome bacterial parasites of the phylum Parcubacteria were also consistently detected. The newly designed computational model allows us to hypothesize that inoculation of predators into the pulmonary microbiome might contribute to the control of chronic colonization by CF pathogens in early colonization stages. IMPORTANCE The application of NGS to sequential samples of CF patients demonstrated the complexity of the organisms present in the lung (156 species) and the constancy of basic individual colonization patterns, although some differences between samples from the same patient were observed, probably related to sampling bias. Bdellovibrio and Vampirovibrio predator bacteria were found for the first time by NGS as part of the CF lung microbiota, although their ecological significance needs to be clarified. The newly designed computational model allows us to hypothesize that inoculation of predators into the lung microbiome can eradicate CF pathogens in early stages of the process. Our data strongly suggest that lower respiratory microbiome fluctuations are not necessarily related to the patient’s clinical status. The application of NGS to sequential samples of CF patients demonstrated the complexity of the organisms present in the lung (156 species) and the constancy of basic individual colonization patterns, although some differences between samples from the same patient were observed, probably related to sampling bias. Bdellovibrio and Vampirovibrio predator bacteria were found for the first time by NGS as part of the CF lung microbiota, although their ecological significance needs to be clarified. The newly designed computational model allows us to hypothesize that inoculation of predators into the lung microbiome can eradicate CF pathogens in early stages of the process. Our data strongly suggest that lower respiratory microbiome fluctuations are not necessarily related to the patient’s clinical status.