The Preventive Role of Glutamine Supplementation in Cardiac Surgery-Associated Kidney Injury from Experimental Research to Clinical Practice: A Narrative Review.

Acute kidney injury represents a significant threat in cardiac surgery regarding complications and costs. Novel preventive approaches are needed, as the therapeutic modalities are still limited. As experimental studies have demonstrated, glutamine, a conditionally essential amino acid, might have a protective role in this setting. Moreover, the levels of glutamine after the cardiopulmonary bypass are significantly lower. In clinical practice, various trials have investigated the effects of glutamine supplementation on cardiac surgery with encouraging results. However, these studies are heterogeneous regarding the selection criteria, timing, dose, outcomes studied, and way of glutamine administration. This narrative review aims to present the potential role of glutamine in cardiac surgery-associated acute kidney injury prevention, starting from the experimental studies and guidelines to the clinical practice and future directions.

Freshwater genome-reduced bacteria exhibit pervasive episodes of adaptive stasis.

The emergence of bacterial species is rooted in their inherent potential for continuous evolution and adaptation to an ever-changing ecological landscape. The adaptive capacity of most species frequently resides within the repertoire of genes encoding the secreted proteome (SP), as it serves as a primary interface used to regulate survival/reproduction strategies. Here, by applying evolutionary genomics approaches to metagenomics data, we show that abundant freshwater bacteria exhibit biphasic adaptation states linked to the eco-evolutionary processes governing their genome sizes. While species with average to large genomes adhere to the dominant paradigm of evolution through niche adaptation by reducing the evolutionary pressure on their SPs (via the augmentation of functionally redundant genes that buffer mutational fitness loss) and increasing the phylogenetic distance of recombination events, most of the genome-reduced species exhibit a nonconforming state. In contrast, their SPs reflect a combination of low functional redundancy and high selection pressure, resulting in significantly higher levels of conservation and invariance. Our findings indicate that although niche adaptation is the principal mechanism driving speciation, freshwater genome-reduced bacteria often experience extended periods of adaptive stasis. Understanding the adaptive state of microbial species will lead to a better comprehension of their spatiotemporal dynamics, biogeography, and resilience to global change.

Phenology and ecological role of aerobic anoxygenic phototrophs in freshwaters.

BACKGROUND: Aerobic anoxygenic phototrophic (AAP) bacteria are heterotrophic bacteria that supply their metabolism with light energy harvested by bacteriochlorophyll-a-containing reaction centers. Despite their substantial contribution to bacterial biomass, microbial food webs, and carbon cycle, their phenology in freshwater lakes remains unknown. Hence, we investigated seasonal variations of AAP abundance and community composition biweekly across 3 years in a temperate, meso-oligotrophic freshwater lake. RESULTS: AAP bacteria displayed a clear seasonal trend with a spring maximum following the bloom of phytoplankton and a secondary maximum in autumn. As the AAP bacteria represent a highly diverse assemblage of species, we followed their seasonal succession using the amplicon sequencing of the pufM marker gene. To enhance the accuracy of the taxonomic assignment, we developed new pufM primers that generate longer amplicons and compiled the currently largest database of pufM genes, comprising 3633 reference sequences spanning all phyla known to contain AAP species. With this novel resource, we demonstrated that the majority of the species appeared during specific phases of the seasonal cycle, with less than 2% of AAP species detected during the whole year. AAP community presented an indigenous freshwater nature characterized by high resilience and heterogenic adaptations to varying conditions of the freshwater environment. CONCLUSIONS: Our findings highlight the substantial contribution of AAP bacteria to the carbon flow and ecological dynamics of lakes and unveil a recurrent and dynamic seasonal succession of the AAP community. By integrating this information with the indicator of primary production (Chlorophyll-a) and existing ecological models, we show that AAP bacteria play a pivotal role in the recycling of dissolved organic matter released during spring phytoplankton bloom. We suggest a potential role of AAP bacteria within the context of the PEG model and their consideration in further ecological models.

Novel Insights in Venous Thromboembolism Risk Assessment Methods in Ambulatory Cancer Patients: From the Guidelines to Clinical Practice.

Many cancer patients will experience venous thromboembolism (VTE) at some stage, with the highest rate in the initial period following diagnosis. Novel cancer therapies may further enhance the risk. VTE in a cancer setting is associated with poor prognostic, a decreased quality of life, and high healthcare costs. If thromboprophylaxis in hospitalized cancer patients and perioperative settings is widely accepted in clinical practice and supported by the guidelines, it is not the same situation in ambulatory cancer patient settings. The guidelines do not recommend primary thromboprophylaxis, except in high-risk cases. However, nowadays, risk stratification is still challenging, although many tools have been developed. The Khrorana score remains the most used method, but it has many limits. This narrative review aims to present the current relevant knowledge of VTE risk assessment in ambulatory cancer patients, starting from the guideline recommendations and continuing with the specific risk assessment methods and machine learning models approaches. Biomarkers, genetic, and clinical features were tested alone or in groups. Old and new models used in VTE risk assessment are exposed, underlining their clinical utility. Imaging and biomolecular approaches to VTE screening of outpatients with cancer are also presented, which could help clinical decisions.

Complete genome of Flavobacterium pectinovorum str. ZE23VCel01 obtained through Nanopore Q20+ chemistry.

This study reports the complete genome of Flavobacterium pectinovorum str. ZE23VCel01 isolated from a freshwater environment. By means of Nanopore Q20+ chemistry, the chromosome was assembled as a circular element with a length of 5.9 Mbp, a GC content of 33.58%, and a coverage of 122×.

A high-quality genome of an undescribed Flavobacterium species uncovered using Q20+ Nanopore chemistry.

Herein, we document the complete genome of the Flavobacterium strain ZE23DGlu08, isolated from Lake Zurich, Switzerland. The circular genome was assembled using long-read Nanopore data (coverage: 226×) with the Q20+ chemistry. The described strain displays a genome size of ~3.9 Mbp with a GC content of 34%.

Pseudomonas kielensis str. Ze23jcel16 complete genome obtained through R10.4.1 Nanopore Flow cell chemistry.

Here, we report the complete genome of Pseudomonas kielensis str. Ze23jcel16 isolated from a freshwater sample. The high-quality chromosome was obtained employing R10.4.1 Nanopore Flow cell chemistry and was assembled as a circular element at 45× coverage, a length of 5.8 Mbp, and a G+C content of 61.15%.

Q20+ Nanopore sequencing data recover a high-quality Asticcacaulis sp. genome.

We present here the complete genome of Asticcacaulis sp. ZE23SCel15. The strain was isolated from the surface water of Lake Zurich, Switzerland. The assembly of high-quality Q20+ Nanopore data yielded a circular genome with ~3.8 Mb (coverage: 34×) and a GC content of 56.81%.

Stereomicroscopic Aspects of Non-Carious Cervical Lesions.

Non-carious cervical lesions (NCCLs) represent a form of tooth wear, characterized by the irreversible loss of dental hard tissues at the enamel-cement junction, without the involvement of caries and dental trauma. The aim of this study was to highlight the morphological elements of NCCLs via their stereomicroscopic examination and to confirm the role of this examination in the diagnosis of early lesions. In addition, the association between the morphological aspects identified during the stereomicroscopic examination of NCCLs and their etiological factors was determined. For this study, extracted teeth with NCCLs were examined with a stereomicroscope. The morphological aspects of NCCLs were evaluated at magnifications up to 75×. In wedge-shaped NCCLs, the stereomicroscopic examination allowed the identification and measurement of scratches, furrows and cracks. In saucer-shaped NCCLs, the stereomicroscopic examination highlighted the smooth appearance of the walls. The presented study highlighted the role of stereomicroscopic examination in the assessment of NCCL morphology and in their early diagnosis. The study confirmed, in particular, the role of occlusal overloads and tooth brushing in determining the morphology of NCCLs.

Morphological and Optical Coherence Tomography Aspects of Non-Carious Cervical Lesions.

Non-carious cervical lesions (NCCLs) are considered the irreversible losses of dental hard tissues at the cemento-enamel junction, in the absence of acute trauma and dental caries. The aim of this study was to highlight the presence of NCCLs in cervical areas based on specific macroscopic aspects in order to establish their clinical form, size and location and to confirm the role of optical coherence tomography (OCT) examination in the early diagnosis of these lesions. For this study, 52 extracted teeth were used, which did not have endodontic treatments, fillings or carious lesions in the cervical area. All teeth were examined macroscopically and OCT was used to evaluate the degree of occlusal wear, the presence and clinical form of NCCLs. Most NCCLs were identified on the buccal surfaces of the premolars. The most frequently encountered clinical form was the wedge-shaped form, with a radicular location. NCCLs present most frequently in the wedge-shaped form. Teeth that presented several NCCLs were identified. The OCT examination is an adjunct method to evaluate the clinical forms of NCCL.

Postglacial adaptations enabled colonization and quasi-clonal dispersal of ammonia-oxidizing archaea in modern European large lakes.

Ammonia-oxidizing archaea (AOA) play a key role in the aquatic nitrogen cycle. Their genetic diversity is viewed as the outcome of evolutionary processes that shaped ancestral transition from terrestrial to marine habitats. However, current genome-wide insights into AOA evolution rarely consider brackish and freshwater representatives or provide their divergence timeline in lacustrine systems. An unbiased global assessment of lacustrine AOA diversity is critical for understanding their origins, dispersal mechanisms, and ecosystem roles. Here, we leveraged continental-scale metagenomics to document that AOA species diversity in freshwater systems is remarkably low compared to marine environments. We show that the uncultured freshwater AOA, "Candidatus Nitrosopumilus limneticus," is ubiquitous and genotypically static in various large European lakes where it evolved 13 million years ago. We find that extensive proteome remodeling was a key innovation for freshwater colonization of AOA. These findings reveal the genetic diversity and adaptive mechanisms of a keystone species that has survived clonally in lakes for millennia.

High-resolution metagenomic reconstruction of the freshwater spring bloom.

BACKGROUND: The phytoplankton spring bloom in freshwater habitats is a complex, recurring, and dynamic ecological spectacle that unfolds at multiple biological scales. Although enormous taxonomic shifts in microbial assemblages during and after the bloom have been reported, genomic information on the microbial community of the spring bloom remains scarce. RESULTS: We performed a high-resolution spatio-temporal sampling of the spring bloom in a freshwater reservoir and describe a multitude of previously unknown taxa using metagenome-assembled genomes of eukaryotes, prokaryotes, and viruses in combination with a broad array of methodologies. The recovered genomes reveal multiple distributional dynamics for several bacterial groups with progressively increasing stratification. Analyses of abundances of metagenome-assembled genomes in concert with CARD-FISH revealed remarkably similar in situ doubling time estimates for dominant genome-streamlined microbial lineages. Discordance between quantitations of cryptophytes arising from sequence data and microscopic identification suggested the presence of hidden, yet extremely abundant aplastidic cryptophytes that were confirmed by CARD-FISH analyses. Aplastidic cryptophytes are prevalent throughout the water column but have never been considered in prior models of plankton dynamics. We also recovered the first metagenomic-assembled genomes of freshwater protists (a diatom and a haptophyte) along with thousands of giant viral genomic contigs, some of which appeared similar to viruses infecting haptophytes but owing to lack of known representatives, most remained without any indication of their hosts. The contrasting distribution of giant viruses that are present in the entire water column to that of parasitic perkinsids residing largely in deeper waters allows us to propose giant viruses as the biological agents of top-down control and bloom collapse, likely in combination with bottom-up factors like a nutrient limitation. CONCLUSION: We reconstructed thousands of genomes of microbes and viruses from a freshwater spring bloom and show that such large-scale genome recovery allows tracking of planktonic succession in great detail. However, integration of metagenomic information with other methodologies (e.g., microscopy, CARD-FISH) remains critical to reveal diverse phenomena (e.g., distributional patterns, in situ doubling times) and novel participants (e.g., aplastidic cryptophytes) and to further refine existing ecological models (e.g., factors affecting bloom collapse). This work provides a genomic foundation for future approaches towards a fine-scale characterization of the organisms in relation to the rapidly changing environment during the course of the freshwater spring bloom. Video Abstract.

Complete Genome Sequence of an Uncultivated Freshwater Bacteroidota Lineage.

We report here a complete metagenome-assembled genome belonging to the AKYH767 order within the Bacteroidota phylum. The recovered genome stems from a nonaxenic Amoebozoa culture from Lake Zürich and was assembled as a circular element at a length of 4.1 Mbp and a coverage of 115×.

Complete Genome Sequence of an Uncultivated Freshwater Flavobacterium sp. Strain.

Here, we report the complete metagenome-assembled genome of an uncultivated freshwater Flavobacterium sp. recovered from a nonaxenic Amoebozoa sp. culture. The chromosome was obtained from a metagenomic long-read sequencing run and was assembled as a circular element at a 51× coverage, length of 3.8 Mbp and a G+C content of 37.37%.

Study of Complete Genome Sequence of Uncultivated Hyphomonadaceae sp.

We report here a complete metagenome-assembled genome sequence belonging to the Proteobacteria phylum within the Hyphomonadaceae family. The circular chromosome was obtained from a metagenomic long-read sequencing run and displays a length of 4.1 Mbp along with a GC content of 62.5% at a coverage of 81×.

The Evolutionary Kaleidoscope of Rhodopsins.

Rhodopsins are widely distributed across all domains of life where they perform a plethora of functions through the conversion of electromagnetic radiation into physicochemical signals. As a result of an extensive survey of available genomic and metagenomic sequencing data, we reported the existence of novel clades and exotic sequence motifs scattered throughout the evolutionary radiations of both Type-1 and Type-3 rhodopsins that will likely enlarge the optogenetics toolbox. We expanded the typical rhodopsin blueprint by showing that a highly conserved and functionally important arginine residue (i.e., Arg82) was substituted multiple times during evolution by an extensive amino acid spectrum. We proposed the umbrella term Alt-rhodopsins (AltRs) for all such proteins that departed Arg82 orthodoxy. Some AltRs formed novel clades in the rhodopsin phylogeny and were found in giant viruses. Some newly uncovered AltRs were phylogenetically close to heliorhodopsins, which allowed a closer examination of the phylogenetic border between Type-1 rhodopsins and heliorhodopsins. Comprehensive phylogenetic trees and ancestral sequence reconstructions allowed us to advance the hypothesis that proto-heliorhodopsins were a eukaryotic innovation before their subsequent diversification into the extant Type-3 rhodopsins. IMPORTANCE The rhodopsin scaffold is remarkably versatile and widespread, coupling light availability to energy production and other light-dependent cellular responses with minor alterations to critical residues. We described an unprecedented spectrum of substitutions at one of the most conserved amino acids in the rhodopsin fold, Arg82. We denoted such phylogenetically diverse rhodopsins with the umbrella name Alt-rhodopsins (AltR) and described a distinct branch of AltRs in giant viruses. Intriguingly, some AltRs were the closest phylogenetic neighbors to Heliorhodopsins (HeRs) whose origins have remained enigmatic. Our analyses of HeR origins in the light of AltRs led us to posit a most unusual evolutionary trajectory that suggested a eukaryotic origin for HeRs before their diversification in prokaryotes.

Complete Genome Sequence from an Uncultivated Freshwater Elusimicrobiota Lineage.

Here, we report the first complete genome of an uncultivated freshwater Elusimicrobiota organism recovered from a nonaxenic Amoebozoa sp. culture. The chromosome was obtained from a metagenomic long-read sequencing run and was assembled as a circular element at a 47× coverage, a length of 3.8 Mbp, and a G+C content of 68.6%.

Ecogenomics sheds light on diverse lifestyle strategies in freshwater CPR.

BACKGROUND: The increased use of metagenomics and single-cell genomics led to the discovery of organisms from phyla with no cultivated representatives and proposed new microbial lineages such as the candidate phyla radiation (CPR or Patescibacteria). These bacteria have peculiar ribosomal structures, reduced metabolic capacities, small genome, and cell sizes, and a general host-associated lifestyle was proposed for the radiation. So far, most CPR genomes were obtained from groundwaters; however, their diversity, abundance, and role in surface freshwaters is largely unexplored. Here, we attempt to close these knowledge gaps by deep metagenomic sequencing of 119 samples of 17 different freshwater lakes located in Europe and Asia. Moreover, we applied Fluorescence in situ Hybridization followed by Catalyzed Reporter Deposition (CARD-FISH) for a first visualization of distinct CPR lineages in freshwater samples. RESULTS: A total of 174 dereplicated metagenome-assembled genomes (MAGs) of diverse CPR lineages were recovered from the investigated lakes, with a higher prevalence from hypolimnion samples (162 MAGs). They have reduced genomes (median size 1 Mbp) and were generally found in low abundances (0.02-14.36 coverage/Gb) and with estimated slow replication rates. The analysis of genomic traits and CARD-FISH results showed that the radiation is an eclectic group in terms of metabolic capabilities and potential lifestyles, ranging from what appear to be free-living lineages to host- or particle-associated groups. Although some complexes of the electron transport chain were present in the CPR MAGs, together with ion-pumping rhodopsins and heliorhodopsins, we believe that they most probably adopt a fermentative metabolism. Terminal oxidases might function in O2 scavenging, while heliorhodopsins could be involved in mitigation against oxidative stress. CONCLUSIONS: A high diversity of CPR MAGs was recovered, and distinct CPR lineages did not seem to be limited to lakes with specific trophic states. Their reduced metabolic capacities resemble the ones described for genomes in groundwater and animal-associated samples, apart from Gracilibacteria that possesses more complete metabolic pathways. Even though this radiation is mostly host-associated, we also observed organisms from different clades (ABY1, Paceibacteria, Saccharimonadia) that appear to be unattached to any other organisms or were associated with 'lake snow' particles (ABY1, Gracilibacteria), suggesting a broad range of potential life-strategies in this phylum. Video Abstract.

Modifications of the Dental Hard Tissues in the Cervical Area of Occlusally Overloaded Teeth Identified Using Optical Coherence Tomography.

Background and objectives: Occlusal overloads produce a series of manifestations in teeth, especially attrition and non-carious cervical lesions (NCCL). Optical Coherence Tomography (OCT) can highlight and evaluate tooth lesions. The aim of this study was to examine the changes of dental hard tissues in the cervical area because of occlusal overload by macroscopic examination and using in vitro Swept Source OCT examination. Materials and Methods: The study was performed on 21 extracted teeth with occlusal trauma. After macroscopic and OCT examination, the 2D OCT images were transformed into 3D images using ImageJ software. Statistical analysis of macroscopic and OCT images was performed with Statistical Package for Social Sciences. Results: On 21 teeth, 88 cervical lesions (cracks) were identified. Upper premolars with an occlusal Smith and Knight tooth wear score of 2 had the most NCCL. Statistical analysis revealed significant differences in the median widths of cervical lesions between teeth with score 1 and score 3. Additionally, we obtained statistically significant differences in median widths between the buccal and oral surfaces. Conclusions: These cracks can be considered precursors of NCCL. NCCL can be located on dental surfaces in the cervical area other than the buccal one. A 3D reconstruction of OCT images emphasized that cracks are located especially at enamel level, evolving towards the enamel-dentin junction, with multiple ramifications.