Elsevier eBooks, Год журнала: 2024, Номер unknown
Опубликована: Янв. 1, 2024
Язык: Английский
Nature, Год журнала: 2025, Номер 639(8055), С. 589 - 601
Опубликована: Март 19, 2025
Язык: Английский
Процитировано
4
Briefings in Bioinformatics, Год журнала: 2024, Номер 25(3)
Опубликована: Март 27, 2024
Abstract The advent of rapid whole-genome sequencing has created new opportunities for computational prediction antimicrobial resistance (AMR) phenotypes from genomic data. Both rule-based and machine learning (ML) approaches have been explored this task, but systematic benchmarking is still needed. Here, we evaluated four state-of-the-art ML methods (Kover, PhenotypeSeeker, Seq2Geno2Pheno Aytan-Aktug), an baseline the ResFinder by training testing each them across 78 species–antibiotic datasets, using a rigorous workflow that integrates three evaluation approaches, paired with distinct sample splitting methods. Our analysis revealed considerable variation in performance techniques datasets. Whereas generally excelled closely related strains, handling divergent genomes. Overall, Kover most frequently ranked top among followed PhenotypeSeeker Seq2Geno2Pheno. AMR antibiotic classes such as macrolides sulfonamides were predicted highest accuracies. quality predictions varied substantially combinations, particularly beta-lactams; species, phenotyping beta-lactams compound, aztreonam, amoxicillin/clavulanic acid, cefoxitin, ceftazidime piperacillin/tazobactam, alongside tetracyclines demonstrated more variable than other benchmarked antibiotics. By organism, Campylobacter jejuni Enterococcus faecium robustly those Escherichia coli, Staphylococcus aureus, Salmonella enterica, Neisseria gonorrhoeae, Klebsiella pneumoniae, Pseudomonas aeruginosa, Acinetobacter baumannii, Streptococcus pneumoniae Mycobacterium tuberculosis. In addition, our study provides software recommendations combination. It furthermore highlights need optimization robust clinical applications, strains diverge used training.
Язык: Английский
Процитировано
14
Nature Reviews Genetics, Год журнала: 2025, Номер unknown
Опубликована: Янв. 8, 2025
Язык: Английский
Процитировано
2
The ISME Journal, Год журнала: 2024, Номер 18(1)
Опубликована: Янв. 1, 2024
In recent years, phylogenetic reconciliation has emerged as a promising approach for studying microbial ecology and evolution. The core idea is to model how gene trees evolve along species tree explain differences between them via evolutionary events including duplications, transfers, losses. Here, we describe provides natural framework genome evolution highlight applications ancestral content inference, the rooting of trees, insights into metabolic ecological transitions they yield. Reconciliation analyses have elucidated diverse lineages, from Chlamydiae Asgard archaea, shedding light on adaptation, host-microbe interactions, symbiotic relationships. However, there are many opportunities broader application in microbiology. Continuing improvements make models more realistic scalable, integration metadata such habitat, pH, temperature, oxygen use offer enormous potential understanding rich tapestry life.
Язык: Английский
Процитировано
4
Molecular Biology and Evolution, Год журнала: 2025, Номер unknown
Опубликована: Янв. 10, 2025
The pangenome of a species is the set all genes carried by at least one member species. In bacteria, pangenomes can be much larger than single organism. Many questions remain unanswered regarding evolutionary forces shaping patterns presence/absence in given We introduce new model for bacterial evolution along phylogeny that explicitly describes timing appearance each gene and accounts three generic types dynamics: persistent are present ancestral genome, private specific to clade, mobile imported once into pool then undergo frequent horizontal transfers. call this Persistent-Private-Mobile (PPM) model. develop an algorithm fitting PPM apply it dataset 902 Salmonella enterica genomes. show best able reproduce global pattern some multivariate statistics like frequency spectrum parsimony vs. plot. Moreover, classification induced allows us study position accessory on chromosome depending their category, as well functions most category. This work paves way mechanistic understanding evolution, developed here could used dynamics-aware classification.
Язык: Английский
Процитировано
0
mSystems, Год журнала: 2025, Номер unknown
Опубликована: Фев. 24, 2025
ABSTRACT Encoded within many microbial genomes, biosynthetic gene clusters (BGCs) underlie the synthesis of various secondary metabolites that often mediate ecologically important functions. Several studies and bioinformatics methods developed over past decade have advanced our understanding both pangenomes BGC evolution. In this minireview, we first highlight challenges in broad evolutionary analysis BGCs, including delineation boundaries clustering BGCs across genomes. We further summarize key findings from comparative genomics on conservation taxa habitats discuss potential fitness effects different settings. Afterward, recent research showing importance genomic context production evolution is highlighted. These draw parallels to recent, broader, investigations gene-to-gene associations pangenomes. Finally, describe mechanisms by which evolve, ranging acquisition or origination entire micro-evolutionary trends individual genes. An outlook how expansions capabilities some might support theories open are result adaptive also discussed. conclude with remarks about future work leveraging longitudinal metagenomics diverse ecosystems likely significantly improve genomes BGCs.
Язык: Английский
Процитировано
0
Journal of Proteins and Proteomics, Год журнала: 2025, Номер unknown
Опубликована: Март 18, 2025
Язык: Английский
Процитировано
0
bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2024, Номер unknown
Опубликована: Май 2, 2024
The pangenome is the set of all genes present in a prokaryotic species. Most pangenomes contain many accessory that are only some species members. Genes need to function together, and it has been suggested selection for certain gene combinations affects structure pangenomes. Nevertheless, might also co-occur simply due being linked on genome, efficient tools needed distinguish linkage from co-selection. Here we Goldfinder, an approach infer co-occurrence co-avoidance between pairs by taking phylogenetic relationships into account. implemented Python script available at https://github.com/fbaumdicker/goldfinder . We provide scripts clustering co-occurring visualizing resulting networks Cytoscape. In comparison inference tool Coinfinder, Goldfinder finds fewer real pangenome, suggesting spurious associations dependencies detected. conclude fast accurate co-avoidance, which will enable large-scale analyses co-selected across bacterial
Язык: Английский
Процитировано
3
Cells, Год журнала: 2024, Номер 13(2), С. 197 - 197
Опубликована: Янв. 21, 2024
Peto’s paradox and the epidemiologic observation of average six degrees tumor prevalence are studied hypothetically solved. A simple consideration, Petho’s challenges our intuitive understanding cancer risk prevalence. Our consideration is that more a cell divides, higher chance acquiring cancerous mutations, so larger or longer-lived organisms have cells undergo divisions over their lifetime, expecting to developing cancer. Paradoxically, it not supported by observations. The allometric scaling species could answer Peto paradox. Another paradoxical human epidemiology in mutations necessary for prevalence, despite random expectations causes. To solve this challenge, game theory be applied. inherited DNA replication process nonlinearly drive development. statistical variance concept does reasonably describe Instead, Darwinian natural selection principle healthy organism’s cellular population can serve species’ evolutionary adaptation selective pressure circumstances. Still, some collect multiple uncorrected adapt extreme stress stromal environment, develop subclinical phases individual. This needs extensive subsequent replications heritage additional which only marginal alone. together, they preparing first stage precancerous condition. In second stage, when one caretaker genes accidentally mutated, caused genetic instability prepares fight its survival avoid apoptosis. described as competitive game. third develops uncontrolled proliferation with damaged gatekeeper gene forces new strategy binary cooperation alimentation. fourth starving conditions cause change again, starting cooperative game, where malignant cooperate force host, too. fifth resetting homeostasis finishes clinical phase starts. prevention development mutated complex than averting exposure mutagens from environment throughout lifetime. Mutagenic increase otherwise imperfect reproduction, increasing likelihood development, but exist. Toxic challenging; may select tolerant on particular toxic stress, these facility apoptosis collected mutational states.
Язык: Английский
Процитировано
2
Reviews in the Neurosciences, Год журнала: 2024, Номер 35(5), С. 503 - 531
Опубликована: Фев. 19, 2024
Abstract An extensive review is presented on mitochondrial structure and function, proteins, the outer inner membranes, cristae, role of F 1 O -ATP synthase, contact site cristae organizing system (MICOS), sorting assembly machinery morphology phospholipids, in particular cardiolipin. Aspects regulation under physiological pathological conditions are outlined, dysregulated MICOS protein subunit Mic60 Parkinson’s disease, relations between quality control mitochondria as signaling organelles. A mathematical modeling approach using mechanical beam theory introduced outlined. The proposed based premise that an optimization framework can be used for a better understanding critical function also to map certain experiments clinical interventions.
Язык: Английский
Процитировано
2