Current Opinion in Microbiology, Год журнала: 2022, Номер 68, С. 102171 - 102171
Опубликована: Июнь 13, 2022
Язык: Английский
Proceedings of the National Academy of Sciences, Год журнала: 2024, Номер 121(21)
Опубликована: Май 14, 2024
Pangenomes vary across bacteria. Some species have fluid pangenomes, with a high proportion of genes varying between individual genomes. Other less different genomes tending to contain the same genes. Two main hypotheses been suggested explain this variation: differences in species' bacterial lifestyle and effective population size. However, previous studies not able test these because features size are highly correlated each other, phylogenetically conserved, making it hard disentangle their relative importance. We used phylogeny-based analyses, 126 species, tease apart causal role factors. found that pangenome fluidity was lower i) host-associated compared free-living ii) obligately dependent on host, live inside cells, more pathogenic motile. In contrast, we no support for competing hypothesis larger sizes lead pangenomes. Effective appears correlate variation is also driven by lifestyle, rather than relationship.
Язык: Английский
Процитировано
12
Microbiology Spectrum, Год журнала: 2022, Номер 11(1)
Опубликована: Дек. 8, 2022
Acinetobacter baumannii is an opportunistic pathogenic bacterium prioritized by WHO and CDC because of its increasing antibiotic resistance. Heterogeneity among strains represents the hallmark A. bacteria. We wondered to what extent extensively used strains, so-called reference reflect dynamic nature intrinsic heterogeneity these analyzed multiple phenotypic traits 43 nonredundant, modern, multidrug-resistant, drug-resistant, pandrug-resistant clinical isolates broadly baumannii. Comparison at genetic levels confirmed a high degree heterogeneity. Importantly, we observed that significant portion modern strongly differs from several historically established in light colony morphology, cellular density, capsule production, natural transformability, vivo virulence. The differences between could hamper study baumannii, especially concerning virulence resistance mechanisms. Hence, propose variable collection are characterized levels, covering wide range spectrum, with six different macrocolony type groups, avirulent hypervirulent phenotypes, naturally noncapsulated hypermucoid intermediate phenotypes as well. Strain-specific mechanistic observations remain interesting per se, "reference" have undoubtedly been shown be very useful basic mechanisms biology. However, any based on specific strain should compared clinically relevant isolates. IMPORTANCE resistance, leading treatment failures. this pathogen isolates, due genome. In context, tested if subset considered was reflecting diversity found currently circulating do not cover whole While formerly successfully generated strong base knowledge field beyond, our shows rational choice strain, related biological question, taken into consideration. Any data obtained also drug screening, contexts.
Язык: Английский
Процитировано
24
Microbial Genomics, Год журнала: 2022, Номер 8(11)
Опубликована: Ноя. 23, 2022
The Escherichia coli species contains a diverse set of sequence types and there remain important questions regarding differences in genetic content within this population that need to be addressed. Pangenomes are useful vehicles for studying gene types. Here, we analyse 21 E. type pangenomes using comparative pangenomics identify variance both pangenome structure content. We present functional breakdowns core genomes enriched metabolism, transcription cell membrane biogenesis genes. also uncover metabolism genes have variable classification, depending on which allele is present. Our approach allows detailed exploration the context species. show ongoing gain loss type-specific, may consequence distinct type-specific evolutionary drivers.
Язык: Английский
Процитировано
21
Frontiers in Microbiology, Год журнала: 2024, Номер 14
Опубликована: Фев. 2, 2024
Ralstonia pickettii , the most critical clinical pathogen of genus has been identified as a causative agent numerous harmful infections. Additionally, demonstrates adaptability to extreme environmental conditions, such those found in drinking water. In this study, we conducted comprehensive genomic analysis investigate characteristics related potential pathogenicity and adaptive evolution water environments . Through phylogenetic population genetic analysis, divided into five Groups, two which were associated with environments. The open pan-genome large flexible gene repertoire indicated high plasticity. Significant differences functional enrichment observed between core- different groups. Diverse mobile elements (MGEs), extensive rearrangements, horizontal transfer (HGT) events played crucial role generating diversity. environments, exhibited strong adaptability, acquisition specific genes was potentially facilitated by islands (GIs) HGT. Furthermore, pressures drove leading accumulation unique mutations key genes. These may have significant impact on various physiological functions, particularly carbon metabolism energy metabolism. presence virulence-related macromolecular secretion systems, virulence factors, antimicrobial resistance making it capable causing multiple nosocomial This study provides insights from perspective.
Язык: Английский
Процитировано
3
The Science of The Total Environment, Год журнала: 2024, Номер 927, С. 172251 - 172251
Опубликована: Апрель 9, 2024
Animal hosts harbor diverse assemblages of microbial symbionts that play crucial roles in the host's lifestyle. The link between symbiosis and host development remains poorly understood. In particular, little is known about adaptive evolution gut bacteria host–microbe symbioses. Recently, symbiotic relationships have been categorized as open, closed, or mixed, reflecting their modes inter-host transmission resulting distinct genomic features. Members genus Bacteroides are most abundant human microbiota possess both probiotic pathogenic potential, providing an excellent model for studying pan-genome systems. Here, we determined complete genome novel clinical strain PL2022, which was isolated from a blood sample performed analyses on representative set cellulosilyticus strains to quantify influence relationship evolutionary dynamics. B. exhibited correlated features with open closed symbioses, suggesting mixed symbiosis. An characterized by accessory gene families, potential horizontal transfer (HGT), mobile genetic elements (MGEs), indicating innovative pool, mainly associated islands plasmids. However, massive parallel loss, weak purifying selection, accumulation positively selected mutations were main drivers reduction cellulosilyticus. Metagenomic read recruitment showed members globally distributed active habitats, line predominant vertical gut. existence and/or high abundance also detected non-intestinal tissues, other animal hosts, non-host environments, occasional new niches, thereby creating arenas acquisition genes. This case study under advances our understanding evolution. Our results highlight complexity this unusual intestinal symbiont.
Язык: Английский
Процитировано
3
Current Research in Food Science, Год журнала: 2024, Номер 9, С. 100867 - 100867
Опубликована: Янв. 1, 2024
Язык: Английский
Процитировано
3
Frontiers in Cellular and Infection Microbiology, Год журнала: 2025, Номер 14
Опубликована: Янв. 20, 2025
Background To explore the genetic characteristics of Mycobacterium abscessus complex (MABC) population in China, given its rising clinical importance among nontuberculous mycobacteria. Methods We conducted analyses on 360 MABC genomes from focusing core genome multilocus sequence typing (cgMLST), pan-genome characterization, genetics, and antimicrobial resistance gene profiling. Results Our analysis identified 273 M. subsp. (Mab A ) 87 massiliense M isolates, uncovering 68 types (STs), with ST5 being most common. cgMLST classified 33.3% isolates into six dominant circulating clones (DCCs) 49.4% 59 genomic clusters at a threshold 25 different alleles, including 18 international linking Chinese seven other countries. The is open, Mab exhibiting greater accessory diversity higher turnover compared to . Mobile elements (MGEs), such as prophages islands, were prevalent across all genomes. 139 151 virulence factors (VFs) per genome, distinct VFs affecting immune modulation metabolism. Resistance profiling revealed ubiquitous mtrA , RbpA bla MAB -specific erm(41) conferring macrolides β-lactams. Common rrs rrl mutations indicated widespread aminoglycosides macrolides, while gyrA suggested emerging fluoroquinolone resistance. An acquired erm(46) gene, likely obtained via phage-mediated horizontal transfer, was detected one strain. Conclusion This study provides key insights dynamics China. distribution DCCs, high clustering rates, open pan-genome, patterns between along MGEs, highlight need for targeted surveillance tailored therapies address challenges infections.
Язык: Английский
Процитировано
0
Environmental Microbiology, Год журнала: 2025, Номер 27(2)
Опубликована: Фев. 1, 2025
ABSTRACT Horizontal genetic transfer (HGT) is a significant driver of genomic novelty in all domains life. HGT has been investigated many studies however, the focus on conspicuous protein‐coding DNA transfers that often prove to be adaptive recipient organisms and are therefore fixed longer‐term lineages. These results comprise subclass HGTs do not represent exhaustive (coding non‐coding) its impact ecology. Uncovering can provide key insights into connectivity genomes communities how these may occur. In this study, we use term frequency‐inverse document frequency (TF‐IDF) technique, used successfully mine within real simulated high‐quality prokaryote genomes, search for an extremophilic microbial community. We establish pipeline validating identified using approach. find most within‐domain involve non‐coding DNA. A relatively high proportion predicted appear encode transposase activity, restriction‐modification system components, biofilm formation functions. Our study demonstrates utility TF‐IDF approach detection provides mechanisms recent transfer.
Язык: Английский
Процитировано
0
Communications Earth & Environment, Год журнала: 2025, Номер 6(1)
Опубликована: Фев. 26, 2025
Язык: Английский
Процитировано
0
mSphere, Год журнала: 2025, Номер unknown
Опубликована: Март 19, 2025
ABSTRACT Below-ground carbon transformations that contribute to healthy soils represent a natural climate change mitigation, but newly acquired traits adaptive stress may alter microbial feedback mechanisms. To better define evolutionary responses long-term warming, we study microorganisms from an ongoing in situ soil warming experiment where, for over three decades, temperate forest are continuously heated at 5°C above ambient. We hypothesize across generations of chronic genomic signatures within diverse bacterial lineages reflect adaptations related growth and utilization. From our culture collection isolated experimental control plots, sequenced genomes representing dominant taxa sensitive including Actinobacteria, Alphaproteobacteria, Betaproteobacteria. investigated attributes functional gene content identify adaptation. Comparative pangenomics revealed accessory clusters central metabolism, competition, substrate degradation, with few annotations explicitly associated warming. Trends patterns suggest plots were relatively enriched carbohydrate nitrogen metabolism pathways, while amino acid fatty pathways. observed had less codon bias, suggesting potential or efficiency. Codon usage bias varied organisms similar 16S rrn operon copy number, these experience different selective pressures on Our work suggests the emergence lineage-specific trends as well common ecological-evolutionary change. IMPORTANCE Anthropogenic threatens ecosystem health part by altering below-ground cycling carried out microbes. Microbial often overshadowed community-level ecological responses, changes function. predict microbes adapting stressors like test this, analyzed bacteria where have been experimentally ambient 30 years. While unchanged indicators These new parameters how ecosystems system.
Язык: Английский
Процитировано
0