Phylogenetic Network Analysis Revealed the Occurrence of Horizontal Gene Transfer of 16S rRNA in the Genus Enterobacter

Isolation and Genomics of Futiania mangrovii gen. nov., sp. nov., a Rare and Metabolically Versatile Member in the Class Alphaproteobacteria

Mangrove microorganisms are a major part of the coastal ecosystem and are directly associated with nutrient cycling. Despite their ecological significance, the collection of culturable mangrove microbes is limited due to difficulties in isolation and cultivation. Here, we report the isolation and genome sequence of strain FT118^T, the first cultured representative of a previously uncultivated order UBA8317 within Alphaproteobacteria, based on the combined results of 16S rRNA gene similarity, phylogenomic, and average amino acid identity analyses. We propose Futianiales ord. nov. and Futianiaceae fam. nov. with Futiania as the type genus, and FT118^T represents the type species with the name Futiania mangrovii gen. nov, sp. nov. The 16S rRNA gene sequence comparison reveals that this novel order is a rare member but has a ubiquitous distribution across various habitats worldwide, which is corroborated by the experimental confirmation that this isolate can physiologically adapt to a wide range of oxygen levels, temperatures, pH and salinity levels. Biochemical characterization, genomic annotation, and metatranscriptomic analysis of FT118^T demonstrate that it is metabolically versatile and active in situ. Genomic analysis reveals adaptive features of Futianiales to fluctuating mangrove environments, including the presence of high- and low-affinity terminal oxidases, N-type ATPase, and the genomic capability of producing various compatible solutes and polyhydroxybutyrate, which possibly allow for the persistence of this novel order across various habitats. Collectively, these results expand the current culture collection of mangrove microorganisms, providing genomic insights of how this novel taxon adapts to fluctuating environments and the culture reference to unravel possible microbe-environment interactions. IMPORTANCE The rare biosphere constitutes an essential part of the microbial community and may drive nutrient cycling and other geochemical processes. However, the difficulty in microbial isolation and cultivation has hampered our understanding of the physiology and ecology of uncultured rare lineages. In this study, we successfully isolated a novel alphaproteobacterium, designated as FT118^T, and performed a combination of phenotypic, phylogenetic, and phylogenomic analyses, confirming that this isolate represents the first cultured member of a previously uncultivated order UBA8317 within Alphaproteobacteria. It is a rare species with a ubiquitous distribution across different habitats. Genomic and metatranscriptomic analyses demonstrate that it is metabolically versatile and active in situ, suggesting its potential role in nutrient cycling despite being scarce. This work not only expands the current phylogeny of isolated Alphaproteobacteria but also provides genomic and culture reference to unravel microbial adaptation strategies in mangrove sediments and possible microbe-environment interactions.

Ribosomal RNA operons define a central functional compartment in the Streptomyces chromosome

Streptomyces are prolific producers of specialized metabolites with applications in medicine and agriculture. These bacteria possess a large linear chromosome genetically compartmentalized: core genes are grouped in the central part, while terminal regions are populated by poorly conserved genes. In exponentially growing cells, chromosome conformation capture unveiled sharp boundaries formed by ribosomal RNA (rrn) operons that segment the chromosome into multiple domains. Here we further explore the link between the genetic distribution of rrn operons and Streptomyces genetic compartmentalization. A large panel of genomes of species representative of the genus diversity revealed that rrn operons and core genes form a central skeleton, the former being identifiable from their core gene environment. We implemented a new nomenclature for Streptomyces genomes and trace their rrn-based evolutionary history. Remarkably, rrn operons are close to pericentric inversions. Moreover, the central compartment delimited by rrn operons has a very dense, nearly invariant core gene content. Finally, this compartment harbors genes with the highest expression levels, regardless of gene persistence and distance to the origin of replication. Our results highlight that rrn operons are structural boundaries of a central functional compartment prone to transcription in Streptomyces.

Intact ribosomal DNA arrays of Potentilla origin detected in Erythronium nucleus suggest recent eudicot-to-monocot horizontal transfer

During our initial phylogenetic study of the monocot genus Erythronium (Liliaceae), we observed peculiar eudicot-type internal transcribed spacer (ITS) sequences in a dataset derived from genomic DNA of Erythronium dens-canis. This raised the possibility of horizontal transfer of a eudicot alien ribosomal DNA (rDNA) into the Erythronium genome. In this work we aimed to support this hypothesis by carrying out genomic, molecular, and cytogenetic analyses. Genome skimming coupled by PacBio HiFi sequencing of a bacterial artificial chromosome clone derived from flow-sorted nuclei was used to characterise the alien 45S rDNA. Integration of alien rDNA in the recipient genome was further proved by Southern blotting and fluorescence in situ hybridization using specific probes. Alien rDNA, nested among Potentilla species in phylogenetic analysis, likely entered the Erythronium lineage in the common ancestor of E. dens-canis and E. caucasicum. Transferred eudicot-type rDNA preserved its tandemly arrayed feature on a single chromosome and was found to be transcribed in the monocot host, albeit much less efficiently than the native counterpart. This study adds a new example to the rarely documented nuclear-to-nuclear jumps of DNA between eudicots and monocots while holding the scientific community continually in suspense about the mode of DNA transfer.

Carbapenem antibiotic stress increases blaKPC -2 gene relative copy number and bacterial resistance levels of Klebsiella pneumoniae

Background

The clinical isolation rates of carbapenem‐resistant Klebsiella pneumoniae (CR‐KP) continue to increase. In China, clinical CR‐KP isolates are mainly attributed to the bla_KPC‐2 gene carried on plasmids, and the bla_KPC‐2 copy number correlates with the expression of KPC enzymes, which can cause elevated carbapenem MICs.

Methods

Thirty‐seven CR‐KP isolates were collected at the Second People’s Hospital of Lianyungang City between January 2020 and March 2021, with no duplicate isolates, and were screened for the bla_KPC‐2 gene with PCR. Analysis of current CRKP resistance to clinically relevant antimicrobials using the bioMérieux VITEK^® 2 bacterial identification card. The multilocus sequence types of the strains were confirmed with PCR and DNA sequencing. Recombinant plasmids pET20b‐bla_KPC‐2 and pET20b‐CpsG were constructed, and the copy numbers of the recombinant plasmids per unit volume was calculated based on the molecular weight of the plasmids. After the genomes DNA of clinical isolates of K. pneumoniae carrying the bla_KPC‐2 gene were purified, the bla_KPC‐2 gene relative copy number in individual K. pneumoniae strains was indicated by the double standard curve method. Detection of MIC values changes of K. pneumoniae under imipenem selection pressure by broth microdilution method.

Results

Among the 37 CR‐KP strains isolated, only the bla_KPC‐2 gene was detected in 30 strains, three strains were positive for the bla_NDM‐1 gene, two strains carried both the bla_KPC‐2 and bla_NDM‐1 genes, and two strains without detectable carbapenem resistance genes. The ST11 clone was predominant among the 37 carbapenem‐resistant K. pneumoniae isolates. Drug sensitivity testing showed that except for polymyxins (100% susceptible) and tigecycline (75.7% intermediate), the 37 CR‐KP strains were resistant to almost all antimicrobial drugs. The bla_KPC‐2 relative copy number in nine ST11 clinical isolates of K. pneumoniae was 7.64 ± 2.51 when grown on LB plates but 27.67 ± 13.04 when grown on LB plates containing imipenem. Among these nine isolates, five CRKP strains exhibited elevated MICs to imipenem, while the remaining four strains showed unchanged MIC values to imipenem.

Conclusion

Carbapenem‐resistant Klebsiella pneumoniae isolates may have multiple pathways to achieve high levels of carbapenem resistance, and moderate carbapenem pressure can increase the copy number of KPC enzyme genes in CRKP strains and enhance the degree of carbapenem resistance in the strains.

Biocontrol Mechanism of Bacillus subtilis C3 Against Bulb Rot Disease in Fritillaria taipaiensis P.Y.Li

Bulb rot disease has become one of the main diseases that seriously affects the yield and quality of Fritillaria taipaiensis P.Y.Li (F. taipaiensis). In this study, F. taipaiensis was used as the research object to explore the effect and mechanism of Bacillus subtilis C3 in preventing and curing bulb rot. Through isolation and verification of the pathogenic fungi, we determined for the first time that the pathogenic fungus that causes bulb rot in F. taipaiensis is Fusarium oxysporum. The results of the study showed that B. subtilis C3 inhibits the growth of pathogenic fungi, and the inhibition rate is as high as 60%. In the inhibition mechanism, strain C3 inhibits the conidiogenesis of pathogenic fungi and destroys the cell structure of its hyphae, causing protoplast exudation, chromatin concentration, DNA fragmentation, and ultimately cell death. Among the secondary metabolites of C3, antimicrobial proteins and main active components (paeonol, ethyl palmitate, and oxalic acid) inhibited the growth of F. oxysporum. The molecular weight of the antibacterial protein with the highest inhibition rate was approximately 50 kD. The results of a field experiment on the Taibai Mountain F. taipaiensis planting base showed that after the application of strain C3, the incidence of bulb rot in Fritillaria was reduced by 18.44%, and the ratio of bacteria to fungi in the soil increased to 8.21, which verified the control effect of C3 on Fritillaria bulb rot disease. This study provides a theoretical basis for the use of B. subtilis C3 to prevent and control bulb rot in Fritillaria.

Development and evaluation of a nanopore 16S rRNA gene sequencing service for same day targeted treatment of bacterial respiratory infection in the intensive care unit

OBJECTIVES

Assess the feasibility and impact of nanopore-based 16S rRNA gene sequencing (Np16S) service on antibiotic treatment for acute severe pneumonia on the intensive care unit (ICU).

METHODS

Speciation and sequencing accuracy of Np16S on isolates with bioinformatics pipeline optimisation, followed by technical evaluation including quality checks and clinical-reporting criteria analysing stored respiratory samples using single-sample flow cells. Pilot service comparing Np16S results with all routine respiratory tests and impact on same-day antimicrobial prescribing.

RESULTS

Np16S correctly identified 140/167 (84%) isolates after 1h sequencing and passed quality control criteria including reproducibility and limit-of-detection. Sequencing of 108 stored respiratory samples showed concordance with routine culture in 80.5% of cases and established technical and clinical reporting criteria. A 10-week same-day pilot Np16S service analysed 45 samples from 37 patients with suspected community (n=15) or hospital acquired (n=30) pneumonia. Np16S showed concordance compared with all routine culture or molecular tests for 27 (82%) of 33 positive samples. It identified the causative pathogen in 32/33 (97%) samples and contributed to antimicrobial treatment changes for 30 patients (67%).

CONCLUSIONS

This study demonstrates feasibility of providing a routine same-day nanopore sequencing service that makes a significant contribution to early antibiotic prescribing for bacterial pneumonia in the ICU.

Performance and Application of 16S rRNA Gene Cycle Sequencing for Routine Identification of Bacteria in the Clinical Microbiology Laboratory

This review provides a state-of-the-art description of the performance of Sanger cycle sequencing of the 16S rRNA gene for routine identification of bacteria in the clinical microbiology laboratory. A detailed description of the technology and current methodology is outlined with a major focus on proper data analyses and interpretation of sequences. The remainder of the article is focused on a comprehensive evaluation of the application of this method for identification of bacterial pathogens based on analyses of 16S multialignment sequences. In particular, the existing limitations of similarity within 16S for genus- and species-level differentiation of clinically relevant pathogens and the lack of sequence data currently available in public databases is highlighted. A multiyear experience is described of a large regional clinical microbiology service with direct 16S broad-range PCR followed by cycle sequencing for direct detection of pathogens in appropriate clinical samples. The ability of proteomics (matrix-assisted desorption ionization-time of flight) versus 16S sequencing for bacterial identification and genotyping is compared. Finally, the potential for whole-genome analysis by next-generation sequencing (NGS) to replace 16S sequencing for routine diagnostic use is presented for several applications, including the barriers that must be overcome to fully implement newer genomic methods in clinical microbiology. A future challenge for large clinical, reference, and research laboratories, as well as for industry, will be the translation of vast amounts of accrued NGS microbial data into convenient algorithm testing schemes for various applications (i.e., microbial identification, genotyping, and metagenomics and microbiome analyses) so that clinically relevant information can be reported to physicians in a format that is understood and actionable. These challenges will not be faced by clinical microbiologists alone but by every scientist involved in a domain where natural diversity of genes and gene sequences plays a critical role in disease, health, pathogenicity, epidemiology, and other aspects of life-forms. Overcoming these challenges will require global multidisciplinary efforts across fields that do not normally interact with the clinical arena to make vast amounts of sequencing data clinically interpretable and actionable at the bedside.

Investigation of antibiotic resistance determinants and virulence factors of uropathogenic Escherichia coli

Multidrug-resistant (MDR) uropathogenic Escherichia coli (UPEC) are prevalent throughout the world resulting in a major public health burden. In this research, we isolated and identified 28 MDR UPEC from one university hospital in China, investigated MDR and pathogenic mechanisms by PCR, including 55 antibiotic resistance determinants (ARDs) genes, 13 genetic markers of mobile genetic elements (MGEs) and 6 virulence factors (VFs) genes. In these isolates, we identified 23 ARDs genes and 6 genetic markers of MGEs that played a key role in MDR phenotypes. In addition, we found 2 VFs genes, hofQ and ompT, which could be associated with pathogenicity and invasiveness of these strains in urinary tract infections (UTIs).

Deciphering the Factors for Nodulation and Symbiosis of Mesorhizobium Associated with Cicer arietinum in Northwest India

The compatibility between rhizobia and legumes for nitrogen-fixing nodules and the stages of root hair curling, formation of infection thread, and nodulation initiation have been vitally studied, but the factors for the sustainable root surface colonization and efficient symbiosis within chickpea and rhizobia have been poorly investigated. Hence, we aimed to analyze phenotypic properties and phylogenetic relationships of root-nodule bacteria associated with chickpea (Cicer arietinum) in the north-west Indo Gangetic Plains (NW-IGP) region of Uttar Pradesh, India. In this study, 54 isolates were recovered from five agricultural locations. Strains exhibited high exopolysaccharide production and were capable of survival at 15–42 °C. Assays for phosphate solubilization, catalase, oxidase, Indole acetic acid (IAA) production, and 1-aminocyclopropane-1-carboxylic acid (ACC) deaminase activity revealed that all the tested isolates possessed plant growth-promoting potential. Metabolic profiling using Biolog plates indicated that patterns of substrate utilization differed considerably among isolates. A biofilm formation assay showed that isolates displayed a nearly four-fold range in their capacity for biofilm development. Inoculation experiments indicated that all isolates formed nodules on chickpea, but they exhibited more than a two-fold range in symbiotic efficiency. No nodules were observed on four other legumes (Phaseolus vulgaris, Pisum sativum, Lens culinaris, and Vigna mungo). Concatenated sequences from six loci (gap, edD, glnD, gnD, rpoB, and nodC) supported the assignment of all isolates to the species Mesorhizobium ciceri, with strain M. ciceri Ca181 as their closest relative.

Occurrence of randomly recombined functional 16S rRNA genes in Thermus thermophilus suggests genetic interoperability and promiscuity of bacterial 16S rRNAs

Based on the structural complexity of ribosomes, 16S rRNA genes are considered species-specific and hence used for bacterial phylogenetic analysis. However, a growing number of reports suggest the occurrence of horizontal gene transfer, raising genealogical questions. Here we show the genetic interoperability and promiscuity of 16S rRNA in the ribosomes of an extremely thermophilic bacterium, Thermus thermophilus. The gene in this thermophile was systematically replaced with a diverse array of heterologous genes, resulting in the discovery of various genes that supported growth, some of which were from different phyla. Moreover, numerous functional chimeras were spontaneously generated. Remarkably, cold-adapted mutants were obtained carrying chimeric or full-length heterologous genes, indicating that horizontal gene transfer promoted adaptive evolution. The ribosome may well be understood as a patchworked supramolecule comprising patchworked components. We here propose the “random patch model” for ribosomal evolution.

Functional metagenomic approach to identify overlooked antibiotic resistance mutations in bacterial rRNA

Our knowledge as to how bacteria acquire antibiotic resistance is still fragmented, especially for the ribosome-targeting drugs. In this study, with the aim of finding novel mechanisms that render bacteria resistant to the ribosome-targeting antibiotics, we developed a general method to systematically screen for antibiotic resistant 16 S ribosomal RNAs (rRNAs), which are the major target for multiple antibiotics (e.g. spectinomycin, tetracycline, and aminoglycosides), and identify point mutations therein. We used Escherichia coli ∆7, a null mutant of the rrn (ribosomal RNA) operons, as a surrogate host organism to construct a metagenomic library of 16 S rRNA genes from the natural (non-clinical) environment. The library was screened for spectinomycin resistance to obtain four resistant 16 S rRNA genes from non-E. coli bacterial species. Bioinformatic analysis and site-directed mutagenesis identified three novel mutations - U1183C (the first mutation discovered in a region other than helix 34), and C1063U and U1189C in helix 34 - as well as three well-described mutations (C1066U, C1192G, and G1193A). These results strongly suggest that uncharacterized antibiotic resistance mutations still exist, even for traditional antibiotics.