Biology subjects

Gan, Y.-H.

Publications and source records attributed to Gan, Y.-H..

8 recordsLinked to original sources

bioRxiv2026

Layered phage therapy exploits capsule-loss escape and altered antibiotic susceptibility in CG23 hypervirulent Klebsiella pneumoniae

The rise of drug-resistant Klebsiella pneumoniae infections is prompting a re-evaluation of phage therapy as an alternative treatment. Phage therapy has achieved successful outcomes, yet important limitations persist, including the rapid emergence of phage resistance and the time required to source suitable phages. Combining multiple phages into a phage cocktail based on genetic diversity, morphology or distinct infection mechanisms is a common strategy to mitigate resistance. Phage pairing based on these criteria neither mitigates nor delays the emergence of resistance, using CG23 hypervirulent Klebsiella pneumoniae (hvKp) EC0675 as a model. In CG23 Kp strains, resistance arises through disruption of the capsular biosynthetic pathway, leading to capsule impairment and global cross-resistance to all capsule-active phages. Combining phages active against encapsulated wild-type bacteria with those active against capsule-deficient escape mutants can overcome this constraint, improving bacterial suppression in vitro and reducing bacterial burdens across multiple organs in a mouse systemic infection model. In parallel, phage-driven capsule loss increased susceptibility of hvKp EC0675 to selected antibiotics targeting the bacterial envelope or cell wall in vitro. These findings highlight the contribution of capsule-associated resistance to phage cross-resistance in the CG23 Kp strains examined, and support further evaluation of phage combinations targeting both wild-type bacteria and resistant derivatives, including their use alongside selected antibiotics, informing future clinical translation.

microbiology↗

bioRxiv2025

Bacterial, fungal and protist communities affect differentially in succession stage of karst soil

Karst soil microbial communities are major drivers of cycling of soil nutrients that sustain plant growth and productivity. Yet, a holistic understanding of the impact of different succession stage on the karst soil microbiome is still pooly understood. Here, we used a field experiment to investigate the loog-term consequences of changes in succession stage: rocky desertification(RD), grassland(GL), shrubs(SH), forest plantation(FP) and natural forest(NF) based on plant frequency on bacteria, protist and fungal communites. We showed that the shannon index of bacteria and fungi were higher in NF compared to GL, while protist shannon index was higher in SH that GL. The bacterial simpson_e index in NF and PF were higher than that in GL, SH and RD, howerer fungal and protist simpson_e index were similar across the five succession stages. Significant differences were observed in observed outs and phylogenetic diversity index in NF, SH were higher than GL, RD for fungi and protist, whereas bacterial observed outs and phylogenetic diversity index were relatively similar in five succession stage. The five succession stage differed markedly in the compositions of bacterial, fungi and protist communities. In bacterial, dominant phyla were Actinobacteriota, Proteoprotist, Acidobacteriota. Protist communities were dominated by Phragmoplastophyta, Arthropoda phyla. Regarding protist taxa, the dominant phyla were Ascomycota and Basidiomycota. Our findings provided evidence indicating that the microbial community compositions of RD, GL, SH, PF, and NF have their respective characteristics. These characteristics stem from differences in vegetation coverage, plant debris, root formation and other factors, leading to changes in the diversity and taxonomic group of bacteria, fungi and protists at different successional stages. Overall, this study provides a comprehensive perspective, showing the differences in microbial communities at different successional stages in karst soil.

microbiology↗

bioRxiv2025

Expanding the toolbox for hypervirulent Klebsiella pneumoniae using the social amoeba Dictyostelium discoideum as a virulence biosensor

Hypervirulent Klebsiella pneumoniae (hvKp) represents a critical global threat due to its capacity to cause severe, community-acquired infections in healthy individuals and its convergence with multidrug resistance. However, current methods to evaluate hvKp virulence are limited by their reliance on mammalian models, which are costly, ethically constrained, and unsuitable for high-throughput applications. Here, we introduce a biosensing approach using the social amoeba Dictyostelium discoideum as a living phenotypic sensor for hvKp virulence. Through a suite of quantitative assays integrating predation resistance, social development, and real-time single-cell motility tracking, we show that D. discoideum can discriminate avirulent, virulent, and hypervirulent K. pneumoniae strains. Using the model hvKp strain SGH10 and its capsule-null mutant {Delta}wcaJ, we demonstrate that capsule production is strongly associated with phagocytosis resistance, developmental arrest, and amoebae paralysis, all quantifiable through imaging and motility-based readouts. Multivariate data integration revealed a clear segregation of virulence phenotypes, validating D. discoideum as a sensitive, scalable, and genetically tractable biosensor for functional virulence detection. This work establishes a conceptual and methodological framework for developing cell-based biosensors that report virulence levels through measurable host behavioral responses and outlines a calibration path to vertebrate endpoints. These systems provide a low-cost alternative to mammalian systems, especially for early-stage evaluation, and a potential foundation for automated high-throughput screening and surveillance of virulence in critical priority bacterial pathogens.

microbiology↗

bioRxiv2025

Bacterial species and surface structures shape gene transfer and the transcriptional landscape during early conjugation

Conjugative plasmids drive bacterial evolution and niche adaptation, yet how their active acquisition reshapes host transcription remains poorly understood. Most studies focus on stable plasmid carriage, overlooking the dynamic transcriptional changes during conjugation itself. Here, we show that active RP4 conjugation triggers an immediate, host- and surface factor-dependent transcriptional response. This includes activation of non-SOS stress pathways, motility, exopolysaccharide production, anaerobic respiration, and metabolic adaptation. These responses do not inhibit conjugation, suggesting they serve to maintain host homeostasis. Capsule expression blocks these responses by preventing conjugation, and also inhibits RP4 activation by physically blocking donor-recipient contact. Unexpectedly, RP4 overcomes this barrier by exploiting single-cell variation in recipient capsule thickness, successfully conjugating with thin-capsulated recipients. These findings reveal a striking interplay between plasmid, host, and surface architecture in shaping the conjugation transcriptional landscape, with broad implications for plasmid dissemination and bacterial evolution.

microbiology↗

bioRxiv2023

Effects of Polyphosphate metabolism Mutations on Biofilm, Capsule Formation and Virulence Traits in Hypervirulent ST23 Klebsiella pneumoniae SGH10

The emergence of hypervirulent Klebsiella pneumoniae (hvKP) strains poses a significant threat to public health due to their high mortality rates and propensity to cause severe community-acquired infections in otherwise healthy individuals. The ability of hvKP to form biofilms and produce a protective capsule contributes to its enhanced virulence and is a significant challenge to effective antibiotic treatment. Therefore, understanding the molecular mechanisms underlying hvKP virulence and biofilm formation is crucial for developing new therapeutic strategies. Polyphosphate Kinase 1 (PPK1) is an enzyme responsible for inorganic polyphosphate synthesis and plays a vital role in regulating various physiological processes in bacteria. In this study, we investigated the impact of polyP metabolism on the biofilm and capsule formation and virulence traits in hvKP using Dictyostelium discoideum amoeba as a model host. We found that the PPK1 null-mutant was impaired in biofilm and capsule formation and showed attenuated virulence in D. discoideum compared to the wild-type strain. We performed a shotgun proteomic analysis of the PPK1 mutant and wild-type strain to gain further insight into the underlying molecular mechanism. The results revealed that the PPK1 mutant had a differential expression of proteins (DEP) involved in capsule synthesis (Wzi - Ugd), biofilm formation (MrkC-D-H), synthesis of the colibactin genotoxin precursor (ClbB), as well as proteins associated with the synthesis and modification of lipid A (ArnB -LpxC - PagP). These proteomic findings corroborate the phenotypic observations and indicate that the PPK1 mutation is associated with impaired biofilm and capsule formation and attenuated virulence in hypervirulent K. pneumoniae. Overall, our study highlights the importance of polyP synthesis in regulating extracellular biomolecules and virulence in K. pneumoniae and provides insights into potential therapeutic targets for treating K. pneumoniae infections.

microbiology↗

bioRxiv2022

Long-term ecological and evolutionary dynamics in the gut microbiomes of carbapenemase-producing Enterobacteriaceae colonized subjects

Long-term colonization of the gut microbiome by carbapenemase-producing Enterobacteriaceae (CPE) is a growing area of public health concern as it can lead to community transmission and rapid increase in cases of life-threatening CPE infections. Leveraging the observation that many subjects are decolonized without interventions within a year, we used longitudinal shotgun metagenomics (up to 12 timepoints) for detailed characterization of ecological and evolutionary dynamics in the gut microbiome of a cohort of CPE-colonized subjects and family members (n=46; 361 samples). Subjects who underwent decolonization exhibited a distinct ecological shift marked by recovery of microbial diversity, key commensals and anti-inflammatory pathways. In addition, colonization was marked by elevated but unstable Enterobacteriaceae abundances, which exhibited distinct strain-level dynamics for different species (Escherichia coli and Klebsiella pneumoniae). Finally, comparative analysis with whole genome sequencing data from CPE isolates (n=159) helped identify sub-strain variation in key functional genes and the presence of highly similar E. coli and K. pneumoniae strains with variable resistance profiles and plasmid sharing. These results provide an enhanced view into how colonization by multi-drug resistant bacteria associates with altered gut ecology and can enable transfer of resistance genes, even in the absence of overt infection and antibiotic usage.

genomics↗

bioRxiv2018

Gut microbiome recovery after antibiotic usage is mediated by specific bacterial species

Dysbiosis in the gut microbiome due to antibiotic usage can persist for extended periods of time, impacting host health and increasing the risk for pathogen colonization. The specific factors associated with variability in gut microbiome recovery remain unknown. Using data from 4 different cohorts in 3 continents comprising >500 microbiome profiles from 117 subjects, we identified 20 bacterial species exhibiting robust association with gut microbiome recovery post antibiotic therapy. Functional and growth analysis showed that microbiome recovery is supported by enrichment in carbohydrate degradation and energy production capabilities. Association rule mining on 782 microbiome profiles from the MEDUSA database enabled reconstruction of the gut microbial food-web, identifying many recovery-associated bacteria (RABs) as primary colonizing species, with the ability to use both host and diet-derived energy sources, and to break down complex carbohydrates to support the growth of other bacteria. Experiments in a mouse model recapitulated the ability of RABs (Bacteroides thetaiotamicron and Bifidobacterium adolescentis) to promote microbiome recovery with synergistic effects, providing a two orders of magnitude boost to microbial abundance in early time-points and faster maturation of microbial diversity. The identification of specific microbial factors promoting microbiome recovery opens up opportunities for rationally fine-tuning pre- and probiotic formulations that prevent pathogen colonization and promote gut health.

genomics↗

bioRxiv2017

Population genomics of hypervirulent Klebsiella pneumoniae clonal group 23 reveals early emergence and rapid global dissemination

Since the mid-1980s there have been increasing reports of severe community-acquired pyogenic liver abscess, meningitis and bloodstream infections caused by hypervirulent Klebsiella pneumoniae, predominantly encompassing clonal group (CG) 23 serotype K1 strains. Common features of CG23 include a virulence plasmid associated with iron scavenging and hypermucoidy, and a chromosomal integrative and conjugative element (ICE) encoding the siderophore yersiniabactin and the genotoxin colibactin. Here we investigate the evolutionary history and genomic diversity of CG23 based on comparative analysis of 98 genomes. Contrary to previous reports with more limited samples, we show that CG23 comprises several deep branching sublineages dating back to the 1870s, many of which are associated with distinct chromosomal insertions of ICEs encoding yersiniabactin. We find that most liver abscess isolates (>80%) belong to a dominant sublineage, CG23-I, which emerged in the 1920s following acquisition of ICEKp10 (encoding colibactin in addition to yersiniabactin) and has undergone clonal expansion and global dissemination within the human population. The unique genomic feature of CG23-I is the production of colibactin, which has been reported previously as a promoter of gut colonisation and dissemination to the liver and brain in a mouse model of CG23 K. pneumoniae infection, and has been linked to colorectal cancer. We also identify an antibiotic-resistant subclade of CG23-I associated with sexually-transmitted infections in horses dating back to the 1980s. These data show that hypervirulent CG23 K. pneumoniae was circulating in humans for decades before the liver abscess epidemic was first recognised, and has the capacity to acquire and maintain AMR plasmids. These data provide a framework for future epidemiological and experimental studies of hypervirulent K. pneumoniae. To further support such studies we present an open access and completely sequenced human liver abscess isolate, SGH10, which is typical of the globally disseminated CG23-I sublineage.

genomics↗