Xin-Hui Xing’s research while affiliated with Tsinghua University and other places

Animals have a strong, reciprocal relationship with the microbes in their gut, but little is known about what traits allow potentially symbiotic bacteria to colonize new hosts. Given the high degree of selective pressure exerted on microbes in a digestive tract–some studies have used serial passage to examine what traits enable microbes to associate with hosts. But to speed up the mutation rate, a recent study combined serial passage with atmospheric and room temperature plasma (ARTP) mutagenesis. The researchers generated mutant libraries of Snodgrassella from bumblebees (Bombus terrestris) using ARTP, and then passed the libraries through a non-native host, gnotobiotic honeybees (Apis mellifera). Strains with mutations in the Mutual gliding locus had a competitive advantage in the honeybees but not bumblebees. Further tests suggested that these mutations promoted colonization by altering the cell’s Type IV pili-dependent motility. While more research is needed, this study demonstrates that ARTP mutagenesis can be used to rapidly identify key microbial mutations–and paves the way for broader application in evolutionary microbiota research.

Background The gut microbiota and their hosts profoundly affect each other’s physiology and evolution. Identifying host-selected traits is crucial to understanding the processes that govern the evolving interactions between animals and symbiotic microbes. Current experimental approaches mainly focus on the model bacteria, like hypermutating Escherichia coli or the evolutionary changes of wild stains by host transmissions. A method called atmospheric and room temperature plasma (ARTP) may overcome the bottleneck of low spontaneous mutation rates while maintaining mild conditions for the gut bacteria. Results We established an experimental symbiotic system with gnotobiotic bee models to unravel the molecular mechanisms promoting host colonization. By in vivo serial passage, we tracked the genetic changes of ARTP-treated Snodgrassella strains from Bombus terrestris in the non-native honeybee host. We observed that passaged isolates showing genetic changes in the mutual gliding locus have a competitive advantage in the non-native host. Specifically, alleles in the orphan mglB, the GTPase activating protein, promoted colonization potentially by altering the type IV pili-dependent motility of the cells. Finally, competition assays confirmed that the mutations out-competed the ancestral strain in the non-native honeybee gut but not in the native host. Conclusions Using the ARTP mutagenesis to generate a mutation library of gut symbionts, we explored the potential genetic mechanisms for improved gut colonization in non-native hosts. Our findings demonstrate the implication of the cell mutual-gliding motility in host association and provide an experimental system for future study on host-microbe interactions. ArN8Xjm3N6Dubzus4DCSQmVideo Abstract

Background CRISPRi screening has become a powerful approach for functional genomic research. However, the off-target effects resulting from the mismatch tolerance between sgRNAs and their intended targets is a primary concern in CRISPRi applications. Results We introduce Guide Library Designer (GLiDe), a web-based tool specifically created for the genome-scale design of sgRNA libraries tailored for CRISPRi screening in prokaryotic organisms. GLiDe incorporates a robust quality control framework, rooted in prior experimental knowledge, ensuring the accurate identification of off-target hits. It boasts an extensive built-in database, encompassing 1,397 common prokaryotic species as a comprehensive design resource. Conclusions GLiDe provides the capability to design sgRNAs for newly discovered organisms. We further demonstrated that GLiDe exhibits enhanced precision in identifying off-target binding sites for the CRISPRi system.

Gas-fermenting Clostridium species hold tremendous promise for one-carbon biomanufacturing. To unlock their full potential, it is crucial to unravel and optimize the intricate regulatory networks that govern these organisms; however, this aspect is currently underexplored. In this study, we employed pooled CRISPR interference (CRISPRi) screening to uncover a wide range of functional transcription factors (TFs) in Clostridium ljungdahlii , a representative species of gas-fermenting Clostridium , with a special focus on the TFs associated with the utilization of carbon resources. Among the 425 TF candidates, we identified 75 and 68 TF genes affecting the heterotrophic and autotrophic growth of C. ljungdahlii , respectively. We directed our attention on two of the screened TFs, NrdR and DeoR, and revealed their pivotal roles in the regulation of deoxyribonucleotides (dNTPs) supply, carbon fixation, and product synthesis in C. ljungdahlii , thereby influencing the strain performance in gas fermentation. Based on this, we proceeded to optimize the expression of deoR in C. ljungdahlii by adjusting its promoter strength, leading to improved growth rate and ethanol synthesis of C. ljungdahlii when utilizing syngas. This study highlights the effectiveness of pooled CRISPRi screening in gas-fermenting Clostridium species, expanding the horizons for functional genomic research in these industrially important bacteria.

Designing highly efficient orally administrated nanotherapeutics with specific inflammatory site-targeting functions in the gastrointestinal (GI) tract for ulcerative colitis (UC) management is a significant challenge. Straightforward and adaptable modular multifunctional nanotherapeutics represent groundbreaking advancements and are crucial to promoting broad application in both academic research and clinical practice. In this study, we focused on exploring a specific targeting modular and functional oral nanotherapy, serving as "one stone", for the directed localization of inflammation and the regulation of redox homeostasis, thereby achieving effects against "two birds" for UC treatment. The designed nanotherapeutic agent OPNs@LMWH, which has a core-shell structure composed of oxidation-sensitive epsilon-polylysine nanoparticles (OPNs) in the core and low-molecular-weight heparin (LMWH) in the shell, exhibited specific active targeting effects and therapeutic efficacy simultaneously. We qualitatively and quantificationally confirmed that OPNs@LMWH possessed high integrin alpha M-mediated immune cellular uptake efficiency and preferentially accumulated in inflamed lesions. Compared with bare OPNs, OPNs@LMWH exhibited enhanced intracellular reactive oxygen species (ROS) scavenging and anti-inflammatory effects. After oral administration of OPNs@LMWH to mice with dextran sulfate sodium (DSS)-induced colitis, robust resilience was observed. OPNs@LMWH effectively ameliorated oxidative stress and inhibited the activation of inflammation-associated signalling pathways while simultaneously bolstering the protective mechanisms of the colonic epithelium. Overall, these findings underscore the compelling dual functionalities of OPNs@LMWH, which enable effective oral delivery to inflamed sites, thereby facilitating precise UC management.

Base editing, the targeted introduction of point mutations into cellular DNA, holds promise for improving genome-scale functional genome screening to single-nucleotide resolution. Current efforts in prokaryotes, however, remain confined to loss-of-function screens using the premature stop codons-mediated gene inactivation library, which falls far short of fully releasing the potential of base editors. Here, we developed a base editor-mediated functional single nucleotide variant screening pipeline in Escherichia coli. We constructed a library with 31,123 sgRNAs targeting 462 stress response-related genes in E. coli, and screened for adaptive mutations under isobutanol and furfural selective conditions. Guided by the screening results, we successfully identified several known and novel functional mutations. Our pipeline might be expanded to the optimization of other phenotypes or the strain engineering in other microorganisms.

Owing to the nondeterministic and nonlinear nature of gene expression, the steady-state intracellular protein abundance of a clonal population forms a distribution. The characteristics of this distribution, including expression strength and noise, are closely related to cellular behavior. However, quantitative description of these characteristics has so far relied on arrayed methods, which are time-consuming and labor-intensive. To address this issue, we propose a deep-learning–assisted Sort-Seq approach (dSort-Seq) in this work, enabling high-throughput profiling of expression properties with high precision. We demonstrated the validity of dSort-Seq for large-scale assaying of the dose-response relationships of biosensors. In addition, we comprehensively investigated the contribution of transcription and translation to noise production in Escherichia coli, from which we found that the expression noise is strongly coupled with the mean expression level. We also found that the transcriptional interference caused by overlapping RpoD-binding sites contributes to noise production, which suggested the existence of a simple and feasible noise control strategy in E. coli.