Biology subjects

Zhang, X.-X.

Publications and source records attributed to Zhang, X.-X..

10 recordsLinked to original sources

bioRxiv2025

Toxoplasma gondii disrupts vitamin B and K2 biosynthetic pathways in feline gut microbiota: microbial adaptation

Vitamins B and K2 (menaquinone) are critical for microbial and host processes, but their biosynthesis in feline gut microbiota and modulation by Toxoplasma gondii remain unclear. We assembled 1,553 high-quality feline intestinal bacterial genomes from metagenomic and public data to study vitamin B and K2 biosynthesis. We identified 86,829 genes and 159 enzymes, revealing regional differences in gene and species diversity for vitamin production. Among these, 782 genomes supported de novo synthesis of at least one vitamin. T. gondii infection altered synthesis pathways: early infection boosted pyridoxine and riboflavin synthesis in the small intestine, while menadione synthesis declined in both intestines. Actinomycetota and Campylobacterota were key to menaquinone biosynthesis, with T. gondii disrupting canonical pathways and activating alternatives. These findings shed light on the complex interplay between host, parasite, and microbiota in shaping vitamin biosynthesis, offering new perspectives for maintaining feline gut health during parasitic infection.

microbiology↗

bioRxiv2025

Comprehensive profiling of antibiotic resistance, virulence genes, and mobile genetic elements in the gut microbiome of Tibetan antelopes

Tibetan antelopes, native to high-altitude plateau regions, play a vital role in the local ecosystem. However, their gut microbiota harbors diverse antibiotic resistance genes (ARGs) and virulence genes (VFGs), raising concerns about the potential spread of antibiotic resistance in wildlife. In this study, in addition to collecting 26,608 metagenome-assembled genomes (MAGs) from public databases, we performed gut metagenomic sequencing on 68 Tibetan antelopes and obtained 7,318 MAGs through binning. A total of 2,968 ARGs were identified, conferring resistance to 23 antibiotic classes, with elfamycin resistance being the most prevalent. Comparative analysis revealed 7 ARGs unique to Tibetan antelopes, suggesting species-specific adaptations. Additionally, during the analysis of shared antibiotic resistance profiles between Tibetan antelopes and humans, two bacterial strains were identified within the Tibetan antelope gut microbiota: Enterococcus gallinarum exhibiting resistance to extended-spectrum class A beta-lactamases and Klebsiella grimontii demonstrating vancomycin resistance. Mobile genetic elements played a key role in ARG dissemination. ARGs were significantly correlated with VFGs, particularly those linked to adherence and effector delivery systems. These findings underscore for the first time the potential ecological and health implications of ARG dissemination in Tibetan antelopes, highlighting the need for further surveillance to assess its impact on wildlife and environmental resistomes.

microbiology↗

bioRxiv2025

Integrated metagenome-resolved profiling of the resistome, virulome, and mobilome in the gut microbiota of wild birds

Wild birds, with their extensive geographic distributions and high mobility, are increasingly recognized as important players in the dissemination of antimicrobial resistance. Their gut microbiota, shaped by exposure to diverse environments, may act as both reservoirs and vectors of antibiotic resistance genes (ARGs), virulence factor genes (VFGs), and mobile genetic elements (MGEs). In this study, we reconstructed 2,516 high-quality metagenome-assembled genomes (MAGs) from 718 gut metagenomes of wild birds to comprehensively profile their resistome and virulome. We identified 5,596 ARG-encoding proteins across 389 distinct ARG types, with multidrug resistance emerging as the most dominant category. Escherichia coli was the principal carrier of ARGs, and genes conferring resistance to elfamycin antibiotics via target alteration were notably widespread--indicating persistent antibiotic selection pressures in avian habitats. Co-occurrence analyses revealed extensive genetic linkage between ARGs, VFGs, and MGEs. Critically, we detected 25 ARG-MGE co-localization events within 5-kilobase genomic regions, highlighting a strong potential for horizontal gene transfer and accelerated resistance dissemination within microbial communities. Of particular concern was the detection of the tetX1 gene--conferring resistance to tigecycline, a last-resort antibiotic--in the gut microbiota of Chroicocephalus ridibundus and Cygnus cygnus. This finding strongly implicates anthropogenic pollution in the spread of clinically relevant ARGs into wildlife and emphasizes the risk of environmental transmission to other hosts, including humans. These results underscore the critical ecological role of wild birds in the global antimicrobial resistance network. As both reservoirs and potential vectors of ARGs, they represent a significant but under-monitored interface between environmental and clinical resistance pathways. Enhanced surveillance and mitigation strategies targeting wildlife are urgently needed to curb the environmental propagation of antimicrobial resistance.

microbiology↗

bioRxiv2025

Metagenomic analysis of antimicrobial resistance, virulence, and mobile genetic elements in the gut microbiota of Caprinae species

The gut microbiota of livestock serves as a reservoir for antimicrobial resistance (AMR), yet Caprinae species remain understudied in this context. In this comprehensive metagenomic study, we analyzed 779 gut samples from Caprinae animals and reconstructed 17,023 high-quality metagenome-assembled genomes (MAGs). From these, we identified 4,685 antimicrobial resistance genes (ARGs) and 5,401 virulence factor genes (VFGs). Escherichia coli emerged as a major host carrying high burdens of both ARGs and VFGs. Strong positive correlations between ARGs, VFGs, and mobile genetic elements (MGEs) suggest potential co-selection and genetic linkage. Although MGEs were found in only 1.45% of MAGs, 23 ARGs were physically co-located with MGEs, indicating mobility potential. Additionally, three ARGs were embedded within viral genomes, two of which were associated with Myoviridae phages and one with an unclassified viral source, implicating phages in AMR dissemination. Comparative analyses revealed 292 ARG types shared between Caprinae and the human gut microbiota, including 20 genes representing six clinically critical resistance types: tetX1, tetX4, tmexD3, vanD, vanR, and vanS--conferring resistance to tigecycline, vancomycin, and polymyxins. These findings expand our understanding of the resistome and virulome in Caprinae animals and highlight potential zoonotic transmission pathways, underscoring the need for targeted AMR surveillance and mitigation strategies.

microbiology↗

bioRxiv2025

Expanding the chicken gut virome: Uncovering viral diversity, host interactions, and regional variations across the intestinal tract

Chicken gastrointestinal virome comprises a complex and diverse viral community with significant implications for host health and microbiome function. We analyzed 3,312 publicly available chicken gut metagenomic datasets to establish the chicken gastrointestinal virome collection (CGVD), which includes 39,380 non-redundant viral operational taxonomic units (vOTUs); notably, 84.90% (33,433/39,380) represent novel sequences absent from current databases. Over half of the CGVD vOTUs were classified as bacteriophages, predominantly from the order Caudovirales. The predicted hosts were mainly prokaryotes, particularly Bacillota and Bacteroidota, revealing a multifaceted landscape of virus-host interactions. Many vOTUs infected multiple bacterial phyla, indicating high adaptability and broad ecological impact. In addition, lifestyle prediction showed that 28.28% (11,137 /39,380) of the vOTUs in CGVD were identified as lytic phages. Functional annotation demonstrated that viral genes contribute to key metabolic processes, including nucleotide and amino acid metabolism, thereby facilitating viral replication and host adaptation. The detection of auxiliary metabolic genes and carbohydrate-active enzymes underscores the role of viruses in modulating the gut microbiome. Although antibiotic resistance genes and mobile genetic elements were present, their contribution to horizontal gene transfer appears limited. Additionally, marked regional differences in virome composition were observed between the small and large intestines, particularly in the abundance of families such as Siphoviridae and Myoviridae. CGVD not only highlights the key role of viruses in shaping the chicken gut microbiome and influencing microbial dynamics and metabolic pathways, but also provides new resources and insights for future research.

microbiology↗

bioRxiv2020

A thousand metagenome-assembled genomes of Akkermansia reveal new phylogroups and geographical and functional variations in human gut

The present study revealed the genomic architecture of Akkermansia in human gut by analyzing 1,119 near-complete metagenome-assembled genomes, 84 public available genomes, and 1 newly sequenced A. glycaniphila strain. We found that 1) the genomes of Akkermansia formed 4 species (including 2 candidate species) with distinct interspecies similarity and differed genomic characteristics, and 2) the population of A. muciniphila was structured by 3 previously identified phylogroups (Amuc I, II, and III) referring to 1,132 genomes and 1 new phylogroup (defined as Amuc IV) that contained 62 genomes. Amuc III was presented in Chinese population and Amuc IV was mainly distributed in western populations. A large number of gene of functions, pathways, and carbohydrate active enzymes that specifically associated to phylogroups. Our findings based on over a thousand genomes strengthened the previous knowledge and provided new insights into the population structure and ecology of Akkermansia in human gut.

genomics↗

bioRxiv2020

In vivo transcriptome analysis provides insights into host-dependent expression of virulence factors by Yersinia entomophaga MH96, during infection of Galleria mellonella

The function of microbes can be inferred from knowledge of genes specifically expressed in natural environments. Here we report the in vivo transcriptome of the entomopathogenic bacterium Yersinia entomophaga MH96, captured during three stages of intrahemocoelic infection in Galleria mellonella. A total of 1,285 genes were significantly upregulated by MH96 during infection; 829 genes responded to in vivo conditions during at least one stage of infection, 289 responded during two stages of infection and 167 transcripts responded throughout all three stages of infection. Genes upregulated during the earliest infection stage included components of the insecticidal toxin complex Yen-TC (chi1, chi2 and yenC1), genes for rearrangement hotspot element containing protein yenC3, cytolethal distending toxin cdtAB and vegetative insecticidal toxin vip2. Genes more highly expressed throughout the infection cycle included the putative heat-stable enterotoxin yenT and three adhesins (usher-chaperone fimbria, filamentous hemagglutinin and an AidA-like secreted adhesin). Clustering and functional enrichment of gene expression data also revealed expression of genes encoding type III and VI secretion system-associated effectors. Together these data provide insight into the pathobiology of MH96 and serve as an important resource supporting efforts to identify novel insecticidal agents.

microbiology↗

bioRxiv2020

Analysis of metagenome-assembled genomes from the mouse gut microbiota reveals distinctive strain-level characteristics

The laboratorial mouse harbors a unique gut microbiota with potential value for human microbiota-associated studies. Mouse gut microbiota has been explored at the genus and species levels, but features rarely been showed at the strain level. The identification of 833,051 and 658,438 nonredundant genes of faeces and gut content samples from the laboratorial C57/BL mice showed over half of these genes were newly found compared to the previous mouse gut microbial gene catalogue. Metagenome-assembled genomes (MAGs) was used to reconstruct 46 nonredundant MAGs belonging to uncultured specieses. These MAGs included members across all phyla in mouse gut (i.e. Firmicutes, Bacteroidetes, Proteobacteria, Deferribacteres, Verrucomicrobia, and Tenericutes) and allowed a strain-level delineating of the mouse gut microbiota. Comparison of MAGs with human gut colonies revealed distinctive genomic and functional characteristics of mouses Bacteroidetes and Firmicutes strains. Genomic characteristics of rare phyla in mouse gut microbiota were demonstrated by MAG approach, including strains of Mucispirillum schaedleri, Parasutterella excrementihominis, Helicobacter typhlonius, and Akkermansia muciniphila. ImportanceThe identification of nonredundant genes suggested the existence of unknown microbes in the mouse gut samples. The metagenome-assembled genomes (MAGs) instantiated the specificity of mouse gut species and revealed an intestinal microbial correlation between mouse and human. The cultivation of faeces and gut contents sample validated the existence of MAGs and estimate their accuracy. Full-length 16S ribosomal RNA gene sequencing enabled taxonomic characterization. This study highlighted a unique ecosystem in the gut of laboratorial mice that obviously differed with the human gut flora at the strain level. The outcomes may be beneficial to researches based on laboratorial mouse models.

microbiology↗

bioRxiv2019

Microbial extracellular polysaccharide production and aggregate stability controlled by Switchgrass (Panicum virgatum) root biomass and soil water potential

Deep-rooting perennial grasses are promising feedstock for biofuel production, especially in marginal soils lacking organic material, nutrients, and/or that experience significant water stress. Perennial grass roots can alter surrounding soil conditions and influence microbial activities, particularly the production of extracellular polymeric substances composed primarily of extracellular polysaccharides (EPS). These polymers can alleviate cellular moisture and nutrient stress, and enhance soil characteristics through improved water retention and aggregate stability, the latter of which may in turn enhance carbon persistence. In this study we used a 13CO2 tracer greenhouse experiment to examine the effect of switchgrass cultivation on the production and origin of EPS in a marginal soil with five fertilization/water treatments (control, +N, +NP, +P, low water). Soils with both added nitrogen and phosphorus had the highest root biomass, EPS and percentage of water-stable soil aggregates. Multiple linear regression analyses revealed root biomass was the most important determinant for soil EPS production, potentially by controlling carbon supply and diurnal changes in soil water potential. Path analysis highlighted the role of soil water potential were and EPS on with water-stable soil aggregates, indicating that EPS concentration and soil aggregation have similar drivers in this soil. High mannose content confirmed the microbial origin of EPS. 13CO2 labeling indicated that 0.18% of newly fixed plant carbon was incorporated into EPS. Analysis of field samples suggests that EPS is significantly enhanced under long-term switchgrass cultivation. Our results demonstrate that switchgrass cultivation can promote microbial production of EPS, providing a mechanism to enhance sustainability of marginal soils.

microbiology↗

bioRxiv2018

Experimental Evolution of Cell Shape in Bacteria

Maintenance of rod-shape in bacterial cells depends on the actin-like protein MreB. Deletion of mreB from Pseudomonas fluorescens SBW25 results in viable spherical cells of variable volume and reduced fitness. Using a combination of time-resolved microscopy and biochemical assay of peptidoglycan synthesis, we show that reduced fitness is a consequence of perturbed cell size homeostasis that arises primarily from differential growth of daughter cells. A 1,000-generation selection experiment resulted in rapid restoration of fitness with derived cells retaining spherical shape. Mutations in the peptidoglycan synthesis protein Pbp1A were identified as the main route for evolutionary rescue with genetic reconstructions demonstrating causality. Compensatory pbp1A mutations that targeted transpeptidase activity enhanced homogeneity of cell wall synthesis on lateral surfaces and restored cell size homeostasis. Mechanistic explanations require enhanced understanding of why deletion of mreB causes heterogeneity in cell wall synthesis. We conclude by presenting two testable hypotheses, one of which posits that heterogeneity stems from non-functional cell wall synthesis machinery, while the second posits that the machinery is functional, albeit stalled. Overall, our data provide support for the second hypothesis and draw attention to the importance of balance between transpeptidase and glycosyltransferase functions of peptidoglycan building enzymes for cell shape determination.

microbiology↗