Biology subjects

Zhou, Y.-L.

Publications and source records attributed to Zhou, Y.-L..

4 recordsLinked to original sources

bioRxiv2023

Artificial intelligence redefines RNA virus discovery

Current metagenomic tools can fail to identify highly divergent RNA viruses. We developed a deep learning algorithm, termed LucaProt, to discover highly divergent RNA-dependent RNA polymerase (RdRP) sequences in 10,487 metatranscriptomes generated from diverse global ecosystems. LucaProt integrates both sequence and predicted structural information, enabling the accurate detection of RdRP sequences. Using this approach we identified 161,979 potential RNA virus species and 180 RNA virus supergroups, including many previously poorly studied groups, as well as RNA virus genomes of exceptional length (up to 47,250 nucleotides) and genomic complexity. A subset of these novel RNA viruses were confirmed by RT-PCR and RNA/DNA sequencing. Newly discovered RNA viruses were present in diverse environments, including air, hot springs and hydrothermal vents, and both virus diversity and abundance varied substantially among ecosystems. This study advances virus discovery, highlights the scale of the virosphere, and provides computational tools to better document the global RNA virome. In briefA deep learning algorithm (LucaProt) that integrates both sequence and predicted structural information was employed to identify highly divergent RNA viral "dark matter" in 10,487 metatranscriptomes from diverse global ecosystems. A total of 161,979 potential RNA virus species and 180 RNA virus supergroups was unveiled using this AI approach, including many understudied groups.

microbiology↗

bioRxiv2022

The effects of pks+ Escherichia coli and bile acid in colorectal tumorigenesis among people with cholelithiasis or cholecystectomy.

Patients with cholelithiasis (CL) or cholecystectomy (CE) would have more chances to get colorectal adenoma (CRA) or cancer (CRC). To figure out the effect of gut microbiota and bile acid on colorectal neoplasm in CL and CE patients, we executed a retrospective observational study recruited 463 volunteers, including 182 people with normal gallbladder (Normal), 135 CL and 146 CE patients. The discovery cohort was established to explore the difference of gut microbiota through 16S rRNA sequencing. The validation cohort aimed to verify the results of sequencing through qPCR. Through this research, significant enrichment of Escherichia coli was found in patients with cholelithiasis or cholecystectomy both in discovery cohort (PNormal-CL=0.013; PNormal-CE=0.042) and in validation cohort (PNormal-CL<0.0001; PNormal-CE<0.0001). The relative abundance of Escherichia coli was also increased in CRA and CRC patients (in discovery cohort, PHC-CRA=0.045, PHC-CRC=0.0016; in validation cohort, PHC-CRA=0.0063, PHC-CRC=0.0007). Pks+Escherichia coli was found enriched in CL and CE patients in validation cohort (PNormal-CL<0.0001; PNormal-CE<0.0001). Through KEGG analysis in discovery cohort, the differences of bile acid metabolism were revealed (Ko00120 primary bile acid biosynthesis P=0.014; Ko00121 secondary bile acid biosynthesis P=0.010). In validation cohort, we also found the elevation of serum total bile acid of CE patients (P<0.0001). And the level of serum total bile acid was found associated with the relative abundance of pks+ Escherichia coli (r=0.1895, P=0.0012). In one word, our research found that Escherichia coli, especially pks+ species, was enriched in CL and CE patients. Pks+ Escherichia coli and bile acid metabolism were associated with CRA and CRC in people after cholecystectomy.

microbiology↗

bioRxiv2020

Phylogenomic insights into distribution and adaptation of Bdellovibrionota in marine waters

Bdellovibrionota is composed of obligate predators that can consume some gram-negative bacteria inhabiting various environments. However, whether genomic traits influence their distribution and marine adaptation remains to be answered. In this study, we performed phylogenomics and comparative genomics studies on 82 Bdellovibrionota genomes along with five metagenome-assembled genomes (MAGs) from deep sea zones. Four phylogenetic groups, Oligoflexia, Bdello-group1, Bdello-group2 and Bacteriovoracia, were revealed by constructing a phylogenetic tree, of which 53.84% of Bdello-group2 and 48.94% of Bacteriovoracia were derived from ocean. Bacteriovoracia was more prevalent in deep sea zones, whereas Bdello-group2 was largely distributed in the epipelagic zone. Metabolic reconstruction indicated that genes involved in chemotaxis, flagellar (mobility), type II secretion system, ABC transporters and penicillin-binding protein were necessary for predatory lifestyle of Bdellovibrionota. Genes involved in glycerol metabolism, hydrogen peroxide (H2O2) degradation, cell wall recycling and peptide utilization were ubiquitously present in Bdellovibrionota genomes. Comparative genomics between marine and non-marine Bdellovibrionota demonstrated that betaine as an osmoprotectant is probably widely used by marine Bdellovibrionota, meanwhile, all the marine genomes have a number of related genes for adapting marine environment. The chitinase and chitin-binding protein encoding genes were identified for the first time in Oligoflexia, which implied that Oligoflexia may prey a wider spectrum of microbes. This study expanded our knowledge on adaption strategies of Bdellovibrionota inhabiting deep sea and their potential usage for biological control. ImportanceBdellovibrionota can prey gram-negative bacteria proposed as biocontrol agent. Available Bdellovibrionota genomes showed that most are from marine environment. However, vertical distribution and adaption of Bdellovibrionota in deep sea has not been reported. Our study of Bdellovibrionota revealed four groups (Oligoflexia, Bdello-group1, Bdello-group2 and Bacteriovoracia) and their distribution pattern in oceans. We also identified the genes for different phases of predation and adaptation in deep-sea environment. Moreover, Oligoflexia genomes contain more genes for carbohydrates utilization and particularly those encoding chitin-binding protein and chitinase. Our analyses of Bdellovibrionota genomes may help understand their special lifestyle and deep-sea adaptation.

microbiology↗

bioRxiv2020

Phylogenomics of expanding uncultured environmental Tenericutes provides insights into their pathogenicity and evolutionary relationship with Bacilli

The metabolic capacity, stress response and evolution of uncultured environmental Tenericutes have remained elusive, since previous studies have been largely focused on pathogenic species. In this study, we expanded analyses on Tenericutes lineages that inhabit various environments using a collection of 840 genomes. Several novel environmental lineages were discovered inhabiting the human gut, ground water, bioreactors and hypersaline lake and spanning the Haloplasmatales and Mycoplasmatales orders. A phylogenomics analysis of Bacilli and Tenericutes genomes revealed that some uncultured Tenericutes are affiliated with novel clades in Bacilli, such as RF39, RFN20 and ML615. Erysipelotrichales and two major gut lineages, RF39 and RFN20, were found to be neighboring clades of Mycoplasmatales. We detected habitat-specific functional patterns between the pathogenic, gut and the environmental Tenericutes, where genes involved in carbohydrate storage, carbon fixation, mutation repair, environmental response and amino acid cleavage are overrepresented in the genomes of environmental lineages. We hypothesize that the two major gut lineages, namely RF39 and RFN20, are probably acetate and hydrogen producers. Furthermore, deteriorating capacity of bactoprenol synthesis for cell wall peptidoglycan precursors secretion is a potential adaptive strategy employed by these lineages in response to the gut environment. This study uncovers the characteristic functions of environmental Tenericutes and their relationships with Bacilli, which sheds new light onto the pathogenicity and evolutionary processes of Mycoplasmatales. IMPORTANCEEnvironmental Tenericutes bacteria were recently discovered in numerous environments. However, our current collection of Tenericutes genomes was overrepresented by those for pathogens. Our phylogenomics study displays the relationships between all the available Tenericutes, as well as those between Tenericutes and the clades in Bacilli, which casts lights into the uncertain boundary between the environmental lineages of Tenericutes and Bacilli. By comparing the genomes of the environmental and pathogenic Tenericutes, we revealed the metabolic pathways and adaptive strategies of the Tenericutes in the different environments and hosts. We also predicted the metabolism of the two major gut lineages RF39 and RFN20 of Tenericutes, indicating their potential importance in stabilization of the gut microbiome and contribution to human health.

microbiology↗