Biomedical subjects

Zhe-Xue Quan

Publications and source records attributed to Zhe-Xue Quan.

11 recordsLinked to original sources

PubMed2026

CoSAG-nf: A Scalable Nextflow Pipeline for Co-assembly, Optimization, and Interactive Visualization of High-Throughput Single-Cell Genomes.

MOTIVATION: Single-cell amplified genomes (SAGs) are crucial for resolving intra-population microbial heterogeneity and accurately understanding the metabolic potential of microbial dark matter populations. However, SAGs generated through multiple displacement amplification (MDA) of genomic DNA from single cells with single-copy chromosomes are highly fragmented and prone to contamination, severely hindering high-quality genome reconstruction and functional analysis, which greatly limits their scientific utility. Co-assembly of related SAGs can substantially improve genome quality, but to our knowledge no automated pipeline exists for high-throughput processing, forcing manual implementation of complex workflows that scale poorly to modern dataset sizes. RESULTS: We present CoSAG-nf, an automated high-throughput co-assembly and optimization pipeline for SAGs, implemented following the nf-core framework standards. The pipeline performs alignment-free clustering using sourmash MinHash signatures, then employs iterative tetranucleotide frequency profiling to identify and exclude outlier SAGs from co-assembly groups. CheckM2 quality assessment guides dynamic selection of optimal SAG combinations to optimize genome completeness and minimize contamination. Fully containerized, CoSAG-nf ensures reproducibility and scalability for the high-throughput processing of large-scale SAG datasets across diverse computing environments, including HPC and cloud platforms. The pipeline generates comprehensive HTML reports with quality metrics and taxonomic annotations, providing an end-to-end solution for automated high-throughput single-cell genome reconstruction. AVAILABILITY: CoSAG-nf is freely available under the MIT License at: https://github.com/linfengxu/CoSAG-nf. Archival code repository snapshots are published at zenodo with doi: https://doi.org/10.5281/zenodo.21525244. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Journal Article↗

PubMed2026

Hypoosmolarity inhibits ammonia oxidation by terrestrial and freshwater Nitrosopumilaceae members.

Salinity strongly influences the physiology and distribution of nitrifying microorganisms, yet the effects of low salinity remain understudied. This study investigates the impact of hypoosmolarity on different groups of ammonia oxidizers in soil and freshwater reservoirs, as well as in pure culture isolates. In soil microcosms amended with ammonium, at low salinity levels (~120 μS/cm), comparable to values commonly found in pristine terrestrial and freshwater environments, the abundance of ammonia-oxidizing bacteria (AOB), dominated by Nitrosomonas oligotropha, significantly increased. In contrast, the growth of ammonia-oxidizing archaea (AOA), dominated by "Candidatus Nitrosotenuis" of the Nitrosopumilaceae family, was stimulated by high salinity (~760 μS/cm). In ammonium-fed freshwater microcosms, the abundance of AOB, dominated by N. oligotropha, significantly increased under both low (~170 μS/cm) and high salinity (~850 μS/cm) conditions. In the presence of allylthiourea (50 μM), used to inhibit bacterial ammonia oxidation, AOA were sensitive to low salinity in both soil and freshwater microcosms. Consistently, culture-dependent studies revealed marked growth inhibition of terrestrial AOA, especially members of Nitrosopumilaceae, under hypoosmolarity, unlike AOB and complete ammonia oxidizer (comammox) strains. Genomic analyses, along with transcriptomic studies, suggested that the sensitivity of AOA to hypoosmolarity stress was possibly due to a lack of osmoregulatory transport systems and their S-layer cell wall structure. Overall, this study indicates hypoosmolarity as an important factor shaping the ecological niches and distribution of ammonia oxidizers, as well as nitrification activities, in terrestrial and freshwater environments that are increasingly affected by intensified water cycles due to global change.

Ammonia↗

PubMed2007

Pseudoalteromonas marina sp. nov., a marine bacterium isolated from tidal flats of the Yellow Sea, and reclassification of Pseudoalteromonas sagamiensis as Algicola sagamiensis comb. nov.

Two Gram-negative, motile and strictly aerobic marine bacteria were isolated from a tidal flat sediment sample obtained from Dae-Chun, Chung-Nam, Korea. They were preliminarily identified as Pseudoalteromonas-like bacteria, based on 16S rRNA gene sequence analysis showing nearly identical sequences (>99.7 % sequence similarity) and the highest similarity (98.4 %) to the species Pseudoalteromonas undina. Some phenotypic features of the newly isolated strains were similar to those of members of the genus Pseudoalteromonas, but several physiological and chemo-taxonomical properties readily distinguished the new isolates from previously described species. DNA-DNA hybridization with type strains of phylogenetically closely related species demonstrated that the isolates represent a novel Pseudoalteromonas species, for which the name Pseudoalteromonas marina sp. nov. is proposed, with the type strain mano4(T) (=KCTC 12242(T)=DSM 17587(T)). In addition, on the basis of this study and polyphasic data obtained from previous work, it is proposed that the species Pseudoalteromonas sagamiensis should be reclassified as Algicola sagamiensis comb. nov. and that strain B-10-31(T) (=DSM 14643(T)=JCM 11461(T)) be designated the type strain.

DNA, Bacterial↗

PubMed2007

Chryseobacterium caeni sp. nov., isolated from bioreactor sludge.

A Gram-negative, non-spore-forming, yellow-pigmented bacterium, strain N4(T), was isolated from a nickel-complexed cyanide-degrading bioreactor and subjected to a polyphasic taxonomic study. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain N4(T) is affiliated to the genus Chryseobacterium of the family Flavobacteriaceae. The levels of 16S rRNA gene sequence similarity between strain N4(T) and the type strains of all known Chryseobacterium species were 93.2-95.8 %, suggesting that strain N4(T) represents a novel species within the genus Chryseobacterium. The strain contained iso-C(15 : 0) and summed feature 4 as the major fatty acids and menaquinone MK-6 as the predominant respiratory quinone. The G+C content of the genomic DNA was 38.2 mol%. On the basis of its phenotypic properties and phylogenetic distinctiveness, strain N4(T) represents a novel species of the genus Chryseobacterium, for which the name Chryseobacterium caeni sp. nov. is proposed. The type strain is N4(T) (=KCTC 12506(T)=CCBAU 10201(T)=DSM 17710(T)).

Bacterial Typing Techniques↗

PubMed2006

Azonexus caeni sp. nov., a denitrifying bacterium isolated from sludge of a wastewater treatment plant.

A polyphasic taxonomic study was carried out to determine the taxonomic position of a newly isolated denitrifying bacterium, designated Slu-05T, which had been isolated from sludge from the main aerobic treatment tanks of a municipal sewage treatment plant. Phylogenetic analysis based on comparative 16S rRNA gene sequencing indicated that strain Slu-05T was closely related to Azonexus fungiphilus LMG 19178T (96.4 % sequence similarity), the sole species in the genus Azonexus. Strain Slu-05T comprised Gram-negative, motile, non-spore-forming and slightly curved rods. The predominant respiratory lipoquinone was Q-8. The major fatty acids were C16:1omega7c, C16:0, C18:1 isomers and C10:0 3-OH. The G+C content of the genomic DNA was 65.6 mol%. The results of DNA-DNA hybridization (15.6 %) together with phenotypic determination showed that strain Slu-5T could be distinguished from A. fungiphilus. Moreover, some phenotypic properties concerning enzyme activity, the substrates utilized as carbon sources and growth conditions distinguish strain Slu-5T from A. fungiphilus. On the basis of the results obtained in this study, Slu-05T (=DSM 17719T=KCTC 12530T=CCBAU 10199T) is the type strain of a novel species of Azonexus, for which the name Azonexus caeni sp. nov. is proposed.

Bacterial Typing Techniques↗

PubMed2006

Oceanisphaera donghaensis sp. nov., a halophilic bacterium from the East Sea, Korea.

A taxonomic study was carried out on two isolates, strains BL1(T) and BL11, from marine sediment collected from the East Sea, Korea. Comparative 16S rRNA gene sequence studies showed that these isolates clearly affiliated with the Gammaproteobacteria. BL1T and BL11 were most closely related to Oceanisphaera litoralis KMM 3654T (97.6 and 97.7 % 16S rRNA gene sequence similarity, respectively). The level of 16S rRNA gene sequence similarity between strains BL1T and BL11 was 99.7 %. The two isolates were Gram-negative, aerobic, moderately halophilic, and grew in 0.5-8.0 % NaCl and at 4-42 degrees C. Strains BL1T and BL11 shared some physiological and biochemical properties with O. litoralis KMM 3654T, although they differed in that BL1T and BL11 were able to utilize ethanol, proline and alanine. The G+C contents of the genomic DNA of strains BL1T and BL11 were 56.6 and 57.1 mol%, respectively. Both strains possessed C(16 : 1)omega7c and/or iso-C(15 : 0) 2-OH, C(16 : 0) and C(18 : 1)omega7c as the major fatty acids. DNA-DNA relatedness data indicated that strains BL1T and BL11 represent a genomic species that is separate from O. litoralis KMM 3654T. On the basis of polyphasic evidence, it is proposed that strain BL1T (=KCTC 12522T = DSM 17589T) represents the type strain of a novel species, Oceanisphaera donghaensis sp. nov.

Aeromonadaceae↗

PubMed2005

Design of long oligonucleotide probes for functional gene detection in a microbial community.

MOTIVATION: Analysis of the functions of microorganisms and their dynamics in the environment is essential for understanding microbial ecology. For analysis of highly similar sequences of a functional gene family using microarrays, the previous long oligonucleotide probe design strategies have not been useful in generating probes. RESULTS: We developed a Hierarchical Probe Design (HPD) program that designs both sequence-specific probes and hierarchical cluster-specific probes from sequences of a conserved functional gene based on the clustering tree of the genes, specifically for analyses of functional gene diversity in environmental samples. HPD was tested on datasets for the nirS and pmoA genes. Our results showed that HPD generated more sequence-specific probes than several popular oligonucleotide design programs. With a combination of sequence-specific and cluster-specific probes, HPD generated a probe set covering all the sequences of each test set. AVAILABILITY: http://brcapp.kribb.re.kr/HPD/

Algorithms↗

PubMed2005

Hydrolyzed molasses as an external carbon source in biological nitrogen removal.

Hydrolyzed molasses was evaluated as an alternative carbon source in a biological nitrogen removal process. To increase biodegradability, molasses was acidified before thermohydrolyzation. The denitrification rate was 2.9-3.6 mg N/g VSSh with hydrolyzed molasses, in which the percentage of readily biodegradable substrate was 47.5%. To consider the hydrolysate as a carbon source, a sequencing batch reactor (SBR) was chosen to treat artificial municipal wastewater. During the 14 days (28 cycles) of operation, the SBR using hydrolyzed molasses as a carbon source showed 91.6 +/- 1.6% nitrogen removal, which was higher than that using methanol (85.3 +/- 2.0%). The results show that hydrolyzed molasses can be an economical and effective external carbon source for the nitrogen removal process.

Biodegradation, Environmental↗

PubMed2005

Rhizobium daejeonense sp. nov. isolated from a cyanide treatment bioreactor.

A polyphasic study was carried out to determine the taxonomic position of two aerobic, cyanide-degrading bacterial strains, designated L61T and L22, which had been isolated from a bioreactor for the treatment of nickel-complexed cyanide. The two isolates exhibited almost identical taxonomic characteristics. Phylogenetic analysis inferred from comparative 16S rRNA gene sequences indicated that the isolates fall in a sublineage of the genus Rhizobium comprising the type strains of Rhizobium giardinii, Rhizobium radiobacter, Rhizobium rubi, Rhizobium larrymoorei, Rhizobium vitis, Rhizobium undicola, Rhizobium loessense, Rhizobium galegae and Rhizobium huautlense. Cells of the two isolates are Gram-negative, aerobic, motile and non-spore-forming rods (0.6-0.7x1.1-1.3 microm), with peritrichous flagella. The DNA G+C content is 60.1-60.9 mol%. Cellular fatty acids are C(16 : 0) (2.2-3.3 %), C(18 : 0) (2.1-3.2 %), C(19 : 0) cyclo omega8c (9.9-16.8 %), C(20 : 3)omega6,9,12c (2.7-3.3 %), summed feature 3 (7.2-7.7 %) and summed feature 7 (67.8-73.7 %). The strains formed nodules on a legume plant, Medicago sativa. A nifH gene encoding denitrogenase reductase, the key component of the nitrogenase enzyme complex, was detected in L61T by PCR amplification by using a nifH-specific primer system. Strains L61T and L22 were distinguished from the type strains of recognized Rhizobium species in the same sublineage based on low DNA-DNA hybridization values (2-4 %) and/or a 16S rRNA gene sequence similarity value of less than 96 %. Moreover, some phenotypic properties with respect to substrate utilization as a carbon or nitrogen source, antibiotic resistance and growth conditions could be used to discriminate L61T and L22 from Rhizobium species in the same sublineage. Based on the results obtained in this study, L61T and L22 are considered to be representatives of a novel species of Rhizobium, for which the name Rhizobium daejeonense sp. nov. is proposed. The type strain is L61T (=KCTC 12121T=IAM 15042T=CCBAU 10050T).

Bioreactors↗

PubMed2004

Toxicity and degradation of metal-complexed cyanide by a bacterial consortium under sulfate-reducing conditions.

Free cyanide at 1 mm decreased the initial sulfate reduction rate of a batch culture of granular sludge from 0.3 to 0.14 mmol d(-1) g(-1) SS (suspended solid), whereas 0.5 mm cyanide had a minimal effect (0.25 mmol d(-1) g(-1) SS). The order of toxicity of metal-complexed cyanides to the sludge was as follows: zinc-complexed cyanide (most toxic) > free cyanide = nickel-complexed cyanide > copper-complexed cyanide (least toxic), which also corresponds well with the order of the stability (dissociation) constants of the metal-cyanide complexes. A consortium degrading cyanide was enriched using nickel cyanide as the sole nitrogen source. This consortium completely removed 0.5 mm of nickel-complexed cyanide under sulfate-reducing conditions in 11 d. Analysis of clone library of 16S rRNA genes shows that the consortium was composed of three major phylotypes including Desulfovibrio.

Bacteria, Anaerobic↗

PubMed2003

Enhancement of sulfate reduction activity using granular sludge in anaerobic treatment of acid mine drainage.

Three laboratory-scale, upflow anaerobic reactors were operated for about 250 d to determine the effect of activated granular sludge with high density of sulfate reducing bacteria in the treatment of artificial acid mine drainage. Sulfate reducing bacteria in the granular sludge taken from the upflow anaerobic sludge blanket reactor were 1-2 x 10(6) c.f.u. g(-1), which is at least 10 times higher than that of organic substrates such as cow manure and oak compost. The reactors with granular sludge effectively removed over 99% of heavy metals, such as Fe, Al, Cu, and Cd during the experiment. This result suggests a feasibility of the application of granular sludge as a source of sulfate reducing bacteria for the treatment of acid mine drainage.

Anaerobiosis↗