Songnian Hu
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View article: Maternal gut microbiota transmission and early-life colonization patterns influence infant CMPA risk
Maternal gut microbiota transmission and early-life colonization patterns influence infant CMPA risk Open
The establishment of gut microbiota in early life represents a critical window for immune system development and the prevention of cow’s milk protein allergy (CMPA). While maternal influence on infant gut colonization is well-documented, t…
View article: A database of glacier prokaryotic genomes and genes for the Three Poles
A database of glacier prokaryotic genomes and genes for the Three Poles Open
Glaciers cover 10 % of Earth's land area and are a pool of carbon and nitrogen for downstream ecosystems. Microbes, including bacteria, fungi, algae, and other microeukaryotes, are the primary inhabitants of glacier ecosystems and are key …
View article: Use of the CHM13-T2T genome improves metagenomic analysis by minimizing host DNA contamination
Use of the CHM13-T2T genome improves metagenomic analysis by minimizing host DNA contamination Open
Human-associated metagenomic data often contain human nucleic acid information, which can affect the accuracy of microbial classification or raise ethical concerns. These reads are typically removed through alignment to the human genome us…
View article: Pharmacogenomic analysis of low-density lipoprotein receptor 3’ untranslated region genetic variants influencing rosuvastatin efficacy in Chinese dyslipidemia patients
Pharmacogenomic analysis of low-density lipoprotein receptor 3’ untranslated region genetic variants influencing rosuvastatin efficacy in Chinese dyslipidemia patients Open
Objectives Dyslipidemia is a crucial risk factor for atherosclerotic cardiovascular disease. Although rosuvastatin is widely used, treatment response varies significantly due to genetic variation. This study investigated the pharmacogenomi…
View article: Large-scale analysis of SARS-CoV-2 genomic data from sewage using eVarEPS reveals that amino acid mutations detected in sewage provide an early warning on population prevalence
Large-scale analysis of SARS-CoV-2 genomic data from sewage using eVarEPS reveals that amino acid mutations detected in sewage provide an early warning on population prevalence Open
Key amino acid mutations in SARS-CoV-2 genomes drive the emergence of variants of concern, impacting virus transmission and immune escape. However, there is still a lack of large-scale monitoring and risk assessment of new amino acid varia…
View article: Whole-genome sequencing and comparative genomic analysis of Irpex lacteus isolated from the female reproductive tract
Whole-genome sequencing and comparative genomic analysis of Irpex lacteus isolated from the female reproductive tract Open
Irpex lacteus is a fungus typically found on angiosperm branches and trunks. Here, we report the isolation of a novel strain of I. lacteus from the cervix uteri of a female patient diagnosed with endometriosis and COVID-19 at Beijing Obste…
View article: hAb-Convergent: an antibody rearrangement analysis system for therapeutic antibody engineering based on convergent evolution
hAb-Convergent: an antibody rearrangement analysis system for therapeutic antibody engineering based on convergent evolution Open
In therapeutic antibody engineering, utilizing naturally occurring mutations in the human body as a reference for modification is an emerging trend. The theory of convergent evolution presents a viable solution. Nevertheless, the nonunifor…
View article: Diverse lifestyles and adaptive evolution of uncultured UBA5794 actinobacteria, a sister order of “Candidatus actinomarinales”
Diverse lifestyles and adaptive evolution of uncultured UBA5794 actinobacteria, a sister order of “Candidatus actinomarinales” Open
View article: Critical contributions of neuronal subtypes to pediatric drug-resistant focal dysplasia
Critical contributions of neuronal subtypes to pediatric drug-resistant focal dysplasia Open
Approximately 75% of epilepsy cases emerge in childhood, and 10%–30% of these pediatric epilepsy cases are resistant to standard drug therapies; however, the underlying causes of resistance remain poorly understood. Focal cortical dysplasi…
View article: VarEPS-MPXV: A risk evaluation system for observed and virtual variations in mpox virus genomes
VarEPS-MPXV: A risk evaluation system for observed and virtual variations in mpox virus genomes Open
View article: Invasion alert: How does Chaetomorpha valida occupy new waters area by ' spore weapons ' and their’s environmental adaptability
Invasion alert: How does Chaetomorpha valida occupy new waters area by ' spore weapons ' and their’s environmental adaptability Open
View article: A Meta-Analysis of the Human Gut Mycobiome Using Internal Transcribed Spacer Data
A Meta-Analysis of the Human Gut Mycobiome Using Internal Transcribed Spacer Data Open
The intestinal mycobiome is closely related to human health. There have been several reports investigating the association between the gut fungi and disease, but there is still a lack of overall assessment of the human gut mycobiome. Here,…
View article: Genomic insights on cgMLST markers, drug resistance, and urease cluster of <i>Proteus mirabilis</i> strains
Genomic insights on cgMLST markers, drug resistance, and urease cluster of <i>Proteus mirabilis</i> strains Open
Proteus mirabilis , a significant pathogenic bacterium within the Enterobacteriaceae family, is widely distributed across various natural environments. This study conducted a genomic comparison analysis of 1,267 strains of P. mirabilis usi…
View article: Probing the diagnostic values of plasma cf-nDNA and cf-mtDNA for Parkinson’s disease and multiple system atrophy
Probing the diagnostic values of plasma cf-nDNA and cf-mtDNA for Parkinson’s disease and multiple system atrophy Open
Background Cell loss and mitochondrial dysfunction are key pathological features of idiopathic Parkinson’s disease (PD) and multiple system atrophy (MSA). It remains unclear whether disease-specific changes in plasma circulating cell-free …
View article: Associations Between the Polymorphisms in the Coding Sequence of SLCO1B1 and Blood Lipid Levels Before and After Treatment by Atorvastatin in the Chinese Han Adults with Dyslipidemia
Associations Between the Polymorphisms in the Coding Sequence of SLCO1B1 and Blood Lipid Levels Before and After Treatment by Atorvastatin in the Chinese Han Adults with Dyslipidemia Open
This study delved into the intricate genetic structure of polymorphisms in SLCO1B1 CDS and their roles in lipid metabolism and atorvastatin's efficacy among Chinese Han adults with dyslipidemia. The findings underscore the crucial role of …
View article: Biological nitrogen fixation driven by methane anaerobic oxidation supports the complex biological communities in cold-seep habitat
Biological nitrogen fixation driven by methane anaerobic oxidation supports the complex biological communities in cold-seep habitat Open
View article: Influence of irrigation with pulp and paper mill wastewater on bacterial communities of reed fields
Influence of irrigation with pulp and paper mill wastewater on bacterial communities of reed fields Open
View article: PIPdb: a comprehensive plasmid sequence resource for tracking the horizontal transfer of pathogenic factors and antimicrobial resistance genes
PIPdb: a comprehensive plasmid sequence resource for tracking the horizontal transfer of pathogenic factors and antimicrobial resistance genes Open
Plasmids, as independent genetic elements, carrying resistance or virulence genes and transfer them among different pathogens, posing a significant threat to human health. Under the ‘One Health’ approach, it is crucial to control the sprea…
View article: Seeing the unseen in characterizing RNA editome during rice endosperm development
Seeing the unseen in characterizing RNA editome during rice endosperm development Open
Rice (Oryza sativa L.) endosperm is essential to provide nutrients for seed germination and determine grain yield. RNA editing, a post-transcriptional modification essential for plant development, unfortunately, is not fully characterized …
View article: Plasma level of alpha-synuclein oligomers as a biomarker for isolated rapid eye movement sleep behavior disorder diagnosis and progression: a prospective cohort study
Plasma level of alpha-synuclein oligomers as a biomarker for isolated rapid eye movement sleep behavior disorder diagnosis and progression: a prospective cohort study Open
Background Alpha-synuclein oligomers (o-α-syn) are pivotal in the pathogenesis of α-synucleinopathy. Isolated rapid eye movement (REM) sleep behavior disorder (iRBD) serves as an early indicator of the disease, offering insights into disea…
View article: Single‐cell landscape revealed immune characteristics associated with disease phases in brucellosis patients
Single‐cell landscape revealed immune characteristics associated with disease phases in brucellosis patients Open
A comprehensive immune landscape for Brucella infection is crucial for developing new treatments for brucellosis. Here, we utilized single‐cell RNA sequencing (scRNA‐seq) of 290,369 cells from 35 individuals, including 29 brucellosis patie…
View article: Co-expression of a pair of interdependent regulators coding genes ovmZ and ovmW awakens the production of angucyclinones antibiotics in Streptomyces neyagawaensis
Co-expression of a pair of interdependent regulators coding genes ovmZ and ovmW awakens the production of angucyclinones antibiotics in Streptomyces neyagawaensis Open
View article: multiMotif: a generalized tool for scanning and visualization of diverse and distant multiple motifs
multiMotif: a generalized tool for scanning and visualization of diverse and distant multiple motifs Open
View article: Exploring CYP2D6 polymorphisms and angiotensin receptor blocker response in the Bai hypertensive population
Exploring CYP2D6 polymorphisms and angiotensin receptor blocker response in the Bai hypertensive population Open
Objective The CYP2D6 enzyme is crucial for the metabolism and disposition of a variety of drugs. This study was conducted to examine the relationship between CYP2D6 gene polymorphisms and the response to angiotensin receptor blocker (ARB)-…
View article: Dissecting and tracing the gut microbiota of infants with botulism: a cross sectional and longitudinal study
Dissecting and tracing the gut microbiota of infants with botulism: a cross sectional and longitudinal study Open
Background Infant botulism is caused by botulinum neurotoxin (BoNT), which is mainly produced by Clostridium botulinum . However, there is a lack of longitudinal cohort studies on infant botulism. Herein, we have constructed a cross-sectio…
View article: Genomic epidemiology reveals multiple mechanisms of linezolid resistance in clinical enterococci in China
Genomic epidemiology reveals multiple mechanisms of linezolid resistance in clinical enterococci in China Open
Background Infections caused by linezolid-resistant enterococci (LRE) are clinically difficult to treat and threaten patient health. However, there is a lack of studies on long time-span LRE strains in China. For this reason, our study com…
View article: Impact of LDLR polymorphisms on lipid levels and atorvastatin’s efficacy in a northern Chinese adult Han cohort with dyslipidemia
Impact of LDLR polymorphisms on lipid levels and atorvastatin’s efficacy in a northern Chinese adult Han cohort with dyslipidemia Open
Background Dyslipidemia, a significant risk factor for atherosclerotic cardiovascular disease (ASCVD), is influenced by genetic variations, particularly those in the low-density lipoprotein receptor (LDLR) gene. This study aimed to elucida…
View article: Dynamic analysis of SARS-CoV-2 evolution based on different countries
Dynamic analysis of SARS-CoV-2 evolution based on different countries Open
Since late 2019, COVID-19 has significantly impacted the world. Understanding the evolution of SARS-CoV-2 is crucial for protecting against future infectious pathogens. In this study, we conducted a comprehensive chronological analysis of …
View article: <i>Anaerostipes hadrus</i> , a butyrate-producing bacterium capable of metabolizing 5-fluorouracil
<i>Anaerostipes hadrus</i> , a butyrate-producing bacterium capable of metabolizing 5-fluorouracil Open
Anaerostipes hadrus ( A. hadrus ) is a dominant species in the human gut microbiota and considered a beneficial bacterium for producing probiotic butyrate. However, recent studies have suggested that A. hadrus may negatively affect the hos…
View article: Comment on essd-2023-395
Comment on essd-2023-395 Open
Abstract. Glaciers cover 10 % of Earth’s land area and are a pool of carbon and nitrogen for downstream ecosystems. Microbes, including bacteria, fungi, algae, and other microeukaryotes, are the primary inhabitants of glac…