GutMetaNet: an integrated database for exploring horizontal gene transfer and functional redundancy in the human gut microbiome.

Metagenomic studies have revealed the critical roles of complex microbial interactions, including horizontal gene transfer (HGT) and functional redundancy (FR), in shaping the gut microbiome's functional capacity and resilience. However, the lack of comprehensive data integration and systematic analysis approaches has limited the in-depth exploration of HGT and FR dynamics across large-scale gut microbiome datasets. To address this gap, we present GutMetaNet (https://gutmetanet.

Identification and characterization of the capsule depolymerase Dpo27 from phage IME-Ap7 specific to .

Among the genus, stands out as an important opportunistic infection causative agent commonly found in hospital settings, which poses a serious threat to human health. Recently, the high prevalence of carbapenem-resistant isolates has created significant therapeutic challenges for clinicians. Bacteriophages and their derived enzymes are promising therapeutic alternatives or adjuncts to antibiotics effective against multidrug-resistant bacterial infections.

Coding genomes with gapped pattern graph convolutional network.

Motivation: Genome sequencing technologies reveal a huge amount of genomic sequences. Neural network-based methods can be prime candidates for retrieving insights from these sequences because of their applicability to large and diverse datasets. However, the highly variable lengths of genome sequences severely impair the presentation of sequences as input to the neural network.

Corrigendum: Genetic characteristics and integration specificity of temperate phages.

[This corrects the article DOI: 10.3389/fmicb.2023.

mStrain: strain-level identification of using metagenomic data.

Motivation: High-resolution target pathogen detection using metagenomic sequencing data represents a major challenge due to the low concentration of target pathogens in samples. We introduced mStrain, a novel strain/lineage-level identification tool that utilizes metagenomic data. mStrain successfully identified at the strain/lineage level by extracting sufficient information regarding single-nucleotide polymorphisms (SNPs), which can therefore be an effective tool for identification and source tracking of based on metagenomic data during a plague outbreak.

Genetic characteristics and integration specificity of temperate phages.

Introduction: Temperate phages can engage in the horizontal transfer of functional genes to their bacterial hosts. Thus, their genetic material becomes an intimate part of bacterial genomes and plays essential roles in bacterial mutation and evolution. Specifically, temperate phages can naturally transmit genes by integrating their genomes into the bacterial host genomes via integrases.

Genomic epidemiological analysis of county-scale Yersinia pestis spread pattern over 50 years in a Southwest Chinese prefecture.

Plague, one of the most devastating infectious diseases in human history, is caused by the bacterium Yersinia pestis. Since the 1950s, the Dehong Dai-Jingpo Autonomous Prefecture (DH) in Yunnan Province, China, has recorded plague outbreaks that have resulted in 1,153 human cases and 379 deaths. The genetic diversity and transmission characteristics of Y.

Transcriptome sequencing and experiments reveal the effect of formyl peptide receptor 2 on liver homeostasis.

Background: Formyl peptide receptor 2 (Fpr2) is an important receptor in host resistance to bacterial infections. In previous studies, we found that the liver of Fpr2 mice is the most severely damaged target organ in bloodstream infections, although the reason for this is unclear.

Aim: To investigate the role of Fpr2 in liver homeostasis and host resistance to bacterial infections.

Vibrio parahaemolyticus from Migratory Birds in China Carries an Extra Copy of tRNA-Gly and Plasmid-Mediated Quinolone Resistance Gene .

Vibrio parahaemolyticus is a marine bacterium coming from estuarine environments, where the migratory birds can easily be colonized by V. parahaemolyticus. Migratory birds may be important reservoirs of V.

Detection of with CRISPR-Cas12a based on specific sequence tags.

Melioidosis is a bacterial infection caused by (), posing a significant threat to public health. Rapid and accurate detection of is crucial for preventing and controlling melioidosis. However, identifying is challenging due to its high similarity to other species in the same genus.

Population genomics implies potential public health risk of two non-toxigenic Vibrio cholerae lineages.

Diarrheal cases caused by non-toxigenic Vibrio cholerae have been reported globally. Lineages L3b and L9, characterized as ctxAB-negative and tcpA-positive (CNTP), pose the highest risk and have caused long-term epidemics in different regions worldwide. From 2001 to 2018, two waves (2001-2012 and 2013-2018) of epidemic caused by non-toxigenic V.

HyperVR: a hybrid deep ensemble learning approach for simultaneously predicting virulence factors and antibiotic resistance genes.

Infectious diseases emerge unprecedentedly, posing serious challenges to public health and the global economy. Virulence factors (VFs) enable pathogens to adhere, reproduce and cause damage to host cells, and antibiotic resistance genes (ARGs) allow pathogens to evade otherwise curable treatments. Simultaneous identification of VFs and ARGs can save pathogen surveillance time, especially epidemic pathogen detection.

Development and application of DETECTR-based rapid detection for pathogenic Bacillusanthracis.

Bacillus anthracis (B. anthracis) is a gram-positive bacterium responsible for the acute disease anthrax. Rapid and reliable identification of pathogenic B.

On triangle inequalities of correlation-based distances for gene expression profiles.

Background: Distance functions are fundamental for evaluating the differences between gene expression profiles. Such a function would output a low value if the profiles are strongly correlated-either negatively or positively-and vice versa. One popular distance function is the absolute correlation distance, [Formula: see text], where [Formula: see text] is similarity measure, such as Pearson or Spearman correlation.

Mining bacterial NGS data vastly expands the complete genomes of temperate phages.

Temperate phages (active prophages induced from bacteria) help control pathogenicity, modulate community structure, and maintain gut homeostasis. Complete phage genome sequences are indispensable for understanding phage biology. Traditional plaque techniques are inapplicable to temperate phages due to their lysogenicity, curbing their identification and characterization.

Small Insertions and Deletions Drive Genomic Plasticity during Adaptive Evolution of Yersinia pestis.

The life cycle of Yersinia pestis has changed a lot to adapt to flea-borne transmission since it evolved from an enteric pathogen, Yersinia pseudotuberculosis. Small insertions and deletions (indels), especially frameshift mutations, can have major effects on phenotypes and contribute to virulence and host adaptation through gene disruption and inactivation. Here, we analyzed 365 Y.

Characterization and Genomic Analysis of Bacteriophage vB_KpnM_IME346 Targeting Clinical Klebsiella pneumoniae Strain of the K63 Capsular Type.

A Klebsiella pneumoniae bacteriophage (vB_KpnM_IME346) was isolated from a hospital sewage sample. This bacteriophage specifically infects a clinical K. pneumoniae strain with a K63 capsular polysaccharide structure.

Genomic Epidemiology and Antimicrobial Susceptibility Profile of Enterotoxigenic From Outpatients With Diarrhea in Shenzhen, China, 2015-2020.

Enterotoxigenic (ETEC) is the leading cause of severe diarrhea in children and the most common cause of diarrhea in travelers. However, most ETEC infections in Shenzhen, China were from indigenous adults. In this study, we characterized 106 ETEC isolates from indigenous outpatients with diarrhea (77% were adults aged >20 years) in Shenzhen between 2015 and 2020 by whole-genome sequencing and antimicrobial susceptibility testing.

Metatranscriptomic analysis identifies different viral-like sequences in two neotropical Mansoniini mosquito species.

Mosquitoes interact with a wide range of viruses including both arboviruses and insect-specific viruses. This study aimed to characterize the RNA viruses that are interacting with Mansonia wilsoni and Coquillettidia hermanoi mosquito species. The total RNA extracted from mosquito pools were sequenced on a Ion torrent platform.

Sequence Analysis of a Jumbo Bacteriophage, That Infects Xanthomonas oryzae pv. oryzae.

A jumbo bacteriophage, , infecting pv. oryzae was isolated from rice fields in China. Here, we report the complete genome sequence of this phage, revealing that it had a linear double-stranded DNA (dsDNA) molecule 232,104 bp long, with a G+C content of 58%.