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. Our previous study showed that
Salmonella enterica
contains the largest number of temperate phages among all publicly available bacterial species.
S. enterica
is an important pathogen that can cause serious systemic infections and even fatalities.
Methods
Initially, we extracted all
S. enterica
temperate phages from the extensively developed temperate phage database established in our previous study. Subsequently, we conducted an in-depth analysis of the genetic characteristics and integration specificity exhibited by these
S. enterica
temperate phages.
Results
Here we identified 8,777
S. enterica
temperate phages, all of which have integrases in their genomes. We found 491 non-redundant
S. enterica
temperate phage integrases (integrase entries).
S. enterica
temperate phage integrases were classified into three types: intA, intS, and phiRv2. Correlation analysis showed that the sequence lengths of
S. enterica
integrase and core regions of
attB
and
attP
were strongly correlated. Further phylogenetic analysis and taxonomic classification indicated that both the
S. enterica
temperate phage genomes and the integrase gene sequences were of high diversities.
Discussion
Our work provides insight into the essential integration specificity and genetic diversity of
S. enterica
temperate phages. This study paves the way for a better understanding of the interactions between phages and
S. enterica
. By analyzing a large number of
S. enterica
temperate phages and their integrases, we provide valuable insights into the genetic diversity and prevalence of these elements. This knowledge has important implications for developing targeted therapeutic interventions, such as phage therapy, to combat
S. enterica
infections. By harnessing the lytic capabilities of temperate phages, they can be engineered or utilized in phage cocktails to specifically target and eradicate
S. enterica
strains, offering an alternative or complementary approach to traditional antibiotic treatments. Our study has implications for public health and holds potential significance in combating clinical infections caused by
S. enterica
.
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. However, the absolute correlation distance fails to fulfill the triangle inequality, which would have guaranteed better performance at vector quantization, allowed fast data localization, as well as accelerated data clustering.
In this work, we propose Formula: see text as an alternative. We prove that Formula: see text satisfies the triangle inequality when Formula: see text represents Pearson correlation, Spearman correlation, or Cosine similarity. We show Formula: see text to be better than Formula: see text, another variant of Formula: see text that satisfies the triangle inequality, both analytically as well as experimentally. We empirically compared Formula: see text with Formula: see text in gene clustering and sample clustering experiment by real-world biological data. The two distances performed similarly in both gene clustering and sample clustering in hierarchical clustering and PAM (partitioning around medoids) clustering. However, Formula: see text demonstrated more robust clustering. According to the bootstrap experiment, Formula: see text generated more robust sample pair partition more frequently (P-value Formula: see text). The statistics on the time a class "dissolved" also support the advantage of Formula: see text in robustness.
Formula: see text, as a variant of absolute correlation distance, satisfies the triangle inequality and is capable for more robust clustering.
Rights and permissions Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in ...any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. Copy to clipboard Provided by the Springer Nature SharedIt content-sharing initiative Volume 23 Supplement 3 Selected articles from the International Conference on Intelligent Biology and Medicine (ICIBM 2021): bioinformatics Correction Open Access Published:31 May 2023 Correction: On triangle inequalities of correlation-based distances for gene expression profiles Jiaxing Chen1,2, Yen Kaow Ng1, Lu Lin1, Xianglilan Zhang 3 & … Shuaicheng Li 1 Show authors BMC Bioinformatics volume 23, Article number: 571 (2022) Cite this article 178 Accesses Metrics details The Original Article was published on 08 February 2023 Correction: BMC Bioinformatics (2023) 24:40 https://doi.org/10.1186/s12859-023-05161-y Following publication of the original article 1, it was reported that the article entitled “On triangle inequalities of correlation-based distances for gene expression profiles” was published in the regular issue of this journal instead of in the supplement issue.
Abstract
Next-generation sequencing expands the known phage genomes rapidly. Unlike culture-based methods, the hosts of phages discovered from next-generation sequencing data remain uncharacterized. ...The high diversity of the phage genomes makes the host assignment task challenging. To solve the issue, we proposed a phage host prediction tool—DeepHost. To encode the phage genomes into matrices, we design a genome encoding method that applied various spaced $k$-mer pairs to tolerate sequence variations, including insertion, deletions, and mutations. DeepHost applies a convolutional neural network to predict host taxonomies. DeepHost achieves the prediction accuracy of 96.05% at the genus level (72 taxonomies) and 90.78% at the species level (118 taxonomies), which outperforms the existing phage host prediction tools by 10.16–30.48% and achieves comparable results to BLAST. For the genomes without hits in BLAST, DeepHost obtains the accuracy of 38.00% at the genus level and 26.47% at the species level, making it suitable for genomes of less homologous sequences with the existing datasets. DeepHost is alignment-free, and it is faster than BLAST, especially for large datasets. DeepHost is available at https://github.com/deepomicslab/DeepHost.
A novel
Vibrio alginolyticus
phage, VAP7, was isolated from seawater collected from Sanya, Hainan province, China. Whole-genome sequencing analysis revealed that phage VAP7 has a linear, ...double-stranded DNA genome of 144,685 bp with an average G+C content of 41.9% and a high degree of sequence similarity to
Vibrio
phage VP-1. Annotation results identified 193 open reading frames and one transfer RNA-encoding gene in the phage genome. The morphology and the results of phylogenetic analysis suggest that VAP7 should be classified as a new member of the family
Ackermannviridae
. Moreover, phage VAP7 grew over a wide pH (5.0-10.0) and temperature (4-40 °C) range. Host-range experiments revealed that VAP7 could infect 31
Vibrio alginolyticus
strains. Thus, VAP7 infecting
Vibrio alginolyticus
strains represents a potential new candidate for use in phage therapy.
Blooms of cyanobacteria cause enormous losses in both the economy and environment. Cyanophages are of great potential for fighting blooming cyanobacteria. Research report on cyanophage of ...bloom-forming cyanobacterium,
Microcystis elabens
is deficient. vB_MelS-Me-ZS1 (abbreviated as Me-ZS1) was isolated from fresh water by double-layer agar plate method using
M. elabens
. TEM exhibited that cyanosiphovirus Me-ZS1 has an icosahedral head about 60 nm in diameter, and a noncontractile tail approximately 260 nm. Experimental infection against 15 cyanobacterial strains showed that Me-ZS1 can infect 12 strains across taxonomic orders (Chroococcales, Nostocales and Oscillatoriales). High-throughput sequencing and bioinformatics analysis revealed that Me-ZS1 has a double-stranded DNA genome of 49,665 bp, with a G + C content of 58.22%, and 73 predicted open reading frames (ORFs). BLASTn and ORF comparisons showed that Me-ZS1 shares very low homology with the public sequences, and the phylogenetic tree based on TerL indicated that Me-ZS1 may delegate a novel and genetically distinct clade of Siphoviridae phages. In microcosm experiment, Me-ZS1 represented apparent effect on reducing relative abundance of cyanobacteria, increasing relative abundance of Saprospiraceae and protecting brocade carp (
Carassius auratus
) in cyanobacterial bloom water. This study isolated and characterized a novel broad-host-range
Microcystis
phage Me-ZS1 presenting a genetically distinct clade of freshwater cyanophage. The features of cyanophage Me-ZS1 provide a potential solution to the loss caused by cyanobacterial bloom.
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. The phage genome was evaluated by next-generation sequencing, which revealed a linear double-stranded DNA genome consisting of 49,482 base pairs with a G+C content of 49.1%. The latent period of vB_KpnM_IME346 was shown to be 20 min, and the burst size was 25–30 pfu (plaque-forming units)/infected cell. Transmission electron microscopy and phylogenetic analysis showed that the JD001-like phage belongs to the genus
Jedunavirus
of the family
Myoviridae
. The newly isolated vB_KpnM_IME346 shows infectivity in the clinical host
K. pneumoniae
KP576 strain, indicating that it is a promising alternative to antibacterial agents for removing
K. pneumoniae
from patients.
A novel virulent phage, vB_KpnP_IME337, isolated from a hospital sewage in Beijing, China, that infects carbapenem-resistant
Klebsiella pneumoniae
KN2 capsular type was identified and characterized. ...Next-generation sequencing and genome analysis revealed that vB_KpnP_IME337 had a linear double-stranded genome with a length of 44,266 base pairs and G+C content of 53.7%. Fifty-two putative open reading frames were identified, and no transfer RNA-encoding genes were detected. BLASTn analysis revealed that phage vB_KpnP_IME337 had the highest sequence similarity with
Klebsiella
phage phiBO1E, with genome coverage of 79%. Based on morphology, phage vB_KpnP_IME337 was determined to belong to the family
Podoviridae
of the order
Caudovirales
. It was shown that phage vB_KpnP_IME337 had an infection duration of ~ 90 min and 10 min latent period, and a highly specific to host strain. In conclusion, phage vB_KpnP_IME337 may be a promising alternative candidate to antibiotic treatment for controlling diseases caused by drug-resistant
K. pneumoniae
.
Considering personal privacy and difficulty of obtaining training material for many seldom used English words and (often non-English) names, language-independent (LI) with lightweight ...speaker-dependent (SD) automatic speech recognition (ASR) is a promising option to solve the problem. The dynamic time warping (DTW) algorithm is the state-of-the-art algorithm for small foot-print SD ASR applications with limited storage space and small vocabulary, such as voice dialing on mobile devices, menu-driven recognition, and voice control on vehicles and robotics. Even though we have successfully developed two fast and accurate DTW variations for clean speech data, speech recognition for adverse conditions is still a big challenge. In order to improve recognition accuracy in noisy environment and bad recording conditions such as too high or low volume, we introduce a novel one-against-all weighted DTW (OAWDTW). This method defines a one-against-all index (OAI) for each time frame of training data and applies the OAIs to the core DTW process. Given two speech signals, OAWDTW tunes their final alignment score by using OAI in the DTW process. Our method achieves better accuracies than DTW and merge-weighted DTW (MWDTW), as 6.97% relative reduction of error rate (RRER) compared with DTW and 15.91% RRER compared with MWDTW are observed in our extensive experiments on one representative SD dataset of four speakers' recordings. To the best of our knowledge, OAWDTW approach is the first weighted DTW specially designed for speech data in adverse conditions.
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