Latent human herpesvirus 6 is reactivated in CAR T cells.

Cell therapies have yielded durable clinical benefits for patients with cancer, but the risks associated with the development of therapies from manipulated human cells are understudied. For example, we lack a comprehensive understanding of the mechanisms of toxicities observed in patients receiving T cell therapies, including recent reports of encephalitis caused by reactivation of human herpesvirus 6 (HHV-6)1. Here, through petabase-scale viral genomics mining, we examine the landscape of human latent viral reactivation and demonstrate that HHV-6B can become reactivated in cultures of human CD4+ T cells. Using single-cell sequencing, we identify a rare population of HHV-6 'super-expressors' (about 1 in 300-10,000 cells) that possess high viral transcriptional activity, among research-grade allogeneic chimeric antigen receptor (CAR) T cells. By analysing single-cell sequencing data from patients receiving cell therapy products that are approved by the US Food and Drug Administration2 or are in clinical studies3-5, we identify the presence of HHV-6-super-expressor CAR T cells in patients in vivo. Together, the findings of our study demonstrate the utility of comprehensive genomics analyses in implicating cell therapy products as a potential source contributing to the lytic HHV-6 infection that has been reported in clinical trials1,6-8 and may influence the design and production of autologous and allogeneic cell therapies.

Day and Night Reversed Feeding Aggravates High-Fat Diet-Induced Abnormalities in Intestinal Flora and Lipid Metabolism in Adipose Tissue of Mice.

BACKGROUND: The incongruity between dietary patterns and the circadian clock poses an elevated risk for metabolic health issues, particularly obesity and associated metabolic disorders. The intestinal microflora engages in regulating various physiological functions of the host through its metabolites. OBJECTIVES: This study aimed to investigate the impact of reversed feeding schedules during the day and night on intestinal flora and lipid metabolism in high-fat diet-induced obese mice. METHODS: Mice aged 8-10 wk were subjected to either daytime or nighttime feeding and were administered a control or high-fat diet for 18 wk. At the end of the experiment, various assessments were conducted, including analysis of serum biochemic indices, histologic examination, evaluation of gene and protein expression in adipose tissue, and scrutiny of changes in intestinal microbial composition. RESULTS: The results showed that day-night reversed feeding caused an increase in fasting blood glucose and exacerbated the high-fat diet-induced weight gain and lipid abnormalities. The mRNA expression levels of Leptin and Dgat1 were increased by day-night reversed feeding, which also reduced the expression level of adiponectin under the high-fat diet. Additionally, there was a significant increase in the protein concentrations of PPARγ, SREBP1c, and CD36. Inverted feeding schedules led to a reduction in intestinal microbial diversity, an increase in the abundance of inflammation-related bacteria, such as Coriobacteriaceae_UCG-002, and a suppression of beneficial bacteria, including Akkermansia, Candidatus_Saccharimonas, Anaeroplasma, Bifidobacterium, Carnobacterium, and Odoribacter. Acinetobacter exhibited a significant negative correlation with Leptin and Fasn, suggesting potential involvement in the regulation of lipid metabolism. CONCLUSIONS: The results elucidated the abnormalities of lipid metabolism and intestinal flora caused by day-night reversed feeding, which exacerbates the adverse effects of a high-fat diet on lipid metabolism and intestinal microflora. This reversal in feeding patterns may disrupt both intestinal and lipid metabolism homeostasis by altering the composition and abundance of intestinal microflora in mice.

Sleep quality as a mediator between family function and life satisfaction among Chinese older adults in nursing home.

BACKGROUND: The life satisfaction of the elderly in nursing home is the focus of social concern.The purpose of this study was to evaluate the effects of family function and sleep quality on life satisfaction among elderly individuals in nursing homes and examine the mediating effect of sleep quality between family function and life satisfaction. METHODS: A cross-sectional observational study was conducted .A total of 127 older adults who completed the Life Satisfaction Index A (LSI-A), the Family APGAR Index and the Pittsburgh Sleep Quality Index (PSQI) were recruited from four nursing homes in Chongqing, China. RESULTS: Life satisfaction was positively correlated with family function (r=0.434, p<0.01) and negatively correlated with PSQI (r = -0.514, p<0.01). PSQI was found to be negatively associated with family function (r=-0.387, p<0.01).Family function had a significant effect on PSQI (path a: ß=-0.8459, 95% CI=-1.2029, -0.4889), and PSQI had a significant effect on life satisfaction (path b: ß=-0.3916, 95% CI=-0.5407, -0.2425). The total effect (path c) and direct effect (path c') of family function on life satisfaction were significant (ß=0.8931, 95% CI=0.5626, 1.2235 and ß=0.56181, 95% CI=0.2358, 0.8879, respectively). The coefficient for the indirect effect of family function on life satisfaction through PSQI was statistically significant (ß=0.3312, 95% CI=0.1628, 0.5588). PSQI played a partial mediating role between family function and life satisfaction, and PSQI mediated 32.58% of the total effect of family function on life satisfaction. CONCLUSIONS: Family function and sleep quality were significant predictors of elderly people's life satisfaction in nursing homes. Sleep quality partially mediated the relationship between family function and life satisfaction.The interventions focused on promoting family function and improving sleep quality may be more helpful in improving elderly people's life satisfaction in nursing homes.

The Relationships Among Family Functioning, Sleep Quality and Quality of Life in Chinese Community-Dwelling Older Adults with Insomnia: A Structural Equation Model.

OBJECTIVES: The proportion of individuals with insomnia is increasing, and many older adults have insomnia. This study aimed to explore the relationships between family functioning and quality of life (QOL) among community-dwelling older adults with insomnia, as well as to explore the mediating role of sleep quality in this relationship. METHODS: The participants were 225 older adults with insomnia from community health service centers in Chongqing, China. The Family Care Index (APGAR) was used to assess family functioning, the Pittsburgh Sleep Quality Index (PSQI) was used to assess sleep quality, and the 36-item Short-Form Health Survey (SF-36) was used to assess QOL. RESULTS: The results showed that family functioning would be positively associated with QOL (p = .005) and that this relationship would be partially mediated by higher sleep quality (p < .001). CONCLUSIONS: Family functioning has a direct effect on QOL and an indirect effect on QOL through the regulation of sleep quality. Maintaining good family functioning is important for improving sleep quality and QOL in older adults with insomnia. CLINICAL IMPLICATIONS: Developing family functioning-based assessments and targeted intervention strategies could be beneficial for older adults with insomnia.

A Ketogenic Diet in Combination with Gemcitabine Mitigates Pancreatic Cancer-Associated Cachexia in Male and Female KPC Mice.

Cancer-associated cachexia (CAC) is a critical contributor to pancreatic ductal adenocarcinoma (PDAC) mortality. Thus, there is an urgent need for new strategies to mitigate PDAC-associated cachexia; and the exploration of dietary interventions is a critical component. We previously observed that a ketogenic diet (KD) combined with gemcitabine enhances overall survival in the autochthonous LSL-KrasG12D/+; LSL-Trp53 R172H/+; Pdx1-Cre (KPC) mouse model. In this study, we investigated the effect and cellular mechanisms of a KD in combination with gemcitabine on the maintenance of skeletal muscle mass in KPC mice. For this purpose, male and female pancreatic tumor-bearing KPC mice were allocated to a control diet (CD), a KD, a CD + gemcitabine (CG), or a KD + gemcitabine (KG) group. We observed that a KD or a KG-mitigated muscle strength declined over time and presented higher gastrocnemius weights compared CD-fed mice. Mechanistically, we observed sex-dependent effects of KG treatment, including the inhibition of autophagy, and increased phosphorylation levels of eIF2α in KG-treated KPC mice when compared to CG-treated mice. Our data suggest that a KG results in preservation of skeletal muscle mass. Additional research is warranted to explore whether this diet-treatment combination can be clinically effective in combating CAC in PDAC patients.

Per1/Per2 knockout Affects Spleen Immune Function in Elderly Mice via Inducing Spleen Lymphocyte Ferroptosis.

Disturbances in circadian rhythms are known to affect immune functions. However, the long-term impact of abnormal circadian rhythms on the immune-related functions of the spleen are poorly understood. Hence, we aimed to investigate the immune-related functions of spleen in Per1/Per2 double-knockout (DKO) and wild-type (WT) mice aged 4, 9, and 14 months. Compared to the WT mice, the DKO mice had smaller spleen white pulp (WP) and lymphocyte germinal area, as well as fewer immune cells with age-these differences were especially clear. The spleen lymphocyte mortality, malondialdehyde (MDA) levels, reactive oxygen species (ROS) levels, and ferritin-binding receptor (TFR1) levels were significantly higher in the 14-month-old DKO mice than in WT mice of the same age. Transcriptome analysis showed that most of the differentially expressed mRNAs were enriched in DNA damage repair-related pathways. In DKO mice, spleen cells showed up-regulation of pro-ferroptosis genes, such as Cd36,Atm, and Acsl4, and down-regulation of anti-ferroptosis genes, such as GPX4. We found that long-term abnormalities in the circadian rhythm can induce DNA damage and ferroptosis in mouse spleen.

Instability mechanism and discharge regime diagnosis of microthrusters based on plasma properties.

In order to make it possible to control the plasma state and predict the regime transitions via coupling optical and electrical diagnosis in aerospace engineering, we have experimentally investigated the regime transitions under 0.1-15 kPa with an input discharge power of 0-25 W in a parallel-plate electrode configuration. An abnormal glow discharge (AGD), filamentary discharge (FD), and arc discharge (AD) are distinguished using the voltage-current characteristics under different gas pressures. The electron excitation temperature (Te), electron density (Ne), spatial resolutions of Te and Ne, and ionization degree are obtained via optical emission spectroscopy to reveal the transition mechanisms. Thermal instability, characterized by Te, plays a dominant role during the transition from an AGD to an FD. The conclusions are supported by analysis of ionization degree, whereas electronic instability becomes the dominant mechanism in the transition from an FD to an AD. This is related to collision kinetics because of an observed drop in Ne, which is verified by the spatial resolution as well. Moreover, planar laser-induced fluorescence provides further insight into the instantaneous location and relative number variation of Ar 1s5 metastable atoms, which agrees well with the plasma properties mentioned above. In addition, a pressure of 1 kPa with a maximum input power of 17.5 W are specified as suitable working parameters for further study when applied to microthrusters due to its higher Ne and better stability.

One-third of lands face high conflict risk between biodiversity conservation and human activities in China.

Biodiversity is declining at an unprecedented rate, and conservation is needed in many places including human-dominated landscapes. Evaluation of conflict risk between biodiversity conservation and human activities is a prerequisite for countries to develop strategies to achieve better conservation outcomes. However, quantitative methods to measure the conflict risk in large-scale areas are still lacking. Here we put forward a quantitative model in large-scale areas and produce the first continuum map of conflict risk in China. Our results show that conflict risk hotspots take up 32.86 % of China's terrestrial area, which may affect 42.98 % of China's population and more than 98 % of threaten vertebrates. Although species richness is high in these hotspot regions, only 10.69 % of them are covered by protected areas. Therefore, alternative conservation measures and proactive spatial planning are needed, especially in regions along the coastlines and around the Sichuan Basin. Especially, extraordinary attentions should be paid to urban agglomerations such as the Pearl River Delta and Yangtze River Delta. Compared to previous studies, our study quantifies the conflict risk of every gird cell, enabling the comparison among any locations. The analysis of 500 times generations shows a low sensitivity of the model as the maximum standard deviation is only 0.017. Furthermore, our model can be applied in other countries or at global scale to provide strategies for conflict governance and biodiversity conservation.

The Effects of Audiovisual Inputs on Solving the Cocktail Party Problem in the Human Brain: An fMRI Study.

At cocktail parties, our brains often simultaneously receive visual and auditory information. Although the cocktail party problem has been widely investigated under auditory-only settings, the effects of audiovisual inputs have not. This study explored the effects of audiovisual inputs in a simulated cocktail party. In our fMRI experiment, each congruent audiovisual stimulus was a synthesis of 2 facial movie clips, each of which could be classified into 1 of 2 emotion categories (crying and laughing). Visual-only (faces) and auditory-only stimuli (voices) were created by extracting the visual and auditory contents from the synthesized audiovisual stimuli. Subjects were instructed to selectively attend to 1 of the 2 objects contained in each stimulus and to judge its emotion category in the visual-only, auditory-only, and audiovisual conditions. The neural representations of the emotion features were assessed by calculating decoding accuracy and brain pattern-related reproducibility index based on the fMRI data. We compared the audiovisual condition with the visual-only and auditory-only conditions and found that audiovisual inputs enhanced the neural representations of emotion features of the attended objects instead of the unattended objects. This enhancement might partially explain the benefits of audiovisual inputs for the brain to solve the cocktail party problem.

The modulatory effect of semantic familiarity on the audiovisual integration of face-name pairs.

To recognize individuals, the brain often integrates audiovisual information from familiar or unfamiliar faces, voices, and auditory names. To date, the effects of the semantic familiarity of stimuli on audiovisual integration remain unknown. In this functional magnetic resonance imaging (fMRI) study, we used familiar/unfamiliar facial images, auditory names, and audiovisual face-name pairs as stimuli to determine the influence of semantic familiarity on audiovisual integration. First, we performed a general linear model analysis using fMRI data and found that audiovisual integration occurred for familiar congruent and unfamiliar face-name pairs but not for familiar incongruent pairs. Second, we decoded the familiarity categories of the stimuli (familiar vs. unfamiliar) from the fMRI data and calculated the reproducibility indices of the brain patterns that corresponded to familiar and unfamiliar stimuli. The decoding accuracy rate was significantly higher for familiar congruent versus unfamiliar face-name pairs (83.2%) than for familiar versus unfamiliar faces (63.9%) and for familiar versus unfamiliar names (60.4%). This increase in decoding accuracy was not observed for familiar incongruent versus unfamiliar pairs. Furthermore, compared with the brain patterns associated with facial images or auditory names, the reproducibility index was significantly improved for the brain patterns of familiar congruent face-name pairs but not those of familiar incongruent or unfamiliar pairs. Our results indicate the modulatory effect that semantic familiarity has on audiovisual integration. Specifically, neural representations were enhanced for familiar congruent face-name pairs compared with visual-only faces and auditory-only names, whereas this enhancement effect was not observed for familiar incongruent or unfamiliar pairs. Hum Brain Mapp 37:4333-4348, 2016. © 2016 Wiley Periodicals, Inc.

Using encrypted genotypes and phenotypes for collaborative genomic analyses to maintain data confidentiality.

To adhere to and capitalize on the benefits of the FAIR (findable, accessible, interoperable, and reusable) principles in agricultural genome-to-phenome studies, it is crucial to address privacy and intellectual property issues that prevent sharing and reuse of data in research and industry. Direct sharing of genotype and phenotype data is often prohibited due to intellectual property and privacy concerns. Thus, there is a pressing need for encryption methods that obscure confidential aspects of the data, without affecting the outcomes of certain statistical analyses. A homomorphic encryption method for genotypes and phenotypes (HEGP) has been proposed for single-marker regression in genome-wide association studies (GWAS) using linear mixed models with Gaussian errors. This methodology permits frequentist likelihood-based parameter estimation and inference. In this paper, we extend HEGP to broader applications in genome-to-phenome analyses. We show that HEGP is suited to commonly used linear mixed models for genetic analyses of quantitative traits including genomic best linear unbiased prediction (GBLUP) and ridge-regression best linear unbiased prediction (RR-BLUP), as well as Bayesian variable selection methods (e.g. those in Bayesian Alphabet), for genetic parameter estimation, genomic prediction, and GWAS. By advancing the capabilities of HEGP, we offer researchers and industry professionals a secure and efficient approach for collaborative genomic analyses while preserving data confidentiality.

The Influence of Genetic and Environmental Factors on Anxiety among Chinese Adolescents: A Twin Study.

This study explored the influence of genetic and environmental factors on adolescent anxiety. Ninety-eight monozygotic and dizygotic twins from Chongqing, China (aged 15-18 years) were assessed for anxiety with the Self-Rating Anxiety Scale (SAS). The Parenting Styles and Dimensions Questionnaire (PSDQ) and Strengths and Difficulties Questionnaire (SDQ) were applied to assess environmental factors. Venous blood was drawn from the twins for zygosity determination. Structural equation modeling was performed to evaluate the effects of additive genetic factors (A), common environmental factors (C), and individual-specific environmental factors (E) on adolescent anxiety. The estimates of A and E on adolescent anxiety were 0.34 (95% CI = 0.12-0.53) and 0.66 (95% CI:0.47-0.89), respectively. The environment played an important role in adolescent anxiety. Adolescent anxiety was significantly positively correlated with peer relations (r = 0.606, p < 0.05) and negatively correlated with prosocial behavior (r = 0.207, p < 0. 05). No sex differences were observed. Adolescent anxiety was influenced by both genetic and environmental factors. The individual-specific environmental factors played an important role. Consideration of these variables will facilitate the targeted and individualized implementation of specific interventions for adolescent anxiety.

Over 1/4 of China's terrestrial area significantly contributed both to biodiversity conservation and carbon neutrality, requiring protection.

Protected areas (PAs) play a crucial role in halting biodiversity loss and mitigating climate change. However, research on the advantages of integrating biodiversity conservation and climate mitigation within PAs remains limited, and there is a deficiency in holistic, scientifically supported management strategies. To address these gaps, we conducted a case study in China, comparing the conservation effectiveness of designating conservation priorities considering either single or multiple objectives, including biodiversity conservation and carbon neutrality. The results showed that integrating multiple values could truly increase the effectiveness of PAs compared to a single value considered. Over 1/4 of China's terrestrial area had a significant contribution for both biodiversity conservation and carbon neutrality, yet remained unprotected. Expanding PAs in these areas holds tremendous win-win biodiversity conservation and carbon neutrality opportunity. We delineated different conservation priorities for comprehensive management and outlined strategies for different types of areas. The framework presented in this study can serve as a reference for other places with comparable scales or management objectives.

A cost-effective approach to identify conservation priority for 30 × 30 biodiversity target on the premise of food security.

There is a growing consensus on expanding protected and conserved areas for biodiversity conservation. Nevertheless, it remains uncertain where to expand conserved areas as well as what appropriate management modalities to choose. Moreover, conserved areas expansion should be balanced with crop-related food security challenges. We developed a framework to identify cost-effective areas for expanding protected areas and other effective area-based conservation measures (OECMs), and applied it to China. By combining templates for biodiversity conservation priorities at global scale and the priority conservation areas based on 2413 vertebrates' extinction risk in China, we identified areas with high biodiversity conservation value. We then categorized the priority areas according to human impact, indicating the potential cost of management. As a result of combining the two aspects above, we identified the most cost-effective areas for expanding protected areas and OECMs while excluding both the current and predicted croplands that can be used for food security. The results show that China could expand its protected areas to 22.81 % of the country's land area and establish OECMs in areas accounting for 9.82 % and 17.37 % of the country's land area in a cost-effective approach in two scenarios. In the ambitious scenario, protected and conserved areas would account for a maximum of 40.18 % of terrestrial area, with an average 62.67 % coverage of the 2413 species' suitable habitat. To achieve the goals of protected and conserved areas in Kunming-Montreal Global Biodiversity Framework, countries could apply this framework to identify their protected areas and OECM expansion priorities.

Impact of Isolation measures on pregnancy outcome during the COVID-19 pandemic.

This study aims to explore the impact of isolation measures implemented during the COVID-19 pandemic on childbirth outcomes in pregnant women. The design was a retrospective cohort study. The pregnant women during the outbreak lockdown and isolation from February 1 to April 30, 2020, were defined as the exposed population, and the pregnant women in the same time frame in 2019 as the non-exposed population. All data for the study were obtained from the National Health Care Data Platform of Shandong University. Generalized linear regression models were used to analyze the differences in pregnancy outcomes between the two study groups. A total of 34,698 pregnant women from Shandong Province, China in the data platform met the criteria and were included in the study. The proportions were 11.53% and 8.93% for macrosomia in the exposed and the non-exposed groups and were 3.47% and 4.37% for low birth weight infants, respectively, which were significantly different. They were 22.55% and 25.94% attributed to average exposed effect for macrosomia and low birth weight infants. Meanwhile, the mean weight and standard deviation of full-term infants in the exposure group were 3414.80 ± 507.43 g, which were significantly higher than in the non-exposed group (3347.22 ± 502.57 g, P < 0.001). The effect of exposure was significant in the third trimester. In conclusion, the isolation during the COVID-19 pandemic increases the birth weight of infants and the probability of macrosomia, regardless of which trimester in isolation a pregnant woman was, while the third trimester is the sensitive window of exposure. Our findings provide a basis for health care and policy development during pregnancy in COVID-19, due to COVID-19 still showing a pandemic trend around the world in 2022.

Effective Macrosomia Prediction Using Random Forest Algorithm.

(1) Background: Macrosomia is prevalent in China and worldwide. The current method of predicting macrosomia is ultrasonography. We aimed to develop new predictive models for recognizing macrosomia using a random forest model to improve the sensitivity and specificity of macrosomia prediction; (2) Methods: Based on the Shandong Multi-Center Healthcare Big Data Platform, we collected the prenatal examination and delivery data from June 2017 to May 2018 in Jinan, including the macrosomia and normal-weight newborns. We constructed a random forest model and a logistic regression model for predicting macrosomia. We compared the validity and predictive value of these two methods and the traditional method; (3) Results: 405 macrosomia cases and 3855 normal-weight newborns fit the selection criteria and 405 pairs of macrosomia and control cases were brought into the random forest model and logistic regression model. On the basis of the average decrease of the Gini coefficient, the order of influencing factors was: interspinal diameter, transverse outlet, intercristal diameter, sacral external diameter, pre-pregnancy body mass index, age, the number of pregnancies, and the parity. The sensitivity, specificity, and area under curve were 91.7%, 91.7%, and 95.3% for the random forest model, and 56.2%, 82.6%, and 72.0% for logistic regression model, respectively; the sensitivity and specificity were 29.6% and 97.5% for the ultrasound; (4) Conclusions: A random forest model based on the maternal information can be used to predict macrosomia accurately during pregnancy, which provides a scientific basis for developing rapid screening and diagnosis tools for macrosomia.

Identifying ecosystem service value and potential loss of wilderness areas in China to support post-2020 global biodiversity conservation.

Preserving wilderness areas is one of the key goals in the Post-2020 Global Biodiversity Framework(GBF). However, far too little attention has been paid to identifying wilderness conservation priorities on the national scale. In this study, we developed a methodological framework to evaluate the ecosystem service values, potential loss and conservation priorities of wilderness areas in China, providing guidance for wilderness conservation. First, we assessed the conservation value of wilderness areas and found that wilderness areas provided more ecosystem services than non-wilderness areas per unit area in most ecoregions. Then we identified threatened wilderness areas under multiple scenarios due to land use and land cover change. We found that 5.82 % of the existing wilderness areas were projected to be lost by 2100. Finally, wilderness conservation priorities were identified considering both conservation values and potential loss, and 11.24 % of existing wilderness areas were highlighted as conservation priorities. This methodological framework could be applied to other countries to support post-2020 global biodiversity conservation.

A ketogenic diet in combination with gemcitabine increases survival in pancreatic cancer KPC mice.

Pancreatic ductal adenocarcinoma (PDAC) continues to be a major health problem. A ketogenic diet (KD), characterized by a very low carbohydrate and high fat composition, has gained attention for its anti-tumor potential. We evaluated the effect and mechanisms of feeding a strict KD alone or in combination with gemcitabine in the autochthonous LSL-KrasG12D/+; LSL-Trp53 R172H/+; Pdx1-Cre (KPC) mouse model. For this purpose, both male and female pancreatic tumor-bearing KPC mice were allocated to a control diet (CD; %kcal: 70% carb, 14% protein, 16% fat), a KD (%kcal: 14% protein, 1% carb, 85% fat), a CD + gemcitabine (CG), or a KD + gemcitabine (KG) group. Mice fed a KD alone or in combination with gemcitabine showed significantly increased blood ß-hydroxybutyrate levels compared to mice fed a CD or CG. KPC mice fed a KG had a significant increase in overall median survival compared to KPC mice fed a CD (increased overall median survival by 42%). Interestingly, when the data was disaggregated by sex, the effect of a KG was significant in female KPC mice (60% increase in median overall survival), but not in male KPC mice (28% increase in median overall survival). Mechanistically, the enhanced survival response to a KD combined with gemcitabine was multifactorial, including inhibition of ERK and AKT pathways, regulation of fatty acid metabolism and the modulation of the gut microbiota. In summary, a KD in combination with gemcitabine appears beneficial as a treatment strategy in PDAC in KPC mice, deserving further clinical evaluation.

Correction: A Ketogenic Diet in Combination with Gemcitabine Increases Survival in Pancreatic Cancer KPC Mice.

[This corrects the article DOI: 10.1158/2767-9764.CRC-22-0256.][This corrects the article DOI: 10.1158/2767-9764.CRC-22-0256.].

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. Existing bioinformatics tools for prophage prediction usually fail to detect accurate and complete temperate phage genomes. This study proposes a novel computational temperate phage detection method (TemPhD) mining both the integrated active prophages and their spontaneously induced forms (temperate phages) from next-generation sequencing raw data. Applying the method to the available dataset resulted in 192 326 complete temperate phage genomes with different host species, expanding the existing number of complete temperate phage genomes by more than 100-fold. The wet-lab experiments demonstrated that TemPhD can accurately determine the complete genome sequences of the temperate phages, with exact flanking sites, outperforming other state-of-the-art prophage prediction methods. Our analysis indicates that temperate phages are likely to function in the microbial evolution by (i) cross-infecting different bacterial host species; (ii) transferring antibiotic resistance and virulence genes and (iii) interacting with hosts through restriction-modification and CRISPR/anti-CRISPR systems. This work provides a comprehensively complete temperate phage genome database and relevant information, which can serve as a valuable resource for phage research.