Metagenomic analysis reveals altered gut virome and diagnostic potential in pancreatic cancer.

Pancreatic cancer (PC) is a highly aggressive malignancy with a poor prognosis, making early diagnosis crucial for improving patient outcomes. While the gut microbiome, including bacteria and viruses, is believed to be essential in cancer pathogenicity, the potential contribution of the gut virome to PC remains largely unexplored. In this study, we conducted a comparative analysis of the gut viral compositional and functional profiles between PC patients and healthy controls, based on fecal metagenomes from two publicly available data sets comprising a total of 101 patients and 82 healthy controls. Our results revealed a decreasing trend in the gut virome diversity of PC patients with disease severity. We identified significant alterations in the overall viral structure of PC patients, with a meta-analysis revealing 219 viral operational taxonomic units (vOTUs) showing significant differences in relative abundance between patients and healthy controls. Among these, 65 vOTUs were enriched in PC patients, and 154 were reduced. Host prediction revealed that PC-enriched vOTUs preferentially infected bacterial members of Veillonellaceae, Enterobacteriaceae, Fusobacteriaceae, and Streptococcaceae, while PC-reduced vOTUs were more likely to infect Ruminococcaceae, Lachnospiraceae, Clostridiaceae, Oscillospiraceae, and Peptostreptococcaceae. Furthermore, we constructed random forest models based on the PC-associated vOTUs, achieving an optimal average area under the curve (AUC) of up to 0.879 for distinguishing patients from controls. Through additional 10 public cohorts, we demonstrated the reproducibility and high specificity of these viral signatures. Our study suggests that the gut virome may play a role in PC development and could serve as a promising target for PC diagnosis and therapeutic intervention. Future studies should further explore the underlying mechanisms of gut virus-bacteria interactions and validate the diagnostic models in larger and more diverse populations.

Hainan four-eyed turtles actively select suitable stones to masquerade according to their own morphology.

Masquerade is a form of camouflage in which animals use their body size, shape, and coloration to resemble inanimate objects in their environment to deceive predators. However, there is a lack of experimental evidence to show that animals actively choose objects that match these body parameters. To explore how the Hainan four-eyed turtle, Sacalia insulensis, masquerades using suitable stones, we used indoor video surveillance technology to study the preferences of juvenile S. insulensis for stones of different sizes, shapes, and colors. The results indicated that under normal conditions, during the day, juvenile S. insulensis preferred larger oval or round stones, while at night, they preferred oval stones that were closer to their own size, with no significant preference for stone color during either time. When disturbed (by a researcher swinging their arm back and forth above the experimental setup every hour to mimic a predator), the turtles showed a preference for brown stones that were closer to their size and oval in shape. These findings suggest that juvenile S. insulensis prefer stones that resemble their carapace size and shape to masquerade when undisturbed, and that this preference is reinforced when they masquerade to reduce the risk of predation. The preference for stones that resemble their carapace color is significant only when there is a disturbance. To the best of our knowledge, this is the first study to provide evidence that vertebrates can selectively choose objects that resemble their own morphology for masquerading to reduce predation risk.

Effects of Freshwater Acidification on the Gut Microbial Community of Trachemys scripta elegans.

Freshwater acidification (FA) has become a global environmental problem, posing a potential threat to freshwater ecosystems. The gut microbiota plays a crucial role in the host's response and adaptation to new environments. In this study, we investigated the changes in microbial communities in Red-eared slider (Trachemys scripta elegans) under acidic conditions to reveal the ecological impacts of acidification on freshwater turtles. The results showed that there were significant differences in ß-diversity (p = 0.03), while there were no significant differences in the α-diversity of gut microbiota in T. s. elegans between the different levels of acidification (pH of 5.5, 6.5, 7.5). Both the Gut Microbiome Health Index (GMHI) and the Microbial Dysbiosis Index (MDI) exhibited significant differences when comparing environments with a pH of 5.5 to those with a pH of 6.5 (p < 0.01). A comparative analysis between pH levels of 5.5 and 6.5 also revealed substantial differences (p < 0.01). Likewise, a comparative analysis between pH levels of 6.5 and 7.5 also revealed substantial differences (p < 0.01). At the phylum level, Firmicutes, Fusobacteria, and Bacteroidota formed a major part of the gut microbial community, Fusobacteria showed significant differences in different acidity environments (p = 0.03). At the genus level, Cetobacterium, Turicibacter, unclassified Eubacteriaceae, and Anaerorhabdus_furcosa_group showed significant differences in different acidity environments. The pH reduced interactivity in the gut microbiota of T. s. elegans. In addition, LEfSe analysis and functional prediction revealed that the potentially_pathogenic and stress_tolerant functional characteristics also showed significant differences in different acidity environments. The findings underscore the pivotal role of the gut microbiota in T. s. elegans in response to freshwater acidification and provide a foundation for further exploration into the impacts of acidification on freshwater ecosystems.

Metagenomic analysis of the gut virome in patients with irritable bowel syndrome.

Irritable bowel syndrome (IBS), a chronic functional gastrointestinal disorder, is recognized for its association with alterations in the gut microbiome and metabolome. This study delves into the largely unexplored domain of the gut virome in IBS patients. We conducted a comprehensive analysis of the fecal metagenomic data set from 277 IBS patients and 84 healthy controls to characterize the gut viral community. Our findings revealed a distinct gut virome in IBS patients compared to healthy individuals, marked by significant variances in between-sample diversity and altered abundances of 127 viral operational taxonomic units (vOTUs). Specifically, 111 vOTUs, predominantly belonging to crAss-like, Siphoviridae, Myoviridae, and Quimbyviridae families, were more abundant in IBS patients, whereas the healthy control group exhibited enrichment of 16 vOTUs from multiple families. We also investigated the interplay between the gut virome and bacteriome, identifying a correlation between IBS-enriched bacteria like Klebsiella pneumoniae, Fusobacterium varium, and Ruminococcus gnavus, and the IBS-associated vOTUs. Furthermore, we assessed the potential of gut viral signatures in predicting IBS, achieving a notable area under the receiver operator characteristic curve (AUC) of 0.834. These findings highlight significant shifts in the viral diversity, taxonomic distribution, and functional composition of the gut virome in IBS patients, suggesting the potential role of the gut virome in IBS pathogenesis and opening new avenues for diagnostic and therapeutic strategies targeting the gut virome in IBS management.

Paeoniflorin protects chicken against APEC-induced acute lung injury by affecting the endocannabinoid system and inhibiting the PI3K/AKT and NF-κB signaling pathways.

Avian pathogenic Escherichia coli (APEC) is the causative agent of chicken colibacillosis. Paeoniflorin, a natural ingredient extracted from Paeonia lactiflora, has a variety of pharmacological effects including anti-inflammatory and immunomodulatory. However, its effects and mechanism in APEC-induced acute lung injury (ALI) in chicken is not clear. The aim of this study was to investigate the protective effect of paeoniflorin on APEC-induced ALI and its possible mechanism. Paeoniflorin (25, 50, and 100 mg/kg) was administered by gavage for 5 d starting at 9 d of age and the chicken were infected with APEC by intraperitoneal injection at 12 d of age. The tissues were collected after APEC infection for 36 h for analysis. The results showed that paeoniflorin significantly alleviated the symptoms, increased the survival rate and body weight gain of APEC-infected chicken, and improved the histopathological damages, and reduced APEC loads in lung tissues. In addition, paeoniflorin restored the gene expression of ZO-1, Occludin and Claudin-3 during APEC infection. Moreover, paeoniflorin pretreatment significantly affected the endocannabinoid system (ECs) by increasing DAGL, decreasing MAGL, increasing secretion of 2-AG. Then, paeoniflorin significantly decreased the secretion of IL-1ß, IL-6 and TNF-α in lung tissues, and decreased the mRNA expression of CXCL8, CXCL12, CCL1, CCL5, and CCL17. In addition, paeoniflorin significantly reduced the phosphorylation levels of PI3K, AKT, P65, and IκB. In summary, we found that paeoniflorin inhibited APEC-induced ALI, and its mechanism may be through affecting ECs and inhibiting the activation of PI3K/AKT and NF-κB signaling pathways, which provides a new idea for the prevention and treatment of chicken colibacillosis.

Automated generation of consistent annual maximum NDVI on coal bases with a new algorithm.

Coal is one of the most important fossil energy sources and is ensuring global energy security. Annual maximum NDVI (Normalized Difference Vegetation Index) data is an important indicator for the research in balancing coal mining and vegetation conservation. However, the existing annual maximum NDVI data displayed lower values with temporally inconsistent and a noticeable mosaic line. Here we propose an algorithm for automatically generating the annual maximum NDVI of China's coal bases in Google Earth Engine called: Auto-NDVIcb. The accuracy of the Auto-NDVIcb algorithm has been verified with an average RMSE of 0.087 for the 14 coal bases from 2013 to 2022. Based on the proposed Auto-NDVIcb algorithm, an annual maximum NDVI dataset for all 14 coal bases in China from 2013 to 2022 was publicly released. This dataset can be fast and automatically updated online. Hence, the public dataset will continuously serve to monitor the vegetation change induced by coal mining, exploring the mechanism of vegetation degradation, and providing scientific data for developing vegetation protection policies in coal mines.

Comparison of the intestinal flora of wild and artificial breeding green turtles (Chelonia mydas).

Gut microbes are pivotal reference indicators for assessing the health status of animals. Before introducing artificially bred species into the wild, examining their gut microbe composition is crucial to help mitigate potential threats posed to wild populations. However, gut microbiological trait similarities between wild and artificially bred green turtles remain unexplored. Therefore, this study compared the gut microbiological characteristics of wild and artificially bred green turtles (Chelonia mydas) through high-throughput Illumina sequencing technology. The α-diversity of intestinal bacteria in wild green turtles, as determined by Shannon and Chao indices, significantly surpasses that of artificial breeding green turtles (p < 0.01). However, no significant differences were detected in the fungal α-diversity between wild and artificially bred green turtles. Meanwhile, the ß-diversity analysis revealed significant differences between wild and artificially bred green turtles in bacterial and fungal compositions. The community of gut bacteria in artificially bred green turtles had a significantly higher abundance of Fusobacteriota including those belonging to the Paracoccus, Cetobacterium, and Fusobacterium genera than that of the wild green turtle. In contrast, the abundance of bacteria belonging to the phylum Actinobacteriota and genus Nautella significantly decreased. Regarding the fungal community, artificially bred green turtles had a significantly higher abundance of Fusarium, Sterigmatomyces, and Acremonium and a lower abundance of Candida and Rhodotorula than the wild green turtle. The PICRUSt2 analyses demonstrated significant differences in the functions of the gut bacterial flora between groups, particularly in carbohydrate and energy metabolism. Fungal functional guild analysis further revealed that the functions of the intestinal fungal flora of wild and artificially bred green turtles differed significantly in terms of animal pathogens-endophytes-lichen parasites-plant pathogens-soil saprotrophs-wood saprotrophs. BugBase analysis revealed significant potential pathogenicity and stress tolerance variations between wild and artificially bred green turtles. Collectively, this study elucidates the distinctive characteristics of gut microbiota in wild and artificially bred green turtles while evaluating their health status. These findings offer valuable scientific insights for releasing artificially bred green turtles and other artificially bred wildlife into natural habitats.

Metagenomics Analysis Reveals the Composition and Functional Differences of Fecal Microbiota in Wild, Farm, and Released Chinese Three-Keeled Pond Turtles (Mauremys reevesii).

The intestine of living organisms harbors different microbiota associated with the biological functioning and health of the host and influences the process of ecological adaptation. Here, we studied the intestinal microbiota's composition and functional differences using 16S rRNA and metagenomic analysis in the wild, farm, and released Chinese three-keeled pond turtle (Mauremys reevesii). At the phylum level, Bacteroidota dominated, followed by Firmicutes, Fusobacteriota, and Actinobacteriota in the wild group, but Chloroflexi was more abundant in the farm and released groups. Moreover, Chryseobacterium, Acinetobacter, Comamonas, Sphingobacterium, and Rhodobacter were abundant in the released and farm cohorts, respectively. Cetobacterium, Paraclostridium, Lysobacter, and Leucobacter showed an abundance in the wild group. The Kyoto Encyclopedia of Genes and Genomes (KEGG) database revealed that the relative abundance of most pathways was significantly higher in the wild turtles (carbohydrate metabolism, lipid metabolism, metabolism of cofactors, and vitamins). The comprehensive antibiotic resistance database (CARD) showed that the antibiotic resistance gene (ARG) subtype macB was the most abundant in the farm turtle group, while tetA was higher in the wild turtles, and srpYmcr was higher in the released group. Our findings shed light on the association between the intestinal microbiota of M. reevesii and its habitats and could be useful for tracking habitats to protect and conserve this endangered species.

Accumulation rate and sources of plastic marine litter at nesting grounds of green turtles on the North Island of Qilianyu, Xisha Islands, South China Sea.

In this study, the accumulation rate of plastic litter was investigated by sampling quadrats placed on the North Island of Qilianyu, and the composition was analyzed and identified to determine its source. The results showed that the annual average accumulation rate of plastic litter on North Island was 0.64 ± 0.32 pieces·m-2·month-1, with a mass accumulation rate of 11.30 ± 7.73 g·m-2·month-1. The accumulation rate of plastic litter was mainly influenced by wind speed and direction, with higher accumulation rates occurring during the southwest monsoon season and tropical cyclones. ATR-FTIR analysis indicated that polyethylene (44 %) and polypropylene (41 %) were the most abundant types of polymers. This study reveals the current status of plastic litter pollution in green turtle nesting grounds on North Island in Qilianyu, which can be used as a reference for management strategies that mitigate plastic litter pollution.

Overexpression of cassava melatonin receptor PMTR1 plays dual roles in development under light and dark conditions in Arabidopsis.

KEY MESSAGE: MePMTR1 is involved in plant development and production as well as photosynthesis in plant. Melatonin is widely involved in plant growth and development as well as stress responses. Compared with the extending studies of melatonin in stress responses, the direct link between melatonin and plant development in the whole stages remains unclear. With the identification of phytomelatonin receptor PMTR1 in plants, melatonin signalling is becoming much clearer. However, the function of MePMTR1 in tropical crop cassava remains elusive. In this study, we found that overexpression of MePMTR1 showed larger biomass than wild type (WT), including higher number and area of leaves, weight, and accompanying with higher photosynthetic efficiency. Consistently, exogenous melatonin accelerated photosynthetic rate in Arabidopsis. In addition, MePMTR1-overexpressed plants exhibited more resistance to dark-induced senescence compared with WT, demonstrated by higher chlorophyll, lower hydrogen peroxide and superoxide content. In summary, this study illustrated that melatonin and its receptor regulate growth, development and senescence in plants, highlighting the potential application of melatonin and its receptor in improving crop yield and photosynthesis.

Gut mechanoimmunology: Shaping immune response through physical cues.

The gut immune system embodies a complex interplay between the gut mucosal barrier, the host's immune cells, and gut microbiota. These components exist within a dynamic environment characterized by a variety of physical cues, e.g., compression, tension, shear stress, stiffness, and viscoelasticity. The physical cues can be modified under specific pathological conditions. Given their dynamic nature, comprehending the specific effects of these physical cues on the gut immune system is critical for pathological and therapeutic studies of intestinal immune-related diseases. This review aims to discuss how physical cues influence gut immunology by affecting the gut mucosal barrier, host immune cells, and gut microbiota, defining this concept as gut mechanoimmunology. This review seeks to highlight that an enhanced understanding of gut mechanoimmunology carries therapeutic implications, not only for intestinal diseases but also for extraintestinal diseases.

KIN10-mediated HB16 protein phosphorylation and self-association improve cassava disease resistance by transcriptional activation of lignin biosynthesis genes.

Cassava bacterial blight significantly affects cassava yield worldwide, while major cassava cultivars are susceptible to this disease. Therefore, it is crucial to identify cassava disease resistance gene networks and defence molecules for the genetic improvement of cassava cultivars. In this study, we found that MeHB16 transcription factor as a differentially expressed gene in cassava cultivars with contrasting disease resistance, positively modulated disease resistance by modulating defence molecule lignin accumulation. Further investigation showed that MeHB16 physically interacted with itself via the leucine-Zippe domain (L-Zip), which was necessary for the transcriptional activation of downstream lignin biosynthesis genes. In addition, protein kinase MeKIN10 directly interacted with MeHB16 to promote its phosphorylation at Ser6, which in turn enhanced MeHB16 self-association and downstream lignin biosynthesis. In summary, this study revealed the molecular network of MeKIN10-mediated MeHB16 protein phosphorylation improved cassava bacterial blight resistance by fine-tuning lignin biosynthesis and provides candidate genes and the defence molecule for improving cassava disease resistance.

The relationship of peak ankle dorsiflexion angle with lower extremity biomechanics during walking.

PURPOSE: Abnormal lower limb movement patterns have been observed during walking in individuals with limited ankle dorsiflexion. The purpose of this study was to investigate the relationships of peak ankle dorsiflexion angle during the stance phase of walking with the lower extremity biomechanics at the corresponding moment and to determine a cutoff value of functional limited ankle dorsiflexion during walking. METHODS: Kinematic and kinetic data of 70 healthy participants were measured during walking. Spearman's correlation coefficients were calculated to establish the association between peak ankle dorsiflexion and angle and moment of ankle, knee, and hip, ground reaction force, and pelvic movement at peak ankle dorsiflexion. All variables significantly related to peak ankle dorsiflexion were extracted as a common factor by factor analysis. Maximally selected Wilcoxon statistic was used to perform a cutoff value analysis. RESULTS: Peak ankle dorsiflexion positively correlated with ankle plantar flexion moment (r = 0.432; p = 0.001), ankle external rotation moment (r = 0.251; p = 0.036), hip extension angle (r = 0.281; p = 0.018), hip flexion moment (r = 0.341; p = 0.004), pelvic ipsilateral rotation angle (r = 0.284; p = 0.017), and medial, anterior, and vertical ground reaction force (r = 0.324; p = 0.006, r = 0.543; p = 0.001, r = 0.322; p = 0.007), negatively correlated with knee external rotation angle (r = -0.394; p = 0.001) and hip adduction angle (r = -0.256; p = 0.032). The cutoff baseline value for all 70 participants was 9.03°. CONCLUSIONS: There is a correlation between the peak ankle dorsiflexion angle and the lower extremity biomechanics during walking. If the peak ankle dorsiflexion angle is less than 9.03°, the lower limb movement pattern will change significantly.