title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=3 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Preliminary insights into the gut microbiota of patients with rheumatoid arthritis in Vietnam link: https://peerj.com/articles/20521 last-modified: 2025-12-18 description: In Vietnam, rheumatoid arthritis accounts for more than 20% of all joint diseases, with a growing number of young patients. The disease progresses rapidly, but its exact cause remains not fully understood. Environmental and lifestyle factors, such as smoking, pollution, obesity, gut microbiota, and infections, play a role in rheumatoid arthritis development. The presence of Gram-positive bacteria in the gut might promote the release of toxic metabolites into the bloodstream, which in turn triggers joint inflammation. Therefore, this pilot study aimed to compare the gut microbiota in 22 patients with newly diagnosed rheumatoid arthritis and 20 healthy individuals recruited at the Bach Mai Hospital, Hanoi, Vietnam. To this end, we analyzed fecal samples from all participants by 16S rRNA metagenomic sequencing. The sequencing data analysis did not reveal any significant differences in alpha diversity between patients and healthy controls. Conversely, unweighted and weighted UniFrac distances (beta diversity metrics) allowed distinct clustering between groups. The abundance of the Lactococcus, Solobacterium, Faecalibaculum, and Corynebacterium genera was increased, and that of Bacteroides was decreased in patients with rheumatoid arthritis compared with healthy controls. Moreover, patients exhibited distinct gut microbiota profiles in function of their disease activity scores (DAS28-CRP, DAS-ESR), rheumatoid factor, and anti-citrullinated protein antibody concentrations. Overall, our study contributes to bridging this knowledge gap and provides a foundation for the study of gut microbial signatures of autoimmune disease in Vietnamese patients. It also highlights the potential role of gut microbes in rheumatoid arthritis diagnosis and management in Vietnam. creator: Bich Ngoc Nguyen creator: Lan Thi Ngoc Nguyen creator: Dinh Thi My Trinh creator: Hien Thao Nguyen creator: Tam Thi Thanh Tran uri: https://doi.org/10.7717/peerj.20521 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Nguyen et al. title: The connection between mindfulness levels and life satisfaction among breast cancer patients: the sequential mediating effects of body appreciation and stress perception link: https://peerj.com/articles/20485 last-modified: 2025-12-18 description: BackgroundResearch indicates a positive relationship between life satisfaction, mindfulness, and emotional perception. While this connection is observed in a variety of groups, it has been less studied in women with breast cancer. The research investigated correlation among mindfulness, body appreciation, emotional perception, and life satisfaction in Chinese breast cancer patients.MethodsIn Xiangyang City, a survey was conducted involving 312 individuals diagnosed with breast cancer. The instruments used for this assessment included the Revised Mindfulness Cognition and Affective Scale (CAMS-R), Body Appreciation Scale (BAS), Perceived Stress Scale (PSS), and Life Satisfaction Scale (SWLS).Results(1) Mindfulness may positively and substantially predict the life satisfaction of breast cancer patients (β = 0.439, P < 0.001); (2) body appreciation (β = 0.152, P < 0.01) and perceived stress (β =  − 0.183, P < 0.01), respectively, acted as a mediator to the influence of being mindful on fulfillment in life, and (3) mindfulness could also indirectly affect the life satisfaction of individuals diagnosed with breast cancer through the sequential influence of body appreciation and perceived stress.ConclusionThe mediating model has been fitted on cross-sectional data in this research. Breast cancer patients’ life satisfaction is significantly positively predicted by mindfulness, which includes indirect as well as direct outcomes of perceived stress and body appreciation. The connection between mindfulness and overall well-being is partially mediated through body appreciation and also perceived stress, and the chain mediation effect provides additional insight into the connection between mindfulness and overall well-being. Therefore, in clinical practice, mindfulness training can enhance the body appreciation levels of breast cancer patients, reduce their perception of stress, and subsequently improve their overall life satisfaction. creator: Junli Zhou creator: Xianhui Huang creator: Dan Yuan creator: Liyuan Wang creator: Minyu Liu creator: Xue Jiang creator: Lijuan Xing creator: Song Xu uri: https://doi.org/10.7717/peerj.20485 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Zhou et al. title: Mechanistic study on integrated water-fertilizer management to alleviate Na+ toxicity and enhance salt tolerance and yield of pakchoi under salt stress link: https://peerj.com/articles/20431 last-modified: 2025-12-18 description: The cultivation of salt-tolerant pakchoi is a promising strategy for utilizing coastal saline soils. However, supporting agronomic technologies are remain underdeveloped. This study investigates how coordinated water-fertilizer regulation mitigates sodium (Na+) toxicity under salt stress, thereby enhancing salt tolerance and yield in pakchoi and providing a scientific basis for optimizing agronomic management. A pot experiment was conducted with three irrigation methods (conventional, drip, and mulched drip) and three fertilizer types (conventional, controlled-release, and mixed), under soil salt stress adjusted by sodium chloride (NaCl) to 0.15% salinity by weight. The results showed that MP treatment (mulched drip irrigation + mixed fertilizer) can significantly improve yield performance, with fresh and dry weight increasing by 39% and 42% respectively, and enhancing ion balance by increasing potassium (K+) and calcium (Ca2+) and reducing Na+. In addition, MP enhanced antioxidant defense by increasing superoxide dismutase (SOD), catalase (CAT), peroxidase (POD), and ascorbate peroxidase (APX) activities and reducing oxidative damage. The treatment also maintains better water status and photosynthetic efficiency. MP treatment can improve growth, physiology, and stress tolerance. This integrated approach represents a novel water-fertilizer strategy with high application potential for sustainable vegetable production in saline regions. creator: Jin Li creator: Hongcheng Li creator: Zizheng Li creator: Huirong Su creator: Tingting Duan creator: Zhong Lin creator: Yinling Zhu creator: Xiaoli Chen creator: Xianmin Wang uri: https://doi.org/10.7717/peerj.20431 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Li et al. title: A systematic review of the role of methylase genes in antibiotic resistance: co-existence with extended spectrum β-lactamase and carbapenemase genes in Klebsiella pneumoniae link: https://peerj.com/articles/20428 last-modified: 2025-12-18 description: BackgroundAntibiotic resistance in multidrug-resistant Klebsiella pneumoniae (MDR-KP), particularly against carbapenems and colistin, is a critical concern, increasing morbidity and mortality among hospitalized patients. This systematic review aims to identify methylase genes in K. pneumoniae and examine their co-existence with β-lactamase and carbapenemase genes contributing to antibiotic resistance.MethodsA literature search was conducted across three electronic databases from inception until 6 December 2023. The quality assessment followed Critical Appraisal Skills Programme (CASP) criteria. Studies focusing on methylase genes and antibiotic resistance in K. pneumoniae were included. Two authors independently screened titles, abstracts, and full texts, with a third resolving disagreements.ResultsThirty-four studies met the inclusion criteria. Methylase genes in K. pneumoniae isolates were predominantly reported in Europe and Asia, particularly in Iran, China, Japan, and India (8.8%, N = 3). The most prevalent 16S rRNA methyltransferase genes identified were armA (76.5%, N = 26), rmtB (61.8%, N = 21), and rmtC (29.4%, N = 10). Common extended-spectrum β-lactamase (ESBL) genes included blaCTXM (64.7%, N = 22) and blaSHV (47%, N = 16), while blaKPC (26.5%, N = 9) and blaNDM (23.5%, N = 8) were the predominant carbapenemase genes. The coexistence of methylase genes with ESBL and carbapenemase genes conferred significant resistance to aminoglycosides (gentamicin, kanamycin, tobramycin, amikacin, arbekacin), cephalosporins (cefazolin, cefoxitin, cefotaxime), and carbapenems (imipenem, meropenem).ConclusionsThe widespread distribution of resistance mechanisms in K. pneumoniae highlights a global challenge, emphasizing the need for strategic antimicrobial use to reduce resistance rates. creator: Nur Husna Shahimi creator: Nabiha Bouafia creator: Mawaddah Mohd Azlan creator: Asma Nadia Ahmad Faris creator: Nur Ayunie Ahmad creator: Ali Rabaan creator: Amal Alfaraj creator: Bandar Albaradi creator: Tasneem Zaidan creator: Abdulsalam Alawfi creator: Amer Alshengeti creator: Zainab Almansour creator: Wadha Alfouzan creator: Amal Sabour creator: Maha Alshiekheid creator: Anizah Rahumatullah creator: Nik Yusnoraini Yusof uri: https://doi.org/10.7717/peerj.20428 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Shahimi et al. title: Effects of glucose spraying and lactic acid bacteria inoculation applied to high-moisture alfalfa during pre- and post-harvest periods on silage fermentation and feed quality link: https://peerj.com/articles/20276 last-modified: 2025-12-18 description: BackgroundThe management of alfalfa silage in livestock production systems is crucial for achieving high-quality silage and optimal livestock production. Alfalfa (Medicago sativa L.) is known to be difficult to ensile due to its high buffering capacity (BC), low water-soluble carbohydrate (WSC) content, and low dry matter (DM) content. Therefore, using biological or chemical additives may be beneficial in improving the silage quality of alfalfa, particularly when it is harvested at relatively low DM content and high protein levels. Lactic acid bacteria (LAB) and glucose are commonly used as silage additives to enhance the ensiling process and improve fermentation quality.MethodsThis study aimed to estimate the effects of pre-harvest and post-harvest application of lactic acid bacteria inoculant (control, L. plantarum, and L. citerum) and glucose doses (0%, 3% and 6%) treatments on the chemical composition and fermentation profile of silage feed of alfalfa grown under field conditions in 2023. After 60 days of ensiling, silages were analyzed for fermentation and quality characteristics.ResultsSignificant two-way and three-way interactions were observed among harvest, inoculant, and glucose dose for several parameters, including pH (T0, T60), dry matter ratio (DMT0, T60) content, and lactic acid bacteria (LAB T0) counts and acid detergent lignin (ADL) content. These interactions indicate that the effect of treatment varied depending on their combinations. The lowest initial pH(T0) was recorded in the pre-harvest combination L. plantarum with 0% glucose (p < 0.001). The silage pH(T60) value the lowest (4.91) was observed in 6% glucose combined with L. plantarum, while the highest pH was found in the control group with %0 glucose (p < 0.02). The highest initial DM(T0) content (25.78%) was achieved with the pre-harvest combination L. citerum + 3% glucose (p < 0.02). The highest silage DM (T60) content was noted with L. citerum (24.00%) and L. plantarum (23.20%) applied pre-harvest (p < 0.001). ADL content was recorded at its lowest value in the pre-harvest L. citerum with 3% glucose added (p < 0.03). The timing of harvest also had a significant effect on the quality parameters of silage (p < 0.001). Yeasts (T60) count and ADF content was lower in the pre-harvest treatments and crude protein content was higher in the pre-harvest (p < 0.01). Increasing glucose dose from 0% to 6% increased DM content, crude protein content and LAB count (p < 0.001).ConclusionThe best results for low pH and improved fermentation stability were achieved with 6% glucose and L. plantarum applied 24 h before harvest, which is recommended for practical use under field conditions. To suppress the yeast population, 3% and 6% glucose contents of L. citerum pre-harvest can be used alternatively. creator: Fatma Akbay uri: https://doi.org/10.7717/peerj.20276 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Akbay title: Vast cryptic diversity in direct-developing frogs Pristimantis (Anura: Strabomantidae): a new subgenus and the description of a new species from the eastern Andes of Ecuador link: https://peerj.com/articles/20512 last-modified: 2025-12-17 description: Pristimantis, a genus of direct-developing frogs within the family Strabomantidae, comprises 617 recognized species, making it the most species-rich genus of vertebrates worldwide. This group include 264 described (43% of the world) species in Ecuador, being one of the countries in the region with the highest rate of species description, greatest diversity and endemism. In this study, we analyze the phylogenetic position and describe a new Pristimantis species from the Colonso Chalupas Biological Reserve and Llanganates National Park in northeastern Ecuador, using phylogenetic, genetic, morphological, and geographic evidence. Additionally, we propose a new subgenus within Pristimantis that includes the Pristimantis prolatus and Pristimantis bicantus species groups. Our results indicate that the new species and related species form a well-supported group with significant genetic divergence based on the 16S rRNA gene (average uncorrected p-distance = 2.8–7.5%), within the Pristimantis bicantus species group. Morphologically, the new species is characterized by a black to dark-gray dorsum and marbled venter (less intense or brown in males), being endemic to the Guacamayos mountain range and the Llanganates region in the northeastern Andean foothills of Ecuador. We emphasize the importance of including topotypic specimens to analyze and compare species groups to delimiting species, like Pristimantis. creator: Keyko D. Loza-Carvajal creator: Mario H. Yánez-Muñoz creator: Walter Quilumbaquin creator: H. Mauricio Ortega-Andrade uri: https://doi.org/10.7717/peerj.20512 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Loza-Carvajal et al. title: Heavy ion beam-induced variation in salt tolerance among Leymus chinensis genotypes during seed germination link: https://peerj.com/articles/20510 last-modified: 2025-12-17 description: Heavy ion beam irradiation (HIBI) is an efficient mutagenic tool characterized by high linear energy transfer and its capacity to induce heritable genetic variation. However, its application in perennial forage species remains limited, especially in terms of genotype-specific responses to radiation and salt tolerance. In this study, nine Leymus chinensis genotypes were irradiated with carbon ion beams at doses of 40, 50, and 80 Gy, with 0 Gy as the control. Germination responses were then evaluated under non-saline (distilled water) and saline (100 mmol·L−1 NaCl) conditions to assess the effects of irradiation and genotype-specific salt tolerance. Both radiation dose and salt stress significantly affected early seedling development, showing pronounced genotype-dependent variation. Under 80 Gy combined with salt stress, emergence percentages of sensitive genotypes (e.g., G2, G4) dropped below 10%, whereas tolerant genotypes (e.g., G3, G9) exhibited a 19.3–65.1% increase under high-dose conditions. The half-lethal dose (LD50), calculated based on emergence data, ranged from 29.6 Gy (G4) to over 80 Gy (G1), allowing classification into three salt tolerance levels: high, medium, and low. Principal component analysis (PCA) supported the trait-based classification and revealed synergistic variation patterns under combined stress conditions. These findings highlight the potential of HIBI to induce beneficial traits for salt tolerance in L. chinensis, providing a theoretical foundation for precision breeding and ecological restoration in saline grasslands. creator: Shiman Chen creator: Yaxiao Li creator: Dandan Zhao creator: Mengdan Sun creator: Wen wen Qi creator: Ming xue Shi creator: Shaoyang Li creator: Hongyuan Ma uri: https://doi.org/10.7717/peerj.20510 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Chen et al. title: Bioinformatics-based identification and validation of mitochondria-related genes associated with neonatal sepsis link: https://peerj.com/articles/20441 last-modified: 2025-12-17 description: BackgroundWhile mitochondrial involvement in sepsis has been widely studied, its role in neonatal sepsis (NESE) remains unclear. This study aimed to explore the molecular mechanisms of mitochondrial-related genes (MRGs) in NESE using bioinformatics analysis.MethodsThis study utilized neonatal sepsis-related datasets GSE69686 and GSE95233. Differentially expressed genes (DEGs) were identified by comparing NESE and control groups. Subsequently, candidate genes were then selected by intersecting DEGs with MRGs. These candidate genes were further refined using least absolute shrinkage and selection operator (LASSO) regression and the Boruta algorithm to identify potential biomarkers. Expression levels and receiver operating characteristic (ROC) curve analyses of the candidate biomarkers were assessed in both datasets. To further investigate their mechanisms, functional enrichment, immune infiltration, and drug prediction analyses were conducted. Finally, biomarker expression was validated using reverse transcription-quantitative polymerase chain reaction (RT-qPCR).ResultsA total of 24 candidate genes were obtained by overlapping 579 DEGs and 1,136 MRGs. ACSL1, ALAS1, ALDH5A1, MTHFD2, PDSS1, and TSPO were identified as biomarkers. The enrichment analysis revealed significant enrichment of ACSL1, ALAS1, ALDH5A1, PDSS1, and TSPO in the lysosome compartment. Moreover, there were significant differences in seven immune cells (M0 macrophage, activated NK cell, neutrophil, etc) between NESE samples and normal samples. Importantly, the correlation analysis revealed that the expression of ACSL1 exhibited a negative correlation with CD8 + T cells, whereas it demonstrated a positive association with neutrophil. Additionally, it also found birch A and Tetrachlorodibenzo-p-dioxin simultaneously targeted TSPO, MTHFD2, ALAS1, ALDH5A1, PDSS1, and ACSL1. Importantly, the RT-qPCR results demonstrated that the expression results of PDSS1, TSPO, and ALAS1 were consistent with the public database, showing significantly over-expressed in the NESE group.ConclusionsIn this study, six mitochondria-related biomarkers in NESE were identified and preliminarily validated, which may provide novel insights into disease mechanisms and serve as a potential basis for future diagnostic and therapeutic exploration. creator: Yu Zhong creator: Guilin Zhao creator: Shanshan Pu creator: Yushan Zhang creator: Dongju Pan creator: Xu Yang creator: Tingting Fu creator: Lu Chen creator: Chaofen Li creator: Xueyu Li creator: Zhi Li creator: Jun Wu creator: Shanping Chen creator: Zupeng Qiu creator: Ying Zhang creator: Fan Li uri: https://doi.org/10.7717/peerj.20441 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Zhong et al. title: Factors constraining natural recovery of Diadema antillarum following a mass die-off: a case study near the island of Saba, Caribbean Netherlands link: https://peerj.com/articles/20418 last-modified: 2025-12-17 description: After the mass mortality of 1983–1984, recovery of the keystone herbivore Diadema antillarum has been limited. Persistently low population densities reduced grazing pressure, leading to algal dominance on many Caribbean reefs. To understand recovery dynamics and support restoration, greater insight into factors constraining sea urchin population recovery is essential. We assessed D. antillarum settlement, predator density, shelter availability, and post-die-off recovery at four locations near Saba, Caribbean Netherlands, following the 2022 D. antillarum die-off. One location, an artificial rock reef, had previously supported high D. antillarum densities, while the natural reefs showed only sporadic recruitment. One-year post-die-off, the D. antillarum density at the artificial reef recovered to 1.4 ± 0.5 D. antillarum per m2, whereas no populations established on the three natural reefs. Despite high overall predator biomass, the artificial reef had lower densities of Spanish hogfish and small wrasses. Previous studies indicate that these species, together with the queen triggerfish, are key determinants of D. antillarum recovery. Invertebrate predator densities were broadly similar across locations, although spotted spiny lobster, an important crab predator and potentially reducing crab predation on D. antillarum, were more abundant on the artificial reef. Shelter availability, depth, and reef structure appeared more favorable at the artificial reef location. We conclude that D. antillarum population establishment is primarily shaped by predation pressure and shelter availability, while larval settlement and the presence of adults appear less influential. A regional-scale study could further detangle the factors affecting natural recovery and identify reefs with a high chance of successful D. antillarum restoration. creator: Alwin Hylkema creator: Oliver J. Klokman uri: https://doi.org/10.7717/peerj.20418 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Hylkema and Klokman title: Elephant seal dive behaviour responds consistently to changes in foraging success regardless of sex or ocean habitat link: https://peerj.com/articles/20378 last-modified: 2025-12-17 description: Understanding how air-breathing diving animals moderate their dive behaviour when foraging successfully is foundational in the study of their foraging ecology. Yet, this fundamental relationship remains unresolved with previous research pointing to inconsistent relationships, differing nominally according to sex, habitat type and scale. Empirically testing the relationships between dive effort responses and foraging success is further hampered because of challenges obtaining concurrent measures of behavioural responses and foraging success at sea. We compiled a multi-decadal dive dataset from 609 southern elephant seals, including their dive responses (transit rate, and relative dive and surface recovery duration) and buoyancy—changes in which provide an indirect measure of body condition change and foraging success. Using this dataset, we tested how seal dive behaviour alters when foraging remotely at sea. We found that as foraging success increased, seals increased transit (ascent, descent) rates and decreased relative dive durations for a given depth, with no response in surface recovery. Our results were consistent across sexes and foraging habitats, and account for the general effects of buoyancy on dive behaviour. The homogeneity of these findings suggests that there is a general functional response in which elephant seals perform, on average, shorter, steeper dives during periods of successful foraging. Importantly, we can align these results with predictions from the marginal value theorem (MVT), that a forager should remain in a patch only until gains drop below the neighbourhood mean. Our findings have broad-based implications for how ecologists interpret dive responses of wild marine animals, demonstrating the value of seeking independent in situ information on foraging success. creator: David B. Green creator: Sophie Bestley creator: Clive R. McMahon creator: Mary-Anne Lea creator: Robert G. Harcourt creator: Christophe Guinet creator: Mark A. Hindell uri: https://doi.org/10.7717/peerj.20378 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Green et al.