The colonization of the infant gut microbiome during the critical window of 0-3 years is influenced by a multitude of prenatal, environmental and host factors, and may be crucial for life-long health. The infant gut microbiome is highly dynamic, with bifidobacteria-dominance generally established during birth and lactation, followed by transition to a more stable and adult-like composition reached around 3 years of age. Bifidobacteria-dominance in infancy is considered protective as they not only display both anti-inflammatory and immunomodulatory effects but also foster the establishment of other beneficial species via cross-feeding interactions. As predominance of bifidobacteria is considered the marker of a healthy breastfed infant, the use of bifidobacteria-based probiotics for the prevention of gut dysbiosis and related conditions has been investigated. This clinically oriented summary highlights the unmet research needs of Bifidobacterium animalis subsp. lactis, BB-12® (BB-12), a well-studied probiotic added to baby formulas, dietary supplements, and fermented milk products; several potentially beneficial attributes, including acid and bile tolerance, strong adherence properties, pathogen inhibition, and immune modulation are considered. Clinical studies have demonstrated the safety and beneficial effects of BB-12 in infants and children across multiple disorders and highlight the need for improved clinical and regulatory guidelines.

With the increase of high-altitude sojourn population, more and more studies on hypoxia have been conducted, but the associated changes in gut bacteriome in different hypoxic environments need to be further investigated. Gut bacteriome plays an important role in host adaptation to high-altitude hypoxia, but the contribution of gut bacteriome in high-altitude hypoxia adaptation is still controversial and may be influenced by multiple factors. In this study, we reviewed the changes in diversity and composition of the gut bacteriome of different populations of animals in different highland hypoxic environments, clarified the dynamics of the gut bacteriome during exposure to high altitude, identified the core bacteriome that may contribute to host adaptation to hypoxic environments, and comprehensively considered the effects of multiple factors on the gut bacteriome.

Fungi play a dual role as indispensable ecological engineers and as major agents of disease in humans, animals, and plants. Recent estimates highlight their substantial impact, with millions of invasive infections annually and severe agricultural losses threatening food security. At the same time, fungi underpin ecosystem services such as decomposition, soil aggregation, and carbon sequestration, while also serving as prolific sources of enzymes, metabolites, and sustainable biomaterials. Advances in single-cell and spatial omics, cryo-electron microscopy, AlphaFold-based structural predictions, and machine learning applied to biosynthetic gene clusters are transforming the study of fungal pathogenicity, symbiosis, and metabolism. These approaches are shifting fungal research from descriptive biology toward predictive, translational pipelines that connect mechanistic insights to drug discovery, resistance management, and biotechnological innovation. Nevertheless, challenges remain, including antifungal resistance, climate-driven emergence of new pathogens, limited therapeutic options, and bottlenecks in scaling fungal applications for sustainability. Addressing these requires integrated One Health strategies that bridge clinical, agricultural, and environmental perspectives. By uniting structural biology, omics, genome editing, and computational tools within a global framework, fungal biology can be harnessed not only to mitigate emerging risks but also to drive innovations in medicine, agriculture, and green technologies.

Phosphorus (P) is an indispensable macronutrient for crop growth and development, but most phosphorus in soil exists in insoluble forms with extremely low availability. Although the application of traditional chemical phosphorus fertilizers can meet the phosphorus demand of crop growth, the extensive exploitation of phosphate rock resources has led to problems such as phosphate rock depletion and environmental pollution, highlighting an urgent need for sustainable phosphorus management strategies. Phosphate-Solubilizing Microorganisms (PSMs) provide an environmentally friendly biological approach to address this challenge. Existing reviews mainly focus on the basic phosphate-solubilizing mechanisms and agricultural applications of PSMs, but lack integration of cutting-edge directions such as omics-based mechanism analysis, stress adaptability regulation, and compound microbial inoculant design. From the innovative perspective of “omics-driven mechanism analysis - stress adaptability regulation - multifunctional inoculant development,” this review systematically summarizes: (1) the distribution characteristics of PSMs and environmental adaptability differences among functional groups; (2) the molecular regulatory networks of core phosphate activation mechanisms (acidification, organic acid secretion, phosphatase production) based on multi-omics, with a focus on comparing mechanism-specificity between bacteria and fungi; (3) the regulatory rules and adaptive mechanisms of PSMs activity under stress factors such as pH, heavy metals, and salinity; (4) the host-specific interaction mechanisms between PSMs and plants, as well as the regulatory effects on rhizosphere microenvironment; (5) the formulation development, field application bottlenecks, and large-scale promotion strategies of PSMs biofertilizers. Finally, the current research limitations (e.g., fragmented molecular mechanisms, significant differences between field and laboratory effects) are critically analyzed, and future research directions are proposed, including integrated multi-omics analysis, breeding of high-efficiency stress-tolerant strains, and long-term field validation. By integrating cutting-edge molecular mechanisms and practical application bottlenecks, this review provides a novel theoretical framework for the precise development and sustainable agricultural application of PSMs, which is of great significance for promoting the construction of an eco-friendly agricultural system.

[This corrects the article DOI: 10.3389/fmicb.2025.1610775.].

Pseudomonas protegens CHA0 and other fluorescent pseudomonads suppress plant diseases by producing a number of metabolites with antibiotic activities in the rhizosphere. However, limited information is available on the physiological functions of most of these metabolites. We herein describe the detection of 3-mercaptopropionic acid (3-MPA), a thiol compound, based on the metabolome of the supernatant of strain CHA0. 3-MPA exhibited antibiotic activity against oomycete and fungal pathogens and suppressed Pythium damping-off and root rot in cucumber. 3-MPA also exhibited antibiotic activity without direct contact with pathogens, indicating the volatilization effect of this compound. We identified a homologous gene encoding 3-MPA dioxygenase in the CHA0 genome and the production level of 3-MPA was elevated in a 3mdo-negative mutant. Growth inhibitory activity against oomycete and fungal pathogens and plant protection efficacy exhibited by the 3mdo-negative mutant were stronger than those of wild-type CHA0. These results suggest that 3-MPA is biocontrol factor of strain CHA0.

Cyanobacterial blooms are increasing in frequency, intensity, and duration in both freshwater and marine environments, potentially enhancing carbon sequestration by producing recalcitrant dissolved organic carbon (RDOC). We conducted monthly analyses of dissolved organic matter (DOM) composition and bacterial community dynamics in Lake Taihu (Meiliang Bay), China, integrating fluorescence DOM and ¹H NMR to quantify carboxyl-rich alicyclic molecules (CRAM) as a molecular proxy for RDOC. Estimated CRAM increased from 51.86 ± 11.22 μM C in the non-bloom period to 60.80 ± 8.21 μM C during blooms (~17% higher). The annual average RDOC was 62.93 ± 10.66 μM C, accounting for ~16% of the total DOC. Bacterial community analysis revealed that labile DOC was actively metabolized and transformed into more recalcitrant compounds through microbial carbon pump mechanisms. Specifically, the CL500-29 marine group and Sphaerotilus contributed to the degradation of protein-like DOM, while the CL500-29 and hgc1 clades played key roles in CRAM formation. The pronounced RDOC enrichment in eutrophic lakes compared to non-eutrophic lakes, rivers, and marine systems underscores the potential of eutrophic lakes to function as significant carbon sinks, highlighting the necessity of integrating bloom-driven RDOC accumulation into carbon budget frameworks to reassess the long-term carbon sequestration potential of these systems.

Peach trees are often threatened by various diseases during cultivation. This study took the roots and rhizosphere soil of diseased peach trees as the research objects and investigated the effects of single and combined treatments of Bacillus (including Bacillus velezensis and Bacillus subtilis) and graphene oxide (GO) on peach trees. The results showed that compared with the diseased control group, the single treatments of Bacillus velezensis (Group V) and Bacillus subtilis (Group S) significantly reduced soil pH (to 8.55 and 8.35, respectively) as well as the contents of calcium (Ca) and zinc (Zn), enhanced organic carbon accumulation (up to 26.43 g/kg), bringing these key indicators close to the rhizosphere levels of healthy peach trees (CK1: pH 8.42, organic carbon (OC) 24.10 g/kg). Additionally, these treatments restored nutrient cycling functions by increasing microbial diversity. The effect of GO treatment showed a concentration dependence: high-concentration GO increased the microbial Shannon index and available phosphorus content, while low-concentration GO inhibited the accumulation of available nitrogen. Among the combined treatments, the combination of Bacillus velezensis and GO, by synergistically regulating the contents of Ca and available nitrogen, restored rhizosphere microecological homeostasis more significantly than the combination involving Bacillus subtilis. This study reveals the mechanism by which the "microbe-GO" combination achieves rhizosphere ecological remediation through the "element balance - microbial community function" linkage and provides a theoretical basis and technical strategies based on healthy microecological targets for the prevention and control of soil-borne diseases in peach trees.

To evaluate the clinical diagnostic ability of iFIND TBR (iFIND) for Mycobacterium tuberculosis (MTB) and resistance to rifampicin (RIF). Sputum samples, prospectively collected from patients with suspected pulmonary tuberculosis between November 2023 and December 2024, were used for comprehensive laboratory testing, including smear microscopy, solid culture, Xpert MTB/RIF, iFIND assays, and proportion method drug susceptibility testing (DST). Among the 452 patients, the positive rates of iFIND (80.31%) and Xpert (76.99%) were significantly higher than those of solid culture (65.49%). Based on solid culture as the reference standard, the sensitivity of iFIND for detection of MTB was slightly higher than that of Xpert, but no statistically significant difference was observed (p = 0.157). The sensitivity and specificity of iFIND for detection of MTB were 99.14 and 84.31% relative to the bacteriology reference standard, respectively. Based on the clinical diagnosis results as reference, the higher sensitivity of iFIND than Xpert was observed in detecting MTB (93.46% vs. 90.58%), although the difference was not statistically significant (p = 0.162). The rifampicin detection failure rate was significantly higher in low bacterial load specimens (1+) compared to those with moderate/high loads (≥2+) (p < 0.001). With the proportion method DST results as reference standard, no statistically significant differences were observed in the sensitivity and specificity between iFIND and Xpert. The iFIND assay is a rapid and automated assay with sensitivity and specificity comparable to Xpert for early TB diagnosis and drug resistance screening, making it particularly suitable for implementation in primary healthcare settings and general hospitals.

In Pakistan, hepatitis B virus (HBV) and hepatitis D virus (HDV) infections remain a major concern. This study assessed the self-reported prevalence, vaccination status, knowledge, risk factors, attitude, and behavioral practices related to both viruses in Pakistan, along with the impact of stigma and cultural norms on disease perception and management. A cross-sectional study was conducted using an online survey, and the data was collected from 980 general Pakistani public (mostly 18-34 age) from January 15 to March 15, 2025. Among respondents, 79.2% were male and 20.8% female, while 58.5% did not know hepatitis (p > 0.05). Only 7.3% reported HBV/HDV self-reported diagnosis, lower than previous studies (16.6%), but 21.3% had a family history, indicating higher self-reported prevalence (p < 0.05). Key risk factors included low vaccination coverage (26.4%, χ2 = 41.17, p < 0.001), chronic infection (χ2 = 16.57, p < 0.001), needle-sharing (9.2%), unlicensed dental (10.6%) and medical (19.3%) procedures, and poor glove usage (14.8%) (p < 0.05). Limited public awareness (35.1%) was noted as the major barrier, while 38.4% of respondents acknowledged the presence of stigma. Participants lack adequate knowledge, gaps in vaccination, risky practices, and stigma persist. A comprehensive public health approach is essential to curb HBV/HDV in Pakistan.