Search Results (288)

The cecal microbiota is essential for intestinal health and performance. This study describes the succession patterns of the cecal microbiota in Japanese quail (Coturnix japonica) until 42 days of age. Sixty quails were raised using standard conditions and fed corn–soybean meal diets. Cecal contents were sampled from five birds weekly from 7 to 42 days of age and submitted to Illumina 16S rRNA sequencing for metabarcoding analysis. Diversity and functional prediction were carried out with QIIME2, PICRUSt2, STAMP and MicrobiomeAnalyst 2.0. Firmicutes increased from 50% at 7 days to more than 80% at 42 days, whereas Bacteroidota decreased from 45% to 12% in the same period. Alpha diversity progressively increased with age, indicating a richer and more balanced microbiota at later ages. Genera such as Bacteroides were predominant in the beginning and later were replaced by Lachnospiraceae, Ruminococcus and Faecalibacterium. These developmental taxonomic features aligned with significant shifts in ten metabolic pathways identified by prediction, revealing a transition from biosynthetic functions to complex carbohydrate metabolism and cell wall biosynthesis. The first seven days are considered a critical window for probiotics intervention, which may favor the establishment of a microbiota that is more stable and beneficial to quail performance. Full article

The gut microbiota plays an essential role in the host’s metabolism. Its composition and structure depend on biological and environmental factors. This work was designed to identify the composition and structure of the wild and captive red grouper (Epinephelus morio) microbiota and make predictions regarding its metabolic functions. Our hypothesis stated that wild and captive individuals would share the most abundant taxonomic groups, forming a core microbiota, and individuals in captivity might have exclusive taxonomic groups. Metagenomic DNA was extracted from the intestinal contents of wild and captive individuals. The 16S rRNA gene was amplified and sequenced using Illumina pair-end technology. QIIME2 pipeline was used for sequence analysis and alpha and beta diversity assessment. PICRUSt was used to infer metabolic functions. Twenty-nine phyla were identified; the most abundant were Pseudomonadota, Bacillota, Fusobacteriota, and Actinomycetota. The dominant genera were Photobacterium, Vibrio, Cetobacterium, and Escherichia-Shigella. The metabolic prediction analysis suggested that the Epinephelus morio gut microbiota is related to food digestion, the immune system, antioxidant enzymes, antibiotic resistance, and vitamin B12 transport. We concluded that the microbiota of E. morio established in captivity is sensitive to environmental changes such as water pollution, which can cause a decrease in diversity. Full article

To explore the interactions within the vegetation–soil–microorganism continuum on the Jingpo Lake lava platform, five vegetation types—grassland (GL), shrubland (SL), deciduous broad-leaved forest (DB), coniferous and broad-leaved mixed forest (CB), and coniferous forest (CF)—were examined. Significant differences in the soil physical and chemical properties were identified among these types (p < 0.05). The soil bacterial community structures also varied significantly (p < 0.05), with Actinobacteriota, Proteobacteria, and Acidobacteria as the dominant phyla, exhibiting notable genus-level differences (p < 0.05). The soil organic matter (SOM), available nitrogen (AN), total nitrogen (TN), and soil water content (SWC) were significantly correlated with the bacterial community structure (p < 0.05 or p < 0.01), acting as key determinants of the microbial community structure and function. PICRUSt2 functional predictions revealed significant variations in the metabolic functions of the soil bacterial communities across vegetation types, indicating distinct functional specializations. In conclusion, the Jingpo Lake lava plateau harbors abundant bacterial resources. When devising vegetation adaptation strategies, it is essential to take into account variations in the rhizosphere soil bacteria across different vegetation types. Furthermore, prioritizing the implementation of forest vegetation is crucial in the adaptive management of the lava plateau. This approach holds significant implications for studying the bacterial diversity in the lava plateau and exploring the cultivation and application of functional bacteria in extreme environments. Full article

Background/Objectives: Breast cancer (BC) is the leading cause of cancer incidence and mortality among women and the recent identification of a resident mammary microbiota has highlighted its potential role in breast carcinogenesis. Given that environmental and socioeconomic factors influence both BC prevalence and tumor-associated bacterial composition, this study aimed to evaluate the compositional and functional features of the mammary microbiota in cancerous (oncobiome) and adjacent healthy BC tissues from patients living in urban and rural areas. Methods: Microbiota composition in both the oncobiome and adjacent healthy BC tissues was analyzed using 16S rRNA sequencing. Results: Significant variations in breast oncobiome composition were observed among BC patients from urban and rural areas. A statistically significant β dispersion among breast oncobiome of patients from urban or rural areas was highlighted. Specifically, the genera Selenomonas, Centipeda, Leptotrichia, Neisseria and Porphyromonas were found exclusively in BC tissues of patients from rural areas. Additionally, bacteria from the Neisseriaceae, Porphyromonadaceae, and Selenomonadaceae families, as well as the Selenomonas genus, were significantly enriched in the oncobiome of rural BC patients. Furthermore, the results of the PICRUSt2 (phylogenetic investigation of communities by reconstruction of unobserved states) revealed a significant increase in phospholipid biosynthesis pathways in breast oncobiome of patients from rural areas compared to those from urban areas. Conclusions: This study provides evidence of distinct compositional and functional differences in the breast oncobiome between BC patients from rural and urban areas. These findings suggest that environmental factors influence local microbiome composition, potentially contributing to BC development and/or progression. Full article

Background/Objectives: Lactobacillus delbrueckii subsp. lactis CKDB001 (LL) has demonstrated anti-inflammatory, antioxidant, and lipid-regulatory effects in vitro and in vivo, including attenuation of hepatic steatosis and modulation of lipid metabolism. Given the known interactions between host metabolism and gut microbiota, these findings suggest a potential role for LL in modulating microbial composition under conditions of diet-induced obesity. This study aimed to investigate the microbiome-related effects of LL using an established murine model. To evaluate the effect of LL supplementation on gut microbial composition and predict microbial metabolic functions in mice with high-fat diet-induced obesity. Methods: Male C57BL/6J mice were fed a high-fat diet and administered LL orally for 12 weeks. Fecal samples were collected and analyzed using 16S rRNA gene sequencing. Microbial taxonomic profiles were assessed using linear discriminant analysis effect size, and functional predictions were performed using PICRUSt2. Results: LL supplementation significantly altered the gut microbiota by increasing the relative abundance of Lactobacillus and other commensal taxa while reducing the prevalence of pro-inflammatory genera such as Alistipes and Bilophila. Functional prediction analysis revealed a downregulation of lipopolysaccharide and ADP-L-glycero-β-D-manno-heptose biosynthesis pathways. Microbial functions associated with carbohydrate metabolism and short-chain fatty acid production were enriched in the LL-treated group. Conclusions: LL modulated gut microbial composition and suppressed pro-inflammatory microbial pathways while enhancing beneficial metabolic functions in high-fat diet-fed mice. These findings support the potential of LL as a safe and effective microbiota-targeted probiotic for managing obesity-related metabolic disorders. Full article

Background: Obesity-associated metabolic disorders represent a critical global health challenge, which necessitates innovative strategies targeting lipid metabolism. Peanut skin procyanidins (PSPs), abundant bioactive compounds derived from agricultural by-products, show potential in lipid regulation, but molecular mechanisms remain unclear. Methods: This study integrated hepatic metabolomics, network pharmacology, and gut microbiota analysis to systematically decipher the mechanisms for PSP to ameliorate high-fat diet (HFD)-induced lipid metabolism disorders. Results: PSP intervention significantly attenuated HFD-induced increases in LDL-C, TG, and TC levels and effectively mitigated hepatic lipid accumulation. Metabolomics revealed that PSP reshaped hepatic lipid dynamics by modulating glycerophospholipid, linoleic acid, arachidonic acid, tryptophan, and nitrogen metabolism. Subsequent network pharmacology identified PLA2G10, PLA2G5, PLA2G2A, and CYP1B1 as the core targets, and PSP could markedly suppress their HFD-induced overexpression. Furthermore, PSP selectively reshaped the gut microbiota, enriching beneficial genera such as Akkermansia and Bacteroides while reducing the abundance of harmful bacteria within Firmicutes. PICRUSt-based functional prediction indicated that PSP alters gut microbial glutamine synthetase activity. Conclusions: Mechanistically, PSP regulates lipid metabolism by downregulating PLA2G10, PLA2G5, PLA2G2A, and CYP1B1 expression, remodeling gut microbiota structure, and increasing hepatic glutamine level. These findings provide novel insights into value-added utilization of agricultural byproducts and development of targeted intervention strategies for metabolic diseases. Full article

Androgenetic alopecia (AGA) is the most common form of patterned hair loss, exhibiting gender-specific clinical features. Recent studies highlight the importance of the skin microbiome in maintaining skin health, but the relationship between the hair follicle microbiome and hair loss, particularly AGA, remains understudied. Hair follicle layer samples were collected directly from the crown region of female pattern hair loss (FPHL), male pattern hair loss (MPHL), and healthy adult women (control) groups. Microbial DNA was extracted and analyzed using Illumina 16S rRNA V3–V4 gene amplicon sequencing. Alpha-diversity and beta-diversity analyses and taxonomic and functional profiling were conducted through relative abundance, LEfSe, and PICRUSt2 analyses. The alpha-diversity analysis showed a significant decrease in microbial richness in the hair loss groups. Unweighted UniFrac-based beta-diversity analysis revealed significant clustering between the control group and the FPHL group. Taxonomic profiling and LEfSe analysis identified differences in microbial composition and biomarkers. PICRUSt2 analysis further revealed altered pathways related to porphyrin metabolism, fatty acid biosynthesis, and steroid hormone metabolism. Additionally, differences in microbiome composition and potential functions were found between the FPHL and MPHL groups. This study provides comprehensive insights into the hair follicle microbiome, revealing unique microbial patterns and functional alterations associated with FPHL. Understanding these microbiome characteristics may contribute to targeted approaches for addressing AGA. Further research is warranted. Full article

Dinoflagellates significantly contribute to the carbon fixation and microbial loop in the ocean with high ecological diversity. While the microbial communities associated with the HABs of dinoflagellates have attracted intensive attention in recent years, little attention has been paid to the microbiomes associated with resting cysts, an important stage in the life cycle and bloom initiation dynamics of dinoflagellates. Using Scrippsiella acuminata as a representative of cyst producers and cyst-relevant research in dinoflagellates, we surveyed the bacteria and fungi microbiomes long associated with different life cycle stages of the dinoflagellate culture through 16S and ITS rRNA amplicon sequencing, and predicted their possible functions using the PICRUSt2 algorithm. The results found high species diversity of the associated bacteria–fungi microbiomes, and species featured with diverse and flexible metabolic capabilities that have stably co-occurred with the laboratory culture of S. acuminata. The host-attached and the free-living groups of bacteria–fungi microbiomes, as operationally defined in the context, showed significant differences in terms of their nutritional preferences. The bacteria–fungi species diversity and community structure associated with cysts are also distinguished significantly from that with vegetative cells, with the latter attracting more bacteria–fungi species specializing in phosphate solubilization. These results suggest that the relative species abundance and thus the community structure of the host-associated microbiome shift with the transition of life cycle stages and environmental conditions. Our findings show the association tightness between bacteria–fungi microbiomes and dinoflagellate hosts and the different life stages of hosts shaping the bacteria–fungi communities, which result in dynamic and specific interactions between bacteria–fungi microbiomes and their hosts. Full article

In this study, the migratory agricultural pest Spodoptera frugiperda was exposed to three periodic short-term heat stress regimes at 37 °C, 40 °C, and 43 °C (2 h daily), with a constant 26 °C control. We systematically evaluated the effects of periodic thermal stress on developmental traits across all life stages. Combined with 16S rRNA high-throughput sequencing, we analyzed the structural and functional characteristics of the gut bacterial community in adults under heat stress. The results demonstrated that 37 °C exposure accelerated egg-to-adult development, whereas 43 °C markedly extended it. Additionally, 43 °C heat stress suppressed pupation and eclosion rates. Increasing stress temperatures were negatively correlated with pupal weight and body size in both sexes. Notably, 43 °C heat stress caused complete loss of hatching ability in offspring eggs, thereby rendering population reproduction unattainable. 16S rRNA sequencing revealed that Proteobacteria (>90%) dominated the gut bacterial community at the phylum level across all treatments. Under 43 °C heat stress, although female and male adults exhibited an increase in specific bacterial species within their gut bacteria, Alpha diversity analysis revealed no significant differences in the diversity (Shannon index) and richness (Chao index) of gut bacterial communities between sexes under temperature treatments. PICRUSt2 functional prediction indicated that metabolic pathways, biosynthesis of secondary metabolites, and microbial metabolism in diverse environments constituted the dominant functions of gut bacteria in both sexes, while heat stress exerted minimal effects on the functional profiles of gut bacteria in S. frugiperda. These findings not only provide a theoretical basis for predicting summer population dynamics and formulating ecological control strategies for S. frugiperda but also offer critical insights into the adaptive interactions between this pest and its gut bacterial community under heat stress. The results lay a foundation for further exploring the interactions between insect environmental adaptability and bacterial symbiosis. Full article

Microplastics (MPs) and heavy metals are commonly present in soil at significant concentrations and can interact in complex ways that pose serious threats to environmental and ecological systems. The effects of combined contamination by different types of heavy metals and microplastics on plants, as well as on soil microbial communities and their functions, remain largely unexplored. In this study, a series of pot experiments was conducted to investigate the effects of composite contamination involving two heavy metals (Cd and Pb) and two types of microplastics polylactic acid (PLA) and polybutylene succinate (PBS) at varying concentrations (0.1% and 0.5%, w/w). The impacts on water spinach (Ipomoea aquatica) growth and heavy metal accumulation were evaluated, and the rhizosphere bacterial and fungal community structure and diversity were analyzed using high-throughput sequencing. The presence of Cd, Pb, and microplastics significantly inhibited the growth of water spinach, reducing both its length and biomass. Under combined microplastic–heavy metal contamination, phytotoxicity increased with rising concentrations of PLA and PBS. Microplastics were found to alter the mobility and availability of heavy metals, thereby reducing their accumulation in plant tissues and decreasing the levels of available potassium and phosphorus in the soil. Furthermore, microplastic–heavy metal interactions significantly influenced the composition and diversity of soil microbial communities, leading to an increased abundance of heavy-metal-tolerant and potential plastic-degrading microorganisms. A strong correlation was observed between microbial community structure (both bacterial and fungal), soil physicochemical properties, and plant growth. Functional predictions using PICRUSt2 suggested that the type and concentration of microplastics significantly affected rhizosphere microorganisms’ metabolic functions. In conclusion, the present study demonstrates that combined microplastic and heavy metal contamination exerts a detrimental effect on soil nutrient availability, resulting in alterations to soil microbial community composition and function. Furthermore, this study shows that these contaminants can inhibit plant growth and heavy metal uptake. The findings provide a valuable contribution to the existing body of knowledge on the ecotoxicological impacts of microplastic–heavy metal composite pollution in terrestrial ecosystems. Full article

Antimicrobial resistance (AMR) is a growing concern in laboratory animals, where antibiotic use can disrupt the gut microbiome and promote resistant strains. Rabbits, commonly used in biomedical research, are particularly susceptible to gut dysbiosis, increasing the risk of infection and subsequent antibiotic use. This study used 16S rRNA amplicon sequencing and PICRUSt2 to predict resistance-related functions in rabbits under standard laboratory conditions. Among 2427 amplicon sequence variants, 42 functional classes were identified, with AMR comprising 1.55% of the predicted functions, including beta-lactam, vancomycin, and cationic antimicrobial peptide resistance. These AMR functions were associated with commensal genera such as Bacteroides and Ruminococcus, while no associations were observed with pathogens such as Escherichia or Salmonella. The study provides functional evidence of intrinsic AMR in the rabbit gut microbiome and underscores the importance of antimicrobial stewardship in laboratory animal research. Full article

Non-starch polysaccharide-degrading enzymes are widely used as feed additives in monogastric and ruminant species, with positive effects reported. In this study, the commercial, fiber-degrading enzyme complex Hostazym^® X, derived from Trichoderma citrinoviride (DSM34663), was included in the total mixed rations of 17 mid-lactating (135 ± 61 days in milk) Holstein cows for 10 weeks. A control group (n = 17) was included. Dry matter intake (DMI), milk yield, 4% fat-corrected milk, solid yield, and milk fatty acid profile were assessed. The structure and composition of fecal bacterial communities, as well as PICRUSt2-based functional prediction of bacterial communities, were also evaluated. Higher DMI and milk yield scores were observed in the supplemented group (27.20 vs. 26.59 kgDM/cow/d; and 39.01 vs. 36.70 L/cow/d, respectively). No effects were observed in fat yield, contrary to lactose and protein, which were greater in the supplemented group compared to the control group (1.18 vs. 1.13 and 1.83 vs. 1.75 kg/cow/d, respectively; p < 0.05). Palmitic and oleic acids, in addition to monounsaturated fat in milk, were increased in the supplemented group (p > 0.05). Enzyme supplementation increased the Patescibacteria (p < 0.5) and Actinobacteriota (p > 0.05) in feces, but slightly reduced the Bacteroidota and Firmicutes. The Turicibacter genus remained at a lower relative abundance after supplementation but Candidatus_Saccharimonas, Clostridioides, Prevotellaceae UCG 003, Corynebacterium, Akkermansia, Syntrophococcus, Erysipelotrichaceae UCG 008, other Lachnospiraceae, other members of the Eubacterium_coprostanoligenes_group, Bifidobacterium, Rumminococcus, Akkermansia, and other Spirochaetaceae increased, modifying the functional predicted profile of bacterial communities. In conclusion, a positive effect on performance and milk composition were observed through modulation of microbiota induced by enzyme supplementation. The enzyme complex could be a viable supplement alternative in the feeding of dairy cows in semi-intensive productive systems, mainly when an ad libitum feeding scheme is used. Full article

The microbial community is one of the key indicators for evaluating the health of alpine marsh wetlands, and understanding the composition and health of alpine wetland communities provides a scientific rationale for conservation and restoration efforts. Taking the alpine marsh wetlands in Qilian Mountain National Park, Qinghai Province, as the research object, 27 soil samples (0–30 cm depth) were collected in July 2024 from three types of wetlands: non-degraded (ND), low-level degraded (LD), and heavily degraded (HD). Using high-throughput sequencing, PICRUSt2 functional prediction, nonmetric multidimensional scaling (NMDS), and redundancy analysis (RDA), we analyzed the bacterial community structure and functional characteristics as well as the soil physicochemical properties across different degradation levels and soil depths. Pearson correlation analysis and RDA were used to identify key soil indicators influencing microbial community characteristics. The results showed that (1) compared to ND, the relative abundance of Acidobacteriota increased from 12.3% to 23.7%, and that of Pseudomonadota increased from 28.5% to 35.1% in HD wetlands. Meanwhile, the Shannon index rose from 5.31 in ND to 6.52 in HD, indicating significantly increased microbial community diversity and complexity with wetland degradation (p < 0.05). (2) Vertically, the six major primary metabolic functions gradually weakened with increasing soil depth in all three types of wetlands, the relative abundance of Proteobacteria decreased from 0 to 30 cm, and the α-diversity indices of soil bacteria also declined with depth. (3) Compared to ND, LD and HD showed significantly lower soil moisture content, organic matter, and total organic carbon (p < 0.05), while total potassium and pH increased significantly (p < 0.05). With increasing depth, total nitrogen significantly decreased across all degradation types (p < 0.05). Bacterial diversity, as measured by the Shannon and Simpson indices, showed a significant correlation with several soil properties (moisture, organic matter, total nitrogen, total potassium, cation exchange capacity, and total organic carbon; p < 0.05). Furthermore, pH emerged as a primary environmental driver shaping microbial community structure across different soil depths. These findings offer technical guidance and a theoretical framework for comprehending the degradation and restoration dynamics of alpine marsh wetland ecosystems in the Qilian Mountains. Full article

This study presented an investigation into the role of ceramsite pore structures in optimizing DNBFs for nitrate-contaminated water treatment. Through systematic comparison of three ceramsite media (CE1, CE2, CE3) with distinct pore structures, we elucidated the microbial mechanisms underlying nitrate removal efficiency by analyzing denitrification performance, biomass accumulation, EPS, microbial community structure, and nitrogen metabolic function. Results demonstrated that the CE2 medium, characterized by an effective porosity (pore size > 0.5 μm) of 55.8% and an optimal porosity (pore size 0.5–25 μm) percentage of 83.1%, achieved superior nitrate removal efficiency (87.8%) with an R_vd of 0.82 kg TN/(m³·d) at HRT = 1.5 h, outperforming CE1 (0.74 kg TN/(m³·d)) and CE3 (0.68 kg TN/(m³·d)). Enhanced performance was mechanistically linked to CE2’s higher biomass accumulation (8.5 vs. 7.8 mg/m² in CE1 and 6.9 mg/m² in CE3) and greater EPS production (48.5 vs. 44.7 in CE1 and 35.4 mg/g in CE3), which facilitated biofilm resilience under hydraulic stress. Microbial analysis revealed CE2’s unique enrichment of a higher relative abundance of Proteobacteria (90.1% vs. 67.2% in CE1 and 47.4% in CE3) and denitrifying taxa (unclassified_f_Comamonadaceae: 42.7%, unclassified_f_Enterobacteriaceae: 35.3%). PICRUST2 showed 1.2- and 1.4-fold higher abundance of denitrification genes (narGHI, nosZ) compared to CE1 and CE3, respectively. These findings establish that optimizing ceramsite pore structure, particularly increasing the optimal porosity ratio (pore size 0.5–25 μm) can enhance denitrification efficiency, offering a scalable strategy for cost-effective groundwater remediation. This work provides actionable criteria for designing high-performance DNBFs, with immediate relevance to industrial and municipal wastewater treatment systems facing stringent nitrate discharge limits. Full article

ACLF is a severe stage of liver cirrhosis, characterized by multiple organ failure, systemic inflammation, and high short-term mortality. The intestinal microbiota (IM) influences its pathophysiology; however, there are currently no studies in Latin American populations. Therefore, we analyzed IM and its relationships with sepsis, organ failure, and mortality. In parallel, we quantified serum lipopolysaccharides as a marker of bacterial translocation. Fecal samples from 33 patients and 20 healthy controls (HCs) were obtained. The IMs were characterized by 16S-rRNA amplicon sequencing, the metagenomic functional predictive profiles were analyzed by PICRUSt2, and LPS quantification was performed by ELISA. Patients with ACLF showed significant alterations in alpha and beta diversity compared to the HCs. A strong dominance index accurately predicted 28-day and 90-day mortalities. The IMs showed a polarization toward Proteobacteria associated with increased LPS. The LPS correlated with clinical severity, organ dysfunction, and higher pathogenic taxa. The Klebsiella/Faecalibacterium ratio showed good performance in identifying sepsis (AUROC = 0.83). Furthermore, Morganella, Proteus, and Klebsiella were enriched in patients with multiorgan failure. Lactobacillus, Escherichia/Shigella, Veillonella, and Ruminococcus gnavus exhibited potential in predicting 28- and 90-day mortalities. The IM alterations in ACLF may be useful as clinical biomarkers of poor prognosis, primarily for mortality and sepsis. These findings are representative of western Mexico. Full article