Search Results (109)

While the gut microbiota of obese children in Mexico has been studied, its relationship with depressive and anxiety symptoms in obese adults remains unexplored. The aim of this study was to describe the gut microbiota profile of Mexican adults with obesity and its association with depression and anxiety. We sequenced the V3-V4 region of the 16S rRNA gene from stool samples of obese adults categorized into four groups: control (OCG), with depressive symptoms (OD), with anxiety symptoms (OAx), or with both (ODAx). Alpha diversity was assessed using t-tests, beta diversity was assessed with PERMANOVA, and taxonomic differences was assessed with LEfSe. Associations between bacterial genera and clinical variables were analyzed using the Maaslin2 library. Bacteroidota was the most prevalent phylum, and Prevotella was the dominant enterotype across all groups. Although overall diversity did not differ significantly, 30 distinct taxonomic biomarkers were identified among groups as follows: 4 in OCG (Firmicutes), 5 in OD (Firmicutes, Bacteroidota), 13 in OAx (Firmicutes, Bacteroidetes, Fusobacteroidota, Proteobacteria), and 8 in ODAx (Firmicutes). This is the first study to identify distinct gut microbiota profiles in obese Mexican adults with depressive and anxiety symptoms. These findings suggest important microbial biomarkers for improving the diagnosis and treatment of mental health conditions in obesity. Full article

Understanding the influence of the sheep breed and roughage source on the composition of rumen bacteria and methanogens is essential for optimizing roughage efficiency. The experiment employed a 2 × 2 factorial design. Twenty-four Dumont and Mongolian sheep (initial body weight of 18.94 ± 1.01 kg) were randomly assigned by breed to two dietary treatment groups (AH: alfalfa hay; CS: corn straw); the experiment lasted 90 days. The results showed that sheep fed alfalfa hay diets had a higher feed intake and weight gain, and Dumont sheep had a higher feed intake than Mongolian sheep (p < 0.05). The diversity and composition of ruminal bacteria and methanogens differed between Dumont and Mongolian sheep fed either AH or CS diets. The taxonomic analysis revealed a distinct clustering pattern based on the roughage source, but not on the breed. When fed a corn straw diet, the bacterial Chao1 index of Dumont sheep increased (p < 0.05), while the diversity and richness of methanogens in Mongolian sheep increased (p < 0.05). Additionally, we have identified unique biomarkers for the rumen bacteria and methanogens of Dumont and Mongolian sheep in response to different roughage sources. The results suggest that the differences in the microbiota of the sheep were associated with the roughage source and breed. The higher growth performance of Dumont sheep might be attributed to the increase in bacterial diversity and the decrease in methanogenic bacteria diversity. 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

Introduction: Anal squamous cell carcinoma (ASCC) is a rare but increasingly common gastrointestinal malignancy, mainly associated with oncogenic human papillomaviruses (HPVs). The role of non-coding RNAs (ncRNAs) in tumorigenesis is recognized, but the impact of viral ncRNAs on host gene expression remains unclear. Methods: We re-analyzed total RNA-Seq data from 70 anal biopsies: 31 low-grade squamous intraepithelial lesions (LGSIL), 16 high-grade SIL (HGSIL), and 23 ASCC cases. Microbial composition was assessed taxonomically. Novel viral miRNAs were predicted using vsRNAfinder and linked to host targets using TargetScan and expression correlation analyses. Results: Microbial profiling revealed significant differences in abundance, with Alphapapillomaviruses types 9, 10, and 14 enriched across lesion grades. We identified 90 novel viral miRNAs and 177 significant anti-correlated miRNA–mRNA interactions. Target genes were enriched in pathways related to cell cycle, epithelial–mesenchymal transition, lipid metabolism, immune modulation, and viral replication. Discussion: Our findings suggest that HPV-derived miRNAs, including those from low-risk types, may contribute to neoplastic transformation by modulating host regulatory networks. Conclusion: This study highlights viral miRNAs as potential drivers of HPV-related anal cancer and supports their utility as early biomarkers and therapeutic targets in ASCC. Full article

Background/Objectives: Emerging evidence suggests that gut microbiota composition is influenced by both age and sex and may contribute to dementia-related brain pathologies. However, comprehensive microbiome-based biomarker discovery stratified by these factors remains limited. Methods: We performed a metagenomic analysis of the gut microbiota of participants stratified by sex (female vs. male) and age (<75 vs. ≥75 years). Alpha diversity (observed operational taxonomic unit, Chao1, Shannon, and Simpson) and linear discriminant analysis effect size analyses were conducted to identify dominant taxa associated with Alzheimer’s pathology, vascular pathology, and dementia-related structural brain changes. Results: Females and non-elderly participants (aged < 75 years) exhibited higher gut microbial diversity, characterized by an increased abundance of Bifidobacterium spp. and Blautia spp., whereas males and elderly participants (aged ≥ 75 years) exhibited increased levels of Bacteroides spp. and Bacteroidia, which have been associated with inflammation and dysbiosis. Several taxa, including Bifidobacterium spp. were consistently identified as potential protective biomarkers, while Bacteroides spp. was linked to a higher risk of dementia-related brain pathologies. Conclusions: Our findings demonstrate distinct age- and sex-specific differences in gut microbiota composition that may be closely associated with the pathophysiology of dementia-related brain pathologies. These results demonstrate that gut microbiota may serve as potential biomarkers for monitoring cerebrovascular conditions, potentially contributing to the development of personalized therapeutic strategies. Full article

Background/Objectives: Aging is characterized by dysregulation of the immune system. A balanced diet and probiotic intake can play significant roles in preventing aging-related chronic degenerative diseases and promoting immune function in the elderly. This community-based intervention study investigated the effects of an eight-week intervention involving a balanced diet with or without probiotics on nutritional parameters and gut microbiota composition in Korean elderly individuals. Methods: A total of 48 participants were enrolled and randomly allocated into two groups: 24 received a balanced diet alone, and 24 received a balanced diet combined with probiotics. Results: The balanced diet showed beneficial impacts on nutritional and inflammatory biomarkers, including fasting glucose, hemoglobin A1c (HbA1c), albumin, gamma-glutamyl transferase (γ-GT), total cholesterol, high-density lipoprotein cholesterol (HDL-C), immunoglobulin E (IgE), and gut microbiota, such as the Bacteroidaceae family and the genera Prevotella and Faecalibacterium. Additionally, providing probiotics alongside a balanced diet influenced the taxonomic profile and abundance of intestinal microbiota. Conclusions: Overall, the combination of a balanced diet and probiotics has beneficial effects on nutritional and inflammatory biomarkers as well as gut microbiota composition in elderly individuals. Future meticulously designed randomized controlled trials are required to further understand the health benefits and underlying mechanisms of balanced diets and probiotics in the Korean elderly. Full article

Pediatric asthma is the most common chronic childhood disease in the US and a major public health concern. It is considered to comprise multiple clinical variants or phenotypes with different etiologies and pathophysiologies. Former research has shown that airway bacteriomes vary in composition and structure across pediatric asthma phenotypes, but their functional diversity and bacterial interactions have hardly been investigated. A previous study of 163 children from Washington DC identified three statistically different asthma phenotypes, each with a unique nasopharyngeal bacterial composition and diversity. Here, I reanalyze 16S rRNA high-throughput sequences from the same cohort to characterize their bacterial metabolism and interactions. I detect 61 to 102 metabolic pathways (PICRUSt2; q ≤ 0.05) differentially expressed across the three asthma phenotypes. Most of those pathways are related to biosynthesis and degradation processes and statistically (p ≤ 0.0012) separated the three clinical groups. Co-occurrence networks also differ in connectivity across phenotypes, suggesting unique bacterial interactions in each group. Five to eight keystone taxa are detected across phenotypes. Insights from this and previous studies, hence, confirm the airway bacteriome heterogeneity across pediatric asthma, increasing our understanding of its etiology and pathophysiology, and provide new taxonomic and functional biomarkers of disease for targeted interventions and therapies. Full article

The role of vaginal dysbiosis in the progression of human papilloma virus (HPV) associated cervical lesions has gained attention in recent years. While many studies use 16S rRNA gene sequencing for microbiota analysis, shotgun metagenomic sequencing offers higher taxonomic resolution and insights into microbial gene functions and pathways. This systematic review evaluates the relationship between compositional and functional changes in the vaginal microbiome during HPV infection and cervical lesion progression. A literature search was performed according to PRISMA guidelines in PubMed, Web of Science, Scopus, and ScienceDirect databases. Seven studies utilizing metagenomic sequencing in patients with HPV infection or HPV-associated cervical lesions were included. Progression from HPV infection to cervical lesions and cancer was associated with a reduction in Lactobacillus species (particularly Lactobacillus crispatus) and an enrichment of anaerobic and pathogenic species, especially Gardnerella vaginalis. Heterogeneous enriched metabolic pathways were also identified, indicating functional shifts during lesion progression. As most studies were conducted in Asia, further research in diverse regions is needed to improve the generalizability of findings. Future studies employing metagenomic sequencing may help identify biomarkers for early pre-cancerous lesions and clarify the role of vaginal microbiota in persistent HPV infection and cervical dysplasia. Full article

Abscesses are among the diseases affecting the survival of captive musk deer and are difficult to identify in their early stages. In this study, metagenomic sequencing, 16S rRNA sequencing, and paraffin sectioning were used to analyze the microbiota in the abscess musk deer pus group (AMP), abscess musk deer oral group (AMO), and healthy musk deer oral group (HMO) to compare the differences in microbiota in musk deer. By detecting differences in the oral microbiota through throat swabs, we aimed to monitor the early onset of abscess disease to facilitate timely intervention and treatment. The results showed that the alpha diversity of HMO microbiota was significantly higher than that of the AMP and AMO samples. Beta diversity results indicated that there were significant differences in the bacterial communities of HMO and AMO samples, and no significant difference was found between AMO and AMP samples. A taxonomic analysis of the bacterial species indicated that differences between HMO and AMP groups were found in the Fusobacterium and Trueperella species. Fusobacterium and Trueperella were the main pathogenic bacteria responsible for the occurrence of abscess diseases in forest musk deer in this study. Furthermore, the appearance of Fusobacterium and Trueperella in the oral cavity can serve as biomarkers for the early diagnosis of abscess disease in musk deer. Full article

Background/Objectives: Generous consumption of phytonutrient-rich foods, including blueberries, provides benefits to multiple physiologic and metabolic systems. This study explored the potential that regular, generous blueberry intake could favorably modulate fecal microbiome composition in sedentary older (>60 years) men and women with overweight or obesity (BMI ≥ 25 to 32 kg/m²). Methods: Participants (n = 55) were randomized to daily consumption of either lyophilized blueberry powder (equivalent to 1.5 cups of blueberries) or an indistinguishable placebo powder; both groups participated in weekly supervised exercise classes. Fecal samples were collected at 0 and 12 weeks and frozen. Following this, 16S rRNA gene sequencing was used to profile each participant’s fecal microbiome. Blood biomarkers of cardiometabolic health were measured via nuclear magnetic resonance spectroscopy (NMR) pre- and post-treatment. Results: Comparing the baseline and endpoint results for the blueberry (n = 15) and placebo (n = 19) groups, there were no significant overall compositional differences or differences in the level of diversity in the fecal microbiome. However, in subjects whose diet included blueberry powder, there was a significant enrichment (p = 0.049) in the relative abundance of Coriobacteriales incertae sedis, a taxonomic group of bacteria that facilitates the metabolism of dietary polyphenols. The placebo group exhibited significant reductions in total cholesterol, LDL-C, non-HDL-C, total LDL-P, large LDL-P, and ApoB, while the blueberry group exhibited significant reductions in total HDL-P and ApoA-I after 12 weeks compared to baseline. Conclusions: Generous blueberry consumption may upregulate the ability of the older human gut to utilize dietary polyphenols by altering the fecal microbiome. Longer, larger-scale studies with blueberries or blueberry powder are needed to observe improvements in cardiometabolic risk factors in older adults with overweight or obesity. Full article

The microbial community in vinegar has primarily been investigated by analyzing short reads to determine operational taxonomic units, but it is also crucial to identify metagenome-assembled genomes (MAGs). In this study, the microbial diversity and functionality in Sichuan Baoning vinegar were examined through deep metagenomic sequencing and metagenomic binning. Results revealed that the most prevalent phylum was Firmicutes, followed by Proteobacteria and unclassified Bacteria. The most abundant bacterial species was Acetilactobacillus jinshanensis, while Saccharomyces cerevisiae was the most prevalent fungal species. The predominant viral species were Hopescreekvirus LfeInf, Myoviridae sp., and Siphoviridae sp. A total of 1395 MAGs were reconstructed, with 660 of them annotated. The majority of MAGs resolved at the species level were attributed to Firmicutes (n = 308), with Acetilactobacillus jinshanensis being the most abundant. According to the average nucleotide identity values, 223 out of the 660 MAGs might represent novel species. The recovered MAGs exhibited biomarker genes indicative of the genetic potential to encode several important secondary metabolites. This study helps to uncover the microbial composition and functional potential of microbial genomes in Sichuan Baoning vinegar. Full article

The significant microbiota variability represents a key feature that makes the full comprehension of the functional interaction between microbiota and the host an ongoing challenge. To overcome this limitation, in this study, fish intestinal microbiota was analyzed through a meta-analysis, identifying the core microbiota and constructing stochastic Bayesian network (BN) models with SAMBA. We combined three experiments performed with gilthead sea bream juveniles of the same hatchery batch, reared at the same season/location, and fed with diets enriched on processed animal proteins (PAP) and other alternative ingredients (NOPAP-PP, NOPAP-SCP). Microbiota data analysis disclosed a high individual taxonomic variability, a high functional homogeneity within trials and highlighted the importance of the core microbiota, clustering PAP and NOPAP fish microbiota composition. For both NOPAP and PAP BNs, >99% of the microbiota population were modelled, with a significant proportion of bacteria (55–69%) directly connected with the diet variable. Functional enrichment identified 11 relevant pathways expressed by different taxa across the different BNs, confirming the high metabolic plasticity and taxonomic heterogeneity. Altogether, these results reinforce the comprehension of the functional bacteria–host interactions and in the near future, allow the use of microbiota as a species-specific growth and welfare benchmark of livestock animals, and farmed fish in particular. Full article

The pervasive presence of microplastics (MPs) in agroecosystems poses a significant threat to soil health and plant growth. This study investigates the effects of varying concentrations and sizes of polystyrene microplastics (PS-MPs) on the Solanum lycopersicum L.’s height, dry weight, antioxidant enzyme activities, soil physicochemical properties, and rhizosphere microbial communities. The results showed that the PS0510 treatment significantly increased plant height (93.70 cm, +40.83%) and dry weight (2.98 g, +100%). Additionally, antioxidant enzyme activities improved across treatments for S. lycopersicum L. roots. Physicochemical analyses revealed enhanced soil organic matter and nutrient levels, including ammonium nitrogen, phosphorus, and effective potassium. Using 16S rRNA sequencing and molecular ecological network techniques, we found that PS-MPs altered the structure and function of the rhizosphere microbial community associated with S. lycopersicum L. The PS1005 treatment notably increased microbial diversity and displayed the most complex ecological network, while PS1010 led to reduced network complexity and more negative interactions. Linear discriminant analysis effect size (LEfSe) analysis identified biomarkers at various taxonomic levels, reflecting the impact of PS-MPs on microbial community structure. Mantel tests indicated positive correlations between microbial diversity and soil antioxidant enzyme activity, as well as relationships between soil physicochemical properties and enzyme activity. Predictions of gene function revealed that PS-MP treatments modified carbon and nitrogen cycling pathways, with PS1005 enhancing methanogenesis genes (mcrABG) and PS1010 negatively affecting denitrification genes (nirK, nirS). This study provides evidence of the complex effects of PS-MPs on soil health and agroecosystem functioning, highlighting their potential to alter soil properties and microbial communities, thereby affecting plant growth. Full article

Paratuberculosis (PTB), primarily caused by Mycobacterium avium subsp. paratuberculosis (MAP), is a chronic infection that affects ruminants and is difficult to prevent, diagnose, and treat. Investigating how MAP infections affect the gut microbiota in sheep can aid in the prevention and treatment of ovine PTB. This study examined fecal samples from eight small-tail Han sheep (STHS) at various stages of infection and from three different field areas. All samples underwent DNA extraction and 16S rRNA sequencing. Among all samples, the phyla p. Firmicutes and p. Bacteroidota exhibited the highest relative abundance. The dominant genera in groups M1–M6 were UCG-005, Christensenellaceae_R-7_group, Rikenellaceae_RC9_gut_group, Akkermansia, UCG-005, and Bacteroides, whereas those in groups A–C were Christensenellaceae_R-7_group, Escherichia–Shigella, and Acinetobacter, respectively. The microbial community structure varied significantly among groups M1–M6. Specifically, 56 microbiota consortia with different taxonomic levels, including the order Clostridiales, were significantly enriched in groups M1–M6, whereas 96 microbiota consortia at different taxonomic levels, including the family Oscillospiraceae, were significantly enriched in groups A–C. To the best of our knowledge, this is the first study to report that MAP infection alters the intestinal microbiota of STHS. Changes in p. Firmicutes abundance can serve as a potential biomarker to distinguish MAP infection and determine the infection stage for its early diagnosis. Our study provides a theoretical basis for the treatment of PTB by regulating the intestinal microbiota, including p. Firmicutes. Full article

Aquatic ecosystems, including rivers, estuaries, and coastal environments, are crucial for maintaining biodiversity, regulating nutrient cycles, and supporting human livelihoods. However, these ecosystems are increasingly being threatened by urbanization, making it essential to understand their microbial communities and their ecological roles. This study employed high-throughput 16S rRNA gene sequencing to characterize the bacterial communities within the riverine, estuarine, and coastal sediments of Adyar Creek, Chennai, India. Proteobacteria were the dominant phylum across most samples, with proportions ranging from 39.65% to 72.09%. Notably, the estuarine environment exhibited a distinct taxonomic profile characterized by a significant abundance of Firmicutes (47.09% of the bacterial population). Distinct bacterial classes were observed across sediment types: Alphaproteobacteria (30.07–34.32%) in riverine sediments, Bacilli dominated estuarine sediments (40.17%), and Gammaproteobacteria (15.71–51.94%) in coastal sediments. The most significant environmental factors influencing the bacterial community composition across these samples were pH, salinity, phosphate, and nitrate. LEfSe (Linear discriminant analysis Effect Size) analysis identified specific genera within the estuary, including Bacillus (20.26%), unclassified_Paenibacillus (12.87%), Clostridium (3.81%), Gailella (3.17%), Paenibacillus (3.02%), Massilia (1.70%), Paraburkholderia (1.42%), and Pantoea (1.15%), as potential biomarkers for habitat health. Functional analysis revealed an elevated expression of the genes associated with ABC transporters and carbon metabolism in the estuary, suggesting a heightened nutrient cycling capacity. Furthermore, co-occurrence network analysis indicated that bacterial communities exhibit a strong modular structure with complex species interactions across the three sediment types. These findings highlight bacterial communities’ critical role and the key drivers in estuarine ecosystems, establishing a baseline for further investigations into the functional ecology of these vulnerable ecosystems. Full article