Search Results (130)

Vermicomposting is a sustainable biotechnological process that transforms organic waste through the synergistic activity of earthworms, such as Eisenia fetida, and their associated microbiota. This study evaluated bacterial and physicochemical dynamics during the vermicomposting of bovine manure by analyzing the microbial composition of the substrate and the gut of E. fetida at three time points (weeks 0, 6, and 12). The V3–V4 region of the 16S rRNA gene was sequenced, and microbial diversity was characterized using QIIME2. Significant differences in alpha diversity (observed features, Shannon index, and phylogenetic diversity) and beta diversity indicated active microbial succession. Proteobacteria, Bacteroidota, and Actinobacteriota were the dominant phyla, with abundances varying across habitats and over time. A significant enrichment of Proteobacteria, Bacteroidota, and the genera Chryseolinea, Flavobacterium, and Sphingomonas was observed in the manure treatments. In contrast, Actinobacteriota, Firmicutes, and the genera Methylobacter, Brevibacillus, Enhygromyxa, and Bacillus, among others, were distinctive of the gut samples and contributed to their dissimilarity from the manure treatments. Simultaneously, the physicochemical parameters indicated progressive substrate stabilization and nutrient enrichment. Notably, the organic matter and total organic carbon contents decreased (from 79.47% to 47.80% and from 46.10% to 27.73%, respectively), whereas the total nitrogen content increased (from 1.70% to 2.23%); these effects reduced the C/N ratio, which is a recognized indicator of maturity, from 27.13 to 12.40. The macronutrient contents also increased, with final values of 1.41% for phosphorus, 1.50% for potassium, 0.89% for magnesium, and 2.81% for calcium. These results demonstrate that vermicomposting modifies microbial communities and enhances substrate quality, supporting its use as a biofertilizer for sustainable agriculture, soil restoration, and agrochemical reduction. Full article

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

This study assessed the viable and culturable microbial diversity that remained on equipment surfaces after hygiene procedures in Brazilian poultry and fish slaughterhouses. Food-contact surface samples were collected using sterile swabs in poultry (n = 50) and fish (Oreochromis niloticus, n = 50) slaughterhouses. The swab samples were used to prepare culture plates to recover viable and culturable cells. The grown plates were washed, and the total DNA of the cell suspension was extracted with a commercial kit. Sequencing of the total DNA extracted from cultures was targeted at the V3 and V4 regions of the 16S rRNA. DNA reads were analyzed by QIIME2 software, with results expressed in relative frequency (%RF). Alpha and beta diversity indexes were analyzed considering the spots of sample collection, type of industry, surfaces (smooth or modular), and materials (polypropylene, stainless steel, or polyurethane). The results showed that in the poultry slaughterhouse, the most abundant genera were Acinetobacter (27.4%), Staphylococcus (7.7%), and Pseudomonas (5.3%), while for the fish slaughterhouse, there was a higher abundance of Staphylococcus (27.7%), Acinetobacter (17.2%), and Bacillus (12.5%). Surface characteristics influenced the microbial diversity, with Acinetobacter spp. dominating modular surfaces and Staphylococcus spp. prevailing on smooth surfaces. The results obtained indicate there is an important resident microbiota that persists even after hygiene processes, and surface-specific cleaning strategies should be developed. Full article

Beta-thalassemia major is an inherited disorder that requires lifelong blood transfusions, with the risk of complications including poor oral health and dental caries. The objective of this study was to compare the oral microbiome diversity and composition in transfusion-dependent thalassemia patients and relate it to oral hygiene and dental caries. A cross-sectional analysis of 35 patients of beta-thalassemia major aged 6–18 years was performed. The status of oral hygiene was examined through the Oral Hygiene Index—Simplified (OHI-S) and Decayed, Missing, and Filled Teeth (DMFT) index. Saliva was taken for DNA extraction, followed by the 16S rRNA sequencing of V3-V4 hypervariable regions. The bioinformatics pipeline in QIIME2 was utilized for analyzing the comparison of microbial composition and diversity in groups of varying oral hygiene status and severity of caries. Metagenomic analysis revealed 3334 Amplicon Sequence Variants (ASVs), of which the most prevalent genera were Streptococcus, Haemophilus, Veillonella, Rothia, and Prevotella. High-oral-hygiene groups presented increased levels of cariogenic bacteria, while moderate-oral-hygiene groups presented an equilibrated microbiome. No statistically significant differences in microbial diversity were found between the study groups (p > 0.05). This study sheds light on the critical importance of oral hygiene in microbiome diversity in patients with beta-thalassemia major. Full article

Objectives: The aim of this study was to assess the taxonomic diversity of the microbiota associated with periapical lesions of endodontic origin and to determine whether microbial profiles vary across different populations and clinical characteristics using a unified in silico analysis of next-generation sequencing (NGS) data. Methods: Raw 16S rRNA sequencing data from three published studies were retrieved from the NCBI Sequence Read Archive and reprocessed using a standardized bioinformatics pipeline. Amplicon sequence variants were inferred using DADA2, and taxonomic assignments were performed using BLASTN against a curated 16S rRNA reference database. Alpha and beta diversity analyses were conducted using QIIME 2 and R, and differential abundance was assessed with ANCOM-BC2. Statistical comparisons were made based on population, sex, symptomatology, and other clinical metadata. Results: A total of 38 periapical lesion samples yielded 566,223 high-confidence reads assigned to 347 bacterial species. Significant differences in microbial composition were observed between geographic regions (China vs. Spain), sexes, and symptoms. Core species such as Fretibacterium sp. HMT 360 and Porphyromonas endodontalis were prevalent across datasets. Porphyromonas gingivalis and Fusobacterium nucleatum were found in abundance across all three studies. Beta diversity metrics revealed distinct clustering by study and country. Symptomatic lesions were associated with higher abundance of Alloprevotella tannerae and Prevotella oris. Conclusions: The periapical lesion microbiota is taxonomically diverse and varies significantly by geographic and clinical features. Full article

Here, we introduce the mbX package: an R-based tool designed to streamline 16S rRNA gene microbiome data analysis following taxonomic classification. It automates key post-sequencing steps, including taxonomic data cleaning and visualization, addressing the need for reproducible and user-friendly microbiome workflows. mbX’s core functions, ezclean and ezviz, take raw taxonomic output (such as those from QIIME 2) and sample metadata to produce a cleaned relative abundance dataset and high-quality stacked bar plots with minimal manual intervention. We validated mbX on 14 real microbiome datasets, demonstrating significant improvements in efficiency and consistency of post-processing of DNA sequence data. The results show that mbX ensures uniform taxonomic formatting, eliminates common manual errors, and quickly generates publication-ready figures, greatly facilitating downstream analysis. For a dataset with 20 samples, both functions of mbX ran in less than 1 s and used less than 1 GB of memory. For a dataset with more than 1170 samples, the functions ran within 125 s and used less than 4.5 GB of memory. By integrating seamlessly with existing pipelines and emphasizing automation, mbX fills a critical gap between sequence classification and statistical analysis. An upcoming version will have an added function which will further extend mbX to automated statistical comparisons, aiming for an end-to-end microbiome analysis solution by integrating mbX with currently available pipelines. This article presents the design of mbX, its workflow and features, and a comparative discussion positioning mbX relative to other microbiome bioinformatics tools. The contributions of mbX highlight its significance in accelerating microbiome research through reproducible and streamlined data analysis. Full article

The greenbug aphid (Schizaphis graminum (Rondani)) is a major pest of wheat and an important vector of wheat viruses. An RNA-seq study was conducted to investigate the microbial effects of two greenbug genotypes, the presence or absence of cereal yellow dwarf virus, and the condition of the wheat host over a 20-day time course of unrestricted greenbug feeding. Messenger RNA reads were mapped to ca. 47,000 bacterial, 1218 archaeal, 14,165 viral, 571 fungal, and 94 protozoan reference or representative genomes, plus greenbug itself and its wheat host. Taxon counts were analyzed with QIIME2 and DESeq2. Distinct early (days 1 through 10) and late (days 15 and 20) communities differed in the abundance of typical enteric genera (Shigella, Escherichia, Citrobacter), which declined in the late community, while the ratio of microbial to greenbug read counts declined 50% and diversity measures increased. The nearly universal aphid endosymbiont, Buchnera aphidicola, accounted for less than 25% of the read counts in both communities. There were 302 differentially expressed (populated) genera with respect to early and late dates, while 25 genera differed between the greenbug genotypes and nine differed between carrier and virus-free greenbugs. The late community was likely responding to starvation as the wheat host succumbed to aphid feeding. Our results add to basic knowledge about aphid microbiomes and offer an attractive alternative method to assess insect microbiomes. Full article

Background/Objectives: Severe infection (sInfection; either late-onset culture-proven sepsis or necrotizing enterocolitis) in very low birth weight (VLBW) infants increases mortality rates and may show long-term progression. The fecal microbiome composition in VLBW infants with and without sInfection was classified in the sInfection and non-sInfection groups. Methods: Gut microbiomes, secondary information from a previous randomized trial, were analyzed using QIIME 2 software. The biodiversity and abundance of the gut microbiota between the sInfection and non-sInfection groups were compared. Results: Fifty-one neonates were included in the sInfection (n = 9) and non-sInfection (n = 42) groups; no significant differences in the fecal microbiome were observed in both alpha and beta diversities. Analysis of relative abundance revealed that in both groups, the predominant gut microbiota phylum, class, and genus were Proteobacteria, Gammaproteobacteria, and Klebsiella, respectively. The main fecal microbiome in the non-sInfection group included Faecalibacterium, Clostridium butyricum, and Bacteroides fragilis. Clostridium_sensu_stricto _1 was significantly more abundant in the non-sInfection group than in the sInfection group. Conclusions: Clostridium_sensu_stricto_1 was the main gut microbiota in the non-sInfection group. Considering the potential taxa as synbiotics (correlations among prebiotics, probiotics, and postbiotics), therapeutics may be useful for preventing and managing necrotizing enterocolitis or late-onset culture-proven sepsis in VLBW infants. Full article

Possible early detection of people at increased risk for severe COVID-19 clinical course is extremely important so that appropriate therapy can be initiated promptly to prevent numerous deaths. Our study included 45 patients treated for COVID-19 at Dubrava University Hospital, with clinical course analysed from medical records and stool samples collected for determination of the gut microbiota diversity using 16S rRNA analysis. Sequencing was successful for 41 samples belonging to four clinical course groups (WHO guidelines): 12 samples—critical, 12—severe, 9—moderate and 8—mild group. Microbial composition was assessed between groups using two approaches—ANCOM (QIIME2) and Kruskal–Wallis (MicrobiomeAnalyst). On the genus level, two taxa were found to be differentially abundant: archaeal Halococcus and Coprococcus (for both W = 37)—the two were most abundant in the critical group (10% and 0.94% of entire abundance, respectively). Coprococcus catus was the only species identified by both methods to be differentially abundant between groups and was most abundant in the critical group. Alpha diversity indicated greater evenness of features in the critical group. Beta diversity showed clustering of samples from the critical group. A relationship between gut microbiota composition and the clinical course of COVID-19 disease was indicated, pointing towards specific distinct features of the critical group. In a broader sense, our findings might be useful in combating potential future similar pandemics and emerging virus outbreaks. Full article

With the explosive growth of sequencing data, rapidly and accurately classifying and identifying species has become a critical challenge in amplicon analysis research. The internal transcribed spacer (ITS) region is widely used for fungal species classification and identification. However, most existing ITS databases cover limited fungal species diversity, and current classification methods struggle to efficiently handle such large-scale data. This study integrates multiple publicly available databases to construct an ITS sequence database encompassing 93,975 fungal species, making it a resource with broader species diversity for fungal taxonomy. In this study, a fungal classification model named FungiLT is proposed, integrating Transformer and BiLSTM architectures while incorporating a dual-channel feature fusion mechanism. On a dataset where each fungal species is represented by 100 ITS sequences, it achieves a species-level classification accuracy of 98.77%. Compared to BLAST, QIIME2, and the deep learning model CNN_FunBar, FungiLT demonstrates significant advantages in ITS species classification. This study provides a more efficient and accurate solution for large-scale fungal classification tasks and offers new technical support and insights for species annotation in amplicon analysis research. Full article

This study investigated the effects of the poly (ADP-ribose) polymerase (PARP) inhibitor Olaparib, alone and in combination with cisplatin, on intestinal integrity, survival, and microbiome composition using a murine model. Statistical analyses were conducted using one-way analysis of variance with Bonferroni correction for multiple comparisons, considering p-values of <0.05 as statistically significant. Microbiome profiling was performed using Qiime 2 software. Histopathological and microbiome analyses revealed Olaparib’s protective effects on intestinal integrity, mitigating cisplatin-induced damage. The single administration of cisplatin caused significant histological damage, biochemical disruptions, and dysbiosis, characterized by an increase in pro-inflammatory microbiome, such as Clostridium_sensu_stricto_1, and a decrease in beneficial short-chain fatty acid (SCFA)-producing microbiome. Conversely, the single administration of Olaparib was associated with an increase in SCFA-producing microbiome, such as Lachnospiraceae NK4A136, and exhibited minimal toxicity. The combination administration showed complicated outcomes, as follows: reduced cisplatin-induced cytotoxicity and increased SCFA-producing microbiome ratios, yet the long-term effects revealed reduced survival rates in the cisplatin group and sustained weight gain suppression. These findings emphasize Olaparib’s potential in enhancing intestinal barrier integrity, reducing inflammation, and positively modulating microbiome diversity. However, the entangled pharmacodynamic interactions in the combination administration underscore the need for further investigation. The study highlights the potential of microbiome-targeted interventions in improving therapeutic outcomes for both cancer treatment and inflammatory bowel disease management. Full article

Microbiota could be of interest in the diagnosis of colorectal and non-small cell lung cancer (CRC and NSCLC). However, how the microbial components of tissues and feces reflect each other remains unknown. In this work, our main objective is to discover the degree of correlation between the composition of the tissue microbiota and that of the feces of patients affected by CRC and NSCLC. Specifically, we investigated tumor and non-tumor tissues from 38 recruited patients with CRC and 19 with NSCLC. DNA from samples was submitted for 16S rDNA metagenomic sequencing, followed by data analysis through the QIIME2 pipeline and further statistical processing with STATA IC16. Tumor and non-tumor tissue selected genera were highly correlated in both CRC and NSCLC (100% and 81.25%). Following this, we established tissue–feces correlations, using selected genera from a LEfSe analysis previously published. In CRC, we found a strong correlation between the taxa detected in feces and those from colorectal tissues. However, our data do not demonstrate this correlation in NSCLC. In conclusion, our findings strongly reinforce the utility of fecal microbiota as a non-invasive biomarker for CRC diagnosis, while highlighting critical distinctions for NSCLC. Furthermore, our data demonstrate that the microbiota components of tumor and non-tumor tissues are similar, with only minor differences being detected. Full article

Ruminants rely on the rumen for the anaerobic fermentation of fibrous plant materials, facilitated by a complex microbial community of bacteria, archaea, fungi, and ciliates. Among them, ruminal ciliates significantly influence ruminal fermentation, methane production, nitrogen utilization efficiency, and microbial interactions. This study examined the impact of ciliate inoculation on ruminal fermentation, microbial composition, and functional profiles in fauna-free conditions. Six treatments were tested: control (no ciliates), small entodinia, Epidinium spp., isotrichids, Ophryoscolex spp., and a mixed inoculum. Using QIIME2 to analyze 16S rRNA gene sequences, the study revealed group-specific effects on methane production, volatile fatty acids (VFAs), and microbial diversity. Small entodinia inoculation increased Streptococcus abundance, while isotrichids enriched Megasphaera, enhancing butyrate production. Alpha diversity indices indicated reduced richness in the ciliate-inoculated groups, reflecting predation on prokaryotes. Beta diversity showed distinct microbial and functional profiles among the treatments. Functional analysis highlighted elevated glycerolipid metabolism in isotrichid groups, associated with Bacteroides and Megasphaera, suggesting roles in lipid metabolism and oxidative stress resistance. Despite limited ciliate cell counts, the study emphasizes ciliate-specific interactions and the role of lactic acid-associated bacteria in shaping ruminal fermentation. Full article

Background: Effective management of primary apical periodontitis depends on understanding the dynamic interactions within the root canal microbiome. This study aimed to investigate the effect of sequential antimicrobial phases on the root canal microbiome during a two-visit treatment approach, with a focus on calcium hydroxide medication. Methods: Samples were collected from three teeth across four treatment phases: initial infection (S1), after chemomechanical preparation (S2), after intracanal medication (S3), and after a final flush (S4). DNA was extracted, and the V3–V4 regions of the 16S rRNA gene were sequenced using Illumina MiSeq. Sequencing data were analyzed with QIIME 2, and differentially abundant taxa were identified using linear discriminant analysis effect size (LEfSe). Results: While microbial community composition did not differ significantly between phases, the Firmicutes/Bacteroidetes ratio decreased after the antimicrobial stages. LEfSe analysis revealed higher abundances of Lactobacillales, Arthrobacter, and Veillonella in the untreated (CMP) group. Bifidobacterium longum was relatively more abundant in the intracanal medication (ICM) phase, and Dorea formicigenerans was more abundant in the final-flush (FF) phase. Conclusions: Although calcium hydroxide treatment did not induce statistically significant changes in overall root canal microbial composition, trends such as a reduction in the Firmicutes/Bacteroidetes ratio and a relative increase in Bifidobacterium longum numbers suggest potential ecological shifts. The observed relative increase in Bifidobacterium longum numbers may represent a hypothesis-driven observation reflecting indirect ecological effects rather than direct pH modulation. While visual patterns (e.g., PCA clustering) were observed, they lacked statistical support. Further studies with larger sample sizes are needed to validate these observations and assess the potential role of beneficial bacteria in root canal treatments. Full article