Search Results (826)

The gross benefit of feeding multi-species probiotics has been reported, but the effect on the gut microbiota in pre-weaned dairy calves has not been elucidated. To address this gap, a randomized controlled trial was conducted in California, USA, to investigate the effect of feeding probiotics on the fecal microbiota of pre-weaned dairy calves. A total of 30 neonatal calves were randomly assigned to either the probiotic (PRO) or control (CON) treatment. Fecal samples were collected at four age timepoints: days 7, 14, 21, and 42. Fecal bacterial population was analyzed using 16S rRNA amplicon sequencing. Differential abundance analysis was conducted to investigate the difference between the PRO and CON treatments, and diarrheic and non-diarrheic calves in each PRO and CON group. The PRO group had decreased Clostridium perfringens and Fusobacterium varium compared to the CON at 7 days of age. At 7 days of age, diarrheic calves in CON had more abundant F. varium compared to non-diarrheic calves, but there was no difference between diarrheic and non-diarrheic calves in the PRO group. In conclusion, probiotics administration decreased the population of pathogenic bacteria in feces from pre-weaned dairy calves on Day 7 of age. However, the treatment did not have an impact on bacterial diversity. These results suggest that the administration of probiotics has the potential to control gastrointestinal pathogens. Full article

Tropical sandy beaches are dynamic ecosystems where microbial communities play crucial roles in biogeochemical processes and tracking human impact. Despite their importance, these habitats remain underexplored. Here, using amplicon-based sequencing of bacterial (V3-V4 16S rRNA) and fungal (ITS2) markers, we first describe microbial communities inhabiting supralittoral–intertidal sediments of two contrasting sandy beaches in the Tadjoura Gulf (Djibouti Republic): Sagallou-Kalaf (SK, rural, siliceous sand) and Siesta Plage (SP, urban, calcareous sand). Sand samples were collected at low tide along 10 m transects perpendicular to the shoreline. Bacterial communities differed significantly between sites and along the sea-to-land gradient, suggesting an influence from both anthropogenic activity and sediment granulometry. SK was dominated by Escherichia-Shigella, Staphylococcus, and Bifidobacterium, associated with human and agricultural sources. SP showed higher richness, with enriched marine-associated genera such as Hoeflea, Xanthomarina, and Marinobacter, also linked to hydrocarbon degradation. Fungal diversity was less variable, but showed significant shifts along transects. SK communities were dominated by Kluyveromyces and Candida, while SP hosted a broader fungal assemblage, including Pichia, Rhodotorula, and Aureobasidium. The higher richness at SP suggests that calcium-rich sands, possibly due to their buffering capacity and greater moisture retention, offer more favorable conditions for microbial colonization. Full article

Fecal water syndrome (FWS) in horses is characterized by two-phase defecation, including both solid and liquid phases. While satisfactory explanations for FWS are unavailable, bacterial dysbiosis has been suggested as a contributing or causative factor. The objectives of this study were to determine whether fecal bacterial dysbiosis is associated with FWS in horses in the midwestern USA. Fecal samples were collected from horses with FWS and from unaffected horses at the same location. In total, 16S rRNA amplicon libraries produced from fecal bacterial DNA were sequenced using the Illumina sequencing platform. Significant differences in beta diversity were detected between affected and control horses (p = 7 × 10⁻⁴, F = 1.51), and differential abundance testing identified several features enriched in affected and control horses. These results agree with prior work regarding specific features in the bacterial microbiome associated with FWS, including Alloprevotella spp., and suggest fecal dysbiosis is associated with FWS. Full article

Cold seep ecosystems harbor unique microbial communities with potential for producing secondary metabolites. However, the metabolic potential of cold seep microorganisms in the South China Sea remains under-recognized. This study employed both culture-dependent and culture-independent approaches, including 16S rRNA amplicon sequencing and metagenomics, to investigate microbial communities and their potential for secondary metabolite production in the South China Sea cold seep. The results indicate microbial composition varied little between two non-reductive sediments but differed significantly from the reductive sediment, primarily due to Planctomycetes and Actinobacteria. Predicting the Secondary Metabolism Potential using Amplicon (PSMPA) predictions revealed 115 strains encoding more than 10 biosynthetic gene clusters (BGCs), with lower BGC abundance in reductive sediment. Culture-dependent studies showed Firmicutes as the dominant cultivable phylum, with strains from shallow samples encoding fewer BGCs. Metagenomic data confirmed distinct microbial compositions and BGC distributions across sediment types, with cold seep type having a stronger influence than geographic location. Certain BGCs showed strong correlations with sediment depth, reflecting microbial adaptation to nutrient-limited environments. This study provides a comprehensive analysis of the metabolic capabilities of South China Sea cold seep microorganisms and reveals key factors influencing their secondary metabolic potential, offering valuable insights for the efficient exploration of cold seep biological resources. Full article

Feed supplementation strategies are essential for optimizing cattle productivity, and the incorporation of non-conventional feed resources may reduce both production costs and environmental impact. This study evaluated the effects of pelletized protein concentrates (including Acacia farnesiana, A. schaffneri, and Agave duranguensis bagasse) on rumen fermentation parameters, microbial communities, and gas emissions. Fistulated bullocks received the concentrate daily, and ruminal contents were collected and filtered before and after supplementation to assess in vitro gas and methane production, pH, and microbial composition using high-throughput sequencing of 16S rRNA and mcrA amplicons. In addition, in situ degradability was evaluated during and after the supplementation period. Supplementation led to a significant (p < 0.05) reduction in degradability parameters and methane production, along with a marked decrease in the abundance of Methanobrevibacter and an increase in succinate-producing taxa. These effects were attributed to the enhanced levels of non-fiber carbohydrates, hemicellulose, crude protein, and the presence of bioactive secondary metabolites and methanol. Rumen microbiota composition was consistent with previously described core communities, and mcrA-based sequencing proved to be a valuable tool for targeted methanogen detection. Overall, the inclusion of non-conventional ingredients in protein concentrates may improve ruminal fermentation efficiency and contribute to methane mitigation in ruminants, although further in vivo trials on a larger scale are recommended. Full article

Neisseria gonorrhoeae, the causative agent of gonorrhea, represents a major public health concern due to its increasing antimicrobial resistance. While often asymptomatic—particularly in extragenital infections—untreated cases can lead to severe complications and further transmission. Despite global efforts to monitor antimicrobial resistance, data on the molecular determinants underlying decreased susceptibility in N. gonorrhoeae remain scarce in Peru. This study aimed to detect mutations in the penA and 23S rRNA genes, which confer decreased susceptibility to cephalosporins and azithromycin resistance. We extracted DNA from 124 N. gonorrhoeae-positive clinical rectal specimens collected in Aptima Combo 2 transport tubes from MSM patients. These DNA samples were then screened using the Mismatch Amplification Mutation Assay-based real-time PCR (MAMA-qPCR) to identify mutations in the 23S rRNA and penA genes. Each sample underwent separate reactions to detect A2059G and C2611T mutations in the 23S rRNA gene, and 86 of these samples were further tested in individual qPCR assays for the penA D345 deletion (D345del) or G545S mutations. Sanger sequencing was performed on all DNA samples positive for 23S rRNA mutations by MAMA-qPCR assay, and on 27 DNA samples that yielded sufficient penA amplicons for additional sequencing. Using the MAMA-qPCR assay for the 23S rRNA gene, 64 of 124 samples amplified in the A2059G reaction: 2 (3.1%) carried the mutation, and 62 were classified as wild type. In the C2611T reaction, 42 of 124 samples amplified, and none of them carried the mutation. Using the MAMA-qPCR assay for the penA gene, we only analyzed 86 samples, as the remaining 38 samples had insufficient DNA yield. A total of 44 of the 86 samples amplified in the D345del reaction: 5 (11.4%) carried the D345del, and 39 were classified as wild type. In the G545S reaction, 4 (6.4%) carried the mutation, and 58 were classified as wild type. Finally, sequencing of the penA gene in the 27 samples revealed mutations related to decreased susceptibility to cephalosporins. This study identified genetic mutations conferring resistance to azithromycin and decreased susceptibility to cephalosporins, providing an overview of the circulating mutations conferring resistance in N. gonorrhoeae strains in Peru. Full article

The long-term monocropping of red kidney beans in agricultural fields can lead to the occurrence of soil-borne diseases. Alterations in the composition of the soil microbial community are a primary cause of soil-borne diseases and a key factor in continuous cropping obstacles. Research exploring how different cultivation modes can modify the diversity and composition of the rhizosphere microbial community in red kidney beans, and thus mitigate the effects of continuous cropping obstacles, is ongoing. This study employed three cultivation modes: the continuous monocropping of red kidney beans, continuous monocropping of soybeans, and red kidney bean–soybean intercropping. To elucidate the composition and diversity of rhizosphere microbial communities, we conducted amplicon sequencing targeting the V3-V4 hypervariable regions of the bacterial 16S rRNA gene and the ITS1 region of fungal ribosomal DNA across distinct growth stages. The obtained sequencing data provide a robust basis for estimating soil microbial diversity. We observed that, under the intercropping mode, the composition of both bacteria and fungi more closely resembled that of soybean monocropping. The monocropping of red kidney beans increased the richness of rhizosphere bacteria and fungi and promoted the accumulation of pathogenic microorganisms. In contrast, intercropping cultivation and soybean monocropping favored the accumulation of beneficial bacteria such as Bacillus and Streptomyce, reduced pathogenic fungi including Alternaria and Mortierell, and exhibited less microbial variation across different growth stages. Compared to the monocropping of red kidney beans, these systems demonstrated more stable microbial structure and composition. The findings of this study will inform sustainable agricultural practices and soil management strategies. Full article

Mandarin fish (Siniperca chuatsi) are known to exhibit distinct physiological and immunological adaptations to environmental stressors, but the underlying molecular and microbial mechanisms remain unclear. In this study, we integrated transcriptome and microbiome analyses to investigate adaptations across three geographically distinct mandarin fish groups: Guangdong (G), Qiupu (Q), and native Taihu (T). Liver RNA sequencing revealed 5339 differentially expressed genes (DEGs) between T and G and 1531 DEGs between T and Q. Functional enrichment analysis revealed group-specific responses. Specifically, DEGs from T vs. G were linked to small-molecule metabolism and innate immunity whereas the DEGs from T vs. Q were related to immune regulation and chromatin organization. The concurrent 16S rRNA sequencing of the intestinal microbiota identified 2680 amplicon sequence variants, with principal coordinate analysis showing distinct clustering (31.77% variance). Group T had higher Firmicutes abundance whereas groups G and Q had a higher relative abundance of Fusobacteriota. Correlation networks revealed key microbe–gene interactions, including positive links between Lactobacillus and immune genes in group T and negative associations with Romboutsia. These findings suggest that enhanced immune homeostasis and metabolic flexibility in group T may result from coordinated host gene expression and Lactobacillus-driven microbiome modulation. We provide new insights into the mechanisms of adaptation in mandarin fish and identify potential biomarkers for enhancing aquaculture resilience. Full article

Global warming represents one of the most pressing environmental challenges to cold-water fish farming. Heat stress markedly alters the mucosal symbiotic microbiota and intestinal microbial metabolites in fish, posing substantial barriers to the healthy artificial breeding of rainbow trout (Oncorhynchus mykiss). However, the relationship between mucosal commensal microbiota, intestinal metabolites, and host environmental adaptability under heat stress remains poorly understood. In this study, rainbow trout reared at optimal temperature (16 °C) served as controls, while those exposed to maximum tolerated temperature (24 °C, 21 d) comprised the heat stress group. Using 16S rRNA amplicon sequencing and ultra-high-performance liquid chromatography–mass spectrometry (UHPLC-MS), we analysed the mucosal commensal microbiota—including gastrointestinal digesta, gastrointestinal mucosa, skin mucus, and gill mucosa—and intestinal metabolites of rainbow trout under heat stress conditions to explore adaptive and regulatory mechanisms. Analysis of microbial composition and diversity revealed that heat stress exerted the greatest impact on the diversity of gill and skin mucus microbiota, followed by gastrointestinal digesta, with relatively minor effects on the gastrointestinal mucosa. At the phylum level, Proteobacteria, Firmicutes, and Bacteroidetes were predominant in the stomach, intestine, and surface mucosa. At the genus level, Acinetobacter showed the greatest increase in abundance in skin and gill mucosa under heat stress, while Enterobacteriaceae exhibited the most pronounced increase in intestinal digesta, gastric digesta, and gastric mucosa. Differential metabolites in the intestinal digesta under heat stress were predominantly enriched in pathways associated with amino acid metabolism, particularly tryptophan metabolism. This study provides a comprehensive characterisation of microbiota and metabolic profile alterations in rainbow trout under heat stress condition, offering a theoretical foundation for understanding the response mechanisms of fish commensal microbiota to thermal stress. 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

The domestication process not only reduced the allelic diversity of tomato genotypes but also affected the genetic traits associated to microbial recruitment, their composition, and their diversity in different compartments of the plant host. Additionally, this process included the transition from natural to agricultural soils, which differ in nutrient availability, physicochemical properties, and agricultural practices. Therefore, modern cultivars may fail to recruit microbial taxa beneficial to their wild relatives, potentially losing important ecological functions. In this study, we analyzed the phylogenetic relationship and the rhizosphere microbiota of four tomato genotypes, Solanum chilense (wild species), S. lycopersicum var. cerasiforme (Cherry tomato), and the S. lycopersicum landrace ‘Poncho Negro’ and the modern cultivar ‘Cal Ace’, grown in both natural and agricultural soils. Microbial communities were identified using 16S rRNA (bacteria) and ITS2 (fungi) amplicon sequencing, allowing cross-domain taxonomic characterization. While the soil type was the main driver of overall microbial diversity, the host genotype influenced the recruitment of specific microbial taxa, which exhibited different recruitment patterns according to the genetic diversification of Solanum genotypes and soil types. Additionally, co-occurrence network analysis identified two main clusters: first, taxa did not show any preferential associations to particular genotypes or soil types, while the second cluster revealed specific microbial patterns associated to fungal taxa in natural soil and bacterial taxa in agricultural soil. Finally, the functional analysis suggested the loss of specific functions through tomato domestication independently of soil type. These findings highlight the role of the plant genotype as a fine-tuning factor in microbiome assembly, with implications for breeding strategies aimed at restoring beneficial plant–microbe interactions. 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

Equine gastric disease (EGD) is a common condition in performance horses (Equus caballus), potentially compromising behaviour, performance, and welfare. EGD is often attributed to high-starch, high-sugar feeds and limited forage. Evidence for diet-induced changes on digestive microbiota is lacking. Nine elite showjumping horses were housed at the same performance yard with standardised diet and management throughout the study. Horses were transitioned from a high-sugar and -starch (31%) feed to a low-starch and -sugar (16.5%) concentrate feed. Gastroscopies, blood, and faecal samples were taken pre- and 12 weeks post-diet change. Squamous and glandular ulceration was blindly graded a posteriori using 0–4 scores and faecal microbiota profiled using 16S rRNA gene amplicon sequencing. Total (t_(1,8) = −6.17, p < 0.001; Pre: 4 [0–5], Post: 1 [0–2]), squamous (t_(1,8) = −5.32, p < 0.001; Pre: 1 [0–3], Post: 0 [0–1]), and glandular (t_(1,8) = −2.53, p = 0.04; Pre: 2.5 [0–4], Post: 0 [0–2]) disease improved following the introduction of a low-starch diet. Diet change did not impact microbiota communities (PERMANOVA: F_(1,16) = 1.37, p = 0.15, r² = 0.08), but Firmicute to Bacteroidota (F/B) ratio reduced (t_(1,8) = −3.13, p = 0.01; Pre: 2.07 ± 0.21 vs. Post: 1.29 ± 0.14). Lower F/B ratios were associated with reduced total EGD scores (ChiSq_(1,17) = 3.83, p = 0.05). Low-starch diets did not influence faecal microbiota diversity but aided gastric disease healing and reduced F/B ratios in elite showjumpers during a competition season without medication. Full article

H. pylori detection via the stool antigen test (SAT) requires 100 times more cells than nested PCR (NPCR) for a 454 bp amplicon, but is significantly more sensitive in identifying positive stool samples. To understand this contradiction, we developed an NPCR assay to amplify a shorter 148 bp segment of the 16S rRNA gene. The assay was extremely sensitive and reliable when adhering to particular rules commonly used in forensic laboratories. The SAT and NPCR for long and short amplicons were compared using stool samples from 208 gastroenterological patients, of which 27.9% were identified as positive according to the SAT and only 6.25% according to the 454 bp NPCR amplicon, but 51.0% in the short 148 bp NPCR. Among 100 asymptomatic volunteers, the prevalence was 35% in the SAT assay and 22% in the long NPCR, but as much as 66.6% of positives were determined in the short 148 bp NPCR. The specificity of the PCR product was determined via DNA sequencing, which confirmed H. pylori’s origin in all NPCR-positive samples. Apparently, the stool contains mostly short fragments of H. pylori DNA, and the most plausible explanation for the SAT/NPCR paradox is the degradation of H. pylori DNA in the digestive system. Full article

The unique microbial communities present on fruit surfaces significantly influence the fermentation process and product quality of artisanal cider production, constituting a microbial terroir analogous to that recognized in viticulture. In this study, we investigated the microbial composition and diversity associated with the apple varietals (Empire, Golden Delicious, and Idared) cultivated by two different orchard producers in the Hudson River Valley of New York. Using 16S rRNA and ITS amplicon sequencing, we identified distinct bacterial and fungal communities that varied significantly according to the apple varietal and orchard location. Notably, the orchard was the dominant factor shaping both the bacterial and fungal communities on the apples’ surfaces, with the varietal differences also playing a significant, albeit secondary, role. For example, we found that the bacterial genera Acidophilim sp. and 1174-901-12 sp., as well as the fungus Sporobolmyces patagonicus, were important markers of the orchard in which the apples were cultivated. These microbial signatures persisted into the early stages of cider fermentation, suggesting their potential influence on the cider quality and flavor profile. Our findings underscore the critical importance of the microbial terroir in cider production, and suggest that targeted management practices can leverage regional microbial diversity to enhance the distinctiveness and marketability of artisanal cider products. Full article