Search Results (993)

The presence of substantial amounts of heavy metals in the environment can result in various significant ecological issues and human health risks. Currently, bioremediation employing microorganisms is garnering significant interest due to its effectiveness. The present investigation aimed to isolate actinobacterial strains from an Italian mine and to characterise them for heavy metals resistance and plant growth-promoting characteristics. The different samples were processed for DNA extraction and 16S rRNA gene metabarcoding to investigate the bacteria and archaea communities. Cultivable microbiota were isolated and evaluated for heavy metals tolerance and different PGP traits. The most pertinent strains were tested for compatibility, merged into a consortium, and tested on Lemna minor L. Metabarcoding analysis revealed that amplicon sequence variants (ASVs) at the phylum level were mostly assigned to proteobacteria and bacteroidota. Uncultured and unknown taxa were the most prevalent in the samples at the genus level. A total of ten strains were obtained from the culture-dependent approach exhibiting interesting heavy metals tolerance and plant growth-promoting traits. The best strains (MTW 1 and MTW 5) were selected and further characterised by 16S barcoding. These strains were identified as Streptomyces atratus (99.57% identity). An in planta experiment showed that the metal-tolerant consortium MTW 1-5 improved plant physiology by significantly optimising plant growth and tolerance to heavy metals. The experiment conducted provided evidence for the possibility of using actinobacteria as bioaugmentation agents to improve the phytoextraction abilities of L. minor. Full article

Background: Gut microbiota plays a critical role in host metabolism, immunity, and intestinal barrier integrity. Both chronic kidney disease (CKD) and kidney transplantation (KTR) are associated with gut dysbiosis, driven by uremic toxins, comorbidities, and immunosuppressive therapy. However, direct comparisons between hemodialysis (HD), KTR, and healthy controls (HC), while accounting for dietary factors, remain limited. Methods: We conducted a cross-sectional study including 48 HD patients, 75 KTR patients, and 13 HC. Stool patient samples were analyzed using 16S rRNA amplicon sequencing targeting the V4-V4 region to assess microbial composition and diversity. Data on clinical status, laboratory parameters, and dietary intake were collected and integrated with microbiome profiling. Results: Firmicutes and Bacteroidota dominated all groups, with Akkermansia enriched in HD and SCFA-producing genera (Faecalibacterium, Roseburia) more abundant in KTR. LEfSe and sPLS-DA analyses identified Akkermansia and Clostridia-related taxa as discriminants of HD, while Acidaminococcus and Megasphaera characterized KTR. HD patients exhibited higher alpha diversity (Faith’s PD and Chao1) than KTR (p < 0.05). Dietary intake differed across groups, but explained only a small proportion of microbial variance. Conclusions: Both HD and KTR patients display persistent gut dysbiosis with distinct microbial signatures. While transplantation partially restores SCFA producers, immunosuppression and diet shape new ecological shifts. These findings underscore the potential of microbiota as a biomarker and therapeutic target in renal replacement therapies. Full article

In this study, gut microorganisms of herbivorous grass carp, omnivorous carp, crucian carp, and aquatic microorganisms were collected from natural salt–alkali lakes and ponds in Xinjiang in winter to analyze their community structures. We sequenced 16S rRNA amplicons to investigate the composition and function of the microorganisms in the gut. PCoA analysis revealed that the gut microbiota of herbivorous and omnivorous fish formed two distinct clusters. Proteobacteria, Actinobacteria, Desulfobacterota, Firmicutes, and Chloroflexia are the dominant bacteria in the gut of fish. Proteobacteria, Bacteroidetes, Actinobacteria, Cyanobacteria, and Gram-negative bacteria are the dominant bacteria in the water. Carbohydrate- and protein-degrading bacteria, such as Desulfofustis, Lactiplantibacillus, and Vibrio, were predominant in omnivorous fish (CC and GRC), while cold-resistant bacteria, such as Shewanella and Psychromonas, were colonized in grass carp. This suggests that the same environment does not lead to similar gut bacteria, and that specific endogenous factors play a far more important role in shaping the microbiota composition than environmental factors. Full article

Sour meat, a traditional fermented meat product, derives its unique attributes from the flavors developed during the fermentation process. This study systematically investigated the dynamic changes in volatile compounds and bacterial succession in pork sour meat during fermentation (0, 15, 30, and 45 days) using a combination of an electric nose (E-nose), an electric tongue (E-tongue), gas chromatography–ion mobility spectrometry (GC-IMS), gas chromatography–mass spectrometry (GC-MS), and 16S rRNA amplicon sequencing. The results showed that the E-nose and E-tongue effectively distinguished samples across fermentation stages. The pork sour meat was analyzed using GC-IMS and GC-MS, which identified 39 and 81 volatile compounds (VOCs), respectively, primarily esters, alcohols, and aldehydes, with esters being most abundant after 45 days of fermentation. A total of 18 and 25 volatile compounds, respectively, were identified by GC-IMS and GC-MS as differential VOCs (p < 0.05, VIP > 1) of the pork sour meat. α-diversity increased in both species’ richness and diversity over the course of fermentation, while β-diversity analysis further differentiated samples across stages. Firmicutes dominated the bacterial community, with Staphylococcus, Lactobacillus, and Weissella as the main genera. Pearson correlation analysis revealed distinct associations between bacteria and volatiles: Staphylococcus was positively associated with butyl acetate-D, ethyl acetate, isoamyl acetate, dihydroactinidiolide, and (E)-2-heptenal, while Lactobacillus and Weissella were positively associated with acetic acid. Additionally, Weissella showed positive correlations with eight volatile compounds: acetic acid, nonanal, benzyl alcohol, ethyl crotonate, isoamyl acetate, dihydroactinidiolide, octanal, and ethyl acetate. This study provides a comprehensive understanding of volatile compound evolution and bacterial succession in pork sour meat, thereby offering a scientific basis for understanding and regulating its flavor quality. Full article

The human endometrium, previously considered a sterile environment, is now recognized as a low-biomass but biologically active microbial niche critical to reproductive health. Advances in sequencing technologies, particularly shotgun metagenomics, have provided unprecedented insights into the taxonomic and functional complexity of the endometrial microbiome. While 16S rRNA sequencing has delineated the distinction between Lactobacillus-dominant and non-dominant microbial communities, shotgun metagenomics has revealed additional diversity at the species and strain level, uncovering microbial signatures that remain undetected by amplicon-based approaches. Current evidence supports the association of Lactobacillus dominance with endometrial homeostasis and favorable reproductive outcomes. Dysbiosis, characterized by increased microbial diversity and enrichment of anaerobic taxa such as Gardnerella, Atopobium, Prevotella, and Streptococcus, is linked to chronic endometritis, implantation failure, and adverse IVF results. Beyond compositional differences, the endometrial microbiome interacts with the host through immunological, metabolic, and epigenetic mechanisms. These interactions modulate cytokine signaling, epithelial barrier integrity, and receptivity-associated gene expression, ultimately influencing embryo implantation. However, discrepancies between published studies reflect the lack of standardized protocols for sampling, DNA extraction, and bioinformatic analysis, as well as the inherent challenges of studying low-biomass environments. Factors such as geography, ethnicity, hormonal status, and antibiotic exposure further contribute to interindividual variability. Culturomics approaches complement sequencing by enabling the isolation of viable bacterial strains, offering perspectives for microbiome-based biotherapeutics. Emerging 3D endometrial models provide additional tools to dissect microbiome–host interactions under controlled conditions. Taken together, the growing body of data highlights the potential of endometrial microbiome profiling as a biomarker for reproductive success and as a target for personalized interventions. Future research should focus on integrating multi-omics approaches and functional analyses to establish causal relationships and translate findings into clinical practice. This review gives a new insight into current knowledge on the uterine microbiome and its impact on implantation success, analyzed through the lenses of microbiology, immunology, and oxidative stress. Full article

Environmental physicochemical factors and microorganisms play critical roles in the health of oysters. However, the impact of high-density oyster farming—a highly efficient filter-feeding bivalve system—on environmental conditions and microbial community structure and function remains poorly understood. This study conducted four-season monitoring of the water and sediment parameters in a semi-enclosed bay commercial oyster aquaculture (OA) system and a control area (CT), coupled with 16S rRNA amplicon sequencing of the environmental microbiota. Oyster aquaculture caused negligible disruption to water column parameters but significantly increased the concentrations of total organic carbon (TOC, annual mean OA vs. CT:1.15% vs. 0.56%), sulfides (annual mean OA vs. CT:67.72 vs. 24.99 mg·kg⁻¹), and heavy metals (Cd, Pb, Cu, Zn, and Cr) in the sediment. α-diversity (Shannon and Chao indices) exhibited minimal overall perturbation, with significant inter-regional differences observed only in winter for both water and sediment. The bacterial community structure of the water column was significantly altered only in winter, whereas sediment communities showed structural shifts in spring, summer, and autumn. Water microbiota were primarily influenced by turbidity, dissolved oxygen, salinity, the Si/N ratio, and silicates. Sediment microbiota were correlated with Pb, Cu, Zn, TOC, Cr, and sediment particle size. Water bacterial functions displayed only four significantly divergent biogeochemical processes annually (sulfur compound respiration; OA vs. CT). In contrast, sediment bacteria exhibited 29 significantly disrupted functions annually, with the greatest seasonal divergence in winter (11/67 functions). Spring, summer, and autumn sediment functions showed distinct patterns. Understanding these environmental–microbial interactions is essential for sustainable oyster aquaculture and ecological optimization. Full article

Although rhizobacteria are known to improve plant adaptation to abiotic stressors, their possible contribution to the inherent resilience exhibited by crops such as Sorghum bicolor is still poorly quantified. Here, three sorghum pre-release lines and three check varieties were established and evaluated at two low-altitude sites of less than 600 masl. Treatments were laid out in a randomized complete block design, replicated two times. Twenty-four rhizospheric soil samples comprising six sorghum genotypes with two replications across two sites were collected, processed using Zymo Research DNA extraction protocols, and the 16S rRNA amplicon sequences were generated for bacterial diversity quantifications following the Divisive Amplicon Denoising Algorithm 2 (DADA2) workflow. Grain yield data were also recorded and expressed in tonnes per hectare. Rhizobacteria recruitment and GY performance significantly (p < 0.05) varied with sorghum genotypes. Bacterial abundance significantly (p < 0.05) associated with sorghum grain yield performance with Actinobacteriota and Firmicutes being identified to be of economic importance, explaining between 52.23 and 85.64% of the variation in grain yield performance. The modelled relationships between rhizobacteria and grain yield performance revealed R² predicted values of up to 75.25% and a 10-fold R² of 75.54%, implying no model overfitting. Sorghum genotypes did not consistently exhibit direct variation between genetic worth values and grain yield performance. Superior grain yield performers, namely ICSV111IN, CHITICHI, and SV4, consistently associated with high incidences of occurrence of the bacteria phyla Chloroflexi (class = Chloroflexia) and Firmicutes (class = Bacilli), whilst integrating the conventional selection method with microbial diversity data, changed the genotype performance ranking, in which all the three pre-release lines, namely, IESV91070DL, ASARECA12-3-1, and ICSV111IN, exhibited superiority over the check varieties. The results demonstrated that the inherent stress resilience exhibited by some sorghum genotypes under climate change-induced stresses such as CDHS may be influenced by specific bacterial taxa recruited in the rhizosphere environment of the plants. Hence, more effort should be made to further exploit these beneficial plant–microbe interactions for enhanced sorghum productivity under abiotic stress conditions. Full article

Symptomatic uncomplicated diverticular disease (SUDD) is the primary clinical manifestation of diverticular disease (DD). Although gut microbiota (GM) perturbation and dietary habits are considered important factors in the development of the disease, there is currently a lack of data on the potential relationship between diet, GM profile and SUDD. An exploratory retrospective study was conducted in a SUDD cohort of 47 patients to investigate this relationship; a diverticulosis cohort of 19 patients served as the control group. Patients were stratified by their self-reported dietary habits, i.e., Mediterranean diet, predominantly plant-based diet or omnivorous diet. GM was profiled using 16S rRNA amplicon sequencing of fecal swabs. SUDD patients following a Mediterranean or predominantly plant-based diet showed higher alpha diversity and enrichment of known fibre degraders and short-chain fatty acid producers, such as members of the Lachnospiraceae, Ruminococcaceae, Oscillospiraceae and Prevotellaceae families. This suggests that their gut (and whole-body) health is less impaired. In contrast, those following an omnivorous diet showed an increased presence of pro-inflammatory taxa, including the mucus degrader R. torques, which suggests impaired gut barrier function and potential systemic implications. Similar associations between GM profile and dietary habits were found when considering SUDD patients with moderate abdominal pain severity (according to visual analogue scale, VAS) and those scored as DICA 1 according to the endoscopic severity of the disease. However, no such associations or trends were observed in SUDD patients scored as DICA 2, which suggests that diet may be unable to impact GM dysbiosis as SUDD severity increases. Despite the study’s limitations, primarily its retrospective design and related biases, our findings suggest that other GM modulation tools should be employed in more severe cases of SUDD to reverse dysbiosis while alleviating symptoms. Full article

Between 1% and 2% of the world’s population is sensitised to mites. Aetiological diagnosis is key to the management of allergic patients. However, methods based solely on morphological criteria are ambiguous in many cases. Polymerase chain reaction of ribosomal genes represents a valuable complementary approach. The 5 most representative species (Dermatophagoides pteronyssinus, Dermatophagoides farinae, Tyrophagus putrescentiae, Blomia tropicalis and Lepidoglyphus destructor) were selected as sources of allergens. They were first identified morphologically and the 18S rRNA gene sequences were obtained from the GenBank database. Alignment of the nucleotide sequences of the 18S rRNA ribosomal gene enabled the identification of the conserved and divergent regions in all of them. The alignment allowed the design of a pair of oligonucleotides in conserved regions of the gene, to amplify the sequence of interest in each of the species. We performed genomic DNA extraction, quantification and purity. PCR, using oligonucleotides designed to amplify the 18S sequence fragment of interest, showed the exact size for each species. Amplification, efficiency curves and melting points resulting from the amplification of the 18S amplicon of the five species were obtained. The oligonucleotides designed for real-time PCR studies, allow species identification by amplifying the specific fragment of each species using real-time PCR. Full article

Background/Objectives: This exploratory study aimed to evaluate the impact of an 80 km ultra-marathon trail running event on changes in faecal bacterial composition, and to investigate whether any correlations exist between exercise-associated gastrointestinal symptoms (Ex-GIS) with faecal bacterial profiles. Such events represent a unique physiological stressor and may impact the composition of the gut microbiota. Studying this impact may provide insights into acute (i.e., <24 h) gut microbiota changes under extreme conditions. Methods: Thirteen endurance athletes (n = 7 males, n = 6 females) aged 41 ± 8 years completed the 80 km Margaret River (Australia) ultra-marathon race in 2022. Faecal samples were collected pre- and post-race. Faecal bacterial profile, as per relative abundance (RA) of operational taxonomic units and the determination of α-diversity (Shannon Equitability Index (SEI)), was achieved by 16S rRNA amplicon gene sequencing. Changes in RA% and SEI pre- to post-race were assessed by the Wilcoxon signed-rank test. Correlations between Ex-GIS with bacterial profile and changes pre-, during, and post-ultra-marathon race were determined by Spearman’s rank correlation coefficients. Results: Bacterial calculations of phyla (n = 5), family (n = 23), and genus (n = 41) were detected for RA (≥0.5%). A significant decrease pre- to post-race of Actinobacteriota (p = 0.035) phyla, Bifidobacteriaceae (p = 0.007), and Clostridiaceae (p = 0.010) family, and Blautia (p = 0.039) and Subdoligranulum (p = 0.023) genus was determined; meanwhile, Oscillospiraceae (p = 0.016) and Monoglobaceae (p = 0.039) family significantly increased pre- to post-race. No other bacterial group changes were observed. No correlations were observed between pre- to post-ultra-marathon RA change and Ex-GIS. Conclusions: The completion of an 80 km ultra-marathon did not invoke substantial changes in the gut microbiota as determined by faecal bacterial profiling. Very strong and strong correlations were observed between certain bacterial groups and Ex-GIS; however, no significant correlations were observed between pre- to post-ultra-marathon changes in RA ≥ 0.5% and Ex-GIS. Full article

Increased seawater temperatures and nutrient loading are stressors that affect coral reefs and their microbiomes. In this study, filamentous algae were collected and exposed to different temperatures and nutrient concentrations through a laboratory experiment. Microbial DNA was extracted and analyzed using amplicon sequencing of the V3-V4 hypervariable region of the 16S rRNA gene. In total, 1 domain, 51 phyla, 131 classes, 335 orders, 549 families, and 1905 species were identified. Proteobacteria and Bacteroidota were the dominant taxa reported. Elevated seawater temperatures and nutrient enrichment impacted microbial communities associated with turf algae under laboratory culture. Bacterial species diversity and abundance differed under different temperature and nutrient conditions. Proteobacteria and Actinobacteria were abundant in lower-temperature conditions, while Desulfobacterota, Spirochaetota, and Firmicutes were abundant in higher-temperature conditions. Ruegeria was abundant in low-temperature conditions, whereas Vibrio abundance was low. Regarding nutrient conditions, Proteobacteria and Cyanobacteria were abundant under high-nutrient conditions, while Firmicutes and Desulfobacterota were abundant under ambient-nutrient conditions. The higher nutrient concentration increased the abundance of pathogenic bacteria, such as Vibrio and Photobacterium, while Pseudoalteromonas, which is beneficial for reefs, was present under ambient nutrient conditions. This study demonstrates that temperature and nutrient enrichment can shape microbial communities under laboratory conditions, providing an experimental setting for further studies of bacterial functions and metabolic processes in natural conditions under thermal and nutrient stresses. Full article

Marine bacteria possess significant potential for numerous applications including environmental remediation, creation of natural products and medicines, agriculture, and various industrial sectors. In this study, the diversity of bacterial populations in the seawater at the nearshore S1 station which is a frequent red-tide occurrence area in the East China Sea, was characterized using 16S rRNA gene amplicon sequencing analysis. The three predominant phyla in the bacterial communities were identified as Proteobacteria, Actinobacteria, and Bacteroidetes, with the families Rhodobacteraceae, Mycobacteriaceae, and Flavobacteriaceae as the dominant groups, respectively. The bacterial community composition at the S1 station significantly differed from those of the other five investigated coastal sites, and demonstrated its own unique taxonomic associations with the Rhodobacteraceae as the keystone species. Functional prediction through KEGG and MetaCyc analyses revealed the presence of an L-tryptophan biosynthesis pathway responsible for indole-3-acetic acid (IAA) production. By using the targeted isolation of cultivable bacterial strains, a novel red-pigmented bacterium, designated S1-TA-50, which produced IAA metabolites, was recovered from the S1 station. It was identified as a potential novel species within the genus Sulfitobacter in the family Rhodobacteraceae. This bacterium demonstrated notable antibacterial activity against four model pathogenic strains and also acted as a new microalgae growth-promoting bacterium with substantial IAA production after bacterial culture optimization. This study contributes to the accumulation of scientific knowledge regarding the dynamics of marine bacterial ecosystems in nearshore eutrophic environments and facilitates a better understanding of phycosphere bacterial roles in coastal ecosystems, as well as the comprehensive utilization of microbial resources. Full article

Background/Objectives: Postoperative pneumonia and other infectious complications after robotic-assisted minimally invasive esophagectomy still contribute to morbidity and mortality. Selective oral decontamination of the esophagus prior to surgery might reduce the rate of infectious complications. However, its impact on the esophageal microbiota is unknown. Therefore, this study aimed to analyze whether selective oral decontamination of the esophagus prior to surgery reduces postoperative pneumonia rates and alters the esophageal microbiome. Methods: We conducted a proof-of-principle study including 22 patients who underwent robotic-assisted minimally invasive esophagectomy. Thirteen patients were treated with 50 mg amphotericin B, 8 mg tobramycin, and 10 mg colistin orally 7 days prior to surgery, intraoperatively, and 5 days postoperatively. The remaining nine patients received standard-of-care treatment (no oral decontamination). The esophageal microbiome was assessed using 16S rRNA gene amplicon libraries which were annotated using the Ribosomal Data Project. The incidence of postoperative (at discharge from hospital or 30 days, whichever was later) infectious complications was assessed. Results: Selective oral decontamination was associated with reduced overall rates of infectious complications (7.7% vs. 55.5%, p = 0.008) and postoperative pneumonia (0% vs. 33.3%, p = 0.007). Alterations in the esophageal microbiome depending on selective oral decontamination were detectable. The microbiomes of patients with infectious complications showed higher abundances of Neisseria and lower abundances of Streptococcus than samples without infectious complications. Conclusions: Selective oral decontamination reduced the rate of postoperative complications, postoperative pneumonia in particular, after robot-assisted esophagectomy. Alterations in the microbiome were also evident following decontamination. Further studies with larger sample sizes are necessary to confirm these data. Full article

Background/Objectives: Chlorhexidine (CHX)-based mouthwashes are the most commonly used chemical methods as adjuvants for the treatment of peri-implant diseases, but there is a lack of information on their effect on the peri-implant microbiota. The objective of this study was to evaluate the impact of short-time (15 days) self-administered 0.05% and 0.12% commercial chlorhexidine mouthwashes on the peri-implant pocket microbiota of patients with peri-implantitis. Methods: In this pilot study, we analyzed the microbial composition of peri-implant lesions in 22 patients before and after a 15-day regimen of thrice-daily use of two commercial chlorhexidine mouthwashes containing 0.05% (n = 11) and 0.12% chlorhexidine (n = 11). Microbial samples were collected using paper points, and the taxonomic composition was determined through sequencing of 16S rRNA gene amplicons using Illumina MiSeq. Results: Although individual responses to chlorhexidine mouthwash treatment varied significantly, neither concentration produced a statistically significant change in the microbial diversity associated with peri-implantitis, suggesting limited treatment penetration into peri-implant lesions. Similarly, changes in the abundance of specific odontopathogens were not statistically significant. Conclusions: We found no significant differences in the effect of mouthwashes with different chlorhexidine concentrations on the peri-implant microbiota in short-period applications. Even though more extensive studies are required, the observed patient-dependent outcomes of both chlorhexidine mouthwashes on the peri-implant microbiota and their limited effect in controlling the abundance of oral pathogens indicate that prescription of chlorhexidine mouthwashes for the treatment of peri-implantitis should be carried out with caution. Novel presentations of chlorhexidine with better penetration capacities should be developed, as they could offer enhanced benefits in managing peri-implant diseases. Full article

This research reports ruminal and fecal microbiota composition of lactating dairy cows enrolled in a study aimed at investigating the effects of a fermentation extract derived from Bacillus licheniformis (BLFE), monensin (Rumensin^®; R), and their interactions on feed efficiency (FE, FE = milk yield/DMI). In a completely randomized design, 48 Holstein cows at 108 ± 35 days in milk were matched for parity and assigned to monensin (0 or 17.6 g/kg of DM) and BLFE (0 or 166 mg/kg of DM) in a 2 × 2 factorial arrangement. Treatments were fed daily for 63 d, including a 21 d adaptation period followed by a 42 d measurement period (P2). On d 38 and d 39 of P2, rumen-fluid (RF) and fecal samples were collected. DNA from RF and feces was sequenced using 16S rRNA gene-amplicon sequencing on an Illumina MiSeq platform. Fecal and RF volatile fatty acid (VFA) concentrations were analyzed, and propionate/acetate (P: A) was determined. The BLFE increased milk yield (3.3 kg/d) and FE (1.20 to 1.28), when fed alone rather than with monensin, while monensin increased energy-corrected milk yield (2.5 kg/d, p < 0.05), regardless of the BLFE in the diet. The BLFE tended to increase ruminal Firmicutes/Bacteroidetes (F: B) when fed alone, while alpha and beta diversities remained unmodified. The BLFE increased the abundances of Bifidobacterium (p = 0.02) and Erysipelotrichaceae_UCG-002 (p = 0.01) in RF, whereas monensin increased and decreased the abundances of Oscillospirales_ge (p = 0.02) and an unclassified Clostridia genus (p = 0.03), respectively. The monensin-suppressed Clostridia were negatively associated with ruminal P: A (r = −0.66; p < 0.01) and feed efficiency (r = −0.30; p = 0.04). The BLFE and monensin interactively affected several fecal genera (p < 0.05), but they had negligible or weak correlations with fecal P: A and FE. Overall, the results showed the ability of dietary supplementations of monensin and BLFE to increase milk production performance and FE by modulating ruminal rather than lower-gut microbiota composition, this is predominantly attributed to the ratio between the Firmicutes and Bacteroidetes abundances in lactating dairy cows. Full article