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14 pages, 1763 KB  
Article
Early Gut and Nasal Bacterial Community Profiles Within 48 h of Birth According to Delivery Mode: Findings from a Mexican Cohort
by Bautista-Carbajal Patricia, García-León Miguel Leonardo, Espinosa-Torres Torija Bogart, Hernández-Pérez Brenda, Rodríguez-Bernabé Alma Angélica, Pérez-Gopar Martha Alicia and Wong-Chew Rosa María
Microbiol. Res. 2026, 17(9), 164; https://doi.org/10.3390/microbiolres17090164 (registering DOI) - 22 Aug 2026
Abstract
The earliest gut and nasal bacterial community profiles after birth remain incompletely characterized, particularly when both sites are examined in parallel. We aimed to characterize these profiles according to delivery mode within the first 48 h of life in a Mexican cohort. Meconium [...] Read more.
The earliest gut and nasal bacterial community profiles after birth remain incompletely characterized, particularly when both sites are examined in parallel. We aimed to characterize these profiles according to delivery mode within the first 48 h of life in a Mexican cohort. Meconium and nasal wash samples from 60 neonates (30 vaginal and 30 cesarean deliveries) were analyzed by V3–V4 16S rRNA gene amplicon sequencing on an Illumina MiSeq platform, followed by QIIME 2 processing. All 60 meconium samples yielded analyzable 16S rRNA profiles. Nasal washes yielded analyzable profiles in 10/30 vaginally delivered and 12/30 cesarean-delivered neonates (p = 0.79). No statistically significant differences in alpha diversity were detected by delivery mode in gut samples (observed ASVs, p = 0.842; Shannon index, p = 0.183; Pielou’s evenness, p = 0.121; Faith’s phylogenetic diversity, p = 0.574) or nasal samples (p = 0.356, 0.947, 0.644, and 0.114, respectively). In unadjusted PERMANOVA comparisons, gut community structure differed by delivery mode for Bray–Curtis (p = 0.001), weighted UniFrac (p = 0.021), and unweighted UniFrac (p = 0.013) distances, whereas nasal comparisons were not statistically significant. Traditional ANCOM identified Staphylococcus as the feature with the highest W statistic in cesarean-delivered neonates (W = 65). Descriptive phylum-level profiles were examined across maternal urinary tract infection, premature rupture of membranes, maternal comorbidities, maternal BMI, hours since birth, and recorded antibiotic exposure; these comparisons were not multivariable and cannot exclude residual confounding. Delivery mode was associated with differences in early gut bacterial community structure in this cohort. Nasal findings were inconclusive because only 22 washes yielded analyzable 16S rRNA profiles and the workflow was not optimized to quantify ultra-low-biomass bacterial DNA. These cross-sectional data do not establish persistence, causality, or the timing at which nasal communities become stable. Full article
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24 pages, 5509 KB  
Article
Implantation Outcome-Specific Associations Between Stromal Senescence and the Endometrial Microbiota
by Dimitar Parvanov, Margarita Ruseva, Rumiana Ganeva, Teodora Tihomirova, Maria Handzhiyska, Stela Chapanova, Jinahn Safir, Sofia Koristashevskaya, Ivan Pavlov, Dimitar Metodiev, Blaga Rukova, Georgi Stamenov and Savina Hadjidekova
Microorganisms 2026, 14(9), 1868; https://doi.org/10.3390/microorganisms14091868 (registering DOI) - 22 Aug 2026
Abstract
Endometrial senescence and the endometrial microbiota have both been implicated in the regulation of endometrial receptivity, yet their relationship remains poorly understood. The aim of this study was to investigate associations between p16-positive endometrial cells and microbiota composition during the implantation window and [...] Read more.
Endometrial senescence and the endometrial microbiota have both been implicated in the regulation of endometrial receptivity, yet their relationship remains poorly understood. The aim of this study was to investigate associations between p16-positive endometrial cells and microbiota composition during the implantation window and to determine whether these relationships differ according to implantation outcome. Endometrial senescence was assessed by p16 immunohistochemistry and digital image analysis, whereas microbial composition was characterized by 16S rRNA gene sequencing in endometrial biopsies collected from 68 women prior to undergoing transfer of a single euploid embryo, which was performed within six months of biopsy under the same hormonal preparation protocol. No significant differences in luminal epithelial or stromal p16 abundance were observed according to subsequent implantation outcome. Although senescence was not directly associated with implantation success, stromal p16 expression demonstrated multiple associations with the endometrial microbiota. Increased stromal p16-positivity was associated with lower relative abundance of Lactobacillus and higher abundance of Delftia. Notably, in exploratory subgroup analyses more pronounced associations were observed in women who achieved pregnancy, including a negative correlation between stromal p16 expression and Lactobacillus abundance (ρ = −0.48, p = 0.005) and positive correlation with Delftia abundance (ρ = 0.42, p = 0.016). Species-level analyses revealed implantation outcome-specific associations involving Lactobacillus iners and Limosilactobacillus vaginalis. In addition, stromal p16 expression was associated with differences in microbial co-occurrence networks, indicating broader effects on microbial community organization. Together, these findings suggest that stromal, but not luminal, senescence is closely linked to endometrial microbiota composition and microbial community organization during the window of implantation. The observation that the strongest senescence–microbiota associations occurred in women who subsequently achieved successful implantation supports the hypothesis that coordinated senescence–microbiota relationships may represent a previously underrecognized feature of the receptive endometrial microenvironment. Full article
(This article belongs to the Special Issue Microbiomes in Human Health and Diseases)
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27 pages, 2126 KB  
Article
Process Stability, Methane Yield, and Microbial Community Structure in Two-Stage Co-Digestion of Plant and Animal Substrates Using Real-World Feedstock from an Agricultural Biogas Plant
by Daria Sławczyk, Beata Bień, Przemysław Liczbiński, Estera Baor and Anna Grobelak
Energies 2026, 19(17), 3944; https://doi.org/10.3390/en19173944 (registering DOI) - 22 Aug 2026
Abstract
In the context of the global shift toward sustainable energy systems and circular economy strategies, anaerobic digestion is a well-established biotechnology for the valorisation of organic residues, the production of biogas as a renewable energy carrier, and the generation of nutrient-rich digestate. This [...] Read more.
In the context of the global shift toward sustainable energy systems and circular economy strategies, anaerobic digestion is a well-established biotechnology for the valorisation of organic residues, the production of biogas as a renewable energy carrier, and the generation of nutrient-rich digestate. This study aimed to evaluate the stability and methane yield of a two-stage co-digestion process using a substrate mixture developed based on the actual feedstock composition of a full-scale agricultural biogas plant. The daily feed mixture consisted of maize silage (8.2%), sugar beet pulp (4.9%), cellulose pulp (6.6%), distillery stillage (38.6%), corn syrup (6.4%), cattle slurry (22.5%) and sterilised animal by-products (12.8%). Digestate was recirculated separately as part of the reactor operation. Laboratory-scale experiments were conducted in a two-stage anaerobic digestion system operated at 42 °C and 50 °C. The physicochemical properties of the substrates and digestate were determined, biogas quantity and composition were monitored, and the microbial community structure was assessed using 16S rRNA gene amplicon sequencing. The process remained stable throughout the experimental period, with pH values ranging from 8.23 to 8.53, alkalinity between 2600 and 2940 mg CaCO3/dm3, and a VFAs/alkalinity ratio of 0.17–0.93. Despite ammonium nitrogen concentrations reaching 4346 mg N-NH4+/L, no clear concurrent reduction in gas or methane production was observed. Methane accounted for approximately 70–80% of the biogas produced. The overall specific methane yield reached 346.4 NL CH4 kg−1 VS added. 16S rRNA gene amplicon sequencing revealed a diverse microbial community containing taxa previously associated with hydrolysis, fermentation and syntrophic interactions, including Proteiniphilum and Syntrophaceticus. The results demonstrate stable process performance and methane production in this site-specific laboratory-scale case study based on the feedstock composition and process configuration of a full-scale agricultural biogas plant. Full article
(This article belongs to the Special Issue Waste to Bioenergy: New Technologies and Applications)
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25 pages, 9696 KB  
Article
Distinct Inflammation-Associated Microbiome Signatures in Pediatric Non-IgE-Mediated Food Allergy
by Maria-Teodora Coșoreanu, Gratiela Gradisteanu Pircalabioru, Irina-Oana Lixandru-Petre, Mara-Ioana Ionescu, Andreea Ioan, Eliza-Elena Cinteză and Felicia Galoș
Int. J. Mol. Sci. 2026, 27(16), 7482; https://doi.org/10.3390/ijms27167482 - 21 Aug 2026
Abstract
Non-IgE-mediated food allergy is characterized by delayed gastrointestinal manifestations and the absence of reliable non-invasive biomarkers. Increasing evidence suggests that gut microbiota may contribute to this disease pathogenesis. The aim of this study was to characterize the gut microbiome composition in thirty pediatric [...] Read more.
Non-IgE-mediated food allergy is characterized by delayed gastrointestinal manifestations and the absence of reliable non-invasive biomarkers. Increasing evidence suggests that gut microbiota may contribute to this disease pathogenesis. The aim of this study was to characterize the gut microbiome composition in thirty pediatric patients diagnosed with non-IgE-mediated food allergy, in comparison to fifteen healthy controls children, and to investigate its association with fecal calprotectin, eosinophil-derived neurotoxin (EDN) and IgA. Gut microbiota profiling was performed by 16S rRNA gene sequencing targeting the V3–V4 region. Compared with healthy controls, higher mean relative abundances of Bacteroides, Faecalibacterium, Alistipes, Parabacteroides, and Sutterella were observed in patients. Conversely, healthy children showed higher mean relative abundances of Pseudobutyrivibrio, Roseburia, Bifidobacterium, Collinsella, Clostridium, Eubacterium, Streptococcus, and Barnesiella. Several genera (Escherichia–Shigella, Agathobacter, and Enterococcus/Streptococcus) were detected only in the allergy cohort. Shannon diversity was higher in patients compared to controls and in the subgroups of patients with elevated fecal calprotectin (p = 0.028), previous antibiotic exposure (p = 0.015), and atopic dermatitis (p = 0.021). Stratification according to inflammatory biomarkers identified a distinct inflammatory microbiome endotype characterized by increased fecal calprotectin and EDN together with enrichment of Veillonellaceae and depletion of Bifidobacteriaceae and Lachnospiraceae. Correlation analyses further revealed positive associations between Veillonella abundance and both fecal calprotectin and EDN. These findings suggest that pediatric non-IgE-mediated food allergy is characterized by distinct microbiome–inflammation relationships rather than a single dysbiotic signature. Full article
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15 pages, 27014 KB  
Article
Genetic Variation and Demographic History of Green Weevil Hypomeces pulviger (Herbst, 1795) (Coleoptera: Curculionidae) in Thailand Examined by Mitochondrial DNA Sequences
by Nakorn Pradit, Warayutt Pilap, Chavanut Jaroenchaiwattanachote, Jatupon Saijuntha, Wittaya Tawong, Watee Kongbuntad, Panida Laotongsan, Komgrit Wongpakam, Khamla Inkhavilay, Isara Thanee, Weerachai Saijuntha and Chairat Tantrawatpan
Biology 2026, 15(16), 1442; https://doi.org/10.3390/biology15161442 - 21 Aug 2026
Abstract
The population genetic diversity and demographic history of Hypomeces pulviger in Thailand were examined based on mitochondrial cytochrome c oxidase subunit 1 (CO1) and 16S ribosomal DNA (16S rDNA) sequence data. A total of 171 and 104 individuals from multiple populations [...] Read more.
The population genetic diversity and demographic history of Hypomeces pulviger in Thailand were examined based on mitochondrial cytochrome c oxidase subunit 1 (CO1) and 16S ribosomal DNA (16S rDNA) sequence data. A total of 171 and 104 individuals from multiple populations were analyzed using CO1 and 16S rDNA sequences, respectively. The CO1 sequence dataset revealed high haplotype diversity (Hd = 0.999) and moderate nucleotide diversity (Nd = 0.0323), whereas the 16S rDNA showed lower diversity (Hd = 0.750, Nd = 0.0026). Population structure analyses showed low to moderate differentiation in CO1 sequences with a significant isolation-by-distance pattern, suggesting distance-limited gene flow, while 16S rDNA sequences showed weaker structure. Neutrality tests and mismatch distribution analyses supported a recent population expansion, as indicated by significantly negative Fu’s Fs and a unimodal distribution. Haplotype network and phylogenetic analyses further demonstrated greater resolution in the CO1 gene compared to the 16S rRNA gene. Collectively, H. pulviger populations in Thailand are genetically diverse, connected, and expanding, likely facilitated by both natural dispersal and agricultural activities. These findings provide important insights for understanding pest dynamics and developing effective management strategies. Full article
(This article belongs to the Special Issue Research Advances on Insect Biodiversity and Ecosystem Function)
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26 pages, 17475 KB  
Article
Unraveling the Microbial Associations of Volatile Flavor Profiles in Spontaneously Fermented Camel Milk from Three Regions of Xinjiang, China
by Yating Wu, He Chen, Fulan Wang, Henigul Osman, Shiqi Zhang, Hongyan Zhang, Shuai Wang, Nan Zheng and Yankun Zhao
Foods 2026, 15(16), 2937; https://doi.org/10.3390/foods15162937 - 21 Aug 2026
Abstract
Spontaneously fermented camel milk from Xinjiang is valued for its nutrition but faces quality inconsistency due to complex microbial ecosystems. This study investigated how regional microbial communities correlate with volatile flavor profiles. Nine samples from three distinct areas—Dabancheng, Hami, and Keping—were analyzed using [...] Read more.
Spontaneously fermented camel milk from Xinjiang is valued for its nutrition but faces quality inconsistency due to complex microbial ecosystems. This study investigated how regional microbial communities correlate with volatile flavor profiles. Nine samples from three distinct areas—Dabancheng, Hami, and Keping—were analyzed using bacterial 16S rRNA gene and fungal ITS region amplicon sequencing combined with comprehensive two-dimensional gas chromatography–time-of-flight mass spectrometry (GC×GC-TOF MS). Bacterial communities were dominated by Firmicutes and Proteobacteria, while Ascomycota and Basidiomycota prevailed among fungi. Dominant genera varied by region: Lactobacillus and Dekkera in Dabancheng; Lactobacillus and Dipodascus in Hami; Lactococcus and Cutaneotrichosporon in Keping. Flavor profiles also diverged, with Dabancheng being rich in esters, alcohols, and ketones; Hami featuring hydrocarbons and alcohols; and Keping containing elevated hydrocarbons, alcohols, and esters. Key statistical associations were identified: Lactobacillus, Rahnella, and Acetobacter were positively associated with propene and 3-decyn-2-ol (VIP > 1.0, |r| > 0.8), while Pseudomonas, Lactococcus, and Klebsiella showed negative correlations with vinyl n-caproate. These findings reveal statistical associations between geographic origin, specific microbial taxa, and flavor attributes, providing a scientific foundation that may inform future efforts toward developing targeted starter cultures pending microbial isolation and functional validation. Full article
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16 pages, 429 KB  
Article
Molecular Detection of Blastocystis ST2 and ST4 and Exploratory 16S rRNA Gene Community Profiles in a 12-Week Dairy-Intervention Pilot Study
by Panayiota Tsokkou, Chad Schou, Catherine O’Dowd Phanis, Kyriacos A. Hasapis, Stella A. Nicolaou, Eleni P. Andreou and Evelina Charidemou
Microorganisms 2026, 14(8), 1860; https://doi.org/10.3390/microorganisms14081860 - 21 Aug 2026
Viewed by 23
Abstract
Blastocystis is a common intestinal protist whose clinical and ecological significance remains uncertain. This secondary exploratory analysis examined Blastocystis PCR detection in paired baseline and Week 12 stool samples collected during a randomized pilot intervention comparing daily goat-milk and cow-milk consumption. Nineteen healthy [...] Read more.
Blastocystis is a common intestinal protist whose clinical and ecological significance remains uncertain. This secondary exploratory analysis examined Blastocystis PCR detection in paired baseline and Week 12 stool samples collected during a randomized pilot intervention comparing daily goat-milk and cow-milk consumption. Nineteen healthy Greek Cypriot adults provided 38 stool samples. Stool DNA was screened by PCR targeting a partial 18S rRNA gene fragment, and positive amplicons were Sanger sequenced for subtype assignment. Blastocystis was detected at both time points in 3 of 19 participants (15.8%); ST2 was identified in two participants and ST4 in one. No Cryptosporidium spp. or Giardia duodenalis PCR-positive samples were identified. In exploratory 16S rRNA gene analyses, median Shannon diversity index was 6.10 versus 4.85 at baseline (p = 0.171) and 5.67 versus 4.17 at Week 12 (p = 0.085) in repeat-detection and no-detection groups, respectively. Bray–Curtis PERMANOVA was non-significant at baseline (R2 = 0.0946, p = 0.0815) and Week 12 (R2 = 0.0597, p = 0.8576); Aitchison-distance sensitivity analyses were likewise non-significant (p = 0.0547 and p = 0.3232, respectively). No selected genus-level comparison met the false-discovery-rate-adjusted threshold. The three-participant repeat-detection subgroup precluded reliable analysis of dairy-arm effects, subtype-specific differences, cardiometabolic outcomes, or bacterial-community associations. In this small pilot cohort, ST2 and ST4 were identified in paired baseline and Week 12 stool samples from three healthy adults, providing molecular evidence of repeat detection over the sampled interval. Larger studies with more frequent sampling, quantitative assays, and adequately powered, prespecified analyses are needed to investigate the temporal dynamics and host-associated correlates of Blastocystis detection. Full article
(This article belongs to the Section Gut Microbiota)
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29 pages, 4042 KB  
Article
Tissue-Specific Bioactive Metabolites and Antioxidant Activity in Minicitrus (Fortunella hindsii) and Responses to a Fruit-Associated Weissella Strain
by Han Yang, Manxi Wu, Xinlin Huang, Hujing Cao, Jinping Cao, Chongde Sun and Yue Wang
Antioxidants 2026, 15(8), 1037; https://doi.org/10.3390/antiox15081037 - 20 Aug 2026
Viewed by 74
Abstract
Minicitrus (Fortunella hindsii) is a wild kumquat with potential nutritional and medicinal value, but its tissue-specific bioactive metabolites, antioxidant activity, and endophytes remain poorly characterized. Here, we integrated LC-MS profiling, HPLC quantification, chemical and cellular antioxidant assays, 16S rRNA gene sequencing, [...] Read more.
Minicitrus (Fortunella hindsii) is a wild kumquat with potential nutritional and medicinal value, but its tissue-specific bioactive metabolites, antioxidant activity, and endophytes remain poorly characterized. Here, we integrated LC-MS profiling, HPLC quantification, chemical and cellular antioxidant assays, 16S rRNA gene sequencing, bacterial isolation, and treatment experiments across five tissues. Among all the metabolites determined by HPLC, 13 were quantified using authentic standards and 24 were semi-quantified as linarin equivalents. Leaves, stems, and fruits accumulated abundant flavone glycosides, with phloretin-3′,5′-di-C-glucoside reaching 1823.19 ± 278.71 μg/g FW in leaves and 847.11 ± 27.28 μg/g FW in fruits, while roots and seeds showed distinct coumarin- and furanocoumarin-rich profiles, respectively. Leaf extracts showed the strongest chemical and cellular antioxidant activities, followed by fruit extracts. Isoorientin 2″-O-rhamnoside and diosmin exhibited strong chemical antioxidant capacity, and several flavone glycosides showed protective effects in cellular assays. Endophytic bacterial communities differed markedly among tissues, with fruit harboring a distinct community dominated by Weissella and Pantoea, which accounted for 65.64% and 19.13% of the relative abundance, respectively. Among two culturable fruit-associated isolates, Weissella sp. SJG-1 treatment was associated with 32.92–104.45% increases in six HPLC-quantified metabolites and higher antioxidant activity of fruit extracts. These findings highlight minicitrus as a source of bioactive metabolites and suggest a potential association between fruit-associated bacteria and fruit functional properties. Full article
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26 pages, 6076 KB  
Article
Microbial Diversity and Hydrocarbon-Oxidizing Bacteria in Coastal Waters and Sands Contaminated by the Fuel Oil Spill in the Black Sea
by Ekaterina M. Semenova, Alexey P. Ershov, Tamara L. Babich, Diyana S. Sokolova, Nataliya G. Loiko, Elena A. Bakay, Ekaterina S. Kazak and Tamara N. Nazina
Microorganisms 2026, 14(8), 1856; https://doi.org/10.3390/microorganisms14081856 - 20 Aug 2026
Viewed by 189
Abstract
In 2024, an accident involving two tankers in the Kerch Strait resulted in the release of approximately 2400 tons of fuel oil into the Black Sea, causing significant contamination of seawater and the coastal zone. This study presents the first microbiological and molecular–ecological [...] Read more.
In 2024, an accident involving two tankers in the Kerch Strait resulted in the release of approximately 2400 tons of fuel oil into the Black Sea, causing significant contamination of seawater and the coastal zone. This study presents the first microbiological and molecular–ecological assessment of prokaryotic community composition and hydrocarbon-oxidizing bacteria (HOB) in coastal seawater and sand near Anapa (Russian Federation) following the spill. The taxonomic composition of nine samples was analyzed using high-throughput sequencing of 16S rRNA genes (V3–V4 regions), identifying Bacteria as the dominant domain (85.3–99.8%). In seawater samples, bacteria of the phyla Pseudomonadota, Cyanobacteriota, and Bacteroidota and archaea of the phyla Thermoplasmatota and Crenarchaeota predominated. Eighteen aerobic bacterial strains, including members of the genera Shewanella, Pseudoalteromonas, Halopseudomonas, Marinomonas, Pseudomonas, Vibrio, Alcanivorax, Ectopseudomonas, Nitratireductor, and Echinicola, were isolated from the zone of fuel oil spill. Several isolates demonstrated heavy oil degradation and biosurfactant production. Screening of collection strains isolated from other habitats revealed that Rhodococcus erythropolis TG65 and Marinobacter lutaoensis Pd1 and Pd2 degraded 92–94% of fuel oil n-alkanes. Elevated dissolved iron concentrations in the seawater indicate the possibility of a metabolic coupling between hydrocarbon oxidation and microbial iron reduction, mediated by indigenous Shewanella and Pseudomonas species. These findings indicate that indigenous HOB may contribute to the natural attenuation of aliphatic hydrocarbons in fuel oil. Full article
(This article belongs to the Special Issue Microbiomes in the Oil Supply Chain: Applications and Drawbacks)
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18 pages, 18980 KB  
Article
Vegetation-Driven Differentiation of Soil Bacterial and Fungal Diversity: Distinct Edaphic Determinants in Atractylodes japonica Cultivation Systems
by Zehao Gan, Ruitong Du, Zhipeng Xu, Xin Fu, Yunwei Liu, Xiangquan Li and Zhibin Wang
Diversity 2026, 18(8), 498; https://doi.org/10.3390/d18080498 - 20 Aug 2026
Viewed by 144
Abstract
As key drivers of soil biogeochemical cycles, soil microbial communities play essential roles in maintaining soil fertility, nutrient cycling, and plant growth. In this study, high-throughput sequencing of 16S rRNA and ITS genes was used to investigate the diversity, the composition, and the [...] Read more.
As key drivers of soil biogeochemical cycles, soil microbial communities play essential roles in maintaining soil fertility, nutrient cycling, and plant growth. In this study, high-throughput sequencing of 16S rRNA and ITS genes was used to investigate the diversity, the composition, and the driving factors of bacterial and fungal communities in bulk soils across four soil groups collected from different vegetation covers (forest soil (FS), soybean field (PGS), and two Atractylodes japonica cultivation soils (ALO and ALR)) under identical climatic conditions. The results showed that the bacterial α-diversity remained stable across all the vegetation types, whereas the fungal α-diversity and richness were more sensitive to the vegetation type, with the PGS generally exhibiting lower Shannon and Chao1 indices. The β-diversity analysis revealed significant differences in the microbial community structure among the vegetation types, with a stronger effect on fungi (R2 = 0.737, p = 0.001) than on bacteria (R2 = 0.493, p = 0.001). At the phylum and genus levels, the fungal communities displayed more pronounced shifts than the bacterial communities, which remained relatively stable. A redundancy analysis indicated that the soil chemical properties significantly shaped the microbial community structure (p = 0.002). The microbial communities in the A. japonica soils (ALO and ALR) were primarily driven by pH, available phosphorus, and available potassium, while the FS and PGS communities were more strongly influenced by soil organic carbon, total nitrogen, and nitrogen forms (NH4+-N and NO3-N). The Spearman correlation and functional prediction analyses further confirmed that the key soil factors differentially regulated the abundance and ecological functions of the dominant microbial taxa. These findings demonstrate the vegetation-specific assembly of soil microbial communities and highlight the distinct edaphic drivers associated with A. japonica cultivation, providing a scientific basis for soil health management and the sustainable cultivation of this medicinal plant. Full article
(This article belongs to the Special Issue Microbial Diversity in Different Environments)
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13 pages, 932 KB  
Article
Distribution and Abundance of the Tick-Borne Piroplasm Theileria cervi Parasitizing White-Tailed Deer (Odocoileus virginianus) in Massachusetts
by Jacqueline O. Borges, Patrick Pearson, Guang Xu, Nolan Stamborski, Patrick Roden-Reynolds, Martin J. R. Feehan and Stephen M. Rich
Pathogens 2026, 15(8), 869; https://doi.org/10.3390/pathogens15080869 - 20 Aug 2026
Viewed by 133
Abstract
Pathogen surveillance contributes to the prediction of outbreaks and implementation of strategies to minimize disease transmission. White-tailed deer (Odocoileus virginianus) host important disease vectors and often support the proliferation of associated pathogens. Such vectors include ticks: hematophagous acarids that facilitate pathogen [...] Read more.
Pathogen surveillance contributes to the prediction of outbreaks and implementation of strategies to minimize disease transmission. White-tailed deer (Odocoileus virginianus) host important disease vectors and often support the proliferation of associated pathogens. Such vectors include ticks: hematophagous acarids that facilitate pathogen transmission between animals through blood feeding. Piroplasmida, an order of blood-borne protozoa including Babesia and Theileria, exploits this feeding to infect definitive hosts. Accordingly, we investigated the prevalence of Theileria cervi infections in Massachusetts white-tailed deer. Conventional polymerase chain reaction (PCR) was used to detect parasite gene fragments encoding the small ribosomal subunit (18S rRNA). Confirmation of species identity was determined by Oxford nanopore sequencing and Sequencher analysis. This revealed a 32.6% prevalence of T. cervi across Massachusetts. Whilst surveillance of deer blood uncovers parasite abundance and distribution, inversely, this allows us to also monitor vector populations. As Amblyomma americanum is the only vector implicated in the transmission of T. cervi, the detection of T. cervi in regions without anticipated Amblyomma presence may indicate expansion of vector populations. These findings provide valuable insights into the prevalence and ecology of this piroplasm and its vector, with possible implications for veterinary and public health. Full article
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17 pages, 11487 KB  
Article
Integrated Analysis of Multiple Databases Identifies Tissue Inhibitor of Metalloproteinase 1 Expression and Its Association with the Immune Microenvironment in Colorectal Cancer
by Yun Xie, Jun Li, Zuwei Yan and Wenguang Zhang
Genes 2026, 17(8), 977; https://doi.org/10.3390/genes17080977 - 20 Aug 2026
Viewed by 181
Abstract
Background: In recent decades, the incidence of colorectal cancer (CRC) has been rising worldwide. CRC ranks second in cancer-related mortality. The identification of reliable biomarkers for early diagnosis and prognosis prediction, along with a deeper understanding of the underlying molecular events, holds substantial [...] Read more.
Background: In recent decades, the incidence of colorectal cancer (CRC) has been rising worldwide. CRC ranks second in cancer-related mortality. The identification of reliable biomarkers for early diagnosis and prognosis prediction, along with a deeper understanding of the underlying molecular events, holds substantial promise for improving patient outcomes. The tissue inhibitor of the metalloproteinase 1 (TIMP1) gene is overexpressed in various gastrointestinal malignancies and contributes to tumor progression. However, its role in regulating the CRC tumor immune microenvironment (TIME) and its potential as a clinically actionable prognostic biomarker remain unclear. Methods: To probe how TIMP1 acts as a prognosis-related candidate biomarker in colorectal carcinoma, TCGA-derived datasets were adopted to conduct Kaplan–Meier survival assessment. We also investigated the connection between the expression abundance of TIMP1 and the infiltration of immune populations and intratumoral lymphocytes; furthermore, immune checkpoint-related genes were systematically assessed across multiple tumor types via the TISIDB and TIMER2.0 platforms, with particular emphasis on CRC. We adopted the ESTIMATE scoring system to figure out how TIMP1 gene expression correlates with the phenotypic properties of the colorectal-cancer TIME. We relied on the limma toolkit for the screening of differential transcripts from high-TIMP1 and low-TIMP1 cohorts. Enrichment assessments covering Gene Ontology terms and Kyoto Encyclopedia of Genes and Genomes entries were then carried out to predict the potential biological pathways associated with TIMP1. We constructed the protein–protein interaction map for TIMP1-interacting partners via the STRING repository. To further explore TIMP1-correlated genes, we performed Venn diagram intersection analysis combined with Spearman’s correlation test. Finally, quantitative reverse-transcription PCR was then implemented to detect TIMP1 messenger-RNA abundance inside the RKO colorectal carcinoma cell line as well as normal colonic epithelial CCD-18Co cells, which offered in vitro experimental verification for our bioinformatic outcomes. Results: According to outcome data, TIMP1 transcripts were markedly up-regulated in CRC specimens and cell lines relative to normal samples. Elevated TIMP1 expression served as a poor-prognosis indicator for overall survival (hazard ratio [HR] = 0.43, 95% confidence interval [CI] = 0.29–0.64, p < 0.001) and disease-specific survival (HR = 0.39, 95% CI = 0.22–0.68, p = 0.001) among colorectal-carcinoma patients. TIMP1-high and TIMP1-low groups exhibited notable differences in immune cell infiltration (CD8+ T, macrophage, mast, neutrophil, B, monocyte, dendritic, and CD4+ T cells). TIMP1 expression was also significantly correlated with tumor-infiltrating lymphocytes, key immune checkpoint genes (e.g., CD274 [PD-L1] and CTLA4), and immunomodulatory chemokines (e.g., CCL3 and CCL5). Twelve TIMP1-interacting DEGs were selected: COL5A1, FN1, PRG4, and a cluster of nine MMPs (MMP1/2/3/7/8/9/11/13/14), all of which showed significant positive correlations with TIMP1 (r = 0.31–0.63, all p < 0.001). Conclusions: TIMP1 expression correlates with features of the tumor immune microenvironment and extracellular matrix remodeling in CRC, suggesting that TIMP1 shows potential as a candidate biomarker. However, its potential as a therapeutic target warrants further experimental investigation. Full article
(This article belongs to the Section Human Genomics and Genetic Diseases)
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19 pages, 14335 KB  
Article
Isolation, Identification, Drug Sensitivity, Pathogenicity and Genomic Analysis of Vibrio mimicus from Pelteobagrus fulvidraco
by Shao Peng, Kai Zhang, Zichun Zhou, Zhi Meng, Chunyu Zhang, Wenjing Li, Tongpu Guo, Lei Tang, Wei Xu, Wenli Zhou, Xuying Jia and Jinwei Gao
Microorganisms 2026, 14(8), 1842; https://doi.org/10.3390/microorganisms14081842 - 19 Aug 2026
Viewed by 142
Abstract
In this study, pathogenic bacteria were isolated from diseased Pelteobagrus fulvidraco collected from a yellow catfish farm in northern China. The recovered isolate was subjected to Gram staining, transmission electron microscopy observation, 16S rRNA gene sequencing and whole-genome sequencing, followed by systematic analyses [...] Read more.
In this study, pathogenic bacteria were isolated from diseased Pelteobagrus fulvidraco collected from a yellow catfish farm in northern China. The recovered isolate was subjected to Gram staining, transmission electron microscopy observation, 16S rRNA gene sequencing and whole-genome sequencing, followed by systematic analyses of its antimicrobial resistance, pathogenicity and genomic characteristics. Combined with artificial infection assays and multiple comparative verifications, the pathogen was identified as Vibrio mimicus. Clinical observation of naturally infected fish revealed that superficial skin ulcers of varying severity constituted the hallmark clinical sign of this disease. Genomic analysis uncovered major virulence-related genes, including tlh, vmh and tdh, as well as key antimicrobial resistance genes such as crp and ugd. Artificial infection trials confirmed the strong virulence of this isolate against P. fulvidraco, with distinct clinical manifestations triggered by injections of bacterial suspensions at different concentrations. Mortality was first observed in the high-dose group at 2–3 days post-injection, yet no cutaneous ulceration was detected at this stage. The peak incidence and mortality occurred between 3 and 7 days post-challenge, with diseased fish exhibiting lesions identical to those seen in naturally infected individuals. The median lethal dose (LD50) of the isolate was determined to be 1.72 × 105 CFU/mL. Growth gradient assays across varying temperatures and pH values identified the optimal culture conditions for this strain: 33 °C and pH 8.5. Antimicrobial susceptibility testing demonstrated that the isolate was highly susceptible to piperacillin, norfloxacin, roxithromycin, azithromycin, furazolidone, ceftriaxone and tetracycline, whereas it displayed high-level resistance to compound sulfamethoxazole and clindamycin. Collectively, this work lays a scientific foundation for the isolation, identification and comprehensive research of Vibrio mimicus-induced ulcerative disease in yellow catfish. Full article
(This article belongs to the Special Issue Research on Bacterial Pathogens in Fish)
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16 pages, 4318 KB  
Article
Age-Related and Lifestyle-Related Differences in Gut Microbiota Composition Among Community-Dwelling Adults
by Siyu Li, Xuefei Zhao, Minjia Chen, Yi Cheng, Qiwei Wu, Yangyang Feng, Ailin Yi, Lu Chen, Yuting Tian and Yanling Wei
Microorganisms 2026, 14(8), 1841; https://doi.org/10.3390/microorganisms14081841 - 19 Aug 2026
Viewed by 185
Abstract
As global aging accelerates, identifying age- and lifestyle-associated gut microbiota alterations has become critical for understanding healthy aging and microbiota-targeted interventions. To explore the associations of age and lifestyle factors with gut microbiota profiles in community-dwelling adults, 159 Chongqing residents were divided into [...] Read more.
As global aging accelerates, identifying age- and lifestyle-associated gut microbiota alterations has become critical for understanding healthy aging and microbiota-targeted interventions. To explore the associations of age and lifestyle factors with gut microbiota profiles in community-dwelling adults, 159 Chongqing residents were divided into young (18–39, n = 44), middle-aged (40–59, n = 71) and elderly (60–89, n = 44) groups. Fecal samples were analyzed by 16S rRNA gene sequencing, and lifestyle factors were assessed using a study-specific structured questionnaire. The Shannon index differed significantly between the young and middle-aged groups (p < 0.05), whereas other α-diversity and β-diversity analyses showed no significant differences. Age-related shift trends included decreased Bacillota and increased abundance of Bacteroidota. Young adults were enriched in Parasutterella, the [Eubacterium] ventriosum group and Anaerostipes; middle-aged adults were enriched in Clostridium sensu stricto 4, Clostridium sensu stricto 1 and Holdemanella; and elderly adults were enriched in Prevotellaceae UCG-004, Helicobacter, Lactobacillus, Streptococcus and Fusobacterium. Lifestyle factors were independently associated with specific microbial signatures, including tea-related enrichment of Catenibacterium and Escherichia–Shigella, exercise-related enrichment of Dialister and Bavariicoccus, and milk-related enrichment of Bacillus and Klebsiella (formerly Raoultella). Overall, these findings provide population-based evidence linking age and lifestyle factors with gut microbial profiles and may inform microbiota-targeted strategies for healthy aging. Full article
(This article belongs to the Special Issue Fecal Microbiota Transplantation in Humans and Animals)
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17 pages, 2730 KB  
Article
Variation in Soil Bacterial and Fungal Diversity, Community Composition, and Co-Occurrence Patterns Across Nearshore Islands in the Northern South China Sea
by Jian Gong, Yechen Qiao, Rui Pan, Hu Du, Xionghui Liao and Wanxia Peng
Microorganisms 2026, 14(8), 1838; https://doi.org/10.3390/microorganisms14081838 - 19 Aug 2026
Viewed by 159
Abstract
Soil microbial biogeography on nearshore islands remains less well understood than that on remote archipelagos, particularly when bacterial and fungal diversity, community composition, and co-occurrence associations are evaluated together. We characterized bacterial 16S rRNA gene and fungal ITS communities in 36 topsoil samples [...] Read more.
Soil microbial biogeography on nearshore islands remains less well understood than that on remote archipelagos, particularly when bacterial and fungal diversity, community composition, and co-occurrence associations are evaluated together. We characterized bacterial 16S rRNA gene and fungal ITS communities in 36 topsoil samples collected from five nearshore islands in the northern South China Sea and examined their associations with plant diversity, soil physicochemical properties, and climatic and geographic conditions. Bacterial Shannon diversity, ACE richness, and Simpson diversity differed significantly among islands, as did fungal ACE richness, whereas fungal Shannon and Simpson diversity showed no significant differences. Bray–Curtis-based analyses revealed island-associated differentiation in bacterial community composition and fungal community composition, although multivariate dispersion also differed among islands. Sample-level subnetworks derived from an integrated co-occurrence network showed that the number of bacteria–bacteria edges differed significantly among islands, whereas the numbers of bacteria–fungi and fungi–fungi edges did not. Exploratory Spearman correlation analyses and variation partitioning indicated that microbial properties were more broadly associated with soil physicochemical properties and climatic–geographic conditions than with plant diversity. By evaluating both microbial kingdoms within the same field campaign, this study identifies partly distinct bacterial and fungal biogeographic and co-occurrence patterns and provides a baseline for future microbial biodiversity monitoring on nearshore islands. Full article
(This article belongs to the Special Issue Soil Microbial Carbon/Nitrogen/Phosphorus Cycling: 2nd Edition)
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