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17 pages, 1802 KiB  
Article
Longitudinal Profiling of the Human Milk Microbiome from Birth to 12 Months Reveals Overall Stability and Selective Taxa-Level Variation
by Ruomei Xu, Zoya Gridneva, Matthew S. Payne, Mark P. Nicol, Ali S. Cheema, Donna T. Geddes and Lisa F. Stinson
Microorganisms 2025, 13(8), 1830; https://doi.org/10.3390/microorganisms13081830 - 5 Aug 2025
Abstract
Human milk bacteria contribute to gut microbiome establishment in breastfed infants. Although breastfeeding is recommended throughout infancy, temporal variation in the milk microbiome—particularly beyond solid food introduction—remains understudied. We analyzed 539 milk samples from 83 mother–infant dyads between 1 week and 12 months [...] Read more.
Human milk bacteria contribute to gut microbiome establishment in breastfed infants. Although breastfeeding is recommended throughout infancy, temporal variation in the milk microbiome—particularly beyond solid food introduction—remains understudied. We analyzed 539 milk samples from 83 mother–infant dyads between 1 week and 12 months postpartum using full-length 16S rRNA gene sequencing. The microbiota was dominated by Streptococcus (34%), Cutibacterium (12%), and Staphylococcus (9%), with marked inter-individual variation. Microbiome profiles remained largely stable across lactation, with only six taxa showing temporal fluctuations, including increases in typical oral bacteria such as Streptococcus salivarius, Streptococcus lactarius, Rothia mucilaginosa, and Granulicatella adiacens. Richness and evenness were higher at 1 week compared to 1 month postpartum (p = 0.00003 and p = 0.007, respectively), then stabilized. Beta diversity also remained stable over time. Maternal pre-pregnancy BMI was positively associated with Gemella haemolysans (p = 0.016), while Haemophilus parainfluenzae was more abundant in milk from mothers with allergies (p = 0.003) and those who gave birth in autumn or winter (p = 0.006). The introduction of solid food was linked to minor taxonomic shifts. Overall, the milk microbiome remained robustly stable over the first year of lactation, with limited but notable fluctuations in specific taxa. This study supports the role of human milk as a consistent microbial source for infants and identifies maternal BMI, allergy status, and birth season as key variables warranting further investigation. Full article
(This article belongs to the Section Microbiomes)
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20 pages, 1773 KiB  
Article
Make Acetylcholine Great Again! Australian Skinks Evolved Multiple Neurotoxin-Proof Nicotinic Acetylcholine Receptors in Defiance of Snake Venom
by Uthpala Chandrasekara, Marco Mancuso, Glenn Shea, Lee Jones, Jacek Kwiatkowski, Dane Trembath, Abhinandan Chowdhury, Terry Bertozzi, Michael G. Gardner, Conrad J. Hoskin, Christina N. Zdenek and Bryan G. Fry
Int. J. Mol. Sci. 2025, 26(15), 7510; https://doi.org/10.3390/ijms26157510 - 4 Aug 2025
Viewed by 689
Abstract
Many vertebrates have evolved resistance to snake venom as a result of coevolutionary chemical arms races. In Australian skinks (family Scincidae), who often encounter venomous elapid snakes, the frequency, diversity, and molecular basis of venom resistance have been unexplored. This study investigated the [...] Read more.
Many vertebrates have evolved resistance to snake venom as a result of coevolutionary chemical arms races. In Australian skinks (family Scincidae), who often encounter venomous elapid snakes, the frequency, diversity, and molecular basis of venom resistance have been unexplored. This study investigated the evolution of neurotoxin resistance in Australian skinks, focusing on mutations in the muscle nicotinic acetylcholine receptor (nAChR) α1 subunit’s orthosteric site that prevent pathophysiological binding by α-neurotoxins. We sampled a broad taxonomic range of Australian skinks and sequenced the nAChR α1 subunit gene. Key resistance-conferring mutations at the toxin-binding site (N-glycosylation motifs, proline substitutions, arginine insertions, changes in the electrochemical state of the receptor, and novel cysteines) were identified and mapped onto the skink organismal phylogeny. Comparisons with other venom-resistant taxa (amphibians, mammals, and reptiles) were performed, and structural modelling and binding assays were used to evaluate the impact of these mutations. Multiple independent origins of α-neurotoxin resistance were found across diverse skink lineages. Thirteen lineages evolved at least one resistance motif and twelve additional motifs evolved within these lineages, for a total of twenty-five times of α-neurotoxic venoms resistance. These changes sterically or electrostatically inhibit neurotoxin binding. Convergent mutations at the orthosteric site include the introduction of N-linked glycosylation sites previously known from animals as diverse as cobras and mongooses. However, an arginine (R) substitution at position 187 was also shown to have evolved on multiple occasions in Australian skinks, a modification previously shown to be responsible for the Honey Badger’s iconic resistance to cobra venom. Functional testing confirmed this mode of resistance in skinks. Our findings reveal that venom resistance has evolved extensively and convergently in Australian skinks through repeated molecular adaptations of the nAChR in response to the enormous selection pressure exerted by elapid snakes subsequent to their arrival and continent-wide dispersal in Australia. These toxicological findings highlight a remarkable example of convergent evolution across vertebrates and provide insight into the adaptive significance of toxin resistance in snake–lizard ecological interactions. Full article
(This article belongs to the Section Biochemistry)
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8 pages, 405 KiB  
Brief Report
Characterization of DNA Viruses in Hindgut Contents of Protaetia brevitarsis Larvae
by Jean Geung Min, Namkyong Min, Binh T. Nguyen, Rochelle A. Flores and Dongjean Yim
Insects 2025, 16(8), 800; https://doi.org/10.3390/insects16080800 - 1 Aug 2025
Viewed by 264
Abstract
The scarab species Protaetia brevitarsis, an edible insect, has been used in traditional medicine, as animal feed, and for converting agricultural organic wastes into biofertilizer. The intestinal tract, which contains a diverse array of microbiota, including viruses, plays a critical role in [...] Read more.
The scarab species Protaetia brevitarsis, an edible insect, has been used in traditional medicine, as animal feed, and for converting agricultural organic wastes into biofertilizer. The intestinal tract, which contains a diverse array of microbiota, including viruses, plays a critical role in animal health and homeostasis. We previously conducted a comparative analysis of the gut microbiota of third-instar larvae of P. brevitarsis obtained from five different farms and found significant differences in the composition of the gut bacterial microbiota between farms. To better understand the gut microbiota, the composition of DNA viruses in the hindgut contents of P. brevitarsis larvae obtained from five farms was investigated using metagenomic sequencing in this study. The β-diversity was significantly different between metagenomic data obtained from the five farms (PERMANOVA, pseudo-F = 46.95, p = 0.002). Family-based taxonomic analysis indicated that the relative abundance of viruses in the gut overall metagenome varied significantly between farms, with viral reads comprising approximately 41.2%, 15.0%, 4.3%, 4.0%, and 1.6% of metagenomic sequences from the farms Tohamsan gumbengi farm (TO), Secomnalagum gumbengi (IS), Gumbengi brothers (BR), Kyungpook farm (KB), and Jhbio (JH), respectively. More than 98% of the DNA viruses in the hindgut were bacteriophages, mainly belonging to the Siphoviridae family. At the species level, Phage Min1, infecting the genus Microbacterium, was detected in all farms, and it was the most abundant bacteriophage in intestinal microbiota, with a prevalence of 0.9% to 29.09%. The detected eukaryotic DNA viruses accounted for 0.01% to 0.06% of the intestinal microbiota and showed little or no relationship with insect viruses. Therefore, they most likely originated from contaminated feed or soil. These results suggest that the condition of substrates used as feed is more important than genetic factors in shaping the intestinal viral microbiota of P. brevitarsis larvae. These results can be used as reference data for understanding the hindgut microbiota of P. brevitarsis larvae and, more generally, the gut virome of insects. Full article
(This article belongs to the Topic Diversity of Insect-Associated Microorganisms)
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36 pages, 3621 KiB  
Review
Harnessing Molecular Phylogeny and Chemometrics for Taxonomic Validation of Korean Aromatic Plants: Integrating Genomics with Practical Applications
by Adnan Amin and Seonjoo Park
Plants 2025, 14(15), 2364; https://doi.org/10.3390/plants14152364 - 1 Aug 2025
Viewed by 365
Abstract
Plant genetics and chemotaxonomic analysis are considered key parameters in understanding evolution, plant diversity and adaptation. Korean Peninsula has a unique biogeographical landscape that supports various aromatic plant species, each with considerable ecological, ethnobotanical, and pharmacological significance. This review aims to provide a [...] Read more.
Plant genetics and chemotaxonomic analysis are considered key parameters in understanding evolution, plant diversity and adaptation. Korean Peninsula has a unique biogeographical landscape that supports various aromatic plant species, each with considerable ecological, ethnobotanical, and pharmacological significance. This review aims to provide a comprehensive overview of the chemotaxonomic traits, biological activities, phylogenetic relationships and potential applications of Korean aromatic plants, highlighting their significance in more accurate identification. Chemotaxonomic investigations employing techniques such as gas chromatography mass spectrometry, high-performance liquid chromatography, and nuclear magnetic resonance spectroscopy have enabled the identification of essential oils and specialized metabolites that serve as valuable taxonomic and diagnostic markers. These chemical traits play essential roles in species delimitation and in clarifying interspecific variation. The biological activities of selected taxa are reviewed, with emphasis on antimicrobial, antioxidant, anti-inflammatory, and cytotoxic effects, supported by bioassay-guided fractionation and compound isolation. In parallel, recent advances in phylogenetic reconstruction employing DNA barcoding, internal transcribed spacer regions, and chloroplast genes such as rbcL and matK are examined for their role in clarifying taxonomic uncertainties and inferring evolutionary lineages. Overall, the search period was from year 2001 to 2025 and total of 268 records were included in the study. By integrating phytochemical profiling, pharmacological evidence, and molecular systematics, this review highlights the multifaceted significance of Korean endemic aromatic plants. The conclusion highlights the importance of multidisciplinary approaches including metabolomics and phylogenomics in advancing our understanding of species diversity, evolutionary adaptation, and potential applications. Future research directions are proposed to support conservation efforts. Full article
(This article belongs to the Special Issue Applications of Bioinformatics in Plant Science)
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17 pages, 1908 KiB  
Article
BDE-47 Disrupts Gut Microbiota and Exacerbates Prediabetic Conditions in Mice: Therapeutic Potential of Grape Exosomes and Antioxidants
by Zaoling Liu, Fang Cao, Aerna Qiayimaerdan, Nilupaer Aisikaer, Zulipiya Zunong, Xiaodie Ma and Yale Yu
Toxics 2025, 13(8), 640; https://doi.org/10.3390/toxics13080640 - 29 Jul 2025
Viewed by 222
Abstract
Background: BDE-47, a pervasive environmental pollutant detected in >90% of human serum samples, is increasingly linked to metabolic disorders. This study investigates the specific impact of BDE-47 exposure on the gut microbiota in prediabetic mice and evaluates the efficacy of therapeutic interventions [...] Read more.
Background: BDE-47, a pervasive environmental pollutant detected in >90% of human serum samples, is increasingly linked to metabolic disorders. This study investigates the specific impact of BDE-47 exposure on the gut microbiota in prediabetic mice and evaluates the efficacy of therapeutic interventions in mitigating these effects. Objectives: To determine whether BDE-47 exposure induces diabetogenic dysbiosis in prediabetic mice and to assess whether dietary interventions, such as grape exosomes and an antioxidant cocktail, can restore a healthy microbiota composition and mitigate diabetes risk. Methods: In this study, a prediabetic mouse model was established in 54 male SPF-grade C57BL/6J mice through a combination of high-sugar and high-fat diet feeding with streptozotocin injection. Oral glucose tolerance tests (OGTT) were conducted on day 7 and day 21 post-modeling to assess the establishment of the model. The criteria for successful model induction were defined as fasting blood glucose levels below 7.8 mmol/L and 2 h postprandial glucose levels between 7.8 and 11.1 mmol/L. Following confirmation of model success, a 3 × 3 factorial design was applied to allocate the experimental animals into groups based on two independent factors: BDE-47 exposure and exosome intervention. The BDE-47 exposure factor consisted of three dose levels—none, high-dose, and medium-dose—while the exosome intervention factor included three modalities—none, Antioxidant Nutrients Intervention, and Grape Exosomes Intervention. Fresh fecal samples were collected from mice two days prior to sacrifice. Cecal contents and segments of the small intestine were collected and transferred into 1.5 mL cryotubes. All sequences were clustered into operational taxonomic units (OTUs) based on defined similarity thresholds. To compare means across multiple groups, a two-way analysis of variance (ANOVA) was employed. The significance level was predefined at α = 0.05, and p-values < 0.05 were considered statistically significant. Bar charts and line graphs were generated using GraphPad Prism version 9.0 software, while statistical analyses were performed using SPSS version 20.0 software. Results: The results of 16S rDNA sequencing analysis of the microbiome showed that there was no difference in the α diversity of the intestinal microbiota in each group of mice (p > 0.05), but there was a difference in the Beta diversity (p < 0.05). At the gate level, the abundances of Proteobacteria, Campylobacterota, Desulfobacterota, and Fusobacteriota in the medium-dose BDE-7 group were higher than those in the model control group (p < 0.05). The abundance of Patellar bacteria was lower than that of the model control group (p < 0.05). The abundances of Proteobacteria and Campylobacterota in the high-dose BDE-7 group were higher than those in the model control group (p < 0.05). The abundance of Planctomycetota and Patescibacteria was lower than that of the model control group (p < 0.05), while the abundance of Campylobacterota in the grape exosome group was higher than that of the model control group (p < 0.05). The abundance of Patescibacteria was lower than that of the model control group (p < 0.05), while the abundance of Firmicutes and Fusobacteriota in the antioxidant nutrient group was higher than that of the model control group (p < 0.05). However, the abundance of Verrucomicrobiota and Patescibacteria was lower than that of the model control group (p < 0.05). At the genus level, the abundances of Bacteroides and unclassified Lachnospiraceae in the high-dose BDE-7 group were higher than those in the model control group (p < 0.05). The abundance of Lachnospiraceae NK4A136_group and Lactobacillus was lower than that of the model control group (p < 0.05). The abundance of Veillonella and Helicobacter in the medium-dose BDE-7 group was higher than that in the model control group (p < 0.05), while the abundance of Lactobacillus was lower (p < 0.05). The abundance of genera such as Lentilactobacillus and Faecalibacterium in the grape exosome group was higher than that in the model control group (p < 0.05). The abundance of Alloprevotella and Bacteroides was lower than that of the model control group (p < 0.05). In the antioxidant nutrient group, the abundance of Lachnospiraceae and Hydrogenophaga was higher than that in the model control group (p < 0.05). However, the abundance of Akkermansia and Coriobacteriaceae UCG-002 was significantly lower than that of the model control group (p < 0.05). Conclusions: BDE-47 induces diabetogenic dysbiosis in prediabetic mice, which is reversible by dietary interventions. These findings suggest that microbiota-targeted strategies may effectively mitigate the diabetes risk associated with environmental pollutant exposure. Future studies should further explore the mechanisms underlying these microbiota changes and the long-term health benefits of such interventions. Full article
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25 pages, 3102 KiB  
Article
Rainfall Drives Fluctuating Antibiotic Resistance Gene Levels in a Suburban Freshwater Lake
by Jack Roddey, Karlen Enid Correa Velez and R. Sean Norman
Water 2025, 17(15), 2260; https://doi.org/10.3390/w17152260 - 29 Jul 2025
Viewed by 381
Abstract
Antibiotic resistance genes (ARGs) in suburban freshwater ecosystems pose a growing public health concern by potentially reducing the effectiveness of medical treatments. This study investigated how rainfall influences ARG dynamics in Lake Katherine, a 62-hectare suburban lake in Columbia, South Carolina, over one [...] Read more.
Antibiotic resistance genes (ARGs) in suburban freshwater ecosystems pose a growing public health concern by potentially reducing the effectiveness of medical treatments. This study investigated how rainfall influences ARG dynamics in Lake Katherine, a 62-hectare suburban lake in Columbia, South Carolina, over one year. Surface water was collected under both dry and post-rain conditions from three locations, and ARGs were identified using metagenomic sequencing. Statistical models revealed that six of nine ARG classes with sufficient data showed significant responses to rainfall. Three classes, Bacitracin, Aminoglycoside, and Unclassified, were more abundant after rainfall, while Tetracycline, Multidrug, and Peptide resistance genes declined. Taxonomic analysis showed that members of the Pseudomonadota phylum, especially Betaproteobacteria, were prevalent among ARG-carrying microbes. These findings suggest that rainfall can alter the distribution of ARGs in suburban lakes, highlighting the importance of routine monitoring and water management strategies to limit the environmental spread of antibiotic resistance. Full article
(This article belongs to the Special Issue Water Safety, Ecological Risk and Public Health)
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22 pages, 2461 KiB  
Article
Environmental Drivers of Phytoplankton Structure in a Semi-Arid Reservoir
by Fangze Zi, Tianjian Song, Wenxia Cai, Jiaxuan Liu, Yanwu Ma, Xuyuan Lin, Xinhong Zhao, Bolin Hu, Daoquan Ren, Yong Song and Shengao Chen
Biology 2025, 14(8), 914; https://doi.org/10.3390/biology14080914 - 22 Jul 2025
Viewed by 312
Abstract
Artificial reservoirs in arid regions provide unique ecological environments for studying the spatial and functional dynamics of plankton communities under the combined stressors of climate change and anthropogenic activities. This study conducted a systematic investigation of the phytoplankton community structure and its environmental [...] Read more.
Artificial reservoirs in arid regions provide unique ecological environments for studying the spatial and functional dynamics of plankton communities under the combined stressors of climate change and anthropogenic activities. This study conducted a systematic investigation of the phytoplankton community structure and its environmental drivers in 17 artificial reservoirs in the Ili region of Xinjiang in August and October 2024. The Ili region is located in the temperate continental arid zone of northwestern China. A total of 209 phytoplankton species were identified, with Bacillariophyta, Chlorophyta, and Cyanobacteria comprising over 92% of the community, indicating an oligarchic dominance pattern. The decoupling between numerical dominance (diatoms) and biomass dominance (cyanobacteria) revealed functional differentiation and ecological complementarity among major taxa. Through multivariate analyses, including Mantel tests, principal component analysis (PCA), and redundancy analysis (RDA), we found that phytoplankton community structures at different ecological levels responded distinctly to environmental gradients. Oxidation-reduction potential (ORP), dissolved oxygen (DO), and mineralization parameters (EC, TDS) were key drivers of morphological operational taxonomic unit (MOTU). In contrast, dominant species (SP) were more responsive to salinity and pH. A seasonal analysis demonstrated significant shifts in correlation structures between summer and autumn, reflecting the regulatory influence of the climate on redox conditions and nutrient solubility. Machine learning using the random forest model effectively identified core taxa (e.g., MOTU1 and SP1) with strong discriminatory power, confirming their potential as bioindicators for water quality assessments and the early warning of ecological shifts. These core taxa exhibited wide spatial distribution and stable dominance, while localized dominant species showed high sensitivity to site-specific environmental conditions. Our findings underscore the need to integrate taxonomic resolution with functional and spatial analyses to reveal ecological response mechanisms in arid-zone reservoirs. This study provides a scientific foundation for environmental monitoring, water resource management, and resilience assessments in climate-sensitive freshwater ecosystems. Full article
(This article belongs to the Special Issue Wetland Ecosystems (2nd Edition))
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16 pages, 2162 KiB  
Article
Exploring Protist Communities in the Rhizosphere of Cultivated and Wild Date Palms
by Dana A. Abumaali, Sara H. Al-Hadidi, Talaat Ahmed, Ameni Ben Zineb, Abdul Rashid P. Rasheela, Amer Fayad Al-khis, Sowaid Ali Al-Malki, Mahmoud W. Yaish, Hassan Hassan, Roda Al-Thani and Juha M. Alatalo
Soil Syst. 2025, 9(3), 79; https://doi.org/10.3390/soilsystems9030079 - 15 Jul 2025
Viewed by 189
Abstract
Protists represent a major component of eukaryotic diversity within the soil microbiome, playing critical roles in mediating carbon and nitrogen cycling and influencing nutrient availability and soil health. Their diversity is shaped by multiple factors, including temperature, pH, organic matter content, and land [...] Read more.
Protists represent a major component of eukaryotic diversity within the soil microbiome, playing critical roles in mediating carbon and nitrogen cycling and influencing nutrient availability and soil health. Their diversity is shaped by multiple factors, including temperature, pH, organic matter content, and land use. In this study, we investigated the protist diversity in rhizosphere soils from both wild and cultivated date palm varieties. Our results identified nitrate, nitrite, calcium, and carbon content as key soil factors significantly correlated with protist diversity. Only 9.2% (42) of operational taxonomic units (OTUs) were shared across all soil samples, suggesting that these taxa possess traits enabling adaptation to extreme environmental conditions. The dominant protist families belonged to Rhizaria, Alveolata, Amoebozoa, and Archaeplastida, primarily comprising bacterial consumers, alongside taxa from Stramenopiles, Opisthokonta, Hacrobia, and Excavata. At the class level, Filosa-Sarcomonadea, Colpodea, Variosea, Tubulinea, and Chlorophyceae were the most abundant. Filosa-Sarcomonadea and Colpodea were positively correlated with bacterial and fungal genera, suggesting their role as consumers, while Variosea showed a negative correlation with bacteria, reflecting predator-prey dynamics. Notably, the protist community composition in wild date palm rhizosphere soils was distinct from that in cultivated soils, with Opisthokonta being particularly abundant, likely reflecting adaptation to drought conditions. Overall, this study highlights the significant differences in protist diversity and community structure between wild and cultivated date palm ecosystems. Full article
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14 pages, 1915 KiB  
Article
Preliminary Study to Understand the Role of Gut Microbiota in Coronary Slow Flow Phenomenon (CSFP)
by Tayfun Gurol, Tayyip Karaman, Yesim Gurol, Osman Ugur Sezerman and Sinem Oktem Okullu
Metabolites 2025, 15(7), 475; https://doi.org/10.3390/metabo15070475 - 14 Jul 2025
Viewed by 364
Abstract
Background/Objectives: Coronary slow flow phenomenon (CSFP) is a cardiovascular condition characterized by delayed passage of contrast medium through the coronary arteries, predominantly affecting young male smokers admitted with acute coronary syndrome. Although over 80% of patients experience recurrent chest pain and more than [...] Read more.
Background/Objectives: Coronary slow flow phenomenon (CSFP) is a cardiovascular condition characterized by delayed passage of contrast medium through the coronary arteries, predominantly affecting young male smokers admitted with acute coronary syndrome. Although over 80% of patients experience recurrent chest pain and more than 20% require readmission, the etiology of CSFP remains poorly understood. Given the emerging role of gut microbiome in cardiovascular diseases, this study investigates the microbial composition associated with CSFP. Methods: Stool samples were collected from patients diagnosed with CSFP and healthy control individuals. Microbiota profiling was performed using 16S rRNA sequencing. Taxonomic differences were evaluated to identify microbial markers potentially associated with CSFP. Results: The analysis revealed a notable enrichment of the genus Gemmiger and the species Anaerobutyricum in CSFP patients, specifically within the selenium metabolism pathway. This is of particular interest given the established link between selenium deficiency and heightened cardiovascular risk, suggesting a possible microbiome-mediated modulation of selenium bioavailability in CSFP pathophysiology. Moreover, a marked increase in taxa associated with the biosynthesis of trimethylamine (TMA), a proatherogenic metabolite implicated in the onset and progression of various cardiovascular disorders, was observed in the CSFP cohort, further supporting a potential mechanistic role of gut microbiota in the disease’s underlying etiology. Conclusions: Although statistical significance could not be established due to the limited sample size, the observed trends support the hypothesis that specific gut microbes and metabolic pathways, particularly those linked to selenium metabolism and TMA production, may serve as potential microbial indicators for CSFP. These preliminary findings warrant further investigation in larger cohorts. Full article
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14 pages, 1089 KiB  
Article
Modeling Plant Diversity Responses to Fire Recurrence in Disjunct Amazonian Savannas
by Mariana Martins Medeiros de Santana, Rodrigo Nogueira de Vasconcelos, Salustiano Vilar da Costa Neto, Eduardo Mariano Neto and Washington de Jesus Sant’Anna da Franca Rocha
Land 2025, 14(7), 1455; https://doi.org/10.3390/land14071455 - 13 Jul 2025
Viewed by 404
Abstract
Fire is a key ecological driver in tropical savannas, yet its effects on plant biodiversity remain understudied in Amazonian savannas. This study investigates how fire recurrence influences taxonomic and functional diversity in savanna ecosystems in northeastern Amazonia. We conducted vegetation surveys across five [...] Read more.
Fire is a key ecological driver in tropical savannas, yet its effects on plant biodiversity remain understudied in Amazonian savannas. This study investigates how fire recurrence influences taxonomic and functional diversity in savanna ecosystems in northeastern Amazonia. We conducted vegetation surveys across five phytophysiognomies in Amapá State, Brazil, and compiled trait data for 226 plant species. Generalized Additive Mixed Models (GAMMs) were used to evaluate the relationships between fire frequency and diversity metrics across five landscape scales. The results showed that taxonomic diversity—particularly Shannon diversity—exhibited a unimodal response to fire recurrence, with peak diversity occurring at intermediate fire frequencies. Abundance increased with fire frequency, indicating potential dominance by fire-tolerant species. Functional diversity responded more subtly: functional richness and dispersion showed weak, non-linear associations with fire, while functional evenness remained stable. These findings suggest that recurrent fire can reduce taxonomic diversity without strongly altering functional structure, possibly due to functional redundancy among species. The use of multiscale models revealed that biodiversity–fire relationships vary with spatial context. In conclusion, this study highlights the moderate resilience of Amazonian savannas to fire recurrence and emphasizes the need to incorporate these ecosystems into fire management plans in climate change scenarios. Full article
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16 pages, 2511 KiB  
Article
Screening of High-Yield 2-Phenylethanol Producing Strain from Wild-Type Saccharomyces cerevisiae and Optimization of Fermentation Parameters
by Chenshuo Zhang, Tingwen Fan, Zhichun Wang, Jiamu Yu, Xiaoming Guo, Wei Jiang, Lili Miao and Huaiyi Yang
Foods 2025, 14(14), 2444; https://doi.org/10.3390/foods14142444 - 11 Jul 2025
Viewed by 371
Abstract
2-Phenylethanol (2-PE), an aromatic alcohol with a rose-like fragrance, is widely used in the food, pharmaceutical, and high-end cosmetic industries. In this study, a high-yield 2-PE-producing strain was isolated and identified as Saccharomyces cerevisiae based on morphological characterization and taxonomic identification. Fermentation medium [...] Read more.
2-Phenylethanol (2-PE), an aromatic alcohol with a rose-like fragrance, is widely used in the food, pharmaceutical, and high-end cosmetic industries. In this study, a high-yield 2-PE-producing strain was isolated and identified as Saccharomyces cerevisiae based on morphological characterization and taxonomic identification. Fermentation medium components (carbon and nitrogen sources) were optimized through single-factor experiments in shaking flasks, and fermentation medium with 40 g/L glucose, 5 g/L malt extract, 1.75 g/L corn steep liquor, 2.5 g/L yeast extract, 5 g/L malt extract, 1.75 g/L corn steep liquor was considered suitable for 2-PE production. RT-qPCR results indicated that corn steep liquor activates expression of genes related to the shikimate pathway and Ehrlich pathway (pha2, aro4, aro8, and aro9), thereby promoting the synthesis of 2-PE through these pathways. Excess yeast extract inhibited the expression of aro8 and aro9, while enhancing the expression of tdh3 and adh2, thus promoting the de novo synthesis of 2-PE. Furthermore, fermentation in a 5 L bioreactor was applied to investigate the effects of feeding strategies, inoculum proportion, and pH on 2-PE production. With a pH of 5.5 and10% inoculum proportion, the supplementation of the substrate L-Phe led to a 2-PE production of 4.81 g/L after 24 h of fermentation. Finally, in situ product recovery (ISPR) techniques was applied to alleviate 2-PE cytotoxicity, achieving a production of 6.41 g/L. This process offers a promising strategy for producing 2-PE efficiently and naturally, paving the way for further industrial applications in food, pharmaceutical, and cosmetic sectors. Full article
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23 pages, 11464 KiB  
Article
Characterization of Water Quality and the Relationship Between WQI and Benthic Macroinvertebrate Communities as Ecological Indicators in the Ghris Watershed, Southeast Morocco
by Ali El Mansour, Saida Ait Boughrous, Ismail Mansouri, Abdellali Abdaoui, Wafae Squalli, Asmae Nouayti, Mohamed Abdellaoui, El Mahdi Beyouda, Christophe Piscart and Ali Ait Boughrous
Water 2025, 17(14), 2055; https://doi.org/10.3390/w17142055 - 9 Jul 2025
Viewed by 454
Abstract
The Ghris watershed in southern Morocco is a significant ecological and agricultural area. However, due to the current impacts of climate change, farming activities, and pollution, data on its quality and biological importance need to be updated. Therefore, this study aimed to evaluate [...] Read more.
The Ghris watershed in southern Morocco is a significant ecological and agricultural area. However, due to the current impacts of climate change, farming activities, and pollution, data on its quality and biological importance need to be updated. Therefore, this study aimed to evaluate the physico-chemical and biological quality of surface water in the Ghris River. The Water Quality Index (WQI) and the Iberian Biological Monitoring Working Group (IBMWP) index were used to assess water quality along four sampling sites in 2024. The collected data were analyzed with descriptive and multivariate statistics. In total, 424 benthic macroinvertebrates belonging to seven orders were identified in the surface waters of the Ghris basin. These microfauna were significantly variable among the studied sites (p < 0.05). Station S4 is significantly rich in species, including seven orders and nine families of macroinvertebrates, followed by Station S2, with seven orders and eight families. Stations S3 and S1 showed less species diversity, with three orders and one family, respectively. The Insecta comprised 95.9% of the abundance, while the Crustacea constituted just 4.1%. The physico-chemical parameters significantly surpassed (p < 0.05) the specified norms of surface water in Morocco. This indicates a decline in the water quality of the studied sites. The findings of the principal component analysis (PCA) demonstrate that the top two axes explain 87% of the cumulative variation in the data. Stations 2 and 3 are closely associated with high concentrations of pollutants, notably Cl, SO42−, NO3, and K+ ions. Dissolved oxygen (DO) showed a slight correlation with S2 and S3, while S4 was characterized by high COD and PO4 concentrations, low levels of mineral components (except Cl), and average temperature conditions. Bioindication scores for macroinvertebrate groups ranging from 1 to 10 enabled the assessment of pollution’s influence on aquatic biodiversity. The IBMWP biotic index indicated discrepancies in water quality across the sites. This study gives the first insight and updated data on the biological and chemical quality of surface water in the Ghris River and the entire aquatic ecosystem in southeast Morocco. These data are proposed as a reference for North African and Southern European rivers. However, more investigations are needed to evaluate the impacts of farming, mining, and urbanization on the surface and ground waters in the study zone. Similarly, it is vital to carry out additional research in arid and semi-arid zones since there is a paucity of understanding regarding taxonomic and functional diversity, as well as the physico-chemical factors impacting water quality. Full article
(This article belongs to the Section Biodiversity and Functionality of Aquatic Ecosystems)
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17 pages, 811 KiB  
Article
A Novel GABA-Producing Levilactobacillus brevis Strain Isolated from Organic Tomato as a Promising Probiotic
by Asia Pizzi, Carola Parolin, Davide Gottardi, Arianna Ricci, Giuseppina Paola Parpinello, Rosalba Lanciotti, Francesca Patrignani and Beatrice Vitali
Biomolecules 2025, 15(7), 979; https://doi.org/10.3390/biom15070979 - 8 Jul 2025
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Abstract
Gamma-aminobutyric acid (GABA) is a non-protein amino acid playing a significant role in the central nervous system and the gut–brain axis. This study investigated the potential to produce GABA by lactic acid bacteria (LAB) isolated from different varieties of organic tomatoes. The isolated [...] Read more.
Gamma-aminobutyric acid (GABA) is a non-protein amino acid playing a significant role in the central nervous system and the gut–brain axis. This study investigated the potential to produce GABA by lactic acid bacteria (LAB) isolated from different varieties of organic tomatoes. The isolated LAB were taxonomically identified by 16S rRNA gene sequencing, the presence of the gadB gene (glutamate decarboxylase) was detected, and GABA production was quantified using HPLC. Levilactobacillus brevis CRAI showed the highest GABA production under optimised fermentation conditions with 4% monosodium glutamate (MSG). The genome sequencing of L. brevis CRAI revealed the presence of gadA and gadB isoforms and assessed the strain’s safety profile. The gene expression analysis revealed that the gadA and gadB genes were upregulated in the presence of 4% MSG. The probiotic potential of L. brevis CRAI was also assessed by functional assays. The strain showed strong antimicrobial activity against representative enteropathogens, i.e., Escherichia coli ETEC, Salmonella choleraesuis, and Yersinia enterocolitica, and anti-inflammatory effect, reducing nitric oxide production in LPS-stimulated RAW264.7 macrophages. In addition, its ability to adhere to intestinal epithelial Caco-2 cells was demonstrated. These results highlight L. brevis CRAI as a promising candidate for the development of GABA-enriched functional foods or probiotic supplements with the perspective to modulate the gut-brain axis. Full article
(This article belongs to the Special Issue Probiotics and Their Metabolites, 2nd Edition)
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13 pages, 2419 KiB  
Article
Modulation of Gut Microbial Composition by Lactobacillus delbrueckii subsp. lactis CKDB001 Supplementation in a High-Fat-Diet-Induced Obese Mice
by Jaeryang Chu, Chae-Won No, Hyunchae Joung, Kyung Hwan Kim, Chang Hun Shin, Jisu Lee and Jung-Heun Ha
Nutrients 2025, 17(13), 2251; https://doi.org/10.3390/nu17132251 - 7 Jul 2025
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Abstract
Background/Objectives: Lactobacillus delbrueckii subsp. lactis CKDB001 (LL) has demonstrated anti-inflammatory, antioxidant, and lipid-regulatory effects in vitro and in vivo, including attenuation of hepatic steatosis and modulation of lipid metabolism. Given the known interactions between host metabolism and gut microbiota, these findings suggest [...] Read more.
Background/Objectives: Lactobacillus delbrueckii subsp. lactis CKDB001 (LL) has demonstrated anti-inflammatory, antioxidant, and lipid-regulatory effects in vitro and in vivo, including attenuation of hepatic steatosis and modulation of lipid metabolism. Given the known interactions between host metabolism and gut microbiota, these findings suggest a potential role for LL in modulating microbial composition under conditions of diet-induced obesity. This study aimed to investigate the microbiome-related effects of LL using an established murine model. To evaluate the effect of LL supplementation on gut microbial composition and predict microbial metabolic functions in mice with high-fat diet-induced obesity. Methods: Male C57BL/6J mice were fed a high-fat diet and administered LL orally for 12 weeks. Fecal samples were collected and analyzed using 16S rRNA gene sequencing. Microbial taxonomic profiles were assessed using linear discriminant analysis effect size, and functional predictions were performed using PICRUSt2. Results: LL supplementation significantly altered the gut microbiota by increasing the relative abundance of Lactobacillus and other commensal taxa while reducing the prevalence of pro-inflammatory genera such as Alistipes and Bilophila. Functional prediction analysis revealed a downregulation of lipopolysaccharide and ADP-L-glycero-β-D-manno-heptose biosynthesis pathways. Microbial functions associated with carbohydrate metabolism and short-chain fatty acid production were enriched in the LL-treated group. Conclusions: LL modulated gut microbial composition and suppressed pro-inflammatory microbial pathways while enhancing beneficial metabolic functions in high-fat diet-fed mice. These findings support the potential of LL as a safe and effective microbiota-targeted probiotic for managing obesity-related metabolic disorders. Full article
(This article belongs to the Special Issue Prebiotics and Probiotics in Metabolism Disorder—2nd Edition)
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12 pages, 1858 KiB  
Article
Botanical Studies Based on Textual Evidence in Eastern Asia and Its Implications for the Ancient Climate
by Haiming Liu, Huijia Song, Fei Duan and Liang Shen
Atmosphere 2025, 16(7), 824; https://doi.org/10.3390/atmos16070824 - 7 Jul 2025
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Abstract
Understanding morphological descriptions of plants documented by ancient peoples over 1000 years ago and identifying the species they described are critical for reconstructing the natural geographic distribution of plant taxa, tracking taxonomic variations, and inferring historical climate dynamics. Analyzing shifts in plant communities [...] Read more.
Understanding morphological descriptions of plants documented by ancient peoples over 1000 years ago and identifying the species they described are critical for reconstructing the natural geographic distribution of plant taxa, tracking taxonomic variations, and inferring historical climate dynamics. Analyzing shifts in plant communities and climatic conditions during this period is essential to unravel the interplay among floristic composition, climate fluctuations, and anthropogenic impacts. However, research in this field remains limited, with greater emphasis placed on plant taxa from hundreds of millions of years ago. Investigations into flora and climate during the last two millennia are sparse, and pre-millennial climatic conditions remain poorly characterized. In this study, a historical text written 1475 years ago was analyzed to compile plant names and morphological features, followed by taxonomic identification. The research identified three gymnosperm species (one in Pinaceae, two in Cupressaceae), 1 Tamaricaceae species (dicotyledon), and 19 dicotyledon species. However, three plant groups could only be identified at the genus level. Using textual analysis and woody plant coexistence methods, the climate of 1475 years ago in western Henan Province, located in the middle-lower Yellow River basin in East Asia, was reconstructed. Results indicate that the mean temperature of the coldest month (MTCM) was approximately 1.3 °C higher than modern values. In comparison, the mean temperature of the warmest month (MTWM) and mean annual temperature (MAT) were lower than present-day levels. This suggests slightly cooler overall conditions with milder seasonal extremes in ancient Luoyang—a finding supported by contemporaneous studies. Furthermore, annual precipitation (AP), precipitation of the warmest quarter (PWQ), and precipitation of the coldest quarter (PCQ) in the Luoyang region 1475 years ago exceeded modern measurements, despite the area’s monsoonal climate. This suggests significantly higher atmospheric moisture content in ancient air masses compared to today. This study provides floristic and climatic baseline data for advancing our understanding of global climate variability at millennial scales. Full article
(This article belongs to the Section Climatology)
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