Search Results (975)

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

Background/Objectives: This study examines how seasonality, pollution, and sample type (water and sediment) influence the presence and distribution of antibiotic resistance genes (ARGs), with a focus on antibiotic resistance genes (ARGs) located on plasmids (the complete set of plasmid-derived sequences, including ARGs) in a tropical urban river. Methods: Samples were collected from three sites along a pollution gradient in the Virilla River, Costa Rica, during three seasonal campaigns (wet 2021, dry 2022, and wet 2022). ARGs in water and sediment were quantified by qPCR, and metagenomic sequencing was applied to analyze chromosomal and plasmid-associated resistance profiles in sediments. Tobit and linear regression models, along with multivariate ordination, were used to assess spatial and seasonal trends. Results: During the wet season of 2021, the abundance of antibiotic resistance genes (ARGs) such as sul-1, intI-1, and tetA in water samples decreased significantly, likely due to dilution, while intI-1 and tetQ increased in sediments, suggesting particle-bound accumulation. In the wet season 2022, intI-1 remained low in water, qnrS increased, and sediments showed significant increases in tetQ, tetA, and qnrS, along with decreases in sul-1 and sul-2. Metagenomic analysis revealed spatial differences in plasmid-associated ARGs, with the highest abundance at the most polluted site (Site 3). Bacterial taxa also showed spatial differences, with greater plasmidome diversity and a higher representation of potential pathogens in the most contaminated site. Conclusions: Seasonality and pollution gradients jointly shape ARG dynamics in this tropical river. Plasmid-mediated resistance responds rapidly to environmental change and is enriched at polluted sites, while sediments serve as long-term reservoirs. These findings support the use of plasmid-based monitoring for antimicrobial resistance surveillance in aquatic systems. Full article

Autism Spectrum Disorder (ASD) is frequently accompanied by gastrointestinal disturbances, dietary selectivity, and altered stress responses, with growing evidence pointing to gut–brain axis involvement. While intestinal microbiota has been extensively studied, the role of the oral microbiota remains underexplored. This study investigates the associations between oral microbiota composition and behavioral, gastrointestinal, dietary, and neuroendocrine parameters in children with ASD. A total of 45 children aged 2–18 years comprised the study group. Data collection included oral swabs for 16S rRNA gene sequencing, salivary cortisol sampling, dietary records, and standardized behavioral assessments using the Vineland Adaptive Behavior Scale. A total of 363 microbial species across 11 phyla were identified. Significant correlations were observed between specific bacterial taxa and functional gastrointestinal disorders (FGIDs), dietary patterns, salivary cortisol rhythms, and functioning. Children with FGIDs, food selectivity, or macronutrient imbalances exhibited enriched pro-inflammatory taxa (e.g., Selenomonas, Megasphaera), whereas those with typical cortisol secretion or higher adaptive functioning showed greater microbial diversity and abundance of health-associated genera (e.g., Bifidobacterium dentium). These findings suggest that oral microbiota profiles may reflect systemic physiological and neurobehavioral traits in children with ASD. Further longitudinal studies are needed to clarify causal relationships and support the development of microbiota-targeted interventions. Full article

Disparities in the functional classification of secretory genes among aphid taxa may be attributed to variations in coding sequences and gene expression profiles. However, the driving factors that regulate sequence evolution remain unclear. This study aimed to investigate the differences in coding sequences and expression patterns of secretory genes between the rose grain aphid (Metopolophium dirhodum) and the pea aphid (Acrythosiphon pisum), with a particular focus on their roles in evolutionary adaptations and functional diversity. The study involved the rearing of aphids, RNA extraction, de novo transcriptome assembly, functional annotation, secretory protein prediction, and comparative analysis of coding sequences and expression patterns across various functional categories using bioinformatics tools. The results revealed that metabolic genes exhibited greater coding sequence divergence, indicating the influence of positive selection. Moreover, significant expression divergence was noted among functional categories, particularly in metabolic and genetic information processing genes, which exhibited higher variability. This study enhances our understanding of the molecular mechanisms that contribute to phenotypic and genetic diversity among aphid species. This study elucidates the relationship between variations in coding sequences and differences in gene expression among functional categories, thereby establishing a foundation for future studies on gene evolution in response to environmental pressures. Full article

Plastic debris is a pervasive and persistent threat to marine ecosystems. Microplastics (plastics < 5 mm) are increasing in a variety of marine habitats, including open water systems, shorelines, and benthic sediments. It remains unclear how microplastics distribute and accumulate in marine systems and the extent to which this pollutant is accessible to marine taxa. We examined subtidal benthic sediments and beach sediments in critical nearshore habitats for forage fish species—Pacific sand lance (Ammodytes personatus), Pacific herring (Clupea pallasi), and surf smelt (Hypomesus pretiosus)—to quantify microplastic concentrations in the spawning and deep-water habitats of these fish and better understand how microplastics accumulate and distribute in nearshore systems. In the San Juan Islands, we examined an offshore subtidal bedform in a high-flow channel and beach sites of protected and exposed shorelines. We also examined 12 beach sites proximate to urban areas in Puget Sound. Microplastics were found in all samples and at all sample sites. Microfibers were the most abundant, and flakes were present proximate to major shipyards and marinas. Microplastics were significantly elevated in Puget Sound compared to the San Juan Archipelago. Protected beaches had elevated concentrations relative to exposed beaches and subtidal sediments. Microplastics were in higher concentrations in sand and fine-grain sediments, poorly sorted sediments, and artificial sediments. Microplastics were also elevated at sites confirmed as spawning habitats for forage fish. The model results indicate that both current speed and proximate urban populations influence nearshore microplastic concentrations. Our research provides new insights into how microplastics are distributed, deposited, and retained in marine sediments and shorelines, as well as insight into potential exposure in benthic, demersal, and shoreline habitats. Further analyses are required to examine the relative influence of urban populations and shipping lanes and the effects of physical processes such as wave exposure, tidal currents, and shoreline geometry. Full article

Caenogastropoda is a highly speciose and ecologically diverse subclass of Gastropoda but its higher order classification remains unclear, especially within its largest constituent group, Hypsogastropoda. Two nominal taxa encompassing most of the great diversity of Hypsogastropoda are in current widespread use: one is Latrogastropoda, which has been repeatedly redefined resulting in changes to the second, Littorinimorpha, which is generally not supposed to be monophyletic. We examined the utility of these divisions by assembling single-gene data sets of nuclear 28S ribosomal RNA (28S rRNA) and mitochondrial 16S ribosomal RNA (16S rRNA) and cytochrome c oxidase subunit I from many genera. Capuloidea was consistently found with strong support within Latrogastropoda, so this taxon is redefined here to include that superfamily. The analyses also suggested the redefinition of some superfamilies within Littorinimorpha, particularly for the clade comprising Truncatelloidea, Vanikoroidea and Rissooidea, and the Littorinoidea. Littorinimorpha was monophyletic (albeit lacking strong support) in the combined analysis of 28S rRNA and 16S rRNA and was resolved as the sister group of Latrogastropoda which was also monophyletic, with bootstrap support of 66%. Littorinimorpha was not monophyletic in other analyses. In these, the sister group of Latrogastropoda comprised clades of multiple littorinimorph superfamilies but these relationships were also not strongly supported. Full article

Organic farming is widely recognized as a promising practice for sustainable agriculture, yet its long-term ecological impacts remain insufficiently investigated. In this study, we evaluated these impacts by comparing heavy metal concentrations, soil invertebrate communities, and microbial profiles between long-term organic and conventional farming systems. A comparative analysis was conducted on 24 plot soils from two paired organic and conventional farm systems in Beijing, each managed continuously for over 20 years. Our results revealed that soils under organic management consistently contained 10.8% to 73.7% lower heavy metals, along with reduced geo-accumulation indices (I_geo, a standardized metric for soil contamination assessment), indicating decreased contamination risks. In terms of soil fauna, while conventional soils showed higher Collembola abundance, organic farming significantly enhanced Collembola richness and diversity by 20.6% to 55.0%. Microbial sequencing likewise revealed enhanced richness and diversity of bacteria and fungi in organic soils. These microbial communities also displayed shifts in dominant taxa and more stable co-occurrence networks under organic management. Principal component analysis and Mantel tests identified soil pH and nutrients as key drivers of soil biodiversity, while heavy metals also imposed negative influences. Collectively, these findings demonstrate that long-term organic farming not only mitigates environmental risks associated with soil contaminants but also promotes belowground ecological integrity by supporting biodiversity of soil fauna and microbiota. This study highlights the ecological significance of sustained organic practices and provides critical insights for advancing sustainable agricultural developments. Full article

The primary aim of this study was to explore the influence of abiotic factors on weed development in maize fields, with the goal of informing more effective weed management practices. We focused on identifying key environmental, edaphic, and agricultural variables that contribute to weed infestations, particularly before the application of spring herbicide treatments. Field investigations were conducted from 2018 to 2021 across selected maize-growing regions in Hungary. Over the four-year period, a total of 51 weed species were recorded, with Echinochloa crus-galli, Chenopodium album, Portulaca oleracea, and Hibiscus trionum emerging as the most prevalent taxa. Collectively, these four species accounted for more than half (52%) of the total weed cover. Altogether, the 20 most dominant species contributed 95% of the overall weed coverage. The analysis revealed that weed cover, species richness, and weed diversity were significantly affected by soil properties, nutrient levels, geographic location, and tillage systems. The results confirm that the composition of weed species was influenced by several environmental and management-related factors, including soil parameters, geographical location, annual precipitation, tillage method, and fertilizer application. Environmental factors collectively explained a slightly higher proportion of the variance (13.37%) than farming factors (12.66%) at a 90% significance level. Seasonal dynamics and crop rotation history also played a notable role in species distribution. Nutrient inputs, particularly nitrogen, phosphorus, and potassium, influenced both species diversity and floristic composition. Deep tillage practices favored the proliferation of perennial species, whereas shallow cultivation tended to promote annual weeds. Overall, the composition of weed vegetation proved to be a valuable indicator of site-specific soil conditions and agricultural practices. These findings underscore the need to tailor weed management strategies to local environmental and soil contexts for sustainable crop production. Full article

Recent advances in microbiome studies have deepened our understanding of endosymbionts and gut-associated microbiota in host biology. Of those, lepidopteran systems in particular harbor a complex and diverse microbiome with various microbial taxa that are stable and transmitted between larval and adult stages, and others that are transient and context-dependent. We highlight key microorganisms—including Bacillus, Lactobacillus, Escherichia coli, Pseudomonas, Rhizobium, Fusarium, Aspergillus, Saccharomyces, Bifidobacterium, and Wolbachia—that play critical roles in microbial ecology, biotechnology, and microbiome studies. The fitness implications of these microbial communities can be variable; some microbes improve host performance, while others neither positively nor negatively impact host fitness, or their impact is undetectable. This review examines the central position played by the gut microbiota in interactions of insects with plants, highlighting the functions of the microbiota in the manipulation of the behavior of herbivorous pests, modulating plant physiology, and regulating higher trophic levels in natural food webs. It also bridges microbiome ecology and applied pest management, emphasizing S. frugiperda as a model for symbiont-based intervention. As gut microbiota are central to the life history of herbivorous pests, we consider how these interactions can be exploited to drive the development of new, environmentally sound biocontrol strategies. Novel biotechnological strategies, including symbiont-based RNA interference (RNAi) and paratransgenesis, represent promising but still immature technologies with major obstacles to overcome in their practical application. However, microbiota-mediated pest control is an attractive strategy to move towards sustainable agriculture. Significantly, the gut microbiota of S. frugiperda is essential for S. frugiperda to adapt to a wide spectrum of host plants and different ecological niches. Studies have revealed that the microbiome of S. frugiperda has a close positive relationship with the fitness and susceptibility to entomopathogenic fungi; therefore, targeting the S. frugiperda microbiome may have good potential for innovative biocontrol strategies in the future. Full article

Assessing microbial community stability and soil quality requires understanding the role of keystone microbial taxa in maintaining diversity and functionality. This study collected soil samples from four major habitats in the urban and peri-urban areas of 20 highly urbanized provinces in China using both the five-point method and the S-shape method and explored their microbiota through high-throughput sequencing techniques. The data was used to investigate changes in the structural diversity and co-occurrence patterns of keystone microbial communities from peri-urban (agricultural land) to urban environments (hospitals, wastewater treatment plants, and zoos) across different regions. Using network analysis, we examined the structure and symbiosis of soil keystone taxa and their association with environmental factors during urbanization. Results revealed that some urban soils exhibited higher microbial diversity, network complexity, and community stability compared to peri-urban soil. Significant differences were observed in the composition, structure, and potential function of keystone microbial taxa between these environments. Correlation analysis showed a significant negative relationship between keystone taxa and mean annual precipitation (p < 0.05), and a strong positive correlation with soil nutrients, microbial diversity, and community stability (p < 0.05). These findings suggest that diverse keystone taxa are vital for sustaining microbial community stability and that urbanization-induced environmental changes modulate their composition. Shifts in keystone taxa composition reflect alterations in soil health and ecosystem functioning, emphasizing their role as indicators of soil quality during urban development. This study highlights the ecological importance of keystone taxa in shaping microbial resilience under urbanization pressure. Full article

Intercropping has been widely proven to boost agricultural yields and control diseases. This study examined the impact of sugarcane monoculture (SM) and sugarcane–pumpkin intercropping (IP) systems on soil physicochemical characteristics and microbial community dynamics. Compared to monoculture, intercropping significantly increased soil pH by 8.82% and total potassium (TK) by 17.92%, while reducing soil organic matter (SOM) by 25.56%. Bacterial communities under intercropping exhibited significantly higher alpha and beta diversity, whereas fungal community diversity remained unaffected. Notably, the relative abundances of certain taxa with known roles in plant growth promotion and pathogen suppression—such as Anaeromyxobacter, Nitrospira, and Massilia—were enriched. Canonical correlation analysis revealed that bacterial community composition was strongly associated with TK, while fungal community structure correlated with variations in soil available nitrogen (AN). These findings indicate that sugarcane–pumpkin intercropping reshapes soil microbial communities and contributes to some improvement in soil nutrient availability. Full article

Background: The gut microbiota is increasingly recognized as a key modulator in obesity management, influencing host energy balance, lipid metabolism, and inflammatory pathways. With obesity prevalence continuing to rise globally, dietary interventions that promote beneficial microbial shifts are essential for enhancing weight loss outcomes and long-term health. Objective: This study investigated the effects of the multicomponent Weight Loss Maintenance 3 Phases Program (WLM3P), which integrates caloric restriction, a high-protein low-carbohydrate diet, time-restricted eating (10h TRE), dietary supplementation (prebiotics and phytochemicals), and digital app-based support on gut microbiota composition compared to a standard low-carbohydrate diet (LCD) in adults with obesity. The analysis focused exclusively on the 6-month weight loss period corresponding to Phases 1 and 2 of the WLM3P intervention. Methods: In this sub-analysis of a randomized controlled trial (ClinicalTrials.gov Identifier: NCT04192357), 58 adults with obesity (BMI 30.0–39.9 kg/m²) were randomized to the WLM3P (n = 29) or LCD (n = 29) groups. Stool samples were collected at baseline and 6 months for 16S rRNA sequencing. Alpha and beta diversity were assessed, and genus-level differential abundance was determined using EdgeR and LEfSe. Associations between microbial taxa and clinical outcomes were evaluated using regression models. Results: After 6-month, the WLM3P group showed a significant increase in alpha diversity (p = 0.03) and a significant change in beta diversity (p < 0.01), while no significant changes were observed in the LCD group. Differential abundance analysis revealed specific microbial signatures in WLM3P participants, including increased levels of Faecalibacterium. Notably, higher Faecalibacterium abundance was associated with greater reductions in fat mass (kg, %) and visceral adiposity (cm²) in the WLM3P group compared to LCD (p < 0.01). Conclusions: These findings suggest a potential microbiota-mediated mechanism in weight loss, where Faecalibacterium may enhance fat reduction effectiveness in the context of the WLM3P intervention. Full article

Background/Objective: Oral lichen planus (OLP) is a chronic inflammatory disorder of the oral mucosa with unclear etiology. Increasing evidence implicates oral microbial dysbiosis in its pathogenesis, but little is known about supragingival plaque communities in relation to clinical subtypes. This cross-sectional case–control study aimed to characterize the supragingival plaque microbiota and microbial interaction networks in erosive OLP (E-OLP), non-erosive OLP (NE-OLP), and healthy controls (HCs), to elucidate microbial patterns associated with disease severity. Methods: Supragingival plaque samples were collected from 90 participants (30 per group) and analyzed using 16S rRNA gene sequencing. Alpha and beta diversity metrics, differential abundance, and co-occurrence network analyses were performed. Results: E-OLP exhibited pronounced dysbiosis, including the enrichment of pro-inflammatory taxa (e.g., Prevotella, Parvimonas) and depletion of health-associated commensals (e.g., Rothia, Capnocytophaga). Network analysis revealed the stepwise disintegration of microbial community structure from HC to NE-OLP to E-OLP, with reduced connectivity and increased dominance of pathogenic clusters in E-OLP. These microbial alterations aligned with clinical findings, as E-OLP patients showed significantly higher Reticulation/keratosis, Erythema, and Ulceration (REU) scores for erythema and ulceration compared to NE-OLP. Conclusions: Supragingival plaque dysbiosis and ecological disruption are strongly associated with OLP severity and subtype. This study highlights the utility of plaque-based microbial profiling in capturing lesion-proximal dysbiotic signals, which may complement mucosal and salivary analyses in future diagnostic frameworks. Multi-omics approaches incorporating fungal, viral, and metabolic profiling are warranted to fully elucidate host–microbe interactions in OLP. Full article

Understanding the biodiversity of aquatic communities and the underlying mechanisms that shape biodiversity patterns and community dynamics is crucial for the effective conservation and management of freshwater ecosystems. However, traditional survey methods often fail to comprehensively capture species diversity, particularly for low-abundance taxa. Moreover, studies integrating both metazoan and fish communities at fine spatial scales remain limited. To address these gaps, we employed a multi-marker eDNA metabarcoding approach, targeting both the 12S and 18S rRNA gene regions, to comprehensively investigate the composition of metazoan and fish communities in the Yujiang River. A total of 12 metazoan orders were detected, encompassing 15 families, 21 genera, and 19 species. For the fish community, 32 species were identified, belonging to 25 genera, 10 families, and 7 orders. Among these, Adula falcatoides and Coptodon zillii were identified as the most prevalent and abundant metazoan and fish species, respectively. Notably, the most prevalent fish species, C. zillii and Oreochromis niloticus, are both recognized as invasive species. The Bray–Curtis distance of metazoa (average: 0.464) was significantly lower than that of fish communities (average: 0.797), suggesting higher community heterogeneity among fish assemblages. Beta-diversity decomposition indicated that variations in the metazoan and fish communities were predominantly driven by species replacement (turnover) (65.4% and 70.9% for metazoa and fish, respectively) rather than nestedness. Mantel tests further revealed that species turnover in metazoan communities was most strongly influenced by water temperature, while fish community turnover was primarily affected by water transparency, likely reflecting the physiological sensitivity of metazoans to thermal gradients and the dependence of fish on visual cues for foraging and habitat selection. In addition, a co-occurrence network of metazoan and fish species was constructed, highlighting potential predator-prey interactions between native species and Corbicula fluminea, which emerged as a potential keystone species. Overall, this study demonstrates the utility of multi-marker eDNA metabarcoding in characterizing aquatic community structures and provides new insights into the spatial dynamics and species interactions within river ecosystems. Full article

Background/Objectives: Our aim was to create a new method for analyzing metagenomics data, named the gut microbiome obesity index, using a set of taxa/biological functions that correlated with BMI. Methods: A total of 109 obese patients (73 women and 36 men, median BMI 43.0 kg/m²), 87 healthy control (HC) individuals (39 females and 48 males, median BMI 22.7 kg/m²), and 109 esports players (five females and 104 males, median BMI 23.0 kg/m²) were included in the study. To conduct metagenomic and metabolomic analyses, DNA and selected metabolites were isolated from fecal samples and used for whole-genome shotgun sequencing and gas chromatography/mass spectrometry, respectively. Results: Compared with HCs and esports players, obese patients with a BMI > 40 kg/m² had a significantly higher alpha diversity, as analyzed by the Shannon index, and significant dissimilarities in beta diversity. Both richness and diversity measures were correlated with BMI. Compared with HCs and esports players, 12 differential bacteria were found in the overall obesity group and 42 were found in those with a BMI > 40 kg/m². Most of the altered species belonged to the Lachnospiraceae family. When the logarithmic relationship of the sums of the bacteria correlated with BMI was calculated to establish a taxonomic health index, it better differentiated between the obesity groups than a standard analytical pipeline; however, it did not differentiate between the HC and the BMI < 35 kg/m² obesity group. Therefore, we created a functional index based on BMI-associated biological pathways, which differentiated between all obesity groups. Conclusions: Of the obesity indices used to distinguish between healthy and obese microbiota analyzed in this study, a function-based index was more useful than a taxonomy-based index. We believe that gut microbiome indexes could be useful as part of routine metagenomics evaluations. However, an index developed in one geographical area might not be applicable to individuals in a different region and, therefore, further studies should develop separate indices for different populations or geographical regions rather than relying on a single index. Full article