Unique Operational Taxonomic Units Research Articles

A global atlas of soil viruses reveals unexplored biodiversity and potential biogeochemical impacts

Historically neglected by microbial ecologists, soil viruses are now thought to be critical to global biogeochemical cycles. However, our understanding of their global distribution, activities and interactions with the soil microbiome remains limited. Here we present the Global Soil Virus Atlas, a comprehensive dataset compiled from 2,953 previously sequenced soil metagenomes and composed of 616,935 uncultivated viral genomes and 38,508 unique viral operational taxonomic units. Rarefaction curves from the Global Soil Virus Atlas indicate that most soil viral diversity remains unexplored, further underscored by high spatial turnover and low rates of shared viral operational taxonomic units across samples. By examining genes associated with biogeochemical functions, we also demonstrate the viral potential to impact soil carbon and nutrient cycling. This study represents an extensive characterization of soil viral diversity and provides a foundation for developing testable hypotheses regarding the role of the virosphere in the soil microbiome and global biogeochemistry.

Unique microbial communities of parasitic fleas on wild animals from the Qinghai-Tibet Plateau.

Fleas, one of the most significant ectoparasites, play a crucial role as vectors in spreading zoonotic diseases globally. The Qinghai Province, as part of the Qinghai-Tibet Plateau, is one of the provinces in China with the largest number of flea species. In this study, we characterized the microbial communities of eighty-five adult fleas, belonging to nineteen species within four families (Ceratophyllidae, Ctenophthalmidae, Leptopsyllidae, and Pulicidae). We identified a total of 1162 unique operational taxonomic units at the genus level, with flea-borne pathogens such as Wolbachia, Bartonella, Rickettsia being the members of top abundant taxa. Except for comparison between Ctenophthalmidae and Leptopsyllidae families, the analyses of both alpha- and beta- diversity indicators suggested that bacterial diversity varied among flea families. This could be attributed to flea phylogeny, which also influenced by their geographical sites and animal hosts. Results of Linear discriminant analysis effect size (LEfSe) indicated that 29 genera in Ceratophylloidea, 11 genera in Ctenophthalmidae, 15 genera in Leptopsyllidae, and 22 genera in Pulicidae were significantly responsible for explaining the differences among the four flea families (linear discriminant analysis score > 2, P < 0.05). Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt2) analyses showed that the functional pathways varied significantly across flea families, which was supported by the significant correlation between the functional pathways and the microbial communities.

Microbiome dysbiosis in patients with chronic endometritis and Clostridium tyrobutyricum ameliorates chronic endometritis in mice

Chronic endometritis is associated with the imbalance of female reproductive tract microbiota and pathogenic microbial infection. This study aimed to identify the specific changes in the endometrial microbiome in patients with endometritis and to explore how Clostridium tyrobutyricum (C.t) influences the progression of endometritis in mice for further elucidating endometritis pathogenesis. For this purpose, endometrial tissues from 100 participants were collected and divided into positive, weakly positive, and negative groups based on CD138 levels, while endometrial microbiome differences were detected and analyzed using 16S rRNA gene sequencing. Staphylococcus aureus (S. aureus)-induced endometritis mouse model was established, followed by treatment with C.t, and inflammatory response, epithelial barrier, and TLR4/NF-κB pathway were evaluated. Results showed that α- and β-diversity was significantly lower in the positive group compared with the weakly positive or negative groups, where the negative group had more unique operational taxonomic units. The abundance of Proteobacteria was found to be increased, while that of Actinobacteria, Firmicutes, and Bacteroidetes was found to be reduced in the positive group, while the area under the curve value was found to be 0.664. Furthermore, C.t treatment resulted in the alleviation of S. aureus-induced inflammatory response, epithelial barrier damage, and activation of the TLR4/NF-κB pathway in mice. Clinical samples analysis revealed that the diversity and abundance of microbiota were altered in patients with endometritis having positive CD138 levels, while mechanistic investigations revealed C.t alleviated S. aureus-induced endometritis by inactivating TLR4/NF-κB pathway. The findings of this study are envisaged to provide a diagnostic and therapeutic potential of microbiota in endometritis.

Towards a Comprehensive DNA Barcode Library of Stenochironomus Kieffer, 1919 (Diptera: Chironomidae) from China

The adoption of DNA-based assessments for biodiversity monitoring has been on the rise. However, the effectiveness of DNA-based taxonomic assignments heavily relies on the availability and reliability of DNA barcode libraries. There is growing demand for a comprehensive understanding of aquatic biodiversity and the critical role of Chironomidae, specifically Stenochironomus in freshwater ecosystems. Therefore, our objective is to develop a reference barcode library for Stenochironomus in China. From 2016 to 2021, we collected Stenochironomus specimens in diverse Chinese landscapes using malaise traps, light traps, and sweep nets. These specimens were carefully preserved for DNA extraction and barcode sequencing. Our analysis unveiled 36 unique operational taxonomic units from 180 COI barcode sequences through a Neighbor-Joining tree and Automatic Barcode Gap Discovery program, highlighting a significant diversity within the Stenochironomus species. The findings emphasize the constraints of conventional morphological identification methods, especially for species with ambiguous morphologies. It also underscores the effectiveness of DNA barcoding in revealing hidden species diversity, known as cryptic species. Consequently, this study advocates for an integrated taxonomic approach, combining morphological and molecular data, to refine species identification and conservation strategies.

Efficacy of intestinal microorganisms on immunotherapy of non-small cell lung cancer

While the 5-year survival rate of patients with advanced non-small cell lung cancer (NSCLC) has seen some improvement, the majority of NSCLC patients fail to respond to immunotherapy with immune checkpoint inhibitors (ICIs). It is critical to identify effective biomarkers that can enhance the efficacy of immunotherapy. The clinical data in the current study were collected from NSCLC patients treated with ICIs, and two groups were classified according to treatment effect: good group with consistent efficacy, poor group with only progressiveness. Differences in intestinal microbiota between the two groups were analyzed using 16s rRNA sequencing. Beta diversity analysis indicated differences between the two groups that were available for differentiation. Comparison of the number of common or unique operational taxonomic units (OTUs) among different groups suggested that there were 53 unique OTUs in the good group and 51 unique OTUs in the poor group. At the phylum level, there was a difference between the two groups for several bacterial groups with the highest abundance values, among which Firmicutes, Actinobacteria and Fusobacteria were more abundant in the good group. Members of the genera Bifidobacterium and Lactobacillus were abundant in the good group, while the abundance of Bacteroides was low. Biomarkers in the poor group included Bacteroides, Bacteroidetes, Bacteroidia, Bacteroidales, Bacteroidaceae and Veillonellaceae. The intestinal microbiota composition affected the immunotherapy process for NSCLC, which might offer more rational instructions for the clinical application of ICIs in NSCLC patients.

The Effects of Salinity and Genotype on the Rhizospheric Mycobiomes in Date Palm Seedlings.

Salinity severely affects the health and productivity of plants, with root-associated microbes, including fungi, potentially playing a crucial role in mitigating this effect and promoting plant health. This study employed metagenomics to investigate differences in the structures of the epiphyte mycobiomes in the rhizospheres of seedlings of two distinct date palm cultivars with contrasting salinity tolerances, the susceptible cultivar, 'Zabad', and the tolerant cultivar, 'Umsila'. Next-generation sequencing (NGS) of the internal transcribed spacer (ITS) rRNA was utilized as a DNA barcoding tool. The sequencing of 12 mycobiome libraries yielded 905,198 raw sequences of 268,829 high-quality reads that coded for 135 unique and annotatable operational taxonomic units (OTUs). An OTU analysis revealed differences in the rhizofungal community structures between the treatments regardless of genotype, and non-metric dimensional scaling (N-MDS) analyses demonstrated distinct separations between the cultivars under saline stress. However, these differences were not detected under the control environmental conditions, i.e., no salinity. The rhizospheric fungal community included four phyla (Ascomycota, Basidiomycota, Chytridiomycota, and Mucoromycota), with differences in the abundances of Aspergillus, Clonostachys, and Fusarium genera in response to salinity, regardless of the genotype. Differential pairwise comparisons showed that Fusarium falciforme-solani and Aspergillus sydowii-versicolor increased in abundance under saline conditions, providing potential future in vitro isolation guidelines for plant growth-promoting fungi. This study highlights the intricate dynamics of the rhizosphere microbial communities in date palms and their responses to salt stress. Additionally, we found no support for the hypothesis that indigenous epiphytic fungal communities are significantly involved in salinity tolerance in date palms.

The soil microbiome of Lolium perenne L. depends on host genotype, is modified by nitrogen level and varies across season

Genotype by environment interactions (G × E) are frequently observed in herbage production. Understanding the underlying biological mechanisms is important for achieving stable and predictive outputs across production environments. The microbiome is gaining increasing attention as a significant contributing factor to G × E. Here, we focused on the soil microbiome of perennial ryegrass (Lolium perenne L.) grown under field conditions and investigated the soil microbiome variation across different ryegrass varieties to assess whether environmental factors, such as seasonality and nitrogen levels, affect the microbial community. We identified bacteria, archaea, and fungi operational taxonomic units (OTUs) and showed that seasonality and ryegrass variety were the two factors explaining the largest fraction of the soil microbiome diversity. The strong and significant variety-by-treatment-by-seasonal cut interaction for ryegrass dry matter was associated with the number of unique OTUs within each sample. We identified seven OTUs associated with ryegrass dry matter variation. An OTU belonging to the Solirubrobacterales (Thermoleophilales) order was associated with increased plant biomass, supporting the possibility of developing engineered microbiomes for increased plant yield. Our results indicate the importance of incorporating different layers of biological data, such as genomic and soil microbiome data to improve the prediction accuracy of plant phenotypes grown across heterogeneous environments.

Fish predation risk alters the microbiota of Daphnia in the process of inducing its life‐history defence traits

Abstract Host‐associated microbiota is an essential mediator of host adaptation to changeable environmental conditions. However, whether fish predation risk alters the gut microbiota composition of Daphnia while also of inducing Daphnia's life‐history defence traits remains unclear. Examination of the effect of predation risk on prey‐associated microbiota may help in improving our understanding of induced anti‐predation defence from a microbial perspective. In this study, Daphnia magna was used as the model organism to investigate the changes in the microbiota in the gut of Daphnia as well as in the whole Daphnia and the culture medium during D. magna life‐history anti‐predation defence. The relationship of these changes with the development stage was also assessed. The results showed that predation risk can simultaneously induce anti‐predation defences and reshape the associated microbiota composition of Daphnia. The gut microbiota of D. magna responded to both developmental stages and predation risk. The Shannon diversity of gut microbiota under predation risk decreased significantly with developmental stage. The abundance of dominant bacteria such as Burkholderiaceae and Flavobacteriaceae decreased under predation risk and was further reduced with developmental stage. Functional prediction results showed that the presence of predation risk mainly weakened overall microbial function, especially metabolic function, in the gut of D. magna. The weakening of microbial function was most obvious during sexual maturity. In addition, the number of unique operational taxonomic units in the whole Daphnia and dissected guts under predation risk was significantly higher than those in control. Based on the screening results, the Pantoea genus (Erwiniaceae family) can clearly distinguish dissected gut samples with or without predation risk. The present study provided more insights into the structural features and functional roles of the Daphnia microbiota and improved our understanding of induced anti‐predation defence from a microbial perspective. Furthermore, this study highlights the possible complex correlations that exist between induced defensive traits and altered microbiota, which warrants further investigation.

The effect of type and combination of fertilizers on eukaryotic microbiome of date palm rhizosphere

The date palm (Phoenix dactylifera) is an important cultivated crop in arid areas. Here, we studied the effect of plant genotype and type of fertilizers on the eukaryotic community structures of the date palm rhizosphere. Samples were collected from one wild population, five cultivars from two farms, and a factorial fertilizer experiment (organic, chemical, and biofertilizer) in Qatar. The eukaryotic communities were sequenced using a next-generation sequencing method. A total of 2422 Operational Taxonomic Units (OTUs) were identified as belonging to 15 phyla, Chlorophyta, Streptophyta, Imbricatea, Chytridiomycota, Ascomycota, Olpidiomycota, being dominant. The wild-type date palms showed a low number of OTUs compared to cultivated date palms, potentially due to the strong influence of soil salinity and low moisture level. However, the wild-type date palm hosted the highest number of unique OTUs. PCA revealed that the eukaryotic microbiome of the wild date palms was separated from the cultivated date palms and that the eukaryotic microbial diversity varied between date palm cultivars in similar environments. Using the highest amounts of biofertilizer and chemical fertilizer decreased the species diversity within the samples. However, a high concentration of biofertilizer combined with a low concentration of chemical fertilizers enhanced the eukaryotic diversity within the samples. We conclude that cultivar type (biotic factor), type of fertilizer, and dosage (abiotic factor) play significant roles in determining the microbiome diversity of the rhizosphere. The wild date palm population could potentially host salt and drought-tolerating eukaryotes that should be further investigated for future development of biofertilizers suitable for drylands.

Comparison of Yamuna (India) and Mississippi River (United States of America) bacterial communities reveals greater diversity below the Yamunotri Glacier.

The Yamuna River in India and the Mississippi River in the United States hold significant commercial, cultural, and ecological importance. This preliminary survey compares the bacterial communities sampled in surface waters at 11 sites (Yamuna headwaters, Mississippi headwaters, Yamuna River Yamunotri Town, Mississippi River at Winona, Tons River, Yamuna River at Paonta Sahib, Yamuna River Delhi-1, Yamuna River Delhi-2, Yamuna River before Sangam, Sangam, Ganga River before Sangam). Bacterial 16S rDNA analyses demonstrate dominance of Proteobacteria and Bacteroidetes phyla. Actinobacteria were also dominant at sites near Sangam in India and sites in Minnesota. A dominance of Epsilonbacteraeota were found in Delhi, India. Principal component analysis (PCA) using unique operational taxonomic units (OTUs) resulted in the identification of 3 groups that included the Yamuna River locations in Delhi (Delhi locations), Yamuna headwaters and Yamuna River at Yamunotri (Yamuna River locations below the Glacier) and Mississippi, Ganga, Tons, and other Yamuna River locations. Diversity indices were significantly higher at the Yamuna River locations below the Glacier (Simpson D = 0.986 and Shannon H = 5.06) as compared (p value <0.001) to the Delhi locations (D = 0.951 and H = 4.23) and as compared (p value < 0.001) to Mississippi, Ganga, Tons, and other Yamuna River locations (D = 0.943 and H = 3.96). To our knowledge, this is the first survey to compare Mississippi and Yamuna River bacterial communities. We demonstrate higher diversity in the bacterial communities below the Yamunotri glacier in India.

Profiling the Bacterial Community of Fermenting Traminette Grapes during Wine Production using Metagenomic Amplicon Sequencing.

Advances in sequencing technology and the relatively easy access to the use of bioinformatics tools to profile microbial community structures have facilitated a better understanding of both culturable and non-culturable microbes in grapes and wine. During industrial fermentation, microbes, known and unknown, are often responsible for product development and off-flavor. Therefore, profiling the bacteria from grape to wine can enable an easy understanding of in situ microbial dynamics. In this study, the bacteria of Traminette grapes must undergoing fermentation, and the final wine were subjected to DNA extraction that yielded 15 ng/µL to 87 ng/µL. The 16S amplicon of the hypervariable region of the V4 region was sequenced, relatively abundant bacteria consisting of phyla Proteobacteria, Actinobacteriota, Firmicutes, Bacteroidota, Fusobacteriota and followed by the Verrucomicrobiota, Halobacterota, Desulfobacterota, Myxococcota, and Acidobacteriota. A Venn diagram analysis of the shared unique operational taxonomic units (OTU) revealed that 15 bacteria phyla were common to both grape must, fermenting stage, and final wine. Phyla that were not previously reported were detected using the 16S amplicon sequencing, as well as genera such as Enterobacteriaceae and Lactobacillaceae. Variation in the organic nutrient use in wine and its impact on bacteria was tested; Traminette R tank containing Fermaid O and Traminette L stimulated with Stimula Sauvignon blanc + Fermaid O. Alpha diversity using the Kruskal-Wallis test determined the degree of evenness. The beta diversity indicated a shift in the bacteria at the fermentation stage for the two treatments, and the final wine bacteria looked similar. The study confirmed that 16S amplicon sequencing can be used to monitor bacteria changes during wine production to support quality and better utilization of grape bacteria during wine production.

Characterization and seasonal variation in biofilms attached to leaves of submerged plant.

The microorganisms and functional predictions of leaf biofilms on submerged plants (Vallisneria natans (Val)) and in water samples (surface water (S) and bottom water (B)) in different seasons were evaluated in this study. S and B groups had 3249 identical operational taxonomic units (OTUs) (50.03%), while the Val group only had 1201 (18.49%) unique OTUs. There was significant overlap between microbial communities of S and B groups in the same season, while Val group showed the greater diversity. The dominant microbial clades were Proteobacteria (18.2-47.3%), Cyanobacteria (3.74-39.3%), Actinobacteria (1.64-29.3%), Bacteroidetes (1.31-21.7%), and Firmicutes (1.10-15.72%). Furthermore, there was a significant relationship between total organic carbon and the distribution of microbial taxa (p = 0.047), and TN may have altered the status of Cyanobacteria by affecting its biological nitrogen fixation capacity and reproductive capacity. The correlation network analysis results showed that the whole system consisted of 249 positive correlations and 111 negative correlations, indicating strong interactions between microbial communities. Functional predictions indicated that microbial functions were related to seasonal variation. These findings would guide the use of submerged plants to improve the diversity and stability of wetland microbial communities.

Synthesis and application of a compound microbial inoculant for effective soil remediation.

Currently, there is a noticeable scarcity of applications that harness composite microbial inoculants to stimulate straw decomposition, nitrogen fixation, and crop growth. This study addresses this gap by selecting and coculturing three bacterial strains to create a composite microbial inoculant named HY-1. This innovative inoculant exhibits multifunctional capabilities, including nitrogen fixation, straw decomposition, and crop growth promotion. Furthermore, we aimed to explore its impact on soil microbial communities. The results showed that the optimal preparation conditions for the compound microbial inoculant HY-1 were 28.5 ± 0.6°C, pH = 7.34 ± 0.40, and bacteriophage ratio 1:2:1 (Microbacterium: Streptomyces fasciatus: Bacillus amyloliquefaciens). Compared to single strains, the combination exhibited higher levels of cellulose-degrading and nitrogen-fixing enzyme activity, increased the straw degradation rate by 37.91% within 180days, and significantly promoted the growth of corn seedlings. Under the condition of straw return, the compound bio-fungicide HY-1 effectively improved the soil microbial diversity. At that time, the soil had the highest number of unique bacterial operational taxonomic units (166), and the abundance of Proteobacteria in the soil increased by 7.24%, while that of Acidobacteriota decreased by 2.27%. The biosynthetic function of the cell wall/membrane/periplasm and the metabolic function of transporting inorganic ions were significantly enhanced. In this study, we discovered that employing coculturing techniques to produce the composite microbial inoculant HY-1 and applying it in the field effectively compensates for the limitations of single-strain inoculants, which often exhibit fewer functions and less pronounced effects. This approach demonstrates significant potential for enhancing the quality of agricultural soils.

Co-occurring tree species drive arbuscular mycorrhizal fungi diversity in tropical forest.

It is still uncertain whether environment or host plant species is more important in determining AMF diversity; although, plant roots are usually associated with abundant AMF species in different environments. This study explored the effect of plant species and environmental factors on AMF diversity based on three co-occurring tree species (Glochidion coccineum, Schefflera octophylla, and Schima superba) on six elevations of Mt. Jianfengling. A total of 185 OTUs (operational taxonomic units) of AMF were found in the three co-occurring dominant tree species. Of which 109 unique OTUs were identified in the three co-occurring plant species, which accounted for the total number of 58.92%. Forty-five OTUs were shared by the three co-occurring tree species, accounting for a total number of 24.32%. The plant species of Schefflera octophylla was identified as having the highest AMF diversity with the largest number of OTUs of 143. The fungi in the genus of Glomus were the dominant AMF species in the three co-occurring tree species. AMF communities and diversity are quite different, either within different plant species at the same elevation or within the same plant species at different elevations. However, the altitude had no significant effect on the ACE index. Therefore, the results suggest that plant species have a more important effect on AMF diversity and community composition.

Intercropping system modulated soil-microbe interactions that enhanced the growth and quality of flue-cured tobacco by improving rhizospheric soil nutrients, microbial structure, and enzymatic activities.

As the promotive/complementary mechanism of the microbe-soil-tobacco (Nicotiana tabacum L.) interaction remains unclear and the contribution of this triple interaction to tobacco growth is not predictable, the effects of intercropping on soil nutrients, enzymatic activity, microbial community composition, plant growth, and plant quality were studied, and the regulatory mechanism of intercropping on plant productivity and soil microenvironment (fertility and microorganisms) were evaluated. The results showed that the soil organic matter (OM), available nitrogen (AN), available phosphorus (AP), available potassium (AK), the urease activity (UE) and sucrase activity (SC), the diversity, abundance, and total and unique operational taxonomic units (OTUs) of bacteria and fungi as well as plant biomass in T1 (intercropping onion), T2 (intercropping endive), and T3 (intercropping lettuce) treatments were significantly higher than those of the controls (monocropping tobacco). Although the dominant bacteria and fungi at the phylum level were the same for each treatment, LEfSe analysis showed that significant differences in community structure composition and the distribution proportion of each dominant community were different. Proteobacteria, Acidobacteria, and Firmicutes of bacteria and Ascomycota and Basidiomycetes of fungi in T1, T2, and T3 treatments were higher than those of the controls. Redundancy analysis (RDA) suggested a close relation between soil characteristic parameters and microbial taxa. The correlation analysis between the soil characteristic parameters and the plant showed that the plant biomass was closely related to soil characteristic parameters. In conclusion, the flue-cured tobacco intercropping not only increased plant biomass and improved chemical quality but also significantly increased rhizospheric soil nutrient and enzymatic activities, optimizing the microbial community composition and diversity of rhizosphere soil. The current study highlighted the importance of microbe-soil-tobacco interactions in maintaining plant productivity and provided the potential fertilization practices in flue-cured tobacco production to maintain ecological sustainability.

Impact of Elevational Gradients and Chemical Parameters on Changes in Soil Bacterial Diversity Under Semiarid Mountain Region.

Elevation gradients, often regarded as "natural experiments or laboratories", can be used to study changes in the distribution of microbial diversity related to changes in environmental conditions that typically occur over small geographical scales. We obtained bacterial sequences using MiSeq sequencing and clustered them into operational taxonomic units (OTUs). The total number of reads obtained by the bacterial 16S rRNA sequencing analysis was 1,090,555, with an average of approximately 45,439 reads per sample collected from various elevations. The current study observed inconsistent bacterial diversity patterns in samples from the lowest to highest elevations. 983 OTUs were found common among all the elevations. The most unique OTUs were found in the soil sample from elevation_2, followed by elevation_1. Soil sample collected at elevation_6 had the least unique OTUs. Actinobacteria, Protobacteria, Chloroflexi were found most abundant bacterial phyla in current study. Ammonium nitrogen (NH4+-N), and total phosphate (TP) are the main factors influencing bacterial diversity at elevations_1. pH was the main factor influencing the bacterial diversity at elevations_2, elevation_3 and elevation_4. Our results provide new visions on forming and maintaining soil microbial diversity along an elevational gradient and have implications for microbial responses to environmental change in semiarid mountain ecosystems.

Gut microbiota signature in children with autism spectrum disorder who suffered from chronic gastrointestinal symptoms

BackgroundChildren diagnosed with autism spectrum disorder (ASD) frequently suffer from persistent gastrointestinal symptoms, such as constipation and diarrhea. Various studies have highlighted differences in gut microbiota composition between individuals with ASD and healthy controls of similar ages. However, it’s essential to recognize that these disparities may be influenced by cultural practices, dietary habits, and environmental factors.MethodsIn this study, we collected fecal samples from both children diagnosed with ASD (n = 42) and healthy individuals (n = 41) residing in the southeastern coastal region of China. Subsequently, 16 S rRNA gene sequencing and advanced bioinformatics analyses were conducted to investigate the distinctive features of gut microbial communities within each group.ResultsThe ASD group consisted of 28 males and 14 females, with a median age of 5.8 years, while the control group included 25 males and 16 females, with a median age of 6.8 years. Among the 83 sequenced fecal samples, a total of 1031 operational taxonomic units (OTUs) were identified. These included 122 unique OTUs specific to the control group and 285 unique OTUs specific to the ASD group. Analyses of α-diversity and β-diversity unveiled significant differences in the abundance and composition of gut microbiota between the two groups. It was found that the dominant bacterial taxa in healthy individuals were UBA1819, Flavonifractor, and Bradyrhizobium. In contrast, the ASD group exhibited a prevalence of Streptococcus, Ruminococcus, and Ruminiclostridium. Further analysis using Kyoto Encyclopedia of Genes and Genomes (KEGG) and Clusters of Orthologous Groups (COG) showed significant differences in the metabolic functionalities of the gut microbiota between the two groups. Notably, the metabolic pathway related to alpha-linolenic acid (ALA) in the gut microbiota of the ASD group was notably diminished compared to the control group. Conversely, the ASD group demonstrated significantly elevated levels of metabolic pathways involving uncharacterized conserved proteins, aminoglycoside phosphotransferase, and inorganic pyrophosphatase compared to the control group.ConclusionsOverall, these results confirm that there are significant differences in the gut microbiota structure between children with ASD and healthy controls in the southeast coastal region of China. This underscores the critical significance of delving into clinical interventions capable of mitigating the gastrointestinal and psychological symptoms encountered by children with ASD. A particularly encouraging path for such interventions lies in the realm of fecal microbiota transplantation, a prospect that merits deeper inquiry.

Molecular Diet Analysis of Asian Clams for Supplementary Biodiversity Monitoring: A Case Study of Nakdong River Estuary.

Environmental DNA (eDNA) extracted from the gut contents of filter feeders can be used to identify biodiversity in aquatic ecosystems. In this study, we used eDNA from the gut contents of the Asian clam Corbicula fluminea to examine biodiversity within estuarine ecosystem. Field sampling was conducted at three points in the Nakdong River Estuary, which is characterised by closed estuarine features resulting from the presence of an estuarine barrage. The collected C. fluminea samples were dissected to separate the gut contents, and the extracted eDNA was amplified using 18S V9 primer targeting all eukaryote-derived DNA. The amplified DNA was sequenced using a next-generation sequencing (NGS) technique, and a BLASTn search was performed based on the National Centre for Biotechnology Information (NCBI) database for taxa identification. We obtained 23 unique operational taxonomic units (OTUs), including fish (approximately 8.70%), copepods (approximately 17.39%), and green algae (approximately 21.74%), representing a wide range of habitats. Furthermore, 8 out of the 20 families were identified through comparisons with reference data from conventional field surveys, and the OTUs of elusive migratory fish were detected. The results support the application of C. fluminea as an eDNA sampler for supplementary biodiversity monitoring.

Unveiling Fungal Community Structure along Different Levels of Anthropic Disturbance in a South American Subtropical Lagoon.

Studies of fungal communities through amplicon metagenomics in aquatic environments, particularly in freshwater ecosystems, are still relatively recent. Unfortunately, many of these water bodies are facing growing threats from human expansion, such as effluent discharge from various human activities. As a result, these effluents have the potential to significantly alter the characteristics of water bodies and, subsequently, impact the diversity of their resident microorganisms. In this context, our objective was to investigate whether the fungal community structure varies according to the presence of different anthropic disturbances. We expect (i) the diversity of fungi will be greater and (ii) more specific unique operational taxonomic units (OTUs) related to each ecotonal system will be found compared to other sites of a lagoon. The study was conducted in the Tramandaí Lagoon (subtropical southern Brazil) at four distinct sampling points (estuary, middle of the lagoon, crop field area, and near a residential area where the Tramandaí River flows into the lagoon). As expected, the estuary and residential zones, which are ecotones, exhibited greater fungal diversity and more specific OTUs compared to the middle of the lagoon and crop field area. Moreover, a substantial proportion of fungal taxa could not be identified at the genus level, with many only classified at the phylum level, indicating potential new lineages. These findings underscore our limited understanding of the subtropical freshwater mycobiota.

Bacterial community structure and predicted function in the rhizosphere of wild and cultivated date palms: Effects of Fertilizers on Composition and Functionality

This study investigated bacterial diversity in date palm rhizosphere and assessed the influence of different fertilizers on diversity using metagenomics. A total of 6356 Operational Taxonomic Units (OTUs) and 1164425 sequences were analyzed across 27 samples. The findings revealed variations in microbial community phylogeny among similar cultivars from different farms, except for the Khalas cultivar, suggesting minor influence of genotype on microbial community structure. Wild date palms exhibited more unique OTUs, in contrast, cultivated date palms had a higher number of OTUs and diversity. Moreover, different fertilizer treatments had varying effects on bacterial diversity. For example, organic and bio-organic fertilizers positively influenced specific bacterial groups, including delta-proteobacteria, acidobacteria-Gp3, Anaerolinaea, and Clostridia. Conversely, combining high concentrations of chemical fertilizers with other types did not show significant effects. Classes such as Bacilli, Nitrospira, Deltaproteobacteria, Spartobacteria, and Thermomacrobia exhibited high relative abundances in treatments with high chemical fertilizer concentrations. Our analysis revealed potential pathways related to carbon, nitrogen, phosphorus, phenol, sulfur, and antimicrobial compounds. Interestingly, these pathways and functions varied across different date palm cultivars. Our findings suggest that date palm cultivars shape the rhizosphere by selectively influencing bacterial communities consistently across other locations. These modulated bacterial communities can potentially provide enhanced benefits to the host. Importantly, this study was the first to investigate the soil bacterial diversity of wild date palms, giving valuable insights into the microbial community associated with this specific context.