Permutational Multivariate Analysis Research Articles

High-throughput sequencing-based analysis of the composition and diversity of the endophyte community in roots of Stellera chamaejasme

Stellera chamaejasme (S. chamaejasme) is an important medicinal plant with heat-clearing, detoxifying, swelling and anti-inflammatory effects. At the same time, it is also one of the iconic plants of natural grassland degradation in northwest China, playing a key role in the invasion process. Plant endophytes live in healthy plant tissues and can synthesize substances needed for plant growth, induce disease resistance in host plants, and enhance plant resistance to environmental stress. Therefore, studying the root endophytes of S. chamaejasme is of great significance for mining beneficial microbial resources and biological prevention and control of S. chamaejasme. This study used Illumina MiSeq high-throughput sequencing technology to analyze the composition and diversity of endophytes in the roots of S. chamaejasme in different alpine grasslands (BGC, NMC and XGYZ) in Tibet. Research results show that the main phylum of endophytic fungi in the roots of S. chamaejasme in different regions is Ascomycota, and the main phyla of endophytic bacteria are Actinobacteria, Proteobacteria and Firmicutes (Bacteroidota). Overall, the endophyte diversity of the NMC samples was significantly higher than that of the other two sample sites. Principal coordinate analysis (PCoA) and permutational multivariate analysis of variance (PERMANOVA) results showed significant differences in the composition of endophytic bacterial and fungal communities among BGC, NMC and XGYZ samples. Co-occurrence network analysis of endophytes showed that there were positive correlations between fungi and some negative correlations between bacteria, and the co-occurrence network of bacteria was more complex than that of fungi. In short, this study provides a vital reference for further exploring and utilizing the endophyte resources of S. chamaejasme and an in-depth understanding of the ecological functions of S. chamaejasme endophytes.

Intraspecific variation in fine-root traits is larger than in aboveground traits in European herbaceous species regardless of drought

Differences within species (Intraspecific trait variation - ITV) contribute substantially to overall trait variability and environmental harshness can reduce among-species variation. While aboveground traits have received considerable attention, knowledge about ITV in fine-root traits and how it differs from ITV in aboveground traits remains limited. This study examined the partitioning of trait variation aboveground and fine-root traits in 52 European herbaceous species and how such proportions change in response to drought, offering valuable insights for accurate functional species characterization and inter-species comparisons. We studied seven morphological aboveground and fine-root traits under drought and well-watered conditions in a greenhouse experiment. Linear mixed effect models and permutational multivariate analysis of variance (PERMANOVA) were employed to decompose trait variation, ensuring the robustness of our results. We also calculated variance partitioning for the combination of aboveground traits and the combination of fine-root traits, as well as pairs of analogous leaf and fine-root traits (i.e., traits that fulfill similar functions) for each treatment (control and drought). Among-species trait differences explained a greater proportion of overall variance than within-species variation, except for root dry matter content (RDMC). Height and leaf area stood out, with species’ identity accounting for 87-90% of total trait variation. Drought had no significant effect on the proportions of variation in any of the traits. However, the combination of fine-root traits exhibited higher intraspecific variability (44-44%) than aboveground traits (19-21%) under both drought and control. Analogous root traits also showed higher ITV (51-50%) than analogous leaf traits (27-31%). Our findings highlight substantial within-species variation and the nuanced responses of fine-root traits, particularly RDMC, suggesting root traits’ flexibility to soil heterogeneity that fosters less differentiation among species. Among-species trait differences, especially aboveground, may underscore distinct strategies and competitive abilities for resource acquisition and utilization. This study contributes to elucidate the mechanisms underlying the multifunctionality of the above- and belowground plants compartments.

Sex-specific associations between AD genotype and the microbiome of human amyloid beta knock-in (hAβ-KI) mice.

Emerging evidence links changes in the gut microbiome to late-onset Alzheimer's disease (LOAD), necessitating examination of AD mouse models with consideration of the microbiome. We used shotgun metagenomics and untargeted metabolomics to study the human amyloid beta knock-in (hAβ-KI) murine model for LOAD compared to both wild-type (WT) mice and a model for early-onset AD (3xTg-AD). Eighteen-month female (but not male) hAβ-KI microbiomes were distinct from WT microbiomes, with AD genotype accounting for 18% of the variance by permutational multivariate analysis of variance (PERMANOVA). Metabolomic diversity differences were observed in females, however no individual metabolites were differentially abundant. hAβ-KI mice microbiomes were distinguishable from 3xTg-AD animals (81% accuracy by random forest modeling), with separation primarily driven by Romboutsia ilealis and Turicibacter species. Microbiomes were highly cage specific, with cage assignment accounting for more than 40% of the PERMANOVA variance between the groups. These findings highlight a sex-dependent variation in the microbiomes of hAβ-KI mice and underscore the importance of considering the microbiome when designing studies that use murine models for AD. Microbial diversity and theabundance of several species differed in human amyloid beta knock-in (hAβ-KI) females but not males. Correlations to Alzheimer's disease (AD) genotype were stronger for the microbiome than the metabolome. Microbiomes from hAβ-KI mice were distinct from 3xTg-AD mice. Cage effects accounted for most of the variance in the microbiome and metabolome.

Seasonal diet partition among top predators of a small island, Iriomote Island in the Ryukyu Archipelago, Japan

Small islands tend to lack predators because species at higher trophic levels often cannot survive. However, two exceptional top predators—the Iriomote cat Prionailurus bengalensis iriomotensis, and the Crested Serpent Eagle Spilornis cheela perplexus—live on the small Iriomote Island in the Ryukyu Archipelago. To understand how these predators coexist with limited resources, we focused on their seasonal diets between which conflicts are considered to occur. To compare the diets, we used DNA metabarcoding analysis of faecal samples. In the summer, we identified 16 unique prey items from Iriomote cat faecal samples and 15 unique prey items from Crested Serpent Eagle faecal samples. In the winter, we identified 37 and 14, respectively. Using a non-metric multidimensional scaling and a permutational multivariate analysis of variance, our study reveals significant differences in the diet composition at the order level between the predators during both seasons. Furthermore, although some prey items at the species-to-order level overlapped between them, the frequency of occurrence of most prey items differed in both seasons. These results suggest that this difference in diets is one of the reasons why the Iriomote cat and the Crested Serpent Eagle are able to coexist on such a small island.

Comparisons of benthic associated fauna assemblages in seagrass meadows across conservation and non-conservation areas in Bali and Lombok, Indonesia

Benthic ecosystem has been widely considered as an important feature of seagrass associated fauna, and its function as a grazer and linkage between primary producers and higher trophic level is well known. Though the importance of benthic fauna in seagrass ecosystems has been indicated in many studies, its biodiversity in spatial scale has often been poorly studied. This study aimed at examining the assemblages and diversity of benthic associated fauna in conservation areas (CA) and non-conservation areas (NCA) across the seagrass meadows in Bali and Lombok. This study found that the assemblages and diversity of benthic fauna greatly varied between the meadows. A total of 430 individuals associated to benthic fauna from 24 species were identified in Bali and Lombok. Of these, Gastropods were the highest class of taxa recorded in this study, followed by Bivalvia, Echinodermata, Decapoda, and Amphipoda. Permutation multivariate analysis of variance (PERMANOVA) revealed a significantly different benthic fauna diversity between sites. Non-metric Multidimensional Scaling (nMDS) and Bray–Curtis analysis showed a clear distinction of benthic fauna assemblages between CA and NCA, both in Bali and Lombok. These results indicated that from spatial perspective, different characteristics of seagrass meadows may represent different biodiversity of associated fauna. These differences might be driven by different anthropogenic pressure and variation of substrates among the meadows which may affect the composition of the benthic fauna ecosystems. The implication of this study was to providing baseline data on guiding the appropriate approach and strategies for management and conservations of seagrass ecosystems.

Abstract 834: Farm animal exposures and the oral microbiome in the Agricultural Health Study

Abstract Raising farm animals involves a variety of exposures, including microbes, antimicrobial agents, bioaerosols, and pesticides that may influence the human microbiome. Exposure to farm animals has also been associated with some cancers including lower risk of lung cancer and elevated risks of certain hematologic malignancies, with heterogeneity by animal species. Increasing epidemiologic evidence suggests that changes in the oral microbiome contribute to cancer development. Few human studies have investigated the potential influence of farm animal exposures on the oral microbiome. We investigated associations between farm animal exposures and the oral microbiome in 1245 Iowa and North Carolina farmers and spouses from the Agricultural Health Study. Participants provided information on types and numbers of farm animals raised in telephone interviews close to the time of oral wash sample collection. DNA was extracted from oral wash specimens and analyzed using 16S rRNA gene (V4 region) sequencing. We evaluated associations between farm animal exposures and alpha diversity metrics [e.g., observed amplicon sequence variants (ASVs)] using linear regression and assessed differences in beta diversity metrics (e.g., weighted Unifrac) using permutational multivariate analysis of variance. In addition, we evaluated associations with the presence and relative abundance of specific genera using zero-inflated negative binomial regression. All analyses adjusted for potential confounders (e.g., sex, age, state of residence, smoking). Overall, 63% of participants reported raising any animals, most commonly cattle (46%) and hogs (20%). Raising sheep/goats was associated with lower alpha diversity [e.g., 18 (95% confidence interval: 3-33) fewer observed ASVs compared to not raising sheep/goats], with an exposure-response trend for increasing number of sheep/goats (13 and 24 fewer observed ASVs for 1-29 and ≥30 sheep/goats vs. none, respectively; Ptrend = 0.048). Increasing numbers of hogs and poultry were associated with higher and lower alpha diversity, respectively. Associations were similar after mutual adjustment for other farm animal types. Based on beta diversity analyses, we did not observe statistically significant differences in microbial compositions between participants with and without farm animals. After adjusting for multiple testing, having any farm animal was associated with an increased relative abundance of Porphyromonas, and several genera were more likely to be absent with specific animal exposures (e.g., Capnocytophaga for cattle and sheep/goats; Corynebacterium and Abiotrophia for sheep/goats). To our knowledge, this was the largest investigation of farm animal exposures and the human microbiome to date. Our preliminary findings suggest that animal farming may alter the oral microbiome and provide new insights into the potential role of animal exposures in cancer etiology. Citation Format: Vicky C. Chang, Vaishnavi Purandare, Rashmi Sinha, Gabriella Andreotti, Shilan Li, Xing Hua, Yukiko Yano, Kathryn R. Dalton, Mikyeong Lee, Christine G. Parks, Stephanie J. London, Dale P. Sandler, Mitchell H. Gail, Jianxin Shi, Jonathan N. Hofmann, Christian C. Abnet, Emily Vogtmann, Laura E. Beane Freeman. Farm animal exposures and the oral microbiome in the Agricultural Health Study [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 834.

Türkiye’den Salmo cinsine ait iki türün karşılaştırmalı otolit morfolojisi

In this study, the morphology of the sagittal otolith of Salmo coruhensis Turan, Kottelat & Engin, 2010 and Salmo fahrettini Turan, Kalayci, Bektaş, Kaya & Bayçelebi, 2020 from Çam Stream (Artvin) and Terme Stream (Samsun) was described by images of scanning electron microscopy. Its shape and contour were also analyzed with shape indices, elliptic Fourier coefficients and wavelet transforms. As the study material, a total of 30 S. coruhensis sample and 20 S. fahrettini sample were obtained. Interspecies differences in otolith shape and morphometry were evaluated by principal components analysis, canonical discrimination analysis, and permutational multivariate analysis of variance. The two salmonid species studied were distinguished by both morphometric and shape analysis methods. However, wavelet transform was found to be more effective than shape indices and elliptic Fourier coefficients in species discrimination, with an overall classification success rate of 80%. Our results showed that saccular otolith morphology could be an additional diagnostic character for trout species differentiation.

Levels of lipid-derived gut microbial metabolites differ among plant matrices in an in vitro model of colon fermentation

This study explored differences in microbial lipid metabolites among sunflower seeds, soybeans, and walnuts. The matrices were subjected to in vitro digestion and colonic fermentation. Defatted digested materials and fiber/phenolics extracted therefrom were added to sunflower oil (SO) and also fermented. Targeted and untargeted lipidomics were employed to monitor and tentatively identify linoleic acid (LA) metabolites. Walnut fermentation produced the highest free fatty acids (FFAs), LA, and conjugated LAs (CLAs). Defatted digested walnuts added to SO boosted FFAs and CLAs production; the addition of fibre boosted CLAs, whereas the addition of phenolics only increased 9e,11z-CLA and 10e,12z-CLA. Several di-/tri-hydroxy-C18-FAs, reported as microbial LA metabolites for the first time, were annotated. Permutational multivariate analysis of variance indicated significant impacts of food matrix presence and type on lipidomics and C18-FAs. Our findings highlight how the food matrices affect CLA production from dietary lipids, emphasizing the role of food context in microbial lipid metabolism.

Environmental heterogeneity influences liana community differentiation across a Neotropical rainforest landscape.

We examined the variation in liana community composition and structure across geopedological land units to test the hypothesis that environmental heterogeneity is a driving force in liana community assembly. The study site was the Los Tuxtlas Tropical Biology Station, SE Mexico, a reserve that encompasses 640 ha of tropical rainforest. We sampled all lianas with basal diameter ≥1 cm in three 0.5-ha plots established in each of five land units (totaling 15 plots and 7.5 ha). We censused 6055 individuals and 110 species. Overall, the most speciose families were also the most abundant ones. Density and basal area of some dominant liana species differed among land units, and a permutational multivariate analysis of variance (PERMANOVA) and a non-metric multidimensional scaling ordination (NMDS) revealed differences in the presence, density, and basal area of liana species across the landscape. Liana composition and structure were highly heterogeneous among land units, suggesting that variations in soil water availability and relief are key drivers of liana community spatial differentiation. By showing that soil and topography play an important role at the landscape scale, we underscore the ecological relevance of environmental heterogeneity for liana community assembly. In the future, as our ability to assess the local environmental complexity increases, we will gain a better understanding of the liana community assembly process and their heterogeneous distribution in tropical forests.

Habitat type strongly influences the structural benthic invertebrate community composition in a landscape characterized by ubiquitous, long-term agricultural stress

ABSTRACT The importance of small waterbodies for biodiversity and ecosystem processes has long been neglected in research and policy development. However, because of their heterogeneous characteristics and habitat structures, these waterbodies are biodiversity hotspots for various aquatic and terrestrial organisms, as previously shown for rotifers, aquatic birds, and amphibians. Knowledge of benthic invertebrate community structures in small waterbodies is scarce. Thus, we performed a comprehensive field study of these structures in an agricultural landscape in the northeastern German lowlands. We obtained a dataset containing biological (taxon abundances) and chemical (pesticide residue and nutrient concentration) data as well as data on environmental parameters (e.g., conductivity and habitat type) for 111 samples. The dataset was analyzed using generalized linear models, permutational multivariate analysis of variance, and partial redundancy analysis to understand the relationships among benthic invertebrate communities, agricultural stressors, and environmental parameters. The factor that best explained structural community composition was habitat type. Pesticide and nutrient concentrations were of minor importance in our analysis. Because of the ubiquitous and long-term occurrence of the agricultural stressors, the structural indices used in benthic invertebrate biomonitoring were not sufficiently sensitive to provide information on the main environmental variables that shape macroinvertebrate communities.

Gut Microbiota Alterations in Adolescent Idiopathic Scoliosis Are Associated with Aberrant Bone Homeostasis.

Low bone mineral density is the major prognostic factor for adolescent idiopathic scoliosis (AIS), but the underlying mechanisms remain unclear. Accumulating evidence suggests that gut microbiota (GM) have the potential to affect bone development, and the GM signatures are altered in AIS patients. However, the effect of GM alterations on aberrant bone homeostasis in AIS remains unclear. This study aims to investigate the GM profile in AIS patients with different bone mineral density (BMD) and explore the association between GM, osteopenia, and aberrant bone turnover. A total of 126 patients with AIS who received surgical treatment were retrospectively included in this study. We analyzed the composition of the GM by 16S rRNA sequencing and BMD by dual X-ray absorptiometry. Based on the BMD of the femur neck, the patients were divided into the osteopenia group (OPN) if the Z score < -1, and the normal (NOR) group if the Z score ≥ -1 SD compared to the healthy control. For the 16S rRNA sequencing, the raw reads were filtered to remove low-quality reads, and operational taxonomic units were identified with the Uparse program. Weighted UniFrac distance matrix for the beta-diversity metrics and principal coordinate analysis (PCoA) was performed, and the statistical comparisons were made with permutational multivariate analysis of variance (PERMANOVA) and analysis of similarity (ANONISM). Linear discriminant analysis effect size (LEfSe) was used to identify the enriched species in two groups. The "Random forest" was applied to determine the optimal biomarker for OPN according to the mean decrease in Gini value. The metabolic function was predicted by the Tax4Fun analysis. The Pearson correlation coefficient was used to evaluate the associations between GM species, bone turnover markers, and BMD. The serum β-CTX was increased in the OPN group (n = 67) compared to the NOR group (n = 59). Patients in OPN groups showed significantly decreased α diversity indicated by the Shannon index. Principal coordinate analysis (PCoA) analysis showed significant clustering of GM between OPN and NOR groups. At genus level, the Escherichia-Shigella and Faecalibacterium were significantly enriched in the OPN group compared to that in the NOR group (p < 0.05), whereas the abundance of Prevotella was significantly decreased (p = 0.0012). The relative abundance of Megamonas and Prevotella was positively correlated with the femur BMD. The abundance of Escherichia-Shigella was negatively correlated with femur BMD and positively correlated with serum β-CTX levels. Functional analysis revealed significant differences in starch and sucrose metabolism, pyruvate and cysteine, and methionine metabolism between NOR and OPN groups. The alterations of GM in AIS patients are correlated with osteopenia. The association between enriched species, BMD, and bone turnover markers provides novel diagnostic and therapeutic targets for the clinical management of AIS.

Identification of keystone taxa in root canals and periapical lesions of post-treatment endodontic infections: Next generation microbiome research.

The aim of this study was to analyse and compare the microbiome present in root canals and periapical lesions of teeth with post-treatment infections, and to identify the presence of keystone taxa in both habitats using next-generation sequencing analysis. Apices and periapical lesions of patients with post-treatment apical periodontitis were surgically extracted. Specimens were cryo-pulverized, bacterial DNA was extracted, and the V3-V4 hypervariable regions of the 16S rRNA gene were sequenced using the Illumina Miseq platform. Bioinformatic analysis was carried out with Mothur software, whilst diversity indices were obtained using operational taxonomic units (OTUs). The diversity indices were compared with the Kruskal-Wallis test, and community composition differences were explored with Permutational Multivariate Analysis of Variance (PERMANOVA). A bacterial functional study was performed with the Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) analysis. Co-occurrence network analyses were performed using the Sparse Correlations for Compositional data (SparCC). Eigencentrality, clr-based abundance and ubiquitousness were applied to infer keystone taxa. P values <.05 were considered statistically significant. Thirty-two apices and thirty-nine periapical lesions were sequenced and analysed. A similar alpha-diversity (p < .05) and community composition (p = .91) was observed for apices and lesion samples. The most abundant OTUs identified amongst all samples included Fusobacterium nucleatum, Prevotella loescheii, Streptococcus intermedius, Porphyromonas gingivalis, Parvimonas micra, Synergistetes bacterium, Tannerella forsythia and Peptostreptococcus stomatis. The metabolic pathways with >0.81% abundances included membrane transport, genetic information processing and metabolic pathways. F. nucleatum was identified as a keystone taxon as it showed ubiquitousness, an eigenvector centrality value of 0.83 and a clr-based abundance >4. The microbiome in apices and periapical lesions of post-treatment endodontic infections showed a similar diversity and taxonomic composition. Co-occurrence network analyses at OTU level identified F. nucleatum as a keystone taxon candidate in these infections.

Environmental drivers of biogeography and community structure in a Mid-Atlantic estuary

Estuaries include some of the most productive yet anthropogenically impacted marine ecosystems on the planet, and provide critical habitat to many ecologically and economically important marine species. In order to elucidate ecological function in estuaries, we must understand what factors drive community dynamics. Delaware Bay is the third largest estuary in the United States and hosts over 200 species of migrant and resident fishes and invertebrates. The Delaware Division of Fish and Wildlife has conducted two long-term trawl surveys at monthly intervals in Delaware Bay since 1966. The two surveys collect data on environmental conditions, species composition, and number of fishes and macroinvertebrates across different size classes and life histories. Using a suite of multivariate approaches including hierarchical cluster analysis, canonical correlation analysis, and permutational multivariate analysis of variance, we characterized the fish and macroinvertebrate community in Delaware Bay and found that community composition and environmental conditions varied across spatial and seasonal scales. We identified four distinct biogeographic regions, based on environmental conditions and community composition, which were consistent across surveys. We found that the community was driven primarily by gradients in temperature and salinity and that abundant, frequently occurring species in the Bay have well-defined environmental associations. Our work represents the first attempt to use an existing historical survey to better understand how environmental parameters influence diversity and distribution of macrofauna within Delaware Bay, providing insight into how abiotic variables, influenced by climate, may impact the Delaware Bay ecosystem and similar estuarine ecosystems worldwide.

Gut microbiota of preterm infants in the neonatal intensive care unit: a study from a tertiary care center in northern India.

Disruptions of the gut microbiota of preterm infants admitted to the neonatal intensive care unit (NICU) during the first 2 weeks of life are of critical importance. These infants are prone to various complications, including necrotizing enterocolitis (NEC) and sepsis. Studying the gut microbiota will improve outcomes in preterm infants. In the present study, we examined the gut microbiota of preterm infants admitted to the NICU in the first month of life. Neonates admitted to the NICU were recruited, and stool samples were collected weekly from the seventh day of the infant's life until the 30th day of life. DNA was extracted using a DNeasy Powersoil DNA isolation kit. 16S rRNA gene sequencing targeting the V3-V4 region was performed using the MiSeq platform. Sequenced reads were processed on DADA2 pipeline to obtain an amplicon sequence variant (ASV) table. All bioinformatic and statistical analyses were performed using different packages in the R statistical framework. Fourteen preterm infants were recruited, and 48 samples were collected. Alpha diversity metrics, observed ASV count, and Shannon index were found to have no differences in any clinical variables. Permutational multivariate analysis of variance (PERMANOVA) showed discrimination of neonates by gestational age and administration of probiotics. Differential abundance analysis showed a decreased abundance of Bifidobacterium Breve in extremely preterm infants (gestational age <28 weeks) compared to moderate preterm infants (gestational age 29-32 weeks). Supplementation with probiotics decreased Acinetobacter and increased Bifidobacterium in the gut of preterm neonates regardless of gestational age. Gestational age and probiotic supplementation alter the gut microbiota of preterm infants admitted to the NICU.

Associations of the Gut Microbiome With Treatment Resistance in Schizophrenia

There is growing interest in the role of gut microbiome composition in schizophrenia. However, lifestyle factors are often neglected, and few studies have investigated microbiome composition in treatment-resistant schizophrenia. To explore associations between the gut microbiome and schizophrenia diagnosis, treatment resistance, clozapine response, and treatment-related adverse effects while adjusting for demographic and lifestyle factors. In this case-control study of adults aged 20 to 63 years, stool samples and data on demographic characteristics, lifestyle, and medication use were collected and gut microbiome measures obtained using shotgun metagenomics. Participants with a schizophrenia diagnosis were referred through psychiatric inpatient units and outpatient clinics. Data were collected for 4 distinct groups: control individuals without a psychiatric diagnosis (past or present), individuals with treatment-responsive schizophrenia taking nonclozapine antipsychotic medications, clozapine-responsive individuals with treatment-resistant schizophrenia, and clozapine-nonresponsive individuals with treatment-resistant schizophrenia. Participants were recruited between November 2020 and November 2021. Control individuals were recruited in parallel through posters and online advertisements and matched for age, sex, and body mass index (BMI) to the individuals with schizophrenia. Participants were excluded if taking antibiotics in the past 2 months, if unable to communicate in English or otherwise follow study instructions, were pregnant or planning to become pregnant, or had any concomitant disease or condition making them unsuited to the study per investigator assessment. Data were analyzed from January 2022 to March 2023. Omics relationship matrices, α and β diversity, and relative abundance of microbiome features. Data were collected for 97 individuals (71 [74%] male; mean [SD] age, 40.4 [10.3] years; mean [SD] BMI, 32.8 [7.4], calculated as weight in kilograms divided by height in meters squared). Significant microbiome associations with schizophrenia were observed at multiple taxonomic and functional levels (eg, common species: b2, 30%; SE, 13%; adjusted P = .002) and treatment resistance (eg, common species: b2, 27%; SE, 16%; adjusted P = .03). In contrast, limited evidence was found for microbiome associations with clozapine response, constipation, or metabolic syndrome. Significantly decreased microbial richness was found in individuals with schizophrenia compared to control individuals (t95 = 4.25; P < .001; mean [SD] for control individuals, 151.8 [32.31]; mean [SD] for individuals with schizophrenia, 117.00 [36.2]; 95% CI, 18.6-51.0), which remained significant after a covariate and multiple comparison correction. However, limited evidence was found for differences in β diversity (weighted UniFrac) for schizophrenia diagnosis (permutational multivariate analysis of variance [PERMANOVA]: R2, 0.03; P = .02), treatment resistance (R2, 0.02; P = .18), or clozapine response (R2, 0.04; P = .08). Multiple differentially abundant bacterial species (19) and metabolic pathways (162) were found in individuals with schizophrenia, which were primarily associated with treatment resistance and clozapine exposure. The findings in this study are consistent with the idea that clozapine induces alterations to gut microbiome composition, although the possibility that preexisting microbiome differences contribute to treatment resistance cannot be ruled out. These findings suggest that prior reports of microbiome alterations in individuals with chronic schizophrenia may be due to medication or lifestyle factors and that future studies should incorporate these variables in their design and interpretation.

The maternal microbiome in pregnancy, delivery, and early-stage development of neonatal microbiome after cesarean section: A prospective longitudinal study.

Changes within the maternal microbiome during the last trimester of pregnancy and the determinants of the subsequent neonatal microbiome establishment after delivery by elective cesarean section are described. Maternal vaginal and rectal microbiome samples were collected in the last trimester and before cesarean section; intrauterine cavity, placenta, neonatal buccal mucosa, skin, and meconium samples were obtained at birth; neonatal sample collection was repeated 2-3 days postnatally. Microbial community composition was analyzed by 16S rRNA gene amplicon sequencing. Relative abundance measurements of amplicon sequencing variants and sum counts at higher taxonomic levels were compared to test for significant overlap or differences in microbial community compositions. gov ID: NCT04489056. A total of 30 mothers and their neonates were included with available microbiome samples for all maternal, intrauterine cavity and placenta samples, as well as for 18 of 30 neonates. The composition of maternal vaginal and rectal microbiomes during the last trimester of healthy pregnancies did not significantly change (permutational multivariate analysis of variance [PERMANOVA], p > 0.05). No robust microbial signature was detected in the intrauterine cavity, placenta, neonatal buccal mucosa, skin swabs, or meconium samples collected at birth. After birth, the neonatal microbiome was rapidly established, and significantly different microbial communities were detectable2-3 days postnatally in neonate buccal mucosa and stool samples (PERMANOVA, p < 0.01). Maternal vaginal and rectal microbiomes in healthy pregnancies remain stable during the third trimester. No microbial colonization of the neonate was observed before birth in healthy pregnancies. Neonatal microbiomes in infants delivered by cesarean section displayed a taxonomic composition distinct from maternal vaginal and rectal microbiomes at birth, indicating that postnatal exposure to the extrauterine environment is the driving source of initial neonatal microbiome development in this cohort.

The exometabolome of microbial communities inhabiting bare ice surfaces on the southern Greenland Ice Sheet.

Microbial blooms colonize the Greenland Ice Sheet bare ice surface during the ablation season and significantly reduce its albedo. On the ice surface, microbes are exposed to high levels of irradiance, freeze-thaw cycles, and low nutrient concentrations. It is well known that microorganisms secrete metabolites to maintain homeostasis, communicate with other microorganisms, and defend themselves. Yet, the exometabolome of supraglacial microbial blooms, dominated by the pigmented glacier ice algae Ancylonema alaskanum and Ancylonema nordenskiöldii, remains thus far unstudied. Here, we use a high-resolution mass spectrometry-based untargeted metabolomics workflow to identify metabolites in the exometabolome of microbial blooms on the surface of the southern tip of the Greenland Ice Sheet. Samples were collected every 6 h across two diurnal cycles at 5 replicate sampling sites with high similarity in community composition, in terms of orders and phyla present. Time of sampling explained 46% (permutational multivariate analysis of variance [PERMANOVA], pseudo-F = 3.7771, p = 0.001) and 27% (PERMANOVA, pseudo-F = 1.8705, p = 0.001) of variance in the exometabolome across the two diurnal cycles. Annotated metabolites included riboflavin, lumichrome, tryptophan, and azelaic acid, all of which have demonstrated roles in microbe-microbe interactions in other ecosystems and should be tested for potential roles in the development of microbial blooms on bare ice surfaces.

Biodiesel production potential of Eichhornia crassipes (Mart.) Solms: comparison of collection sites and different alcohol transesterifications

Renewable resources have stood out as raw materials in producing biofuels. This study aimed to evaluate the parameters of alcohol transesterification (ethanol and methanol) and localization of collection of aquatic macrophyte Eichhornia crassipes (Mart.) Solms in the production of biodiesel by in situ transesterification. E. crassipes was collected in Dourados and Corumbá (Brazil) municipalities. The fatty acid ester composition of the biodiesel was characterized and quantified by gas chromatography. The biodiesel properties were estimated using the BiodieselAnalyzer© program prediction. The ethyl transesterification resulted in higher yields, but the localization of collection was the most relevant parameter in biodiesel production according to the Permutation Multivariate Analysis of Variance. The simulation and comparison of the physical–chemical properties of E. crassipes biodiesel and BD 100 (commercial biodiesel) were promising for commercial application.

Influence of perinatal and childhood exposure to tobacco and mercury in children's gut microbiota.

Early life determinants of the development of gut microbiome composition in infants have been widely investigated; however, if early life pollutant exposures, such as tobacco or mercury, have a persistent influence on the gut microbial community, its stabilization at later childhood remains largely unknown. In this exposome-wide study, we aimed at identifying the contribution of exposure to tobacco and mercury from the prenatal period to childhood, to individual differences in the fecal microbiome composition of 7-year-old children, considering co-exposure to a width of established lifestyle and clinical determinants. Gut microbiome was studied by 16S rRNA amplicon sequencing in 151 children at the genus level. Exposure to tobacco was quantified during pregnancy through questionnaire (active tobacco consumption, second-hand smoking -SHS) and biomonitoring (urinary cotinine) at 4 years (urinary cotinine, SHS) and 7 years (SHS). Exposure to mercury was quantified during pregnancy (cord blood) and at 4 years (hair). Forty nine other potential environmental determinants (12 at pregnancy/birth/infancy, 15 at 4 years and 22 at 7 years, such as diet, demographics, quality of living/social environment, and clinical records) were registered. We used multiple models to determine microbiome associations with pollutants including multi-determinant multivariate analysis of variance and linear correlations (wUnifrac, Bray-Curtis and Aitchison ß-diversity distances), single-pollutant permutational multivariate analysis of variance adjusting for co-variates (Aitchison), and multivariable association model with single taxa (MaAsLin2; genus). Sensitivity analysis was performed including genetic data in a subset of 107 children. Active smoking in pregnancy was systematically associated with microbiome composition and ß-diversity (R2 2-4%, p < 0.05, Aitchison), independently of other co-determinants. However, in the adjusted single pollutant models (PERMANOVA), we did not find any significant association. An increased relative abundance of Dorea and decreased relative abundance of Akkermansia were associated with smoking during pregnancy (q < 0.05). Our findings suggest a long-term sustainable effect of prenatal tobacco exposure on the children's gut microbiota. This effect was not found for mercury exposure or tobacco exposure during childhood. Assessing the role of these exposures on the children's microbiota, considering multiple environmental factors, should be further investigated.

Influence of hydraulic clam dredging and seasonal environmental changes on macro-benthic communities in the Southern Adriatic (Central Mediterranean Sea)

Macro-benthic communities on the shallowest soft bottoms are impacted by hydraulic dredgers used for the harvesting of the striped venus clam (Chamelea gallina). Changes in macro-benthic assemblages were analysed across four areas in the Southern Adriatic Sea (Central Mediterranean Sea) during the winter and summer 2022 (low and high fishing pressures, respectively). Two sampling surveys were carried out collecting abundance data (N/100m2) of 69 species. Diversity indices (Shannon–Weiner and Equitability) were calculated and differences between seasons and areas were tested using non-parametric tests. Changes in the assemblage and feeding habits were explored by adopting permutational multivariate analysis of variance on 34 species. Moreover, environmental conditions of all areas in the two seasons were characterized by a set of 8 variables. Seasonal changes in diversity were only detected for the Shannon–Weiner index, with values significantly higher in winter than summer. Macro-benthic assemblages differed between the two seasons, and the winter assemblages were well-distinct in each area. In contrast, a high overlap was shown in the summer assemblages of the four areas. Changes in feeding habits showed an increase in filter feeding polychaetes and opportunistic/scavenger species during the summer. Temperature, Salinity and primary production were positively correlated to summer stations indicating potential thermic stress on the assemblages. The results provide information on the benthic community impacted by dredge disturbance and seasonal changes driven by environmental conditions, stressing the need to integrate these aspects in assessments on the health status of marine ecosystems required by European directives and fishery management plans.