Taxonomic Features Research Articles

Tuber magnatum Picco: a new record for the Turkish mycobiota

Tuber magnatum Picco, the Italian white truffle mushroom recorded for the first time in Türkiye, is a rare and economically valuable mushroom. Samples were collected from Sakarya province during field studies in 2024. The samples were identified as T. magnatum according to their macro- and microscopic features. To make molecular confirmation of the species, the samples' ITS1 and ITS4 gene regions were analysed and registered in Genbank with the number PP239641. The sample showed 100% compatibility with other T. magnatum accessions in Genbank. The distributions of Tuber species in Türkiye were given, and their taxonomic features were compared.

PSLBII-7 Meta-analysis of the whole-body microbiota in cattle

Abstract Distinctive and self-sustainable microbial communities are present along the digestive, respiratory, and reproductive tracts, as well as in the mammary gland, and mucosal surfaces of the eye and hoof in cattle. Although the taxonomic and functional features of each of these communities have been relatively well characterized, this has been largely limited to the microbiome of an individual organ/site. However, recent developments suggest the presence of core taxa shared across the gut, respiratory, and reproductive microbiotas in cattle, and there is a need for a more holistic evaluation of microbial communities in and on cattle. Here, we performed a meta-analysis using all publicly available bovine 16S rRNA gene datasets deposited since 2019 to provide a holistic view of the whole-body microbiota. In total, we retrieved 16S rRNA gene sequences from 6,215 samples (53 studies originating from 29 different anatomical sites within beef and dairy cattle from Africa, Asia, Europe, South America, and North America. The 29 different anatomical sites including gut (ruminal fluid, ruminal tissues, feces, ileum, jejunum, cecum, colon and duodenum), respiratory (nasal cavity, deep nasopharynx, trachea and lung tissue), and reproductive tracts (female: vagina, endometrium and uterus; male: semen and prepuce), as well as the mammary gland (udder, teat apex, teat barrel, teat canal), eye (conjunctiva, ocular fluid and ocular surface swab), blood, hoof, joints and liver. Microbial community structure was distinct among different sample types (PERMANOVA, P < 0.05). Microbial richness differed by sample type (P < 0.0001) with mucosal surfaces (e.g. udder, eye and feet) having the greatest microbial richness followed by the gut. The lungs, liver, joints, semen and prepuce had the least microbial richness. Microbial diversity was greatest in the microbiota of the colon, cecum, teat apex, ruminal tissue and duodenum (Shannon diversity index > 5) while the liver (1.5), joint (2.3), and prepuce microbiota (2.7) were the least diverse. Bacillota had the highest relative abundance among phyla in the majority of microbial communities except for in the blood, prepuce, trachea and nasal cavity (dominated by Pseudomonadota), and liver (dominated by Fusobacteriota). The relatively most abundant genera across all samples were Mycoplasma (12.9%), Prevotella (3.9%), Bacteroides (2.4%), Escherichia (2.1%), Fusobacterium (2.0%), Ruminococcaceae UCG-005 (1.9%), Streptococcus (1.8%), Rikenellaceae RC9 (1.6%), and Corynebacterium (1.4%). However, their relative abundance varied greatly by body site, with the ocular and respiratory system samples dominated by Mycoplasma. Fusobacterium was relatively most abundant in the liver and semen, Corynebacterium in the mammary gland-associated samples, Bacteroides in the gut, and Streptococcus in the lower reproductive tract microbiota. Overall, our meta-analysis provides a comprehensive evaluation of the multiple bacterial communities in and on cattle, which will be useful for harnessing the whole-body microbiome to improve animal health and productivity.

Redescription and Molecular Characterization of the External Attaching Fish Parasitic Cymothoid, Nerocila phaiopleura Bleeker, 1857 (Crustacea: Isopoda) off the Southwest Coast of India.

The identification of the external attaching fish parasitic cymothoid, Nerocila phaiopleura Bleeker 1857, is still based on the brief description of Australian specimens provided by Bruce (1987). The present study aimed to provide a redescription and molecular characterisation of Indian specimens of N. phaiopleura. Morphological identification was carried out based on microscopic examinations and taxonomic drawings. mitochondrial DNA cox1 was selected as the target gene for sequencing and molecular identification. Nucleotide genetic divergence (p-distance) and base-pair differences among the different species were determined using MEGA11. Nerocila phaiopleura can be well separated from its congeners by the following combination of characteristics: Body about 2.4 times as long as wide, cephalon broadly rounded anteriorly; coxae posteriorly directed, acute and extending beyond their corresponding pereonite; pereonite 7 posterior angle produced, extending to the pleonite 1; pleonites 1 and 2 ventrolateral process posteriorly directed; uropod exopod straight and elongate, 1.7-2.0 times longer than endopod; uropod endopod lateral margin not serrate, no notch on medial margin; pereopods with short ischium; pleotelson triangular. The p-distance among N. phaiopleura and other available Nerocila spp. ranged from 21 to 19%. This study represents the first detailed taxonomic redescription of Indian specimens of N. phaiopleura. Key taxonomic features of the life stages and molecular data are provided here to identify the species properly. Interspecific genetic divergence between N. phaiopleura and other Nerocila spp. is assessed for the first time. Studies in cymothoid life histories, genetics, and morphology are necessary to understand one of the least understood parasite families.

Taxonomic studies on the genus Ophiopogon (Asparagaceae) I:—identity of O. albimarginatus and O. pseudotonkinensis, and a new species O. guangzhouensis from Guangdong, China

One new species of Ophiopogon, O. guangzhouensis, from Guangdong Province in southern China, is described and illustrated. The new species is similar to O. bockianus, but differs markedly by its pedicel (1.3–1.7 cm long) longer than the stalky part of the floral base, adjacent anthers and filaments all completely connate, and style exerted beyond the tepals. This paper not only details their taxonomic features and relationships among similar species, but also provides data on the habitat and phenology of the new species. Based on critical observations on herbarium specimens (including type material) of nine other similar species, we also demonstrate that O. pseudotonkinensis is conspecific with O. bockianus and O. albimarginatus is synonymous with O. stenophyllus. We therefore reduce O. pseudotonkinensis and O. albimarginatus to the synonymy of O. bockianus and O. stenophyllus respectively.

New insight in secretory structures and secretion composition in Rhus typhina L. – Anatomical, histochemical, and ultrastructural studies

Rhus typhina is a valuable plant used in the pharmaceutical, cosmetic, and food industries due to the presence of biologically active substances accumulated in its organs, especially in secretory structures, i.e. trichomes and secretory ducts. Light microscopy, scanning electron microscopy, and transmission electron microscopy were used to examine the structure of glandular and non-glandular trichomes, as well as secretory ducts present in inflorescence peduncles of R. typhina. The chemical composition of the secretion produced by trichomes and ducts was assessed using histochemical techniques, including observations under brightfield and fluorescence microscopes. Two types of capitate glandular trichomes producing secretions with a similar composition and non-glandular trichomes exhibiting secretory activity were identified. The secretion of glandular trichomes was dominated by acidic and neutral lipids, essential oil, sesquiterpenes, and steroid-containing terpenes. The schizogenic secretory ducts located in the phloem produced a viscous milky substance with acidic polysaccharides, acidic lipids, phenolic compounds, and proteins. The secretion was released into the duct lumen through notches in the walls of the secretory epithelial cell facing the duct lumen. The location, type, and traits of the non-glandular trichomes and secretory structures, as well as the composition of the secreted products are considered important taxonomic features in the family Anacardiaceae and the Rhus genus. Additionally, these characters are important diagnostic markers for the pharmacobotanical identification of the species in medicinal and cosmetic raw materials. The various compounds present in the secretory structures of R. typhina may contribute to plant protection against pathogens or herbivory and probably play a role as attractants for pollinators and seed dispersers.

Influence of the Saccharomyces cerevisiae-based probiotic complex on gut microbiota, serum biochemistry, and circulating trace element and mineral levels in lactating dairy cows.

The existing data demonstrate that gut microbiota is involved in regulating mineral metabolism in cattle, although the data are quite contradictory. The study aimed to evaluate Saccharomyces cerevisiae-based probiotic's effects on gut microbiota, systemic metabolism, and dairy cows' essential trace element and mineral body burden. Fifteen cows received a daily supplement of a 50 g S. cerevisiae-based probiotic, fortified with methionine, choline, eugenol, cinnamaldehyde, and Capsicum oleoresin, for a month. 16S metagenomic sequencing was used to evaluate the taxonomic features of fecal microbiota. Serum trace elements and minerals levels were determined through inductively coupled plasma mass spectrometry. Supplementation with S. cerevisiae-based probiotic complex significantly increased alpha and beta diversity, as well as the abundance of Mediterranea and Clostridium IV within the Bacillota phylum, whereas that of Bacteroidota and specifically unclassified Bacteroidales and unclassified Oscillospiraceae decreased. Following probiotic supplementation with the S. cerevisiae-based complex, gut microbiota modulation led to a significant boost in circulating levels of calcium, copper, selenium, and zinc. Creatinine levels decreased while total cholesterol levels increased within normal limits in the serum analysis. The observed improvement in trace elements and minerals in dairy cows might be due to changes in intestinal microflora caused by supplementation. Therefore, probiotic supplementation in cattle may be considered a potential tool for improvement of mineral nutrition in cattle. However, the influence of probiotic treatment and modulation of mineral metabolism on milk productivity and overall performance in cattle is yet to be estimated.

A Comparative Metagenomic Analysis of Specified Microorganisms in Groundwater for Non-Sterilized Pharmaceutical Products

In pharmaceutical manufacturing, ensuring product safety involves the detection and identification of microorganisms with human pathogenic potential, including Burkholderia cepacia complex (BCC), Escherichia coli, Pseudomonas aeruginosa, Salmonella enterica, Staphylococcus aureus, Clostridium sporogenes, Candida albicans, and Mycoplasma spp., some of which may be missed or not identified by traditional culture-dependent methods. In this study, we employed a metagenomic approach to detect these taxa, avoiding the limitations of conventional cultivation methods. We assessed the groundwater microbiome’s taxonomic and functional features from samples collected at two locations in the spring and summer. All datasets comprised 436–557 genera with Proteobacteria, Bacteroidota, Firmicutes, Actinobacteria, and Cyanobacteria accounting for > 95% of microbial DNA sequences. The aforementioned species constituted less than 18.3% of relative abundance. Escherichia and Salmonella were mainly detected in Hot Springs, relative to Jefferson, while Clostridium and Pseudomonas were mainly found in Jefferson relative to Hot Springs. Multidrug resistance efflux pumps and BlaR1 family regulatory sensor-transducer disambiguation dominated in Hot Springs and in Jefferson. These initial results provide insight into the detection of specified microorganisms and could constitute a framework for the establishment of comprehensive metagenomic analysis for the microbiological evaluation of pharmaceutical-grade water and other non-sterile pharmaceutical products, ensuring public safety.

Microbiome variations induced by delta9-tetrahydrocannabinol predict weight reduction in obese mice

IntroductionObesity and high-fat diets induce consistent alterations in gut microbiota composition. Observations from epidemiological reviews and experiments also illustrate weight regulation effects of delta9-tetrahydrocannabinol (THC) with microbiome shifts. Therefore, we investigated the weight-loss potential of THC in obese mice models and to elucidate the contribution of specific gut microbiome changes in THC-induced weight loss.MethodsHigh-fat diet induced obese mice were treated with oral THC supplementation for two weeks and compared with controls. In addition to measuring weight, fecal samples were obtained at various timepoints, sequenced for bacterial 16s rRNA content and analyzed using QIIME2. Alpha and beta diversity were computed followed by linear mixed effects (LME) modeling of bacterial relative abundance relationship to THC treatment and weight change.ResultsIn both male and female mice, the THC group had significantly greater average weight loss than controls (−17.8% vs. −0.22%, p<0.001 and −13.8% vs. +2.9%, p<0.001 respectively). Male mice had 8 bacterial taxonomic features that were both significantly different in relative abundance change over time with THC and correlated with weight change. An LME model using three bacterial features explained 76% of the variance in weight change with 24% of variation explained by fixed effects of feature relative abundance alone. The model also accurately predicted weight change in a second male mouse cohort (R=0.64, R2=0.41, p=<0.001). Female mice had fewer significant predictive features and were difficult to model, but the male-produced 3-feature model still accurately predicted weight change in the females (R=0.66, R2=0.44, p<0.001).ConclusionUsing a stepwise feature selection approach, our results indicate that sex-specific gut microbiome composition changes play some role in THC-induced weight loss. Additionally, we illustrated the concept of microbiome feature-based modeling to predict weight changes.

Comprehensive assessment of machine learning methods for diagnosing gastrointestinal diseases through whole metagenome sequencing data

ABSTRACT The gut microbiome, linked significantly to host diseases, offers potential for disease diagnosis through machine learning (ML) pipelines. These pipelines, crucial in modeling diseases using high-dimensional microbiome data, involve selecting profile modalities, data preprocessing techniques, and classification algorithms, each impacting the model accuracy and generalizability. Despite whole metagenome shotgun sequencing (WMS) gaining popularity for human gut microbiome profiling, a consensus on the optimal methods for ML pipelines in disease diagnosis using WMS data remains elusive. Addressing this gap, we comprehensively evaluated ML methods for diagnosing Crohn’s disease and colorectal cancer, using 2,553 fecal WMS samples from 21 case-control studies. Our study uncovered crucial insights: gut-specific, species-level taxonomic features proved to be the most effective for profiling; batch correction was not consistently beneficial for model performance; compositional data transformations markedly improved the models; and while nonlinear ensemble classification algorithms typically offered superior performance, linear models with proper regularization were found to be more effective for diseases that are linearly separable based on microbiome data. An optimal ML pipeline, integrating the most effective methods, was validated for generalizability using holdout data. This research offers practical guidelines for constructing reliable disease diagnostic ML models with fecal WMS data.

Evaluating Morphology-based Taxonomic Features for the Identification of Genera within the Anthemidinae (Asteraceae) Subtribe in European Türkiye

Evaluating Morphology-based Taxonomic Features for the Identification of Genera within the Anthemidinae (Asteraceae) Subtribe in European Türkiye

Exploratory multi-omics analysis reveals host-microbe interactions associated with disease severity in psoriatic skin

Psoriasis (Pso) is a chronic inflammatory skin disease that poses both physical and psychological challenges. Dysbiosis of the skin microbiome has been implicated in Pso, yet a comprehensive multi-omics analysis of host-microbe interactions is still lacking. To bridge this gap, we conducted an exploratory study by adopting the integrated approach that combines whole metagenomic shotgun sequencing with skin transcriptomics. This was a cross-sectional study, adult patients with plaque-type Psoriasis (Pso) and healthy volunteers were included. Skin microbiota samples and biopsies were collected from both lesional and non-lesional skin areas on the lower back. Weighted Gene Correlation Network Analysis (WGCNA) was employed for co-expression network analysis, and cell deconvolution was conducted to estimate cell fractions. Taxonomic and functional features of the microbiome were identified using whole metagenomic shotgun sequencing. Association between host genes and microbes was analyzed using Spearman correlation. Host anti-viral responses and interferon-related networks were identified and correlated with the severity of psoriasis. The skin microbiome showed a greater prevalence of Corynebacterium simulans in the PASI severe-moderate groups, which correlated with interferon-induced host genes. Two distinct psoriatic clusters with varying disease severities were identified. Variations in the expression of cell apoptosis-associated antimicrobial peptides (AMPs) and microbial aerobic respiration I pathway may partly account for these differences in disease severity. Our multi-omics analysis revealed for the first time anti-viral responses and the presence of C.simulans associated with psoriasis severity. It also identified two psoriatic subtypes with distinct AMP and metabolic pathway expression. Our study provides new insights into understanding the host-microbe interaction in psoriasis and lays the groundwork for developing subtype-specific strategies for managing this chronic skin disease. The research has received funding from the FP7 (MAARS-Grant 261366) and the Innovative Medicines Initiative 2 Joint Undertaking (JU) under grant agreement No 821511 (BIOMAP). The JU receives support from the European Union's Horizon 2020 research and innovation programme and EFPIA. This publication reflects only the author's view and the JU is not responsible for any use that may be made of the information it contains. GAM was supported by a scholarship provided by CAPES-PRINT, financed by the Coordenação de Aperfeiçoamento de Pessoal de Nível Superior - CAPES (Brazilian Government Agency). The authors thank all patients who participated in our study.

Integrated Analysis of Microbiome and Metabolome Reveals Disease-Specific Profiles in Inflammatory Bowel Diseases and Intestinal Behçet's Disease.

The gut microbial and metabolic characteristics of intestinal Behçet's disease (BD), a condition sharing many clinical similarities with ulcerative colitis (UC) and Crohn's disease (CD), are largely unexplored. This study investigated the gut microbial and metabolic characteristics of intestinal BD as well as potential biomarkers, comparing them with those in UC, CD, and healthy controls. Colon tissue and stool samples from 100 patients (35 UC, 30 CD, and 35 intestinal BD) and 41 healthy volunteers were analyzed using 16S ribosomal RNA sequencing to assess microbial diversity, taxonomic composition, and functional profiling. Plasma metabolomic analyses were performed using gas chromatography and ultra-performance liquid chromatography-mass spectrometry. Results indicated reduced microbial diversity in CD but not in intestinal BD, with intestinal BD showing fewer changes compared to controls yet distinct taxonomic features from UC, CD, and controls. Common alterations across all diseases included a reduction in beneficial bacteria producing short-chain fatty acids. Intestinal BD-specific changes featured a decreased abundance of Bacteroides fragilis. Metabolomic profiles in intestinal BD were similar to those in CD but distinct from those in UC, displaying significant changes in energy metabolism and genetic information processing. This integrative analysis revealed both shared and unique profiles in intestinal BD compared with UC, CD, and controls, advancing our understanding of the distinctive features of these diseases.

Molar crown morphometrics in Paucituberculata (Mammalia: Marsupialia)

ABSTRACT The Paucituberculata are a group of marsupials endemic to South America, recorded from the Early Eocene to the present. In terms of taxonomy and qualitative morphology, paucituberculatans are a quite diverse and disparate group, especially considering their extinct representatives. This study aimed to investigate the variability in the quantitative morphology of paucituberculatans in the context of the largest morphometric study of the group performed to date. Due to the fragmentary fossil record, this work focused on lower dental morphology which allowed us to compare around 95% of paucituberculatan species through the measurement and analysis of almost 1500 specimens. Dental measurements of 27 variables were analysed by Principal Component Analysis and Partial Least Squares correlation as exploratory methods. As a result, it is shown that the continuous variability is expressed not only in size differences among species but also in morphological variability of individual teeth, and differences in size and proportions along the molar row. We conclude that paucituberculatans are a group of important morphological diversity regarding quantitative morphology. Many of the quantitative taxonomic features discussed in the literature were corroborated in this study. In addition, we discussed potential evolutionary and palaeoecological implications of this study, highlighting prospects for future studies.

Exploring gut microbiome markers in predicting efficacy of immunotherapy against lung cancer.

8525 Background: Immunotherapy has profoundly changed the treatment landscape for lung cancer (LC) due to its tolerable safety profile and longer sustained therapeutic response. However, only about 20% of patients with locally advanced and metastatic disease can derive long-term clinical benefit from ICIs. Previous studies have suggested that the microbiome is involved in the development of LC in some way. We aimed to use the gut microbiome (GM) to model the benefit of immunotherapy and to mine the biomarkers with a global impact on immune response. Methods: We performed human gut metagenomic analysis on the responder patients and non-responder patients with immunotherapy. A total of 296 fecal samples, including baseline samples (71 responders, 98 non-responders and 72 healthy controls), and 55 samples during treatment were enrolled in our study, the taxonomic and functional features of these samples also were excavated. A machine-learning model was developed to identify responders and non-responders. At the same time, we also explored the influence of antibiotic use on the above results. Results: Specific species, Bacteroides caccae and Bacteroides uniformis, were positively correlated with responders. In non-responders, Prevotella copri was the main enrichment species. The α diversity of microbiota in responding patients was significantly higher than that in non-responding groups, and antibiotic use increased this trend. There was no significant difference in β diversity between the two groups, but LEFSE analysis also could obtain biomarkers of biological significance between the two groups. We used the biomarkers from the above analysis to construct a random forest model, and the area under the receiver operating characteristic curve (AUC) (species level: 82.10%; genus level: 79.4%). In addition, our studies suggested that metabolism such as amino acid metabolism, valine, leucine might be important in regulating the immunotherapy response that warrants further investigation. Conclusions: Overall, our study explored the relationship between microbial composition and immunotherapy efficacy in LC patients and mined relevant markers, and further research is needed to investigate the mechanisms of action of these key strains in influencing immunotherapy in the future.

MORPHOLOGICAL AND TAXONOMICAL DESCRIPTIONS OF COCCINELLIDS OF GENUS ILLEIS (COLEOPTERA: COCCINELLIDAE) WITH ONE NEW RECORD FROM UTTARAKHAND, INDIA

Coccinellids of Genus Illeis are among the most familiar beetles that belong to the tribe Coccinellini of subfamily Coccinellinae under the family Coccinellidae of order Coleoptera. The present study was conducted to understand the distributional, taxonomical, and morphological features of four species of Coccinellids of Genus Illeis recorded from four different Doon Valley, Uttarakhand study sites. Four species of coccinellids of the genus Illeis were recorded during the study period. During the study period, Illeis confusa (Timberlake), Illeis cincta (Fabricius), Illeis indica (Timberlake), and Illeis koebelei (Timberlake) were the four observed species of the genus. From the study, it was observed that among all four species of coccinellids, Illeis confusa was the dominant species (267 individuals), followed by Illeis indica (110), Illeis koebelei (40), and Illeis cincta (35) in term of number of individuals. Out of the four species, Illeis koebelei (Timberlake) was recorded for the 1st time from Doon Valley, Uttarakhand, India.. KEYWORDS :Coccinellids, Illeis confuse, Illeis cincta, Illeis indica, Illeis koebelei, Taxonomy

First record of the spider family Trechaleidae Simon, 1890 (Araneae) from China

The family Trechaleidae Simon, 1890 is reported for the first time from China, including one new species: Shinobius conasp. nov. (♂♀). Morphological descriptions, photos and illustrations of the new species are provided. Taxonomic features of species belonging to the genus are briefly discussed. Photos of the female of Shinobius orientalis (Yaginuma, 1967) are also presented to compare it with the new species.

Ruminal microbiome changes across lactation in primiparous Holstein cows with varying methane intensity: Heritability assessment

Methane is a potent greenhouse gas produced during the ruminal fermentation and is associated with a loss of feed energy. Therefore, efforts to reduce methane emissions have been ongoing in the last decades. Methane production is highly influenced by factors such as the ruminal microbiome and host genetics. Previous studies have proposed to use the ruminal microbiome to reduce long-term methane emissions, as ruminal microbiome composition is a moderately heritable trait and genetic improvement accumulates over time. Lactation stage is another important factor that might influence methane production, but potential associations with the ruminal microbiome have not been evaluated previously. This study sought to examine the changes in ruminal microbiome over the lactation period of primiparous Holstein cows differing in methane intensity (MI) and estimate the heritability of the abundance of relevant microorganisms. Ruminal content samples from 349 primiparous Holstein cows with 14 to 378 DIM were collected from May 2018 to June 2019. Methane intensity of each cow was calculated as methane concentration/milk yield. Up to 64 taxonomic features (TF) from 20 phyla had a significant differential abundance between cows with low and high MI early in lactation, 16 TF during mid lactation, and none late in lactation. Taxonomical features within the Firmicutes, Proteobacteria, Melainabacteria, Cyanobacteria, Bacteroidetes, and Actinobacteria phyla were associated with low MI, whereas eukaryotic TF and those within the Euryarchaeota, Verrucomicrobia, Kiritimatiellaeota, and Lentisphaerae phyla were associated with high MI. Out of the 60 TF that were found to be differentially abundant between early and late lactation in cows with low MI, 56 TF were also significant when cows with low and high MI were compared in the first third of the lactation. In general, microbes associated with low MI were more abundant early in lactation (e.g., Acidaminococcus, Aeromonas, and Weimeria genera) and showed low to moderate heritabilities (0.03 to 0.33). These results suggest some potential to modulate the rumen microbiome composition through selective breeding for lower MI. Differences in the ruminal microbiome of cows with extreme MI levels likely result from variations in the ruminal physiology of these cows and were more noticeable early in lactation, probably due to important interactions between the host phenotype and environmental factors associated with that period. Our results suggest that the ruminal microbiome evaluated early in lactation may be more precise for MI difference, and hence, this should be considered to optimize sampling periods to establish a reference population in genomic selection scenarios.

Host factors are associated with vaginal microbiome structure in pregnancy in the ECHO Cohort Consortium

Using pooled vaginal microbiota data from pregnancy cohorts (N = 683 participants) in the Environmental influences on Child Health Outcomes (ECHO) Program, we analyzed 16S rRNA gene amplicon sequences to identify clinical and demographic host factors that associate with vaginal microbiota structure in pregnancy both within and across diverse cohorts. Using PERMANOVA models, we assessed factors associated with vaginal community structure in pregnancy, examined whether host factors were conserved across populations, and tested the independent and combined effects of host factors on vaginal community state types (CSTs) using multinomial logistic regression models. Demographic and social factors explained a larger amount of variation in the vaginal microbiome in pregnancy than clinical factors. After adjustment, lower education, rather than self-identified race, remained a robust predictor of L. iners dominant (CST III) and diverse (CST IV) (OR = 8.44, 95% CI = 4.06–17.6 and OR = 4.18, 95% CI = 1.88–9.26, respectively). In random forest models, we identified specific taxonomic features of host factors, particularly urogenital pathogens associated with pregnancy complications (Aerococcus christensenii and Gardnerella spp.) among other facultative anaerobes and key markers of community instability (L. iners). Sociodemographic factors were robustly associated with vaginal microbiota structure in pregnancy and should be considered as sources of variation in human microbiome studies.

On a Collection of Ferns from Shevaroy Hills, Salem District, Madras State

The Shevaroys are situated to the north-east of Salem town at a distance of 26 km., the main bill station being Yercaud. Two seasonal explorations were made in the year 1958 and in all a total number of 51 species of ferns representing 14 families and 35 genera were collected.In Shevaroys, the evergreen moist type of forest is seen where the vegetation is undisturbed and it is interesting to note that all the important fern families are represented here like Ophioglossaceae, Marattiaceae, Osmundaceae, Schizaeaceae, Gleicheniaceae, Hymenophyllaceae, Cyatheaceae and Polypodiaceae (sensu lato). Among the rare and interesting ferns, mention may be made of: Anemia tomentosa (Sav.) Sw, Antrophyum plantagineum (Cav.) Kaulf., Athyrium macrocarpum Bedd., Botrychium daucifolium Wall., B. lanuginosum Wall., Cyrtomium falcatum Presl var. caryotideum Wall., Dryopteris cochleata C., Chr., Hymenophyllum exsertum Wall, Leptochilus decurrens Blume, Lindsaea heterophylla Dry., Lygodium scandens Sw., Niphobolus gardneri (Mett.) Kunze, Osmunda regalis L., Pteris cretica L., P. quadriaurita Retz., var. argentea Bedd., and Trichomanes proliferum Blame.The classification of Copeland is followed and the salient taxonomic features of the ferns collected are mentioned in the enumeration. Out of the plants listed Pteridaceae is well represented, the next in order being Aspidiaceae and Polypodiaceae (sensu stricto). The collections include a number of species which are new distributions to Salem District.

The gut microbiome and HLA-B27-associated anterior uveitis: a case-control study

BackgroundThe human gut microbiome (GM) is involved in inflammation and immune response regulation. Dysbiosis, an imbalance in this ecosystem, facilitates pathogenic invasion, disrupts immune equilibrium, and potentially triggers diseases including various human leucocyte antigen (HLA)-B27-associated autoinflammatory and autoimmune diseases such as inflammatory bowel disease (IBD) and spondyloarthropathy (SpA). This study assesses compositional and functional alterations of the GM in patients with HLA-B27-associated non-infectious anterior uveitis (AU) compared to healthy controls.MethodsThe gut metagenomes of 20 patients with HLA-B27-associated non-infectious AU, 21 age- and sex-matched HLA-B27-negative controls, and 6 HLA-B27-positive healthy controls without a history of AU were sequenced using the Illumina NovaSeq 6000 platform for whole metagenome shotgun sequencing. To identify taxonomic and functional features with significantly different relative abundances between groups and to identify associations with clinical metadata, the multivariate association by linear models (MaAsLin) R package was applied.ResultsSignificantly higher levels of the Eubacterium ramulus species were found in HLA-B27-negative controls (p = 0.0085, Mann-Whitney U-test). No significant differences in microbial composition were observed at all other taxonomic levels. Functionally, the lipid IVA biosynthesis pathway was upregulated in patients (p < 0.0001, Mann-Whitney U-test). A subgroup analysis comparing patients with an active non-infectious AU to their age- and sex-matched HLA-B27-negative controls, showed an increase of the species Phocaeicola vulgatus in active AU (p = 0.0530, Mann-Whitney U-test). An additional analysis comparing AU patients to age- and sex-matched HLA-B27-positive controls, showed an increase of the species Bacteroides caccae in controls (p = 0.0022, Mann-Whitney U-test).ConclusionIn our cohort, non-infectious AU development is associated with compositional and functional alterations of the GM. Further research is needed to assess the causality of these associations, offering potentially novel therapeutic strategies.