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INTRODUCTION: A large proportion of patients with inflammatory bowel disease (IBD) experience IBD-related inflammatory conditions outside of the gastrointestinal tract, termed extraintestinal manifestations (EIMs) which further decreases quality of life and, in extreme cases, can be life threatening. The pathogenesis of EIMs remains unknown, and although gut microbiota alterations are a well-known characteristic of patients with IBD, its relationship with EIMs remains sparsely investigated. This study aimed to compare the gut microbiota of patients with IBD with and without EIMs. METHODS: A total of 131 Danish patients with IBD were included in the study, of whom 86 had a history of EIMs (IBD-EIM) and 45 did not (IBD-C). Stool samples underwent 16S rRNA sequencing. Amplicon sequence variants (ASVs) were mapped to the Silva database. Diversity indices and distance matrices were compared between IBD-EIM and IBD-C. Differentially abundant ASVs were identified using a custom multiple model statistical analysis approach, and modules of co-associated bacteria were identified using sparse correlations for compositional data (SparCC) and related to patient EIM status. RESULTS: Patients with IBD and EIMs exhibited increased disease activity, body mass index, increased fecal calprotectin levels and circulating monocytes and neutrophils. Microbiologically, IBD-EIM exhibited lower fecal microbial diversity than IBD-C (Mann-Whitneys test, p = .01) and distinct fecal microbiota composition (permutational multivariate analysis of variance; weighted UniFrac, R2 = 0.018, p = .01). A total of 26 ASVs exhibited differential relative abundances between IBD-EIM and IBD-C, including decreased Agathobacter and Blautia and increased Eggerthella lenta in the IBD-EIM group. SparCC analysis identified 27 bacterial co-association modules, three of which were negatively related to EIM (logistic regression, p

Seasonal floodplains in the Amazon basin are important sources of methane (CH4), while upland forests are known for their sink capacity. Climate change effects, including shifts in rainfall patterns and rising temperatures, may alter the functionality of soil microbial communities, leading to uncertain changes in CH4 cycling dynamics. To investigate the microbial feedback under climate change scenarios, we performed a microcosm experiment using soils from two floodplains (i.e., Amazonas and Tapajós rivers) and one upland forest. We employed a two-factorial experimental design comprising flooding (with non-flooded control) and temperature (at 27 °C and 30 °C, representing a 3 °C increase) as variables. We assessed prokaryotic community dynamics over 30 days using 16S rRNA gene sequencing and qPCR. These data were integrated with chemical properties, CH4 fluxes, and isotopic values and signatures. In the floodplains, temperature changes did not significantly affect the overall microbial composition and CH4 fluxes. CH4 emissions and uptake in response to flooding and non-flooding conditions, respectively, were observed in the floodplain soils. By contrast, in the upland forest, the higher temperature caused a sink-to-source shift under flooding conditions and reduced CH4 sink capability under dry conditions. The upland soil microbial communities also changed in response to increased temperature, with a higher percentage of specialist microbes observed. Floodplains showed higher total and relative abundances of methanogenic and methanotrophic microbes compared to forest soils. Isotopic data from some flooded samples from the Amazonas river floodplain indicated CH4 oxidation metabolism. This floodplain also showed a high relative abundance of aerobic and anaerobic CH4 oxidizing Bacteria and Archaea. Taken together, our data indicate that CH4 cycle dynamics and microbial communities in Amazonian floodplain and upland forest soils may respond differently to climate change effects. We also highlight the potential role of CH4 oxidation pathways in mitigating CH4 emissions in Amazonian floodplains.

ObjectivesTo enable interactive visualization of the vaginal microbiome across the pregnancy and facilitate discovery of novel insights and generation of new hypotheses.Material and methodsVaginal Microbiome Atlas during Pregnancy (VMAP) was created with R shiny to generate visualizations of structured vaginal microbiome data from multiple studies.ResultsVMAP (http://vmapapp.org) visualizes 3880 vaginal microbiome samples of 1402 pregnant individuals from 11 studies, aggregated via open-source tool MaLiAmPi. Visualized features include diversity measures, VALENCIA community state types, and composition (phylotypes, taxonomy) that can be filtered by various categories.DiscussionThis work represents one of the largest and most geographically diverse aggregations of the vaginal microbiome in pregnancy to date and serves as a user-friendly resource to further analyze vaginal microbiome data and better understand pregnancies and associated outcomes.ConclusionVMAP can be obtained from https://github.com/msirota/vmap.git and is currently deployed as an online app for non-R users.

Host–microbiota interactions play a critical role in the hosts’ biology, and thus, it is crucial to elucidate the mechanisms that shape gut microbial communities. We leveraged threespine stickleback fish ( Gasterosteus aculeatus ) as a model system to investigate the contribution of host and environmental factors to gut microbiota variation. These fish offer a unique opportunity for experiments in naturalistic conditions; we reared benthic and limnetic ecotypes from three different lakes in experimental ponds, allowing us to assess the relative effects of shared environment (pond), geographic origin (lake-of-origin), trophic ecology and genetics (ecotype) and biological sex on gut microbiota α- and β-diversity. Host ecotype had the strongest influence on α-diversity, with benthic fish exhibiting higher diversity than limnetic fish, followed by the rearing environment. β-diversity was primarily shaped by rearing environment, followed by host ecotype, indicating that environmental factors play a crucial role in determining gut microbiota composition. Furthermore, numerous bacterial orders were differentially abundant across ponds, underlining the substantial contribution of environmental factors to gut microbiota variation. Our study illustrates the complex interplay between environmental and host ecological or genetic factors in shaping the stickleback gut microbiota and highlights the value of experiments conducted under naturalistic conditions for understanding gut microbiota dynamics.

Background: Premature infants are more prone to brain injuries owing to incomplete nervous system development and poor adaptation outside the mother's body. Without timely intervention, premature infants with brain injuries often develop intellectual disabilities, causing significant burdens on families and the society. Multiple studies have shown that gut dysbiosis can affect the nervous system, and vice versa. This study aimed to explore the changes in gut microbiota of typical premature infants and those with brain injuries on the third and seventh days after birth using 16 S rRNA technology. Methods: Fecal samples from typical premature infants (non-brain injury group, n = 17) and those with brain injuries (brain injury group, n = 21) were collected on days 1, 3, and 7 after birth for 16 S rRNA sequencing. Alpha diversity analysis was used to evaluate the diversity of gut microbiome. LEfSe and DESeq2 were used to analyze of the microorganisms' characteristics and differentiate the microorganisms between the two groups. Results: At the phylum level, Firmicutes, Proteobacteria, and Actinobacteria were the dominant flora in both groups. At the genus level, the proportion of Enterococcus in fecal samples of the brain injury group was higher than that of the non-brain injury group on day three after birth; however, the opposite was observed on day seven. Rothia and Lactobacillales were characteristic bacteria of the non-brain injury group on days three and seven after birth, whereas Enterococcus and Bifidobacteria were characteristic bacteria of the brain injury group on days three and seven after birth, respectively. Three days after birth, the Shannon and Simpson indices of the non-brain injury group were significantly higher than those of the brain injury group. Conclusion: Premature infants with brain injuries have a unique gut microbiota that is different from that of typical premature infants, indicating correlation between brain injuries and gut microbiota. [ABSTRACT FROM AUTHOR]

Background: Wood-feeding termites have been employed as sources of novel and highly efficient lignocellulolytic enzymes due to their ability to degrade lignocellulose efficiently. As a higher wood-feeding termite, Globitermes sulphureus (Blattaria: Termitidae) plays a crucial role as a decomposer in regions such as Vietnam, Singapore, Myanmar, and Yunnan, China. However, the diversity of its gut microbiome and carbohydrate-active enzymes (CAZymes) remains unexplored. Here, we analyzed the diversity of hindgut microbial communities and CAZymes in a higher wood-feeding termite, G. sulphureus, and a lower wood-feeding termite, Coptotermes formosanus (Blattaria: Rhinotermitidae). Results: 16S rRNA sequencing revealed that Spirochaetota, Firmicutes, and Fibrobacterota were the dominant microbiota in the hindgut of the two termite species. At the phylum level, the relative abundances of Proteobacteria and Bacteroidota were significantly greater in the hindgut of C. formosanus than in G. sulphureus. At the genus level, the relative abundances of Candidatus_Azobacteroides and Escherichia-Shigella were significantly lower in the hindgut of G. sulphureus than in C. formosanus. Metagenomic analysis revealed that glycoside hydrolases (GHs) with cellulases and hemicellulases functions were not significantly different between G. sulphureus and C. formosanus. Interestingly, the cellulases in G. sulphureus were mainly GH5_2, GH5_4, GH6, GH9, and GH45, while the hemicellulases were mainly GH11, GH8, GH10, GH11, GH26, and GH53. In C. formosanus, the cellulases were mainly GH6 and GH9, and the hemicellulases were mainly GH5_7, GH5_21, GH10, GH12, and GH53. In addition, β-glucosidase, exo-β-1,4-glucanase, and endo-β-1,4-glucanase activities did not differ significantly between the two termite species, while xylanase activity was higher in G. sulphureus than in C. formosanus. The bacteria encoding GHs in G. sulphureus were mainly Firmicutes, Fibrobacterota, and Proteobacteria, whereas Bacteroidota and Spirochaetota were the main bacteria encoding GHs in C. formosanus. Conclusions: Our findings characterized the microbial composition and differences in the hindgut microbiota of G. sulphureus and C. formosanus. Compared to C. formosanus, G. sulphureus is enriched in genes encoding for hemicellulase and debranching enzymes. It also highlights the rich diversity of GHs in the hindgut microbiota of G. sulphureus, including the GH5 subfamily, GH6, and GH48, with the GH6 and GH48 not previously reported in other higher termites. These results strengthen the understanding of the diversity of termite gut microbiota and CAZymes. [ABSTRACT FROM AUTHOR]

Lichen sclerosus is a chronic inflammatory condition of unknown etiology that affects the genital and extragenital skin, which can lead to sexual dysfunction and has been associated with vulvar cancer. The vaginal microbiome has a critical role in gynecologic health, but little is known about the microbiome in lichen sclerosus. This study investigated the vaginal and vulvar microbiomes of 27 post-menopausal women with lichen sclerosus. The most abundant genera detected in the vaginal microbiome were Lactobacillus, Gardnerella, and Anaerococcus, while Lactobacillus, Anaerococcus, and Staphylococcus were the most abundant in the vulvar microbiome. The vaginal samples clustered into two main groups, Lactobacillus dominant (n = 6, > 50% microbiome Lactobacillus) and polymicrobial (n = 21) with no dominant genus. The vulvar samples were mainly polymicrobial (n = 25). Actinomyces, Anaerococcus, and Ezakiella in the vaginal microbiome and Actinomyces and Ezakiella in the vulvar microbiome were significantly associated with lichen sclerosus symptoms (adjusted p < 0.05). In this population of post-menopausal women with lichen sclerosus the majority have diverse, non-Lactobacillus dominant microbiomes, which is considered less optimal for gynecologic health based on studies of pre-menopausal women. Actinomyces, Ezakiella, and Anaerococcus were associated with lichen sclerosus symptoms. Understanding the role of these bacteria in lichen sclerosus pathogenesis will be an essential future investigation. [ABSTRACT FROM AUTHOR]

This study examined the risk of intrauterine infection associated with radical trachelectomy (RT) in early‐stage cervical cancer patients. This procedure preserves fertility but is linked to increased risk of intrauterine infection due to cervical defects during pregnancy. DNA was extracted from the formalin‐fixed paraffin‐embedded (FFPE) placental specimens of 23 pregnant post‐RT patients and 16S rRNA gene sequencing was used for bacterial identification. The prevalence of Lactobacillus crispatus and Burkholderia stabilis was significantly higher in the non‐chorioamnionitis group. In contrast, alpha diversity analysis using the PD index showed significantly higher diversity in the chorioamnionitis group (P = 0.04). The demonstrated relationship between chorioamnionitis and microbial diversity affirms the importance of controlling the genital bacterial flora in pregnancies following RT. [ABSTRACT FROM AUTHOR]

ABSTRACT The vertebrate gut microbiota is a critical determinant of organismal function, yet whether and how gut microbial communities affect host fitness under natural conditions remains largely unclear. We characterised associations between a fitness proxy—individual growth rate—and bacterial gut microbiota diversity and composition in threespine stickleback fish introduced to large semi‐natural ponds. We detected a 63% higher richness of bacterial taxa (α‐diversity) in the guts of high‐fitness fish compared to low‐fitness fish, which might be driven by stronger bacterial dispersal among high‐fitness fish according to the fit of a neutral community model. Further, microbial communities of high‐fitness fish were more similar to one another (i.e., exhibited lower β‐diversity) than those of low‐fitness fish. The lower β‐diversity found to be associated with higher host fitness is consistent with the Anna Karenina principle—that there are fewer ways to have a functional microbiota than a dysfunctional microbiota. Our study links differences in α‐ and β‐diversity to a fitness‐related trait in a vertebrate species reared under naturalistic conditions and our findings provide a basis for functional tests of the fitness consequences of host‐microbiota interactions. [ABSTRACT FROM AUTHOR]

Background: Sepsis is defined as a life‐threatening disease. Autophagy and the microbiome are increasingly connected with sepsis. The aim of this study was to investigate the protective effect of autophagy and the possible mechanisms. Methods: The septic rat model was established by cecal ligation perforation (CLP). Rapamycin (Rap), 3‐methyladenine (3‐MA), and chloroquine (CQ) were administered to interfere autophagy. Western blot (WB) was used to detect the expression of key proteins in autophagy. Hematoxylin and eosin (H&E) staining and enzyme‐linked immunosorbent assays (ELISAs) were used to identify the effect of autophagy on various organs. 16S ribosomal RNA gene sequencing was used to analyze the changes of the gut microbiota. Results: Rap significantly upregulated the expression of key autophagy proteins, and 3‐MA reduced the relative expression compared to the CLP group. The autophagic flux showed a corresponding trend. Interestingly, the autophagy inducer significantly decreased the mortality and the lipopolysaccharide (LPS) level in serum compared with the CLP group. Autophagy activation significantly improves the inflammatory response in sepsis. Histopathological sections showed that CLP destroyed the tight junctions between ileal epithelial cells, while autophagy induction reversed the damage. The sequencing results showed that autophagy activation increased the alpha diversity and alterted the composition and structure of gut microbiota. The abundance of Proteobacteria was markedly decreased in the Rap group, whereas Bacteroidetes was notably increased compared with the CLP group. Additionally, the protective effect of autophagy further changed the biomarkers in the microbial community. The top 35 functions in each sample were analyzed to obtain 18 genes including RNA synthesis, ATP binding and transport, chromosome assignment, osmotic polysaccharide transport, transcytosis, and methylation. Conclusion: Autophagy is able to improve inflammation and may directly or indirectly regulate the microbiota of septic rats. Autophagy may be an important target for future clinical interventions in the treatment of sepsis. [ABSTRACT FROM AUTHOR]

Simple Summary: Coccidiosis affects broiler chickens, causing economic losses since infected chickens grow less efficiently than healthy birds. Coccidiosis is caused by a parasite Eimeria that infects the gastrointestinal tract. In the current study, changes in the bacteria of the jejunum and ileum following infection with Eimeria maxima were determined. Samples were taken between 0 and 14 days post-infection. The infection resulted in decreased body weight gain, increased feed conversion ratio, compromised gut morphology, and decreased plasma carotenoid levels. Microbiota composition was determined by sequencing a portion of the 16s rDNA gene. The results indicate that infection affected the diversity within and between bacterial communities, particularly at the height of infection. In samples from infected birds, species of bacteria that can be opportunistic pathogens were more abundant than in healthy birds. In uninfected birds, bacteria that produce short-chain fatty acids and are associated with improved growth were more abundant. Eimeria maxima affects the ecology of the small intestine by disrupting its integrity and changes the types of bacteria present to those that could be opportunistic pathogens. Coccidiosis is a complex gastrointestinal disease, and understanding its effects on the host will help find effective control methods in the future. Coccidiosis in broiler chickens continues to be a major disease of the gastrointestinal tract, causing economic losses to the poultry industry worldwide. The goal of this study was to generate a symptomatic Eimeria maxima (1000 oocysts) infection to determine its effect on the luminal and mucosal microbiota populations (L and M) in the jejunum and ileum (J and IL). Samples were taken from day 0 to 14 post-infection, and sequencing of 16S rRNA was performed using Illumina technology. Infected birds had significantly (p < 0.0001) lower body weight gain (BWG), higher feed conversion ratio (FCR) (p = 0.0015), increased crypt depth, and decreased villus height (p < 0.05). The significant differences in alpha and beta diversity were observed primarily at height of infection (D7). Analysis of taxonomy indicated that J-L and M were dominated by Lactobacillus, and in IL-M, changeover from Candidatus Arthromitus to Lactobacillus as the major taxon was observed, which occurred quicky in infected animals. LEfSe analysis found that in the J-M of infected chickens, Lactobacillus was significantly more abundant in infected (IF) chickens. These findings show that E. maxima infection affects the microbiota of the small intestine in a time-dependent manner, with different effects on the luminal and mucosal populations. [ABSTRACT FROM AUTHOR]

This study investigates airborne bacterial and fungal communities in south-eastern Italy and Albania using advanced DNA-based techniques and compositional data analysis (CoDa). We assess the significance of airborne microbial communities, detailing our methodologies for site selection, sample collection, DNA extraction, and data analysis. Our results reveal distinct differences in microbial composition between the two regions, driven by local environmental factors. Specifically, Albanian samples showed higher abundances of bacterial species such as Rubellimicrobium roseum and Sphingomonas cynarae, while Italian samples were characterized by a prevalence of Truepera radiovictrix and Rubrobacter radiotolerans. In terms of fungi, Albanian sites exhibited greater abundance of Mycosphaerella tassiana, Aureobasidium pullulans, and Ascochyta herbicola. Aitchison distance-based dendrograms and principal component analysis (PCA) biplots, utilizing singular value decomposition, clearly delineated a geographical separation of microbial communities, underscoring the impact of regional atmospheric conditions on microbial composition. In the discussion, we interpret these findings in the context of regional environmental factors, highlighting their implications for understanding regional differences in airborne microbial communities. The conclusion emphasizes the effectiveness of advanced DNA techniques and CoDa in environmental microbiology, offering insights into how local environmental conditions shape microbial communities and suggesting directions for future research and public health considerations. [ABSTRACT FROM AUTHOR]

Objectives: Recurrent aphthous ulcer (RAU) is a prevalent oral mucosal disease, affecting around 20% of the global population. It can greatly impair the quality of life for affected individuals. However, the exact etiology of RAU remains unknown. Subjects and Methods: 16S rRNA sequencing (16S rRNA‐seq) and non‐targeted liquid chromatography‐mass spectrometry (LC–MS) were employed to investigate the salivary microbiota and metabolic phenotype between RAU patients (N = 61) and healthy controls (HCs) (N = 105). Results: Findings from 16S rRNA ‐seq indicated reduced oral microbial diversity in RAU patients compared to HCs, but increased interactions. Clinical variables did not show any significant association with the overall diversity of oral microbiota in RAU patients. However, significant correlations were observed between specific microorganisms and clinical variables. LC–MS results revealed dysregulation of amino acid, lipid, nucleotide, and caffeine metabolism in RAU patients. Furthermore, correlation analysis of 16S rRNA‐seq and LC–MS data revealed a significant association between salivary microbiota and metabolites in RAU patients. Conclusions: Our study revealed notable differences in salivary microbiota and metabolic profiles between RAU patients and HCs, indicating a strong link between oral microbiota dysbiosis, metabolic disturbances, and the onset and progression of RAU. [ABSTRACT FROM AUTHOR]

Studies of the composition of the gut microbiome have consistently shown that psychiatric disorders such as schizophrenia are associated with gut dysbiosis. However, research focusing on adolescents with early-onset psychosis remains limited. This study aimed to characterize the microbial communities and their potential metabolic functions in these populations. We identified that genera Desulfovibrionaceae_Incertae_Sedis, Paraprevotella, and several genera from the Oscillospiraceae family were significantly more abundant in patients with schizophrenia compared to non-psychotic individuals, while Dorea showed decreased levels in schizophrenia patients. Furthermore, patients with early-onset psychosis demonstrated a significant reduction in Staphylococcus abundance. Additionally, we observed an increase in Prevotellaceae Leyella and Prevotellaceae Incertae Sedis in patients receiving atypical antipsychotic treatment, along with a rise in the genus Weissella among those treated with sertraline. Conversely, patients on valproate treatment exhibited decreased levels of Desulfovibrionaceae Incertae Sedis, while showing increased levels of Kandleria and Howardella. Functional prediction analysis using PICRUSt2 revealed significant differences in the expression of key enzymes associated with fatty acid metabolism. Gene orthology analysis identified 10 differentially expressed genes in the early-onset psychosis and schizophrenia groups. Our findings underscore the importance of considering dietary factors, pharmacological treatments, and microbial composition in understanding the gut–brain axis in psychiatric disorders. [ABSTRACT FROM AUTHOR]

Human health and the human microbiome are inevitably intertwined, increasing their relevance in clinical research. However, the collection, transportation and storage of faecal samples may introduce bias due to methodological differences, especially since postal shipping is a common practise in large-scale clinical cohort studies. Using four different Omics layer, we determined the structural (16S rRNA sequencing, cytometric microbiota profiling) and functional integrity (SCFAs, global metabolome) of the microbiota in relation to different easy-to-handle conditions. These conditions were storage at −20 °C, −20 °C as glycerol stock, 4 °C and room temperature with and without oxygen exposure for a maximum of one week. Storage time affected the microbiota on all Omics levels. However, the magnitude was donor-dependent, highlighting the need for purpose-optimized sample collection in clinical multi-donor studies. The effects of oxygen exposure were negligible for all analyses. At ambient temperature, SCFA and compositional profiles were stable for 24 h and 48 h, respectively, while at 4 °C, SCFA profiles were maintained for 48 h. The global metabolome was highly susceptible, already changing at 24 h in non-frozen conditions. Thus, faecal microbiota was best preserved on all levels when transported as a native sample frozen within 24 h, leading to the least biased outcomes in the analysis. We conclude that the immediate freezing of native stool samples for transportation to the lab is best suited for planned multi-Omics analyses that include metabolomics to extend standard sequencing approaches. [ABSTRACT FROM AUTHOR]

Background: Early childhood caries (ECC) are a prevalent chronic disease in young children. However, there has been limited research on the microbiota in different tissue levels of the same tooth in children with ECC. This study aimed to investigate the dynamic changes in bacterial diversity during the progression of Severe Early Childhood Caries (S-ECC) within the same tooth, from the tooth surface to the root canal, by collecting tissue samples from different areas of the affected tooth. Methods: Twenty primary teeth with periapical periodontitis were selected from 20 children aged 3-5 years, with 100 samples collected from the different layers: uncavitated buccal enamel surface without white spot lesion (surface), the outermost layer of the dentin carious lesion (superficial), the inner layer of carious dentin (deep), necrotic pulp tissue (pulp), and root exudate (exudate). The taxonomy of each OTU representative sequence was analyzed against the 16S rRNA database. Comparisons of alpha diversity between groups were performed. The number of shared and unique genera between groups counted. Beta diversity was contrasted to evaluate differences in bacterial community composition, and the relationships between the microbiota and samples were analyzed. The heatmap analysis of the 30 most abundant genera was used, which highlighted their relative distribution and abundance. The significantly abundant taxa (phylum to genera) of bacteria among the different groups were identified. The differences of relative abundance between bacterial genera among the five groups were analyzed. Significant Spearman correlations were noted, and visualization of the co-occurrence network was conducted. Results: Bacterial 16S rRNA gene sequencing showed that most genera were present in all layers, with the number of shared genera increasing as the disease advanced. The bacterial communities and core genera in the co-occurrence network changed with progression to severe ECC. Conclusion: An increase in both the quantity and complexity of bacterial interactions was observed. This study emphasized the importance of paying attention to the relationship between microbial species rather than just checking changes in bacterial species structure when investigating the role of bacteria in disease progression. [ABSTRACT FROM AUTHOR]

Microplastics (MPs) have garnered global attention as emerging contaminants due to their adaptability, durability, and robustness in various ecosystems. Still, studies concerning their combination with heavy metals (HMs), their interactions with soil biota, and how they affect soil physiochemical properties and terrestrial plant systems are limited. Our study was set to investigate the combined effect of HMs (cadmium, arsenic, copper, zinc and lead) contaminated soil of Tongling and different sizes (T1 = 106 µm, T2 = 50 µm, and T3 = 13 µm) of polystyrene microplastics on the soil physiochemical attributes, both bacterial and fungal diversity, compositions, AMF (arbuscular mycorrhizal fungi), plant pathogens in the soil, and their effect on Lactuca sativa by conducting a greenhouse experiment. According to our results, the combination of HMs and polystyrene microplastic (PS-MPs), especially the smaller PS-MPs (T3), was more lethal for the lettuce growth, microbes and soil. The toxicity of combined contaminants directly reduced the physio-biochemical attributes of lettuce, altered the lettuce's antioxidant activity and soil health. T3 at the final point led to a significant increase in bacterial and fungal diversity. In contrast, overall bacterial diversity was higher in the rhizosphere, and fungal diversity was higher in the bulk soil. Moreover, the decrease in MPs size played an important role in decreasing AMF and increasing both bacterial and fungal pathogens, especially in the rhizosphere soil. Functional prediction was found to be significantly different in the control treatment, with larger MPs compared to smaller PS-MPs. Environmental factors also played an important role in the alteration of the microbial community. This study also demonstrated that the varied distribution of microbial populations could be an ecological indicator for tracking the environmental health of soil. Overall, our work showed that the combination of HMs and smaller sizes of MPs was more lethal for the soil biota and lettuce and also raised many questions for further studying the ecological risk of PS-MPs and HMs. [ABSTRACT FROM AUTHOR]

Introduction: Symbiotic bacteria play key roles in a variety of important life processes of insects such as development, reproduction and environmental adaptation, and the elucidation of symbiont population structure and dynamics is crucial for revealing the underlying regulatory mechanisms. The marmalade hoverfly (Episyrphus balteatus) is not only a remarkable aphid predator, but also a worldwide pollinator second to honeybees. However, its symbiont composition and dynamics remain unclear. Methods: Herein, we investigate the symbiotic bacterial dynamics in marmalade hoverfly throughout whole life cycle, across two sexes, and in its prey Megoura crassicauda by 16S rRNA sequencing. Results: In general, the dominant phyla were Proteobacteria and Firmicutes, and the dominant genera were Serratia and Wolbachia. Serratia mainly existed in the larval stage of hoverfly with the highest relative abundance of 86.24% in the 1st instar larvae. Wolbachia was found in adults and eggs with the highest relative abundance of 62.80% in eggs. Significant difference in species diversity was observed between the adults feeding on pollen and larvae feeding on M. crassicauda, in which the dominant symbiotic bacteria were Asaia and Serratia, respectively. However, between two sexes, the symbionts exhibited high similarity in species composition. In addition, our results suggested that E. balteatus obtainded Serratia mainly through horizontal transmission by feeding on prey aphids, whereas it acquired Wolbachia mainly through intergeneration vertical transmission. Taken together, our study revealed the effects of development stages, diet types and genders of E. balteatus on symbionts, and explored transmission modes of dominant bacteria Serratia and Wolbachia. Discussion: Our findings lay a foundation for further studying the roles of symbiotic bacteria in E. balteatus life cycle, which will benefit for revealing the co-adaptation mechanisms of insects and symbiotic bacteria. [ABSTRACT FROM AUTHOR]

Climatic extremes, especially extreme droughts, are occurring more frequently and profoundly impacting biogeochemical processes. However, the relative importance of microbial communities on soil nutrient cycling and community maintenance under natural extreme drought events remains elusive. During a record-breaking drought in the Yangtze River Basin (YRB) in the summer of 2022, we collected ambient soils and drought-affected bare and vegetated soils in ecological buffer zones from two sites with similar soil and vegetation characteristics along the YRB, and examined the relative contribution of soil bacterial communities in supporting multi-nutrient cycling index (MNCI) involving carbon-, nitrate- and phosphorus-cycling and their associations with microbial network. Extreme drought decreased (p < 0.05) bacterial a-diversity but increased MNCI in vegetated soils at both sites, while both remained unchanged (p > 0.05) in bare soils, possibly as a result of vegetation releasing rhizodeposits under drought which selectively recruited bacterial communities. Bacterial community compositions were shifted (p < 0.05) only in vegetated soils, and they exerted more influence than a-diversity on soil MNCI. Notably, the Anaerolineae, identified as a biomarker enriched in vegetated soils, had close associations with enzyme activities and soil MNCI at both sites, suggesting their potential recruitment by vegetation to withstand drought. Furthermore, key ecological clusters (Module 1) in bacterial co-occurrence networks at both sites supported (p < 0.05) higher MNCI, despite no substantial variation in network structure due to drought. Specifically, the most important taxa within Module 1 for predicting soil MNCI revealed by random forest modeling analysis (R² = 0.44 - 0.63, p < 0.001), such as B1-7BS, SBR1031 and Nocardioides, could be deeply involved in soil nitrogen-cycling, suggesting an essential role of specialized interactions of bacterial communities in maintaining soil multifunctionality. Overall, this study demonstrates that changes in biomarkers and functional taxa under extreme drought may better reflect the biological mechanisms involved in microbial communities impacting ecosystem function, which may aid in forecasting the ecological consequences of ongoing climate change in the ecological buffer zones along the YRB. [ABSTRACT FROM AUTHOR]

Simple Summary: The gut microbiota has provided valuable insights into understanding an animal's adaptation to its environment. Additionally, it has a significant effect on the animal's performance. Comprehending the composition of the microbiota and its interaction with its host is essential for formulating knowledge-based strategies aimed at improving animal adaptability and productivity. This study aimed to investigate the diversity of the microbiota of local Egyptian cattle in three different ecosystems to gain insights into the potentiality of the adaptation of local Egyptian cattle's microbiota. The results suggest an adaptive response of the animals to their respective/specific environments, with a clear effect of both heat stress and feed type. These findings could be useful in enhancing animal adaptations and productivity. The animal gastrointestinal tract contains a complex microbiome whose composition ultimately reflects the co-evolution of microorganisms with their animal host and their host's environment. This study aimed to gain insights into the adaptation of the microbiota of local Egyptian cattle to three different ecosystems (Upper Egypt, Middle Egypt, and Lower Egypt) distributed across 11 governorates (with an average of 12 animals per governorate) using amplicon sequencing. We analyzed the microbiota from 136 fecal samples of local Egyptian cattle through a 16S rRNA gene sequencing approach to better understand the fecal microbial diversity of this breed which developed under different ecosystems. An alpha diversity analysis showed that the fecal microbiota of the Egyptian cattle was not significantly diverse across areas, seasons, sexes, or farm types. Meanwhile, microbiota data revealed significant differences in richness among age groups (p = 0.0018). The microbial community differed significantly in the distribution of its relative abundance rather than in richness across different ecosystems. The taxonomic analysis of the reads identified Firmicutes and Actinobacteriota as the dominant phyla, accounting for over 93% of the total bacterial community in Egyptian cattle. Middle Egypt exhibited a different microbial community composition compared to Upper and Lower Egypt, with a significantly higher abundance of Firmicutes and Euryarchaeota and a lower abundance of Actinobacteriota in this region than the other two ecosystems. Additionally, Middle Egypt had a significantly higher relative abundance of the Methanobacteriaceae family and the Methanobrevibacter genera than Lower and Upper Egypt. These results suggest a difference in the adaptation of the fecal microbial communities of Egyptian cattle raised in Middle Egypt. At the genus level, eleven genera were significantly different among the three ecosystems including Bacillus, DNF00809, Kandleria, Lachnospiraceae_NK3A20_group, Methanobrevibacter, Mogibacterium, Olsenella, Paeniclostridium, Romboutsia, Turicibacter, and UCG-005. These significant differences in microbiota composition may impact the animal's adaptation to varied environments. [ABSTRACT FROM AUTHOR]

In recent years, pelagic Sargassum has invaded the Caribbean coasts, and anaerobic digestion has been proposed as a sustainable management option. However, the complex composition of these macroalgae acts as a barrier to microbial degradation, thereby limiting methane production. Microbial adaptation is a promising strategy to improve substrate utilization and stress tolerance. This study aimed to investigate the adaptation of a microbial consortium to enhance methane production from the pelagic Sargassum. Microbial adaptation was performed in a fed-batch mode for 100 days by progressive feeding of Sargassum. The evolution of the microbial community was analyzed by high-throughput sequencing of 16S rRNA amplicons. Additionally, 16S rRNA data were used to predict functional profiles using the iVikodak platform. The results showed that, after adaptation, the consortium was dominated by the bacterial phyla Bacteroidota, Firmicutes, and Atribacterota, as well as methanogens of the families Methanotrichaceae and Methanoregulaceae. The abundance of predicted genes related to different metabolic functions was affected during the adaptation stage when Sargassum concentration was increased. At the end of the adaptation stage, the abundance of the predicted genes increased again. The adapted microbial consortium demonstrated a 60% increase in both biomethane potential and biodegradability index. This work offers valuable insights into the development of treatment technologies and the effective management of pelagic Sargassum in coastal regions, emphasizing the importance of microbial adaptation in this context. [ABSTRACT FROM AUTHOR]

The interest in region-specific ethnic fermented foods and their functional microbiota is rising. The demands for functional foods are continuously rising, so research is going on to develop nutritious food with many beneficial attributes and low safety concerns. The present study was designed to isolate and characterize lactobacilli probiotic candidates from locally resourced fermented foods (dahi, lassi, and raabadi) to make ready-to-eat fermented functional products later. Cultures were isolated from 82 fermented food samples collected from different villages. The initial experiments of gram staining, catalase test, and carbohydrate fermentation were assessed for the morphology, purity, and primary characterization on the genus level, which was verified through molecular characterization using PCR. Seven lactobacilli strains (no. MS001-MS007) were then assessed for safety, probiotic candidacy, phytase degradation, and biofilm forming abilities. All seven bacterial cultures showed no hemolytic activity and antibiotic sensitivity against more than 14 antibiotics out of 20. All seven lactobacilli isolates were able to tolerate pH 3.0, 0.3% bile 0.5% pancreatin, lysozyme (100 mg/L to 300 mg/L) and also shown possessed phytase degradation ability. All the cultures showed antioxidative potential and biofilm formation ability. Culture MS007 showed considerably higher bile salt hydrolase activity among all the isolates, whereas MS005 possessed excellent phytate degradation ability among others. Bacterial strains were identified using 16S rRNA gene sequencing. Moreover, the order of preference of isolates was calculated using the multidimensional Technique for Order of Preference by Similarity to Ideal Solution (TOPSIS) based on probiotic and other functional properties. The most promising attributes showing cultures were recognised as Limosilactobacillus fermentum MS005 and Lactiplantibacillus plantarum MS007, which could be further used for functional food product development. [ABSTRACT FROM AUTHOR]

Hepatolenticular degeneration (HLD), also known as Wilson's disease (WD), is a rare autosomal recessive disorder regarding copper metabolism. Whether gut microbiota imbalance is involved in developing HLD remains unknown. A comprehensive 16S rRNA amplicon sequencing, metagenomic sequencing, and metabonomic analysis were undertaken in patients with WD to analyze the composition and function profiles of gut microbiota in patients with WD. The data demonstrated differences in gut microbiota and metabolic pathways between WD patients and normal individuals, significantly decreasing bacterial richness and diversity. The levels of Selenomonaceae and Megamonas in WD patients are significantly higher than those in healthy individuals. The relative abundances of Roseburia inulinivorans in patients with WD are lower than in healthy individuals. Compared with healthy people, the level of metabolites in patients with WD is abnormal. Leucylproline, 5-Phenylvaleric Acid and N-Desmethylclobazam, which have nutritional and protective effects, are significantly reduced fecal metabolites in patients with WD. D-Gluconic acid, which can chelate metal ions, may be a potential treatment for WD. The positive correlation it demonstrates with Alistipes indistinctus and Prevotella stercora indicates potential bacteria able to treat WD. These metabolites are mainly related to the biosynthesis of antibiotics, alpha-linolenic acid metabolism, one carbon pool by folate, nicotinate and nicotinamide metabolism. In conclusion, the data from this study elucidate novel mechanisms describing how abnormal gut miccrobiota contribute to the pathogenesis of WD and outlines new molecules for the treatment of WD. [ABSTRACT FROM AUTHOR]

Objective: The aim of this study is to comprehensively investigate the temporal dynamics of faecal gut microbiota and metabonomics in early postnatal with a focus on very low or extremely low birth weight (VLBW/ELBW) infants. Methods: We collected faecal samples from 157 VLBW/ELBW infants at three time points: days 1, 14, and 28 in a prospective cohort study. The faecal microbial diversity, abundance, composition, and metabolomic analyses were determined using 16S rRNA sequencing and liquid chromatography tandem mass spectrometry (LC-MS/MS). Microbiome functional analyses were conducted utilizing PICRUSt2. The ecological association networks were employed to investigate the interactions between gut microbiota and identify the core genus within 28 days of birth, as well as to unveil correlations between taxa and metabolites. Result: (1) The alpha diversity of gut microbiota significantly decreased from D1 to D28, accompanied by an interrupted trajectory lacking obligate anaerobes. At the phylum level, the 16S RNA sequencing results showed an increase in Proteobacteria and a decrease in Firmicutes and Bacteroidota from D1 to D28. At the genus level, there was a decrease in the relative abundance of Staphylococcus, Acinetobacter and Ureaplasma, with Klebsiella and Enterococcus emerging as the most abundant genera. (2) The analysis revealed a total of 561 metabolic markers that exhibited significant and distinct alterations between D1 and D14. (3) Ecological association networks revealed that the gut microbiota in D1 exhibited a significantly higher degree of microbial interactions compared to those in D14 and D28. Additionally, Enterococcus, Klebsiella, and Enterobacter were major contributors to the co-occurring network at these three time points. (4) Steroid hormone biosynthesis, including tetrahydrocortisone, androsterone glucuronide, androstenedione and etiocholanolone glucuronide, decreased within 28 days after birth. Conclusion: We have successfully demonstrated a significant dysbiosis in the gut microbiota and a subsequent decrease in its diversity within 4 weeks postpartum in VLBW/ELBW infants. Monitoring the gut microbiota of VLBW/ELBW infants and promptly rectifying dysbiosis in the early stages may represent a potential therapeutic strategy. [ABSTRACT FROM AUTHOR]

The classical microbiology techniques have inherent limitations in unraveling the complexity of microbial communities, necessitating the pivotal role of sequencing in studying the diversity of microbial communities. Whole genome sequencing (WGS) enables researchers to uncover the metabolic capabilities of the microbial community, providing valuable insights into the microbiome. Herein, we present an overview of the rapid advancements achieved thus far in the use of WGS in microbiome research. There was an upsurge in publications, particularly in 2021 and 2022 with the United States, China, and India leading the metagenomics research landscape. The Illumina platform has emerged as the widely adopted sequencing technology, whereas a significant focus of metagenomics has been on understanding the relationship between the gut microbiome and human health where distinct bacterial species have been linked to various diseases. Additionally, studies have explored the impact of human activities on microbial communities, including the potential spread of pathogenic bacteria and antimicrobial resistance genes in different ecosystems. Furthermore, WGS is used in investigating the microbiome of various animal species and plant tissues such as the rhizosphere microbiome. Overall, this review reflects the importance of WGS in metagenomics studies and underscores its remarkable power in illuminating the variety and intricacy of the microbiome in different environments. [ABSTRACT FROM AUTHOR]

Anthropogenic activities have escalated CH4 emissions, exacerbating global warming, yet specialized bacteria known as Methanotrophs play a key role in mitigating atmospheric CH4 levels by consuming 30-70% of emitted methane. This study focuses on exploring the culturable methanotrophic population within Muthukuda mangrove sediments, an unexplored reservoir of methanotrophic diversity. The sediment sample yielded a methanotrophic bacterial count of 1.5 x 103 CFU/g, leading to the selection of three unique bacterial morphotypes (NCT270, NCT271, and NCT272) for in-depth investigation. Optimal growth was observed at pH 8, with peak growth at 30°C, while extreme temperatures of 4°C and 40°C inhibited growth across all isolates. Salinity levels between 20 and 30 ppt supported optimal growth, with strains displaying tolerance to various stressors. Methane served as the sole carbon source for all experiments, with positive urease production noted after 7 days of incubation. Microscopic and biochemical analyses suggested the classification of strains NCT270, NCT271, and NCT272 within Group I methanotrophic genera: Methylomicrobium, Methyloscarcina, and Methylomonas, respectively. BLASTn analysis of 16S rRNA gene sequences shared high similarities with known methanotrophic species Methyloscarcina fibrate (ON834586) with 99.28%, Methylomicrobium album (ON834587) with 98.77% and Methylomonas methanica (ON834588) with 99.15%. The resulting insights enhance our understanding of culturable methanotrophic diversity and underscore its potential for environmental applications. [ABSTRACT FROM AUTHOR]

Acute gastroenteritis (AGE) is a common cause of pediatric morbidity and mortality worldwide. AGE can cause an imbalance in the intestinal microbiota. This study aimed to investigate the diversity of the gut microbiome in Korean children hospitalized for infectious AGE at a university hospital. A total of 23 stool samples from patients aged 5 months to 11 years with AGE were analyzed. Thirteen convalescent stool samples were collected 1 month after discharge. Multiplex polymerase chain reaction (PCR) for the five viruses and 16 bacteria-specific AGE pathogens (PowerChek Multiplex Real time PCR Kit, Seoul, Korea), and 16s rRNA sequencing (Illumina MiSeq Sequencing system, Illumina, USA) were performed. According to the results of multiplex PCR for causative pathogens, the microbiome taxonomic profile (MTP) of the gut microbiome in three groups of AGE, norovirus AGE (n = 11), Campylobacter AGE (n = 7) and Salmonella AGE (n = 5) was compared. The phylum Actinobacteria was significantly more abundant in the norovirus AGE (P = 0.011), whereas the phylum Proteobacteria was significantly more abundant in Salmonella AGE (P = 0.012). Alpha diversity, which indicates species richness and diversity, showed no statistical differences. However, beta diversity, representing the similarity in MTP between norovirus, Campylobacter , and Salmonella AGE, was significantly different (P = 0.007). In convalescence, compared with their corresponding AGE samples, the phylum Firmicutes; and the lower taxa Christensenellaceae (P = 0.0152) and Lachnospiraceae (P = 0.0327) were significantly increased. In pediatric AGE, the type of infectious agent can affect the diversity and dominance of gut microbiota in pediatric patients. Furthermore, healthy gut bacteria increased during the period of 1 month after infection, allowing a return to a healthy state without causing long-term dysbiosis. [ABSTRACT FROM AUTHOR]

In subway stations, where passengers are crowed in enclosed spaces with restricted ventilation, airborne microorganisms have been detected, potentially contributing to the spread of infectious aerosols. In South Korea's metropolitan subways, air purifiers are installed on platforms to reduce particulate matter. Efficiency particulate air (EPA) filters in air purifiers lack disinfection capabilities and can serve as a source of airborne pathogens during filter replacement. In this field study, antimicrobial filters were applied to air purifiers installed on a subway platform to assess their ability to reduce the captured microorganisms. After 1 week of operation, the microbiomes were collected from both the control and test filters, followed by microbial identification. Additionally, the composition of metal elements was analyzed using particulate matter collected by the EPA filters. While 19 types of bacterial species were detected in control filters, the antimicrobial filters showed the presence of 15 bacterial species, with overall 64.71% of antibacterial efficacy. Specifically, the antimicrobial filter exhibited 100% reduction in Micrococcus and 93.75% reduction in Staphylococcus genus, related to anthropogenic sources. [ABSTRACT FROM AUTHOR]

Abstract Background Wood-feeding termites have been employed as sources of novel and highly efficient lignocellulolytic enzymes due to their ability to degrade lignocellulose efficiently. As a higher wood-feeding termite, Globitermes sulphureus (Blattaria: Termitidae) plays a crucial role as a decomposer in regions such as Vietnam, Singapore, Myanmar, and Yunnan, China. However, the diversity of its gut microbiome and carbohydrate-active enzymes (CAZymes) remains unexplored. Here, we analyzed the diversity of hindgut microbial communities and CAZymes in a higher wood-feeding termite, G. sulphureus, and a lower wood-feeding termite, Coptotermes formosanus (Blattaria: Rhinotermitidae). Results 16S rRNA sequencing revealed that Spirochaetota, Firmicutes, and Fibrobacterota were the dominant microbiota in the hindgut of the two termite species. At the phylum level, the relative abundances of Proteobacteria and Bacteroidota were significantly greater in the hindgut of C. formosanus than in G. sulphureus. At the genus level, the relative abundances of Candidatus_Azobacteroides and Escherichia-Shigella were significantly lower in the hindgut of G. sulphureus than in C. formosanus. Metagenomic analysis revealed that glycoside hydrolases (GHs) with cellulases and hemicellulases functions were not significantly different between G. sulphureus and C. formosanus. Interestingly, the cellulases in G. sulphureus were mainly GH5_2, GH5_4, GH6, GH9, and GH45, while the hemicellulases were mainly GH11, GH8, GH10, GH11, GH26, and GH53. In C. formosanus, the cellulases were mainly GH6 and GH9, and the hemicellulases were mainly GH5_7, GH5_21, GH10, GH12, and GH53. In addition, β-glucosidase, exo-β-1,4-glucanase, and endo-β-1,4-glucanase activities did not differ significantly between the two termite species, while xylanase activity was higher in G. sulphureus than in C. formosanus. The bacteria encoding GHs in G. sulphureus were mainly Firmicutes, Fibrobacterota, and Proteobacteria, whereas Bacteroidota and Spirochaetota were the main bacteria encoding GHs in C. formosanus. Conclusions Our findings characterized the microbial composition and differences in the hindgut microbiota of G. sulphureus and C. formosanus. Compared to C. formosanus, G. sulphureus is enriched in genes encoding for hemicellulase and debranching enzymes. It also highlights the rich diversity of GHs in the hindgut microbiota of G. sulphureus, including the GH5 subfamily, GH6, and GH48, with the GH6 and GH48 not previously reported in other higher termites. These results strengthen the understanding of the diversity of termite gut microbiota and CAZymes.

Abstract Lichen sclerosus is a chronic inflammatory condition of unknown etiology that affects the genital and extragenital skin, which can lead to sexual dysfunction and has been associated with vulvar cancer. The vaginal microbiome has a critical role in gynecologic health, but little is known about the microbiome in lichen sclerosus. This study investigated the vaginal and vulvar microbiomes of 27 post-menopausal women with lichen sclerosus. The most abundant genera detected in the vaginal microbiome were Lactobacillus, Gardnerella, and Anaerococcus, while Lactobacillus, Anaerococcus, and Staphylococcus were the most abundant in the vulvar microbiome. The vaginal samples clustered into two main groups, Lactobacillus dominant (n = 6, > 50% microbiome Lactobacillus) and polymicrobial (n = 21) with no dominant genus. The vulvar samples were mainly polymicrobial (n = 25). Actinomyces, Anaerococcus, and Ezakiella in the vaginal microbiome and Actinomyces and Ezakiella in the vulvar microbiome were significantly associated with lichen sclerosus symptoms (adjusted p

Abstract Background Fetal growth restriction (FGR) is typically characterised as the fetus’ inability to reach its inherent growth potential. A growing body of evidence points to the important role of the maternal gut microbiota in FGR development. However, comprehensive research on changes in maternal–fetal gut and intrauterine microbiota related to FGR is lacking. Methods In this case–control study, we sequenced bacterial 16S rRNA from 35 maternal faecal, 35 meconium, and 31 amniotic fluid samples collected from 19 pregnant women diagnosed with FGR and 16 healthy controls. We identified putative bacterial taxonomic and functional characteristics associated with FGR by comparing these to control samples. Results We identified 34 differential operational taxonomic units (OTUs) in amniotic fluid, seven differential OTUs in maternal faecal matter, and two differential OTUs in meconium. Compared to controls, FGR subjects exhibited enriched bacterial OTUs of the genus Bacteroides in the maternal gut. They also had depleted OTUs of the order Enterobacterales and genus Pseudomonas in the amniotic fluid and genus Stenotrophomonas in the fetal gut. These altered bacterial OTUs showed a significant correlation with neonatal weight and fetal ultrasonographic indexes. Additionally, we identified differential microbial functional pathways related to glycan and lipid metabolism in the maternal gut. We developed diagnostic biomarkers for FGR based on the maternal–fetal gut and amniotic fluid microbiota. Conclusions This study offers a comprehensive overview of the shifts in microbial composition and functional pathways in the maternal–fetal gut and amniotic fluid microbiota related to FGR, and present novel insights into the development and screening of FGR. However, the assessment of contamination’s impact on meconium and amniotic fluid remains inconclusive, necessitating further rigorous experimentation to address this scientific inquiry in future studies.

This study examined the risk of intrauterine infection associated with radical trachelectomy (RT) in early‐stage cervical cancer patients. This procedure preserves fertility but is linked to increased risk of intrauterine infection due to cervical defects during pregnancy. DNA was extracted from the formalin‐fixed paraffin‐embedded (FFPE) placental specimens of 23 pregnant post‐RT patients and 16S rRNA gene sequencing was used for bacterial identification. The prevalence of Lactobacillus crispatus and Burkholderia stabilis was significantly higher in the non‐chorioamnionitis group. In contrast, alpha diversity analysis using the PD index showed significantly higher diversity in the chorioamnionitis group (P = 0.04). The demonstrated relationship between chorioamnionitis and microbial diversity affirms the importance of controlling the genital bacterial flora in pregnancies following RT.

Objective: To provide the mechanism-based pharmacotherapy of the Huatan Qushi formula (HTQS formula), for the health management and treatment of non-alcoholic fatty liver disease (NAFLD). Methods: A rat model of NAFLD was employed to examine the efficacy and safety of the HTQS formula. In vivo active components and potential mechanisms of the HTQS formula were identified using UPLC‒MS/MS combined with network pharmacology. The influence of the HTQS formula on the dominating proteins in PI3K/Akt pathway was validated in vivo using western blot. Finally, 16S rRNA sequencing of the gut microbiome was conducted followed by targeted metabolomics detecting fecal short-chain fatty acids (SCFAs) and bile acids to determine the impact of the HTQS formula on gut microbiota. Results: The HTQS formula reduced weight gain and hepatic steatosis in NAFLD rats and decreased serum total cholesterol (TC), triglycerides, blood glucose, and insulin resistance (IR) without causing liver or kidney injury. We detected 28 components using UPLC‒MS/MS and identified 439 shared targets between NAFLD and the HTQS formula. Primarily, we focused on the PI3K/Akt signaling pathway based on protein‒protein interaction network analysis. We validated that the HTQS formula inhibited liver steatosis and inflammation by increasing the phosphorylation levels of PI3K, AKT, P27, GSK3β in the PI3K/Akt signaling pathway. 16S rRNA sequencing revealed that the HTQS formula reduced the abundance of the genus Family_XIII_AD3011_group, which was positively correlated with IR and taurodeoxycholic acid. In addition, Lachnospiraceae_UCG_010 inversely correlated with TC and five bile acids, which could be essential to the therapeutic effect of the HTQS formula against NAFLD. Conclusions: The HTQS formula proved to be an effective pharmacotherapy for NAFLD without causing liver or kidney injury. Multiple potent components of the HTQS formula could alleviate liver steatosis and lipid metabolism disorder by modulating the PI3K/Akt signaling pathway and restoring gut microbiota composition.

Abstract Species with different genetic backgrounds exhibit distinct metabolic traits. Nine beef cattle were selected for the experiment to study changes in serum metabolic phenotypes, rumen microbiota diversity, and composition in beef cattle from different genetic backgrounds. Three groups were Chinese Simmental (S group), Simmental×Chinese Holstein (SH group), and Simmental × Mongolian (SM group) cattle. We used ELISA to detect serum biochemical indicators. The Short-chain fatty acids (SCFAs) in the rumen were examined, and a significant difference was observed in the acetic acid content of the three experimental groups (p

Anthropogenic activities have escalated CH4 emissions, exacerbating global warming, yet specialized bacteria known as Methanotrophs play a key role in mitigating atmospheric CH4 levels by consuming 30-70% of emitted methane. This study focuses on exploring the culturable methanotrophic population within Muthukuda mangrove sediments, an unexplored reservoir of methanotrophic diversity. The sediment sample yielded a methanotrophic bacterial count of 1.5 x 103 CFU/g, leading to the selection of three unique bacterial morphotypes (NCT270, NCT271, and NCT272) for in-depth investigation. Optimal growth was observed at pH 8, with peak growth at 30°C, while extreme temperatures of 4°C and 40°C inhibited growth across all isolates. Salinity levels between 20 and 30 ppt supported optimal growth, with strains displaying tolerance to various stressors. Methane served as the sole carbon source for all experiments, with positive urease production noted after 7 days of incubation. Microscopic and biochemical analyses suggested the classification of strains NCT270, NCT271, and NCT272 within Group I methanotrophic genera: Methylomicrobium, Methyloscarcina, and Methylomonas, respectively. BLASTn analysis of 16S rRNA gene sequences shared high similarities with known methanotrophic species Methyloscarcina fibrate (ON834586) with 99.28%, Methylomicrobium album (ON834587) with 98.77% and Methylomonas methanica (ON834588) with 99.15%. The resulting insights enhance our understanding of culturable methanotrophic diversity and underscore its potential for environmental applications.

Abstract Hepatolenticular degeneration (HLD), also known as Wilson's disease (WD), is a rare autosomal recessive disorder regarding copper metabolism. Whether gut microbiota imbalance is involved in developing HLD remains unknown. A comprehensive 16S rRNA amplicon sequencing, metagenomic sequencing, and metabonomic analysis were undertaken in patients with WD to analyze the composition and function profiles of gut microbiota in patients with WD. The data demonstrated differences in gut microbiota and metabolic pathways between WD patients and normal individuals, significantly decreasing bacterial richness and diversity. The levels of Selenomonaceae and Megamonas in WD patients are significantly higher than those in healthy individuals. The relative abundances of Roseburia inulinivorans in patients with WD are lower than in healthy individuals. Compared with healthy people, the level of metabolites in patients with WD is abnormal. Leucylproline, 5-Phenylvaleric Acid and N-Desmethylclobazam, which have nutritional and protective effects, are significantly reduced fecal metabolites in patients with WD. D-Gluconic acid, which can chelate metal ions, may be a potential treatment for WD. The positive correlation it demonstrates with Alistipes indistinctus and Prevotella stercora indicates potential bacteria able to treat WD. These metabolites are mainly related to the biosynthesis of antibiotics, alpha-linolenic acid metabolism, one carbon pool by folate, nicotinate and nicotinamide metabolism. In conclusion, the data from this study elucidate novel mechanisms describing how abnormal gut miccrobiota contribute to the pathogenesis of WD and outlines new molecules for the treatment of WD.

Abstract The interest in region-specific ethnic fermented foods and their functional microbiota is rising. The demands for functional foods are continuously rising, so research is going on to develop nutritious food with many beneficial attributes and low safety concerns. The present study was designed to isolate and characterize lactobacilli probiotic candidates from locally resourced fermented foods (dahi , lassi, and raabadi) to make ready-to-eat fermented functional products later. Cultures were isolated from 82 fermented food samples collected from different villages. The initial experiments of gram staining, catalase test, and carbohydrate fermentation were assessed for the morphology, purity, and primary characterization on the genus level, which was verified through molecular characterization using PCR. Seven lactobacilli strains (no. MS001-MS007) were then assessed for safety, probiotic candidacy, phytase degradation, and biofilm forming abilities. All seven bacterial cultures showed no hemolytic activity and antibiotic sensitivity against more than 14 antibiotics out of 20. All seven lactobacilli isolates were able to tolerate pH 3.0, 0.3% bile 0.5% pancreatin, lysozyme (100 mg/L to 300 mg/L) and also shown possessed phytase degradation ability. All the cultures showed antioxidative potential and biofilm formation ability. Culture MS007 showed considerably higher bile salt hydrolase activity among all the isolates, whereas MS005 possessed excellent phytate degradation ability among others. Bacterial strains were identified using 16S rRNA gene sequencing. Moreover, the order of preference of isolates was calculated using the multidimensional Technique for Order of Preference by Similarity to Ideal Solution (TOPSIS) based on probiotic and other functional properties. The most promising attributes showing cultures were recognised as Limosilactobacillus fermentum MS005 and Lactiplantibacillus plantarum MS007, which could be further used for functional food product development. Graphical Abstract

Background: Acute gastroenteritis (AGE) is a common cause of pediatric morbidity and mortality worldwide. AGE can cause an imbalance in the intestinal microbiota. This study aimed to investigate the diversity of the gut microbiome in Korean children hospitalized for infectious AGE at a university hospital. Methods: A total of 23 stool samples from patients aged 5 months to 11 years with AGE were analyzed. Thirteen convalescent stool samples were collected 1 month after discharge. Multiplex polymerase chain reaction (PCR) for the five viruses and 16 bacteria-specific AGE pathogens (PowerChek Multiplex Real time PCR Kit, Seoul, Korea), and 16s rRNA sequencing (Illumina MiSeq Sequencing system, Illumina, USA) were performed. Results: According to the results of multiplex PCR for causative pathogens, the microbiome taxonomic profile (MTP) of the gut microbiome in three groups of AGE, norovirus AGE (n = 11), Campylobacter AGE (n = 7) and Salmonella AGE (n = 5) was compared. The phylum Actinobacteria was significantly more abundant in the norovirus AGE (P = 0.011), whereas the phylum Proteobacteria was significantly more abundant in Salmonella AGE (P = 0.012). Alpha diversity, which indicates species richness and diversity, showed no statistical differences. However, beta diversity, representing the similarity in MTP between norovirus, Campylobacter, and Salmonella AGE, was significantly different (P = 0.007). In convalescence, compared with their corresponding AGE samples, the phylum Firmicutes; and the lower taxa Christensenellaceae (P = 0.0152) and Lachnospiraceae (P = 0.0327) were significantly increased. Conclusions: In pediatric AGE, the type of infectious agent can affect the diversity and dominance of gut microbiota in pediatric patients. Furthermore, healthy gut bacteria increased during the period of 1 month after infection, allowing a return to a healthy state without causing long-term dysbiosis.

An organism's gut microbiota can change in response to novel environmental conditions, in particular when colonisation of new habitats is accompanied by shifts in the host species' ecology. Here, we investigated the gut microbiota of three lizard species (A. inornata, H. maculata and S. cowlesi) from their ancestral-like habitat in the Chihuahuan desert and two colonised habitats with contrasting geological and ecological compositions: the White Sands and Carrizozo lava flow. The host species and the lizards' environment both shape gut microbiota composition, but host effects were overall stronger. Further, we found evidence that colonisation of the same environment by independent host species led to parallel changes of the gut microbiota, whereas the colonisation of two distinct environments by the same host species led to gut microbiota divergence. Some of the gut microbiota changes that accompanied the colonisation of the White Sands were associated with shifts in diet (based on diet information from previous studies), which is congruent with the general observation that trophic ecology has a strong effect on gut microbiota composition. Our study provides insights into how shifts in host ecology accompanying colonisation of novel environments can affect gut microbiota composition and diversity.

ABSTRACTInhalation of ambient particulate matter (PM) can disrupt the gut microbiome, while exercise independently influences the gut microbiome by promoting beneficial bacteria. In this study, we analyzed changes in gut microbial diversity and composition in response to combined interventions of PM exposure and aerobic exercise, extending up to 12 weeks. This investigation was conducted using mice, categorized into five groups: control group (Con), exercise group (EXE), exercise group followed by 3-day exposure to PM (EXE + 3-day PM), particulate matter exposure (PM), and PM exposure with concurrent treadmill exercise (PME). Notably, the PM group exhibited markedly lower alpha diversity and richness compared to the Con group and our analysis of beta diversity revealed significant variations among the intervention groups. Members of the Lachnospiraceae family showed significant enhancement in the exercise intervention groups (EXE and PME) compared to the Con and PM groups. The biomarker Lactobacillus, Coriobacteraceae, and Anaerofustis were enriched in the EXE group, while Desulfovibrionaceae, Mucispirillum schaedleri, Lactococcus and Anaeroplasma were highly enriched in the PM group. Differential abundance analysis revealed that Paraprevotella, Bacteroides, and Blautia were less abundant in the 12-week PM exposure group than in the 3-day PM exposure group. Moreover, both the 3-day and 12-week PM exposure groups exhibited a reduced relative abundance of Bacteroides uniformis, SMB53, and Staphylococcus compared to non-PM exposure groups. These findings will help delineate the possible roles and associations of altered microbiota resulting from the studied interventions, paving the way for future mechanistic research.

The purpose of this study was to investigate the effects of acute nitrate (NO3−)-rich beetroot juice ingestion on explosive and high-intensity exercise performance, oral microbiota composition, and cognitive flexibility (i.e., function), before and after maximal intermittent running exercise. Fifteen women team-sport athletes were assigned in a randomized, double-blind, crossover design to consume concentrated NO3–-depleted beetroot juice (PL; 0.1 mmol NO3−) and NO3−-rich beetroot juice (BR; 12.0 mmol NO3−) 2.5 h prior to performing a battery of exercise performance tasks and cognitive testing before and after the Yo–Yo intermittent recovery level 1 (YYIR1) running test. Resting plasma [NO3−] and plasma nitrite ([NO2−]) were elevated following BR (P < 0.001). BR did not impact global composition or relative abundance of taxa in the oral microbiome (P > 0.05) or cognitive flexibility before or after exercise (P > 0.05). There was no significant difference in performance during 20-m (PRE, PL: 4.38 ± 0.27 vs. BR: 4.38 ± 0.32 s; POST, PL: 4.45 ± 0.29 vs. BR: 4.43 ± 0.35 s) and 10-m sprints (PRE, PL 2.78 ± 0.15 vs. BR 2.79 ± 0.18 s; POST, PL: 2.82 ± 0.16 vs. BR: 2.81 ± 0.19 s), isokinetic handgrip dynamometry, medicine ball throw, horizontal countermovement jump, or YYIR1 (PL: 355 ± 163 m vs. BR: 368 ± 184 m) between BR and PL (P > 0.05). These findings indicate that acute dietary NO3− may not influence the oral microbiome, explosive and high-intensity exercise performance, or cognitive function in women team-sport athletes. [ABSTRACT FROM AUTHOR]

Background: The oral microbiome‐dependent nitrate (NO3−)–nitrite (NO2−)–nitric oxide (NO) pathway may help regulate blood pressure. NO2−‐producing bacteria in subgingival plaque are reduced in relative abundance in patients with untreated periodontitis compared with periodontally healthy patients. In periodontitis patients, the NO2−‐producing bacteria increase several months after periodontal treatment. The early effects of periodontal treatment on NO2−‐producing bacteria and the NO3−–NO2−–NO pathway remain unknown. The aim of this study was to determine how periodontal treatment affects the oral NO2−‐producing microbiome and salivary NO3− and NO2− levels over time. Methods: The subgingival microbiota of 38 periodontitis patients was analysed before (baseline [BL]) and 1, 7 and 90 days after periodontal treatment. Changes in NO2−‐producing bacteria and periodontitis‐associated bacteria were determined by 16s rRNA Illumina sequencing. Saliva samples were collected at all‐time points to determine NO3− and NO2− levels using gas‐phase chemiluminescence. Results: A significant increase was observed in the relative abundance of NO2−‐producing species between BL and all subsequent timepoints (all p < 0.001). Periodontitis‐associated species decreased at all timepoints, relative to BL (all p < 0.02). NO2−‐producing species negatively correlated with periodontitis‐associated species at all timepoints, with this relationship strongest 90 days post‐treatment (ρ = −0.792, p < 0.001). Despite these findings, no significant changes were found in salivary NO3− and NO2− over time (all p > 0.05). Conclusions: Periodontal treatment induced an immediate increase in the relative abundance of health‐associated NO2−‐producing bacteria. This increase persisted throughout periodontal healing. Future studies should test the effect of periodontal treatment combined with NO3− intake on periodontal and cardiovascular health. [ABSTRACT FROM AUTHOR]

Tilapia, a valuable fish species, ranks as the world's second-largest farmed fish. In Thailand, it is a prominent cultured species, specifically the red tilapia hybrids (Oreochromis spp.). Understanding the factors influencing tilapia's microbiome is essential to mitigate fish mortality and production decline. The study assesses the rearing water and fish gill microbiome in red tilapia culture, comparing closed earthen pond and open river cage culture systems across five provinces in Central Thailand. We conducted 16S rRNA amplicon sequencing (V3-V4 hypervariable regions) on bacterial DNA from 30 gills and 27 rearing water samples The results revealed that the location had a more significant impact (p < 0.05) than the culture system on both gills and water microbiomes. No association between abiotic factors and gill microbiome diversity was observed, while significant associations were observed between the water microbiome with ambient temperature (Ta) (p < 0.00), water temperature (Tw) (p < 0.00), pH (p < 0.03), and salinity (p < 0.01). Fish pathogens such as Streptococcus agalactiae and Mycobacterium spp. were consistently among the top 5 most abundant bacteria found in both water and fish gill samples across all provinces. Furthermore, several significant fish pathogens, including Vibrio spp., Aeromonas hydrophila, Flavobacterium spp., and Edwardsiella spp., which pose a threat to public health and food safety and security, were detected, albeit in relatively low abundance (< 0.04%). In summary, this study has identified several bacterial species present in both rearing water and red tilapia gills, some of which can cause human disease as well. Interestingly, the culture system did not have a significant impact on microbial diversity, while the farm's location played a significant role. Further investigations into other factors such as farming practices and environmental conditions that may contribute to the presence of pathogenic bacteria in both rearing water and gill samples are warranted. [ABSTRACT FROM AUTHOR]

An actinobacterium newly isolated from soil during a screening study was identified as Streptomyces sp. MC12 (GenBank accession number: PP757795) based on 16S rRNA analysis. For secondary metabolite production, fermentation was carried out in ISP 2 broth at 30°C, pH 7.3, for seven days under shaking conditions at 180 rpm. As a result of fermentation studies, the antagonistic effect of the crude extract, obtained through ethyl acetate extraction, against various microorganisms was determined. The MIC values of the extract against Staphylococcus aureus and Escherichia coli were 101.3 µg/mL and 153.6 µg/mL, respectively. It was also found to exhibit strong antifungal activity against Penicillium spp. Streptomyces sp. MC12, which displays both antifungal and antibacterial properties, is considered a potential secondary metabolite producer for future studies, particularly in pharmacology and the biocontrol of fungal pathogens. [ABSTRACT FROM AUTHOR]

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Bovine respiratory disease (BRD) is a multifaceted condition that poses a primary challenge in calf rearing. Viruses and bacteria are etiological agents of BRD. Viral BRD is typically managed symptomatically, whereas bacterial BRD is predominantly managed through the empirical administration of antimicrobials. However, this empirical administration has raised concerns regarding the emergence of antimicrobial-resistant bacteria. Thus, rapid identification of pathogenic bacteria and judicious selection of antimicrobials are required. This study evaluated the usefulness of 16S rRNA analysis through nanopore sequencing for the rapid identification of BRD-causing bacteria. A comparative evaluation of nanopore sequencing and traditional culture method was performed on 100 calf samples detected with BRD. Nanopore sequencing facilitated the identification of bacteria at the species level in bovine nasal swabs, ear swabs, and lung tissue samples within approximately 6 h. Of the 92 samples in which BRD-causing bacteria were identified via nanopore sequencing, 82 (89%) were concordant with the results of culture isolation. In addition, the occurrence of multiple infections exceeded that of singular infections. These results suggest that 16S rRNA sequencing via nanopore technology is effective in reducing analysis time and accurately identifying BRD-causing bacteria. This method is particularly advantageous for the initial detectable screening of BRD. [ABSTRACT FROM AUTHOR]

Abstract Gel lubrication is routinely used during gynecological examination to prevent or reduce pain, yet its impact on microbial composition during sampling remains unclear. This study aimed to investigate whether lubricating gel affects the microbial composition of vaginal samples. We included 31 pregnant women presenting during their third trimester to clinics or emergency room and collected 143 unique vaginal samples for 16S amplicon microbial analysis. Vaginal samples were obtained using sterile swabs under various conditions: without gel—immediately frozen (n = 30), with gel—immediately frozen, without gel—at room temperature (RT) for 5 h before freezing, with gel—at RT for 5 h before freezing, and additional sampling after 24 h without gel—immediate freezing. We found that sample collection with gel lubrication influenced specimen quality—half of the gel samples failing to meet processing limitation compared to those without gel. The effect of gel on testing quality dissipated after 24 h. However, when samples met post-sequencing filters, gel lubrication did not alter the microbial composition, individual taxa abundance or alpha and beta diversity. We recommend sampling either before gel exposure or 24 h after. These findings underscore the importance of considering sample collection methodologies in vaginal microbiome studies to ensure high-quality microbial data for accurate analysis.

Abstract Gaining a comprehensive understanding of the role played by the oral microbiome in moderate to severe plaque psoriasis and its potential implications for disease management and development holds significant importance. With the objective of exploring correlations between the oral microbiota and severe psoriasis, this study involved 72 severe psoriasis patients and 16 healthy individuals, whose clinical manifestations and living habits were carefully recorded. Cutting-edge techniques such as 16S rRNA gene sequencing and bioinformatics analysis were employed to compare the microbial flora, investigating dynamic changes among severe plaque psoriasis patients, psoriatic arthritis patients and healthy individuals. The findings revealed noteworthy patterns including increased levels of Aggregatibacter in the psoriatic arthritis group, accompanied by a decrease in the level of Prevotella. Moreover, the enrichment o Capnocytandophaga (P = 0.009), Campylobacter (P = 0.0022), and Acetobacter (P = 0.0292) was notably more substantial in the psoriasis group compared to the control group, whereas certain bacterial species such as Bacteroides (P = 0.0049), Muribaculaceae (P = 0.0048) demonstrated decreased enrichment. Additionally, the psoriatic arthritis group exhibited significantly higher levels of Ralstonia, Bifidobacterium and Micromonospora. Based on these findings, it can be inferred that individuals with lower levels of Prevotella and higher levels of Corynebacterium may be more susceptible to psoriasis exacerbation.

Abstract Background Recently, the oral oncobacterium Fusobacterium nucleatum (F. nucleatum), has been linked with ulcerative colitis (UC). Here, we aim to investigate whether Fecal Microbiota Transplantation (FMT) can alleviate UC by restoring gut microbiota and eliminating oral-derived F. nucleatum and virulence factor fadA. Method C57BL/6J mice were randomly divided into a healthy control group (HC), Dextran Sulfate Sodium group (DSS), oral inoculation group (OR), upper FMT group (UFMT), and lower FMT group (LFMT). Disease activity index, body weight, survival rate, and histopathological scores were used to measure the severity of colitis. The function of the intestinal mucosal barrier was evaluated by performing immunohistochemical staining of the tight junction protein Occludin. Real-time PCR was used to assess the relative abundance of the nusG gene and the virulence gene fadA. Cytokine levels were detected by ELISA. Full-length sequencing of 16S rRNA was used to analyze the changes and composition of gut microbiota. Findings Oral incubation of F. nucleatum further exacerbated the severity of colitis and gut dysbiosis. Peptostreptococcaceae, Enterococcaceae, and Escherichia coli were significantly enriched in OR mice. However, LFMT mice showed an obvious decrease in disease activity and were more effective in restoring gut microbiota and eliminating F. nucleatum than UFMT mice. Bacteroidota, Lachnospiraceae, and Prevotellaceae were mainly enriched bacteria in LFMT mice. In addition, Genera such as Lactobacillus, Allobaculum, and Bacteroidales were found negative correlation with TNF-α, IL-1β, and IL-6. Genera like Romboutsia, Escherichia Shigella, Enterococcus, and Clostridium were found positively correlated with TNF-α, IL-1β, and IL-6. Conclusions Oral incubation of F. nucleatum further exacerbates the severity and dysbiosis in DSS-induced colitis mice. Besides, lower tract FMT can ameliorate colitis by restoring the gut microbiota diversity and eliminating F. nucleatum and virulence factor fadA.

Objective Compared to Mimas pigeons, Shiqi pigeons exhibit greater tolerance to coarse feeding because of their abundant gut microbiota. Here, to investigate the potential of utilizing intestinal flora derived from Shiqi pigeons, the intestinal flora and body indices of Mimas squabs were evaluated after fecal microbiota transplantation (FMT) from donors. Methods A total of 90 one-day-old squabs were randomly divided into the control group (CON), the low-concentration group (LC) and the high-concentration group (HC): gavaged with 200 μL of bacterial solution at concentrations of 0, 0.1, and 0.2 g/15 mL, respectively. Results The results suggested that FMT improved the body weight of Mimas squabs in the HC and LC groups (p