16S rRNA Gene Sequence Research Articles

Microencapsulated Microbial Seed Coating Could Improve Soil Environment and Maize Grain Yield in Saline Soil

Soil salinization is one of the major challenges for modern agriculture, posing a great threat to soil health and food security. Field experiments were conducted to evaluate the effect of seed coating on soil environment and maize growth in saline soils. Three treatments were applied to maize seeds: coating with a microencapsulated microbial agent (ME), coating with microbial only (MB), and no coating (CK). High-throughput sequencing of soil bacterial and fungal 16S and ITS rRNA genes was performed using the Illumina HiSeq platform to analyze the effects of these treatments on soil bacterial and fungal diversity and community structure. Additionally, the influence of different treatments on endogenous hormones and yield of maize were investigated. It was found that the coating with a microencapsulated microbial agent led to decreases in pH and electrical conductivity (EC), while increasing the content of soil available phosphorus. This coating improved soil microbial diversity, significantly increasing the relative abundance of the main bacteria genera, Bacillus (34.9%), and the main fungal genera, Mortierella (190.4%). The treatment also significantly enhanced indole-3-acetic acid (IAA) by 51.2%, contributing to improvements in resistance to salt stress. The germination rate increased by 22.9%, the 100-grain weight increased by 12.7%, and grain yield increased by 14.3%. The use of the microencapsulated microbial agent effectively mitigated the adverse effects of salt stress on maize plants. This approach is beneficial for promoting sustainable agriculture in saline soils.

Western diet promotes endometriotic lesion growth in mice and induces depletion of Akkermansia muciniphila in intestinal microbiota.

Endometriosis, affecting 10% of women in their reproductive years, remains poorly understood. Both individual and environmental unexplained factors are implicated in this heterogenous condition. This study aims to examine the influence of a Western diet on endometriosis lesion development in mice and to uncover the mechanisms involved. Mice were fed either a control diet or a Western diet (high in fatty acids and low in fiber) for 4weeks. Endometriosis was then surgically induced, and lesion development was monitored by ultrasound. After 7weeks, the mice were sacrificed for analysis of lesion characteristics through RT-qPCR, immunohistochemistry, and flow cytometry. Additionally, the intestinal microbiota was assessed using 16S rRNA gene sequencing. Mice on the Western diet developed lesions that were significantly twice as large compared to those on the control diet. These lesions exhibited greater fibrosis and proliferation, alongside enhanced macrophage activity and leptin pathway expression. Changes in the intestinal microbiota were significantly noted after endometriosis induction, regardless of diet. Notably, mice on the Western diet with the most substantial lesions showed a loss of Akkermansia Muciniphila in their intestinal microbiota. A Western diet significantly exacerbates lesion size in a mouse model of endometriosis, accompanied by metabolic and immune alterations. The onset of endometriosis also leads to substantial shifts in intestinal microbiota, suggesting a potential link between diet, intestinal health, and endometriosis development.

Genome-based classification of Halobellus rubicundus sp. nov., a novel extremely halophilic archaeon isolated from a Korean solar saltern.

A novel extremely halophilic archaeon designated, MBLA0158T, was isolated from a solar saltern in Sorae, Republic of Korea. The colonies are red-pigmented, Gram-stain-negative, pleomorphic, non-motile, and lysed in distilled water. The strain grows at 25-45°C (optimum, 37°C), in 15-30% (w/v) NaCl (optimum, 20%) and 0.1-1.0M Mg2+ (optimum, 0.2-0.3M) at pH 6.0-10.0 (optimum, 7.0-8.0). Comparative analysis based on the 16S rRNA gene sequence revealed that this strain is most closely related to the Halobellus inordinatus YC20T with a sequence identity of 96.0%. Strain MBLA0158T contained phosphatidylglycerol and phosphatidylglycerol phosphate methyl ester as major polar lipids. The genome size is 3.29Mb and the DNA G + C content is 66.9mol%. Phylogenomic analysis confirmed that strain MBLA0158T is distinct from previously reported type strains of the genus Halobellus. Pan-genome analysis showed that strain MBLA0158T contains 419 genes that are not present in other type strains of the genus Halobellus. Based on overall analyses, strain MBLA0158T is considered to represent a new species of the genus Halobellus, for which the name Halobellus rubicundus sp. nov. is proposed. The type strain is MBLA0158T (= KCTC 4318T = JCM 36642T).

Acid mine drainage bioremediation using bacteria enriched from the confluence zone between its flow and treated sewage

AbstractSediments from the confluence zone between an acid mine drainage stream and a water stream receiving the effluent from a municipal wastewater treatment plant were inoculated in a Postgate B medium base having methanol, glycerol, or ethanol as carbon source/electron donor, over a pH range between 2.00 and 6.00, aiming to obtain native cultures enriched in acidophilic/acid-tolerant sulfate-reducing bacteria. The most effective sulfate reduction observed in acidic conditions was in the enrichment cultures with methanol. Thus, the microbial consortium enriched in these conditions was further used in acid mine drainage bioremediation experiments at an initial pH of 4.50 and using different doses of nutrients medium base and methanol as carbon source/electron donor. The most promising results, with more than 99% removal of metals, were obtained in the mixture of 20% Postgate B medium base plus 80% acid mine drainage (v/v), which corresponds to 0.115% basal salts and 0.02% yeast extract (w/v). Metataxonomic analysis based on 16S rRNA gene sequences showed the presence of Desulfosporosinus spp. in all enrichment cultures, with the highest relative abundance in cultures at pH 4.00 with methanol. Furthermore, metataxonomic analysis in the acid mine drainage remediation tests revealed the presence of Desulfosporosinus spp. in all tested conditions. In addition, the study also revealed Clostridium members in all tests. Plus, their relative abundances were related to the dose of nutrient medium base and in balance with the abundances of Desulfosporosinus spp.

Black raspberry modulates cecal and oral microbiome at the early stage of a dibenzo[def,p]chrysene-induced murine oral cancer model.

While tobacco smoking is a risk factor in the development of oral squamous cell carcinoma (OSCC), only a fraction of smokers develop the disease. Compelling evidence shows that microbial community composition is associated with carcinogenesis, suggesting that the microbiome may play a role in cancer development of smokers. We previously showed that black raspberry (BRB) protects against OSCC induced by the tobacco constituent dibenzo[def,p]chrysene (DBP) altering genetic and epigenetic markers in a manner consistent with its cancer preventive activity. In the present study, we conducted a mouse experiment to investigate the effects of BRB and DBP individually and in combination on the oral and gut microbiota. DBP-induced DNA damage in the mouse oral cavity which is an essential step for the development of OSCC in mice. 16S rRNA gene sequencing revealed that BRB significantly increased microbial diversity and shifted microbiome composition in the gut and oral cavity, whereas DBP had no significant effect. In both gut and oral microbiota, Akkermansia muciniphila was significantly reduced after BRB treatment; however, this was not consistent with pure culture in vitro assays suggesting that the impact of BRB on A. muciniphila may be mediated through indirect mechanisms including the host or other microbes. Indeed BRB, but not DBP, was found to modulate the growth kinetics of human gut microbes in vitro including lactic acid bacteria and Bacteroides spp. The results of the current study further emphasize the interplay of microbiome and environmental factors in the development and prevention of OSCC.

Gut Bacterial Composition and Nutritional Implications in Mexican and Spanish Individuals with Inflammatory Bowel Disease Compared to Healthy Controls

The intestinal microbiota plays a key role in the pathogenesis of inflammatory bowel disease (IBD), with its composition varying based on geographic location and dietary factors. This study was performed to examine and compare the bacterial composition of the gut microbiota in Mexican and Spanish individuals with IBD and healthy controls, while also considering the nutritional aspects. This study involved 79 individuals with IBD and healthy controls from Mexico and Spain. The fecal microbiota composition was analyzed using 16S rRNA gene sequencing, and the dietary intake and anthropometric measurements were collected. Alpha diversity analysis revealed a lower Chao1 index of the bacterial genera in the IBD groups. Beta diversity analysis showed significant differences in the bacterial composition, suggesting inter-individual variability within the healthy and IBD groups. Additionally, the relative abundance of the bacterial genera varied across the four groups. Faecalibacterium was more abundant in the IBD groups; Prevotella was found exclusively in the Mexican groups, and Akkermansia was found only in the Spanish groups. Akkermansia was positively correlated with meat and protein intake, Prevotella with lean mass, and Bacteroides with calorie intake. These findings highlight the importance of considering geographic and nutritional factors in future research on the gut microbiome’s role in IBD pathogenesis.

Fecal tryptophan metabolite profiling in newborns in relation to microbiota and antibiotic treatment

In the first days of life, the newborns’ intestinal microbiota develops simultaneously with the intestinal gut barrier and follows intestinal immunity. The mode of delivery shows significant impact on microbial development and, thus, the initiation of the tryptophan catabolism pathway. Further antibiotics (ATB) treatment of mothers before or during delivery affects the microbial and tryptophan metabolite composition of stool of the caesarean- and vaginal-delivered newborns. The determination of microbiome and levels of tryptophan microbial metabolites in meconium and stool can characterize intestinal colonization of a newborn. From 134 samples from the Central European Longitudinal Studies of Parents and Children: The Next Generation (CELSPAC: TNG) cohort study, 16S rRNA gene sequencing was performed, and microbial tryptophan metabolites were quantified using ultra-high-performance liquid chromatography with triple-quadrupole mass spectrometry. Microbial diversity and concentrations of tryptophan metabolites were significantly higher in stool compared to meconium. Treatment of mothers with ATB before or during delivery affects metabolite composition and microbial diversity in stool of vaginal- and caesarean-delivered newborns. Correlation of microbial and metabolite composition shows significant positive correlations of indol-3-lactic acid, N-acetyl-tryptophan and indol-3-acetic acid with Bifidobacterium, Bacteroides and Peptoclostridium. The positive effect of vaginal delivery on newborns’ microbiome development is degraded when mother is treated with ATB before or during delivery.Key points• Antibiotic treatment diminishes the positive effects of vaginal delivery.• Antibiotic treatment affects metabolite and microbial composition in newborns.• Bifidobacterium and Peptoclostridium could be the producer of indole-lactic acid.

Alterations in subgingival microbiome and advanced glycation end-products levels in periodontitis with and without type 1 diabetes mellitus: a cross-sectional study.

Existing studies predominantly focused on the relationship between periodontitis and type 2 diabetes mellitus (T2DM), with limited data on the association between periodontitis and type 1 diabetes mellitus (T1DM). This study aimed to examine the impact of T1DM and periodontitis on the subgingival microbiome and levels of advanced glycation end-products (AGEs). Samples were collected from four groups: T1DM, periodontitis (P), T1DM with periodontitis (DP), and periodontally and systemically healthy controls (Control). Subgingival microbiome composition and AGE levels were assessed using 16S rRNA gene sequencing and enzyme-linked immunosorbent assay (ELISA), respectively. Correlations between clinical indexes, microbiome composition, and AGEs were analyzed using Spearman correlation coefficient. Alpha and beta diversity analyses revealed significant differences in bacterial diversity between the DP group and other groups. Linear discriminant analysis effect size (LEfSe) analysis identified specific bacteria influencing each group: Acinetobacter, Leptotrichia, Raoultibacter, and Veillonella in the Control group; Tannerella, Porphyromonas, Filifactor, and Treponema in the P group; and Lactobacillales in T1DM individuals. Prevotella and Selenomonas were notably influential in the DP group. PICRUSt2 analysis showed pathways alterations were concentrated in cell motility, translation, cell growth and death and metabolism in the DP and P groups. Spearman correlation analysis indicated a positive correlation between AGEs and periodontitis or diabetes-related parameters and AGEs were positively correlated with Haemophilus and Arachnia. The findings suggested that the composition and function of the subgingival microbiome in the P group with or without T1DM were significantly different. Additionally, AGEs were involved in the development of periodontitis even in absence of hyperglycemia.

Seasonality influences skin bacterial community structure and anti-Bd function in two anuran species

Microorganisms on amphibian skin reduce disease susceptibility and play an important role in pathogen defense. We hypothesized that anuran skin bacterial communities would change in response to seasonal variation and host species. To test this hypothesis, we used 16S rRNA amplicon sequencing to identify cutaneous bacterial communities of two frogs from the Qinling Mountains of China, Pelophylax nigromaculatus and Nanorana quadranus. We matched the amplicon sequence variants (ASVs) of microbes exhibiting protective effects against the pathogen Batrachochytrium dendrobatidis (Bd), using a database containing over 1900 16S rRNA gene sequences from amphibian skin bacteria. The results showed that seasonal variation had a stronger effect than host species on the structure (alpha-diversity, beta-diversity, species composition and abundance, and biomarkers) and anti-Bd function of cutaneous bacterial communities. These communities were highly dynamic but varied similarly between hosts. Their structural similarities were more consistent at the phylum level, but markedly less so at finer taxonomic levels. The highest relative abundance of anti-Bd reads was observed in P. nigromaculatus during summer, but anti-Bd reads were present in both frog species during different seasons. Therefore, the protective function of cutaneous microbial communities appears to be continuous despite between-species differences in anti-Bd ASV abundance. This observation does not directly explain why Bd infections have not been recorded in the region, butprovides important insight on anuran pathogen defense mechanisms. Our findings also suggest that specific seasons can be periods of high infection risk, with major implications for research on amphibian ecology and conservation.

Associations of various healthy dietary patterns with biological age acceleration and the mediating role of gut microbiota: results from the China Multi-Ethnic Cohort study.

To investigate the associations between dietary patterns and biological aging, identify the most recommended dietary pattern for coping with biological aging and explore the potential mediating role of gut microbiota in less-developed ethnic minority regions (LEMRs). This prospective cohort study included 8288 participants aged 30-79 years from the China Multi-Ethnic Cohort study (CMEC). Anthropometric measurements and clinical biomarkers were utilized to construct biological age based on Klemera and Doubal's method (KDM-BA) and KDM-BA acceleration (KDM-AA). Dietary information was obtained through the baseline food frequency questionnaire (FFQ). Six dietary patterns were constructed: plant-based diet index (PDI), healthful plant-based diet index (hPDI), unhealthful plant-based diet index (uPDI), healthy diet score (HDS), Dietary Approaches to Stop Hypertension (DASH), and alternative Mediterranean diets (aMED). Follow-up adjusted for baseline analysis were employed to assess the associations between dietary patterns and KDM-AA. Additionally, quantile G-computation was utilized to evaluate the significant beneficial and harmful food groups. In the subsample of 764 participants with gut microbiota data obtained through 16S rRNA gene sequencing, we used causal mediation model to explore the mediating role of gut microbiota in the associations between dietary patterns and KDM-AA. The results showed that all dietary patterns were associated with KDM-AA. Transitioning from non-compliance to compliance, DASH exhibited the strongest negative association with KDM-AA [β = -0.91, 95%CI (-1.19, -0.63)]. The component analyses revealed that tea and soybean products were the significant beneficial food groups, while salt, preserved vegetables, red and processed meats were identified as the major harmful food groups. In mediation analysis, the decreased abundance of Synergistetes phylum and Pyramidobacter genus possibly mediated the negative associations between plant-based diets and KDM-AA (5.61%-9.19%). Overall, healthy dietary patterns, especially DASH, are negatively associated with biological aging in LEMRs. The Synergistetes and Pyramidobacter may mediate the associations between plant-based diets and biological aging. Developing appropriate strategies may promote healthy aging in LEMRs.

Cultivation of deep-sea bacteria from the Northwest Pacific Ocean and characterization of Limnobacter profundi sp. nov., a phenol-degrading bacterium

Despite previous culture-independent studies highlighting the prevalence of the order Burkholderiales in deep-sea environments, the cultivation and characterization of deep-sea Burkholderiales have been infrequent. A total of 243 deep-sea bacterial strains were isolated from various depths in the Northwest Pacific Ocean, with 33 isolates (13.6%) from a depth of 4000 m classified into Burkholderiales. Herein, we report the isolation and genome characteristics of strain SAORIC-580T, from a depth of 4000 m in the Northwest Pacific Ocean. The strain showed a close phylogenetic relationship with Limnobacter thiooxidans CS-K2T, sharing 99.9% 16S rRNA gene sequence identity. The complete whole-genome sequence of strain SAORIC-580T comprised 3.3 Mbp with a DNA G+C content of 52.5%. Comparative genomic analysis revealed average nucleotide identities between 79.4–85.7% and digital DNA-DNA hybridization values of 19.9–29.5% when compared to other Limnobacter genomes, indicating that the strain represents a novel species within the genus. Genomic analysis revealed unique adaptations to deep-sea conditions, including genes associated with phenol degradation, stress responses, cold adaptation, heavy metal resistance, signal transduction, and carbohydrate metabolism. The SAORIC-580T genome was found to be more abundant in the deep sea than at the surface in the trenches of the Northwest Pacific Ocean, suggesting adaptations to the deep-sea environment. Phenotypic characterization highlighted distinct differences from other Limnobacter species, including variations in growth conditions, enzyme activities, and phenol degradation capabilities. Chemotaxonomic markers of the strain included ubiquinone-10, major fatty acids such as C16:0, C16:1, and C18:1, and major polar lipids including phosphatidylethanolamine, phosphatidylglycerol, and diphosphatidylglycerol. Based on the polyphasic taxonomic data, it is concluded that strain SAORIC-580T (= KACC 21440T = NBRC 114111T) represents a novel species, for which the name Limnobacter profundi sp. nov. is proposed.

Deciphering the microbial communities in ticks of Inner Mongolia: ecological determinants and pathogen profiles

BackgroundTicks are vectors of numerous pathogens, with their bacterial composition, abundance, diversity, and interaction influencing both their growth and disease transmission efficiency. Despite the abundance of ticks in Inner Mongolia, China, comprehensive data on their microbial communities are lacking. This study aims to analyze the microbial communities within ticks from Inner Mongolia to inform innovative control strategies for interrupting pathogen transmission.MethodsTick samples were collected from animals and vegetation in multiple locations across Inner Mongolia and stored at − 80 °C. Ticks were identified using morphological keys and molecular biology methods. Full-length 16S rRNA gene sequencing was performed on collected samples. Bacterial community composition and diversity were mainly analyzed using bioinformatic tools such as QIIME, phyloseq, and DESeq2. Alpha diversity was assessed using Chao1, ACE, and Shannon indices, while beta diversity was evaluated using Bray-Curtis dissimilarity matrices. LEfSe analysis was applied to identify taxa associated with ecological and biological variables.ResultsA total of 5,048,137 high-quality read counts were obtained, forming an average of 789.3 OTUs per sample. Proteobacteria, Firmicutes, and Bacteroidetes were the most dominant phyla. Bacterial community composition varied significantly with geography, with Dermacentor nuttalli showing a higher abundance of Rickettsia in Xilingol League, while other regions had different dominant genera. The microbial community also differed based on the feeding status of ticks. Additionally, the microbiota of engorged ticks showed organ specificity. Pathogen detection efforts revealed the presence of nine pathogens across all three tick species. D. nuttalli was found to carry a significantly higher burden of pathogenic bacteria, making it the most potentially threatening tick species in Inner Mongolia.ConclusionsThe study highlights significant variations in tick microbiomes influenced by geographic location, feeding status, and tick species. It underscores the importance of enhancing tick and tick-borne disease surveillance in Inner Mongolia for early detection and control of emerging pathogens.Graphical

Recurrent association between Trichodesmium colonies and calcifying amoebae

Abstract Colonies of the N2-fixing cyanobacterium Trichodesmium spp. constitute a consortium with multiple microorganisms that collectively exert ecosystem-level influence on marine carbon and nitrogen cycling, shunting newly fixed nitrogen to low nitrogen systems, and exporting both carbon and nitrogen to the deep sea. Here we identify a seasonally recurrent association between puff colonies and amoebae through a two-year survey involving over 10 000 Trichodesmium colonies in the Red Sea. This association was most commonly found in near-shore populations during spring. Microscopic observations revealed consistent amoebae morphology throughout the study, and both morphological characteristics and 18S rRNA gene sequencing suggested that these amoebae are likely to belong to the species Trichosphaerium micrum, an amoeba that forms a CaCO3 shell. Co-cultures of Trichosphaerium micrum and Trichodesmium grown in the laboratory suggest that the amoebae feed on heterotrophic bacteria and not Trichodesmium, which adds a consumer dynamic to the complex microbial interactions within these colonies. Sinking experiments with fresh colonies indicated that the presence of the CaCO3-shelled amoebae decreased colony buoyancy. As such, this novel association may accelerate Trichodesmium sinking rates and facilitate carbon and nitrogen export to the deep ocean. Amoebae have previously been identified in Trichodesmium colonies in the western North Atlantic (Bermuda and Barbados), suggesting that this type of association may be widespread. This association may add a new critical facet to the microbial interactions underpinning carbon and nitrogen fixation and fate in the present and future ocean.

Dietary supplementation with Rehmannia glutinosa catalpol improves broiler performance by regulating intestinal immune microenvironment

Plant extracts have been widely considered as a feed additive. Rehmannia glutinosa catalpol can promote the growth performance of the host, improve the immune response, and strengthen the intestinal barrier function of the host. The broilers were fed with Rehmannia glutinosa catalpol (0.01%), and the composition of caecum microbiota in broilers was explored by 16S rRNA gene sequencing. Finally, the changes of intestinal mucosa morphology and immune function were analysed by tissue staining and RT-qPCR. The proportion of thick-walled bacteria in the treatment group was higher than that in the control group. At the genus level, the relative abundance of Faecalibacterium, Paraacteroides and Barnesiella increased after the addition of Rehmannia glutinosa catalpol. The function prediction results of PICRUSt2 showed that the microbiota mainly participated in the biosynthesis and degradation/utilization/association pathway. The results of tissue staining and RT-qPCR showed that the caecum tissue morphology and immune barrier function of broilers were significantly improved after the addition of catalpol. The results of this study show that Rehmannia glutinosa catalpol in the diet may be beneficial to the intestinal health of broilers, which may be achieved by regulating the intestinal microbiota and enhancing the immune function of broilers.

Impact of Dietary Fatty Acid Composition on the Intestinal Microbiota and Fecal Metabolism of Rats Fed a High-Fructose/High-Fat Diet

Background/Objectives: An inappropriate intake of dietary fats can disrupt the homeostasis of intestinal microbiota, affect the host’s metabolic status, and increase the risk of chronic diseases. The impact of dietary fat types on the composition and metabolic functionality of the intestinal microbiota has become a research focus over recent years. The objective of this study was to explore the effects of regular peanut oil (PO) and high-oleic-acid peanut oil (HOPO) on the composition and metabolic function of the intestinal microbiota. Methods: A dietary intervention test was conducted on SD rats fed a high-fat/high-fructose (HFF) diet. The composition and metabolic functionality of the intestinal microbiota of the experimental rats were investigated by 16S rRNA gene sequencing and fecal metabolomics. Results: Compared with saturated fat, PO and HOPO enhanced the diversity of intestinal microbiota in HFF diet-fed rats. Compared with PO, HOPO significantly increased the relative abundance of Lachnospiraceae_NK4A136_group and Harryflintia (p < 0.05), which are able to generate butyrate and acetate. Compared with saturated fat, 318 and 271 fecal biomarkers were identified in PO and HOPO groups, respectively. In contrast, 68 fecal biomarkers were identified between the PO and HOPO groups. The inhibition of harmful proteolytic fermentation in the colon may represent the main regulatory mechanism. With regard to metabolic status, HOPO provided better control of body weight and insulin sensitivity than PO. Conclusions: Compared with saturated fat, peanut oils better regulated the composition and metabolic function of the intestinal microbiota. In addition, HOPO exhibited better regulatory effects than PO.

Polluticaenibacter yanchengensis gen. nov., sp. nov., A Novel Taxon Within the Family Chitinophagaceae Isolated from Activated Sludge.

A Gram-stain-negative bacterium, designated strain LY-5T, was isolated from an activated sludge sample collected from a river in Yancheng city, Jiangsu province, China. Cells of strain LY-5T, were strictly aerobic, non-motile and rod-shaped. Growth occurred at 15-37°C (optimum, 30°C), at pH 5.0-9.0 (optimum 7.0) and at 0-3% (w/v) NaCl (optimum, 0%). Phylogenetic analysis based on 16S rRNA gene and genome sequences indicated that strain LY-5T formed a distinct phyletic branch within the family Chitinophagaceae, with closest relatives being members of the genera Phnomibacter, Aurantisolimonas, and Chitinophaga, sharing 88.5-90.3% sequence similarity. Moreover, the average amino acid identity (AAI) between strain LY-5T and its closed phylogenetic neighbors was below 70%, indicating it belongs to a novel genus. The predominant cellular fatty acids of LY-5T were iso-C15:0, iso-C15:1 G and summed feature 3 (C16:1 ω7c and/or C16:1 ω6c), and the only isoprenoid quinone was menaquinone-7 (MK-7). The major polar lipids identified in strain LY-5T comprised phosphatidylethanolamine, two unidentified aminolipids and five unidentified lipids. The genome size of strain LY-5T was 4.8 Mbp with a G + C content of 38.9%. Based on the evidence presented in this study, strain LY-5T represents a novel species of a new genus in the family Chitinophagaceae, for which the name Polluticaenibacter yanchengensis gen. nov., sp. nov. (Type strain LY-5T = CCTCC AB 2023260T = KCTC 102218T) is proposed.

Comparative Ecotoxicity Assessment of highly bioactive Isomeric monoterpenes carvacrol and thymol on aquatic and edaphic indicators and communities

The growing demand for sustainable natural products to replace harmful synthetic ones requires comprehensive ecotoxicity assessments to ensure their eco-friendly nature. This study explored for the first time the changes in microbial community growth and metabolic profiles from river and natural soil samples exposed to the two structural isomers, thymol (THY) and carvacrol (CARV), utilizing Biolog EcoPlate™ assays and 16S rRNA gene sequencing for taxonomic analysis. In addition, we addressed existing ecotoxicity data gaps for these two compounds by using aquatic (Daphnia magna and Vibrio fischeri) and soil (Eisenia fetida and Allium cepa) indicators. Results show acute toxicity of both CARV and THY on all indicators. V. fischeri (LC50=0.59 mg/L) >D. magna (4.75 mg/L) >A. cepa (6.47 mg/L) for CARV, and V. fischeri (LC50=1.71 mg/L) >A. cepa (4.05 mg/L) >D. magna (8.13 mg/L) for THY. E. fetida showed LC50 = 7.68 mg/Kg for THY and 1.04 for CARV. River and soil microbial communities showed resilience, likely because they contain taxa capable of biodegrading these products. No significant growth inhibition effects were observed up to 100 mg/L, though substrate utilization decreased at higher concentrations, particularly for polymers and amines in soil microorganisms and polymers in aquatic communities. Soil microorganisms were more affected than aquatic ones, with CARV being more toxic than THY (EC50120h = THY 94.13 and CARV 29.79 mg/L in soil microorganisms). These findings suggest that an increase in the consumption of these products and their subsequent ecotoxicity effects from environmental discharge should still be monitored before being ruled out. However, long-term effects are unlikely due to microbial degradation of these natural products, potentially reducing risks to other target species and opening the way for their use as substitutes for commercial antibiotics.

Mercury-tolerant metalophiles: A bio tool for remediation of mercury (Hg) affected Environs

Due to their low solubility, carcinogenic and mutagenic effects, heavy metals are of critical concern to humans and the environment. Mercury (Hg) is one of the rarest and least concentrated elements in the world, but it is ranked third in terms of toxicity. The present investigation evaluates the response and tolerance limit of bacteria isolated from the saffron soil of the Kashmir Valley to various mercury concentrations (50 ppm to 400 ppm). The minimum inhibitory concentration (MIC) was calculated after 24hours by measuring the optical density. Isolated bacteria have been characterized using two efficient methods, i.e. 16S rRNA gene sequence and MALDI-TOF MS. A total of 72 isolates were investigated for the mercury tolerance and among them, only 8 isolates (Staphylococcus equorum, Leclercia adecarboxylata, Staphylococcus warneri, Klebsiella pneumoniae, Serratia plymuthica, Bacillus megaterium, Pseudomonas putida and Bacillus safensis) were found tolerant to mercury with varying MIC. In comparison, Pseudomonas putida has been found to have the maximum resistance (400 ppm) for mercury and S. plymuthica and L. adecarboxylate had the lowest resistance level (200 ppm). The sequestration potential results revealed that P. putida executed the highest sequestration potential (73%) while K. pneumoniae showed the lowest sequestration potential (51.63%). Thus mercury tolerance capacity of these species may be utilised for detoxification and removal of mercury from polluted sites, providing an eco-friendly technique for bioremediation of mercury-affected environments.

Anthropogenic activities affect the diverse autotrophic communities of coastal sediments

Coastal sediments are a critical domain for carbon sequestration and are profoundly impacted by human activities. Therefore, it is essential to understand the structure and components of benthic autotrophs that play a crucial role in carbon sequestration processes, as well as the influence of anthropogenic activities on their communities. This study utilized an urban estuary, an industrial sea bay, a maricultural sea region, and two mangrove coastlines within the coastal areas of Guangdong Province, China. The micro-benthos in these environments, including prokaryotes and eukaryotes, were identified through high-throughput sequencing of 16S rRNA and 18S rRNA genes. The findings show that the autotrophic composition was altered by the interactions of anthropogenic heavy metals (Cd and Zn) and micro-eukaryotes (protazoa, metazoa, and parasitic organisms). Industrial pollution reduced the abundance of both prokaryotic and eukaryotic autotrophs. Mangroves induced a substantial transformation in the sediment eukaryotic and prokaryotic composition, increasing the proportion of autotrophs, notably sulfur-oxidizing and iron-oxidizing bacteria and microalgae. This alteration suggests an increase in specific sulfur and iron cycling with simultaneous carbon sequestration within mangrove sediments. These results indicate that anthropogenic activities affect sediment carbon sequestration by altering autotrophic assemblages along coastlines, thereby inducing consequential shifts in overall elemental cycling processes.

Features of the oropharyngeal microbiota of healthy children and those with acute respiratory infections. A prospective single-center randomized study

Background. The oropharyngeal microbiota is involved in the development of colonization resistance, affecting viral adhesion and metabolism. Any deviations in the stability of the environmental microbial niches of the oropharynx alter the local immune response and can trigger severe chronic somatic disorders. Aim. To compare the composition of the microbiota of children during an episode of respiratory infection and healthy volunteers examined in different periods of convalescence. The obtained data can be used to predict the course of the disease, analyze the risk of complications, and assess the frequency of the diseases in the future. Materials and methods. From 20.01.2022 to 23.12.2022, an open-label prospective single-center randomized comparative study was conducted, which included 120 children aged 5-10 who presented with symptoms of acute respiratory infection. The control group consisted of 15 asymptomatic children examined at different periods of convalescence. The study compared changes in the oral microbiota composition of patients and healthy children. The evaluation was performed using complete 16S rRNA gene sequencing on the Oxford Nanopore platform. Taxonometric analysis at the species and genera level was performed using the Knomics-Biota platform. The R programming language was used for statistical processing. In addition, the parameters of α- and β-diversity of the microbiota were assessed. The Chao1 and Shannon indices were calculated to assess α-diversity (diversity within one community). The Chao1 index is based on the number of species found in the sample and also rare species that are found only 1 or 2 times, thus preventing underestimation of diversity. The Shannon index includes both the number of species and their uniformity in the community. A change in the index indicates the dominance of one or more species. The following indicators were used to assess the β-diversity describing the differences between two microbiota samples at the species and genera level: Bray–Curtis dissimilarity (characterizing the ratios of common and different microorganisms between the samples) and the Aitchison distance (reflecting the differences in the proportions of microorganisms). In addition, the balance between the two groups of microorganisms was evaluated using the NearesBalance method, which characterizes the differences between the microbiota of the main and control groups. Results. The results of our study show that during respiratory infection, the state of the oropharyngeal microbiota is characterized by an increase in α-diversity, which is associated with an increase in the proportion of species of Streptococcus salivarius, Streptococcus pneumoniae, Streptococcus pseudopneumoniae, Streptococcus pyogenes, Streptococcus thermophilus and A12 versus the proportion of Streptococcus mitis, Streptococcus oralis, Streptococcus gwangjuense, Streptococcus sanguinis, Streptococcus gordonii and FDAARGOS_192. In the control group, the oropharyngeal microbiota was divided into two clusters. The dominance of streptococci was observed in the first group (control), while the second group had a more uniform representation. Analysis of the changes in microbial communities in the main and control groups can show the stages of oral microbiota recovery after an acute respiratory infection episode. Conclusion. More research is needed in the field of the oropharyngeal microbiome on a larger sample of healthy children, to standardize the communities of the oropharyngeal microbiota, to study the interaction within communities and with the body as a whole. Analysis of the impact of the microbiota on the frequency and course of respiratory infections and the rate of complications opens up new prospects in treating, rehabilitating, and preventing diseases. These research areas can contribute to improving children's health and quality of life and introducing new approaches into clinical practice.