High-throughput 16S rRNA Gene Sequencing Research Articles

Microbiome and network analysis reveal potential mechanisms underlying Carassius auratus diseases: The interactions between critical environmental and microbial factors

Despite the rapid development of research on aquatic environment microbiota, limited attention has been paid to exploring the complex interactions between microbial communities and aquatic environments. Particularly, the mechanisms underlying fish diseases based on such dynamic interactions remain unknown. This study aimed to address the gap by conducting microbiome and co-occurrence network analyses on the typical freshwater aquaculture systems. High-throughput 16S rRNA gene sequencing results revealed significant differences in the microbiota between the disease and healthy groups. Notably, disease mortality varied consistently with the gradient of relative abundance of Proteobacteria (intestine, R2 = 0.46, p < 0.05) and Cyanobacteria (gill, R2 = 0.67, p < 0.01), indicating their potential use as diagnostic criteria. Furthermore, the elevated hepatosomatic index, NO3-N, COD and TC (sediment) were directly correlated with diseases (r > 0.54, p < 0.01). Mean concentrations of NO3-N, COD and TC were elevated by 78.87%, 25.63% and 44.2%, respectively, in ponds where diseases occurred. Quantitative analysis (qPCR) revealed that Aeromonas sobria infected hosts through a potential pathway of “sediment (4.4 × 105 copy number/g)-water (1.1 × 103 copy number/mL)-intestine (1.2 × 106 copy number/g)”. Similarly, the potential route for Aeromonas veronii was sediment (4.9 × 106 copy number/g) to gill (5.1 × 105 copy number/g). Additionally, the complexity of microbial networks in the intestine, water, and sediment was significantly lower in the disease group, although no similar phenomenon was observed in the gill microbial network. In summary, these findings reveal that elevated concentrations of crucial environmental factors disrupt the linkages within microbiota, fostering the growth of opportunistic bacteria capable of colonizing fish gut or gills. This offers new insights into potential mechanisms by which environmental factors cause disease in fish.

Fimbriimonadales performed dissimilatory nitrate reduction to ammonium (DNRA) in an anammox reactor

Bacteria belonging to the order Fimbriimonadales are frequently detected in anammox reactors. However, the principal functions of these bacteria and their potential contribution to nitrogen removal remain unclear. In this study, we aimed to systematically validate the roles of Fimbriimonadales in an anammox reactor fed with synthetic wastewater. High-throughput 16S rRNA gene sequencing analysis revealed that heterotrophic denitrifying bacteria (HDB) were the most abundant bacterial group at the initial stage of reactor operation and the abundance of Fimbriimonadales members gradually increased to reach 38.8 % (day 196). At the end of reactor operation, Fimbriimonadales decreased to 0.9 % with an increase in anammox bacteria. Correlation analysis demonstrated nitrate competition between Fimbriimonadales and HDB during reactor operation. Based on the phylogenetic analysis, the Fimbriimonadales sequences acquired from the reactor were clustered into three distinct groups, which included the sequences obtained from other anammox reactors. Metagenome-assembled genome analysis of Fimbriimonadales allowed the identification of the genes narGHI and nrfAH, responsible for dissimilatory nitrate reduction to ammonium (DNRA), and nrt and nasA, responsible for nitrate and nitrite transport. In a simulation based on mass balance equations and quantified bacterial groups, the total nitrogen concentrations in the effluent were best predicted when Fimbriimonadales was assumed to perform DNRA (R2 = 0.70 and RMSE = 18.9). Moreover, mass balance analysis demonstrated the potential contribution of DNRA in enriching anammox bacteria and promoting nitrogen removal. These results prove that Fimbriimonadales compete with HDB for nitrate utilization through DNRA in the anammox reactor under non-exogenous carbon supply conditions. Overall, our findings suggest that the DNRA pathway in Fimbriimonadales could enhance anammox enrichment and nitrogen removal by providing substrates (nitrite and/or ammonium) for anammox bacteria.

Changes in the intestinal microbiome of the preterm baby associated with stopping non-invasive pressure support: a prospective cohort study

BackgroundIntestinal dysbiosis is implicated in the pathogenesis of necrotising enterocolitis and late-onset sepsis in preterm babies. The provision of non-invasive positive pressure ventilation is a common clinical intervention in preterm...

Linking Microbiota Profiles to Disease Characterization in Common Variable Immunodeficiency: The Case of Granulomatous-Lymphocytic Interstitial Lung Disease.

Background and objectives: Common variable immunodeficiency (CVID) is a primary immunodeficiency characterized by decreased immunoglobulins and recurrent infections, with non-infectious complications such as granulomatous-lymphocytic interstitial lung disease (GLILD) affecting up to 30% of patients. Methods: Using high-throughput 16S rRNA gene sequencing, salivary, sputum, and fecal microbiome from CVID patients with GLILD, comparing them to CVID patients without GLILD-with immune dysregulation (dCVID) and only infections (iCVID)-and healthy controls was analyzed. Results: A total of 41 CVID patients, 7 with GLILD, and 15 healthy donors were included. Global fecal biodiversity was significantly lower in GLILD patients compared to CVID subgroups and controls. GLILD patients harbored different specific bacterial communities in all niches, with some keystone species common to dCVID. Conchiformibius, Micrococcales, and Capnocytophaga are more frequent in the sputum of GLILD patients. Saliva in GLILD shows higher frequencies of Conchiformibius and Haemophilusparainfluenzae. Fecal samples from GLILD patients have higher levels of Gemella morbilorum, Lacticaseibacillus, and Cellulosimicrobium. A non-assigned Conchiformibius spp. is consistently associated with GLILD across different niches and could be a potential pathobiont or relevant microbiological marker for GLILD. Cluster network and correlation analyses show profound dysbiosis in the sputum, saliva, and feces of GLILD patients. Conclusions: These findings highlight significant microbiome alterations in CVID patients with GLILD, particularly in the respiratory tract, suggesting a possible link to both local and systemic immune dysregulation.

Distinct Communities of Bacteria and Unicellular Eukaryotes in the Different Water Masses of Cretan Passage Water Column (Eastern Mediterranean Sea).

Elucidating marine microbiota diversity and dynamics holds significant importance due to their role in maintaining vital ecosystem functions and services including climate regulation. This work aims to contribute in the understanding of microbial ecology and networking in one of the world's most understudied marine regions, the Eastern Mediterranean Sea. High-throughput 16S and 18S rRNA gene sequencing analysis was applied to study the diversity of bacteria and unicellular eukaryotes in the different water masses of the Cretan Passage during two seasonally-different sampling expeditions. We assumed that microbial associations differ between the surface and deepwater masses and created co-occurrence networks to evaluate this hypothesis. Our results unveiled vertical variations in both bacterial and unicellular eukaryotic diversity with species fluctuations indicative of seasonality being recorded in the surface water mass. Heterotrophic taxa and grazers related to organic matter degradation and nutrient cycling were enriched in the deepest water layers. Moreover, surface waters presented a higher number of microbial associations indicating abundant ecological niches compared to the deepest layer, possibly related to the lack of bottom-up resources in the oligotrophic deep ocean. Overall, our data provide insight in a heavily stressed, yet underexplored, marine area that requires further research to unravel the ecological roles of marine microbes. To our knowledge, this is the first study that combines molecular biology tools to provide data on both planktic prokaryotes and unicellular eukaryotes across the different water masses in this marine region of the Eastern Mediterranean basin.

Unveiling the microbial diversity across the northern Ninety East Ridge in the Indian Ocean.

Prokaryotes play a crucial role in marine ecosystem health and drive biogeochemical processes. The northern Ninety East Ridge (NER) of the Indian Ocean, a pivotal yet understudied area for these cycles, has been the focus of our study. We employed high-throughput 16S rRNA gene sequencing to analyze 35 water samples from five stations along the ridge, categorized into three depth- and dissolved oxygen-level-based groups. Our approach uncovered a clear stratification of microbial communities, with key bioindicators such as Prochlorococcus MIT9313, Sva0996 marine group, and Candidatus Actinomarina in the upper layer; Ketobacter, Pseudophaeobacter, Nitrospina, and SAR324 clade in the middle layer; and Methylobacterium-Methylorubrum, Sphingomonas, Sphingobium, and Erythrobacter in the deep layer. Methylobacterium-Methylorubrum emerged as the most abundant bacterial genus, while Nitrosopumilaceae predominated among archaeal communities. The spatial and depth-wise distribution patterns revealed that Ketobacter was unique to the northern NER, whereas Methylobacterium-Methylorubrum, UBA10353, SAR324 clade, SAR406, Sva0996_marine_group, Candidatus Actinomarina were ubiquitous across various marine regions, exhibiting niche differentiation at the OTU level. Environmental factors, especially dissolved oxygen (DO), silicate, nitrate, and salinity, significantly influence community structure. These findings not only reveal the novelty and adaptability of the microbial ecosystem in the northern NER but also contribute to the broader understanding of marine microbial diversity and its response to environmental heterogeneity.

Impact of floods and landslides on rhizosphere bacterial communities: a high-throughput 16S rRNA gene sequencing study.

This study investigates the diversity and composition of soil bacterial communities in the rhizosphere of Attapadi and Nelliyampathy, prominent hill stations in Palakkad district, Kerala, India. The persistent flooding and landslides in 2018 and 2019 significantly impacted agricultural productivity in these regions. Utilizing high-throughput 16S rRNA gene sequencing (Illumina MiSeq), we conducted a comprehensive analysis of soil samples. Correlative assessments between soil parameters and microbial relative abundance at the phylum level revealed noteworthy positive associations. Notably, nitrogen (N) exhibited a positive relation with Crenarchaeota, Chloroflexi, Actinobacteriota, and Acidobacteriota; pH correlated with Firmicutes; organic carbon (OC) with WPS-2; and phosphorous with Proteobacteria. A total of 31,402 operational taxonomic units (OTUs) were identified, with the highest feature counts observed in undisturbed soils from Attapadi (AUD) and Nelliyampathy (NUD) (13,007 and 12,915, respectively). Disturbed soils in Nelliyampathy (ND) and Attapadi (AD) displayed a substantial decline in microbial diversity and composition, harbouring 1409 and 4071 OTUs, respectively. Alpha and beta diversity indices further underscored the more severe impairment of ND soils compared to AD soils. Interestingly, a majority of ND samples were landslide-affected (four out of five), while flood-affected soils accounted for four out of six AD samples. This indicates that landslides exert a more pronounced impact on microbial diversity and composition than floods. The observed decline in microbial count, composition, and diversity, even after 2years of the disaster, raises concerns about potential threats to agricultural output. The findings emphasize the need for corrective measures, including the incorporation of microbial inoculum, to restore soil fertility in post-disaster landscapes.

Full-length 16S rRNA gene sequencing combined with adequate database selection improves the description of Arctic marine prokaryotic communities

BackgroundHigh-throughput sequencing of the full-length 16S rRNA gene has improved the taxonomic classification of prokaryotes found in natural environments. However, sequencing of shorter regions from the same gene, like the V4-V5 region, can provide more cost-effective high throughput. It is unclear which approach best describes prokaryotic communities from underexplored environments. In this study, we hypothesize that high-throughput full-length 16S rRNA gene sequencing combined with adequate taxonomic databases improves the taxonomic description of prokaryotic communities from underexplored environments in comparison with high-throughput sequencing of a short region of the 16S rRNA gene.ResultsTo test our hypothesis, we compared taxonomic profiles of seawater samples from the Arctic Ocean using: full-length and V4-V5 16S rRNA gene sequencing in combination with either the Genome Taxonomy Database (GTDB) or the Silva taxonomy database. Our results show that all combinations of sequencing strategies and taxonomic databases present similar results at higher taxonomic levels. However, at lower taxonomic levels, namely family, genus, and most notably species level, the full-length approach led to higher proportions of Amplicon Sequence Variants (ASVs) assigned to formally valid taxa. Hence, the best taxonomic description was obtained by the full-length and GTDB combination, which in some cases allowed for the identification of intraspecific diversity of ASVs.ConclusionsWe conclude that coupling high-throughput full-length 16S rRNA gene sequencing with GTDB improves the description of microbiome profiling at lower taxonomic ranks. The improvements reported here provide more context for scientists to discuss microbial community dynamics within a solid taxonomic framework in environments like the Arctic Ocean with still underrepresented microbiome sequences in public databases.

The Improving Effects of Probiotic-Added Pollen Substitute Diets on the Gut Microbiota and Individual Health of Honey Bee (Apis mellifera L.).

Honey bee (Apis mellifera L.) health is crucial for honey bee products and effective pollination, and it is closely associated with gut bacteria. Various factors such as reduced habitat, temperature, disease, and diet affect the health of honey bees by disturbing the homeostasis of the gut microbiota. In this study, high-throughput 16S rRNA gene sequencing was used to analyze the gut microbiota of honey bees subjected to seven diets over 5 days. Lactobacillus dominated the microbiota in all diets. Cage experiments (consumption, head protein content, and vitellogenin gene expression level) were conducted to verify the effect of the diet. Through a heatmap, the Diet2 (probiotic-supplemented) group was clustered together with the Beebread and honey group, showing high consumption (177.50 ± 26.16 mg/bee), moderately higher survival duration (29.00 ± 2.83 days), protein content in the head (312.62 ± 28.71 µg/mL), and diet digestibility (48.41 ± 1.90%). Additionally, we analyzed the correlation between gut microbiota and health-related indicators in honey bees fed each diet. Based on the overall results, we identified that probiotic-supplemented diets increased gut microbiota diversity and positively affected the overall health of individual honey bees.

Deciphering the geochemical influences on bacterial diversity and communities among two Algerian hot springs.

Northeastern Algeria boasts numerous hot springs, yet these hydrothermal sites remain largely unexplored for their microbial ecology. The present study explores the bacterial abundance and diversity within two distinct Algerian hot springs (Hammam Saïda and Hammam Debagh) and investigates the link between the prevailing bacteria with geochemical parameters. High-throughput 16S rRNA gene sequencing of water and sediment samples revealed a bacterial dominance of 99.85-91.16% compared to Archaea (0.14-0.66%) in both springs. Interestingly, Saïda hot spring, characterized by higher temperatures and sodium content, harbored a community dominated by Pseudomonadota (51.13%), whereas Debagh, a Ca-Cl-SO4 type spring, was primarily populated by Bacillota with 55.33%. Bacteroidota displayed even distribution across both sites. Additional phyla, including Chloroflexota, Deinococcota, Cyanobacteriota, and Chlorobiota, were also present. Environmental factors, particularly temperature, sodium, potassium, and alkalinity, significantly influenced bacterial diversity and composition. These findings shed light on the interplay between distinct microbial communities and their associated geochemical properties, providing valuable insights for future research on biogeochemical processes in these unique ecosystems driven by distinct environmental conditions, including potential applications in bioremediation and enzyme discovery.

Sediment microbial communities of a technogenic saline-alkaline reservoir

Various natural saline and alkaline habitats have recently been widely investigated, but knowledge of anthropogenic habitats with more complex environmental conditions is still lacking. This research looks at the structure of microbial communities in 18 bottom sediment samples from a technogenic water body with saline and alkaline composition. The core samples were collected from 2 columns in the western and eastern parts of an artificial water body at the Verkhnekamskoe Salt Deposit (Russia). The microbial community structure was studied using high-throughput 16S rRNA gene sequencing. The bottom sediment composition (salinity, pH, and toxic element content) varies greatly with depth and laterally throughout the study area. The study found a considerable difference in bacterial community diversity between the 2 columns, but no considerable difference was found between the communities at various depths of the studied layers. Proteobacteria, Firmicutes, and Actinobacteria, which are common in both natural and artificial saline and alkaline environments, make up the majority of the bacteria found in the samples. Studies have shown that salinity and total alkalinity are the key factors influencing the formation of microbial communities. Ralstonia and Pseudomonas were the two most common genera in the sediment samples. These two genera are known for having high metabolic flexibility, which means they can survive in extreme environments and use a variety of carbon compounds as energy sources. The study also found that Ralstonia is indicator bacteria in samples with the highest concentrations of toxic elements compared to the other samples. A relatively high microbial diversity was discovered in the studied anthropogenic water reservoir despite the extreme alkaline and saline conditions, but it is considerably lower than that found in natural, less alkaline habitats. This research offers insight into the mechanisms behind microbial community formation in complex anthropogenic environments and covers key factors in microbial community distribution.

The effect of Astragalus polysaccharides on the repair of adverse effects in largemouth bass (Micropterus salmoides) under enrofloxacin stress

Antibiotics have important role in controlling the outbreak of bacterial diseases in fish farming, but long-term use or persistent existence of antibiotics in water can cause adverse effects on aquatic animals. In order to evaluate repairing effect of Astragalus polysaccharides (APS) on damaged intestine of fish under enrofloxacin (ENR) stress, ENR-pretreated (1.0 mg/L, 7 days) largemouth bass were randomly divided into two groups, and subsequently were fed basal diet and diet supplemented with 1.0 g/kg APS for 14 days. Intestine tissue and content were sampled on day 0 (D0), days 7 (D7), days 21 (D21_APS and D21) to detect the intestinal structure, intestinal microbiota structure, oxidative stress, non-specific immune and inflammatory response.Intestinal tissue section showed that the height, width of intestinal villi, and muscular thickness in D21_APS were significantly greater than those on D0, D7, and D21 (P < 0.05). APS-supplemented diet was significantly increased expression of tight junction protein related genes occludin, claudin-1, ZO-1 (P < 0.05). APS addition significantly improved the activities of catalase (CAT) and peroxidase (POD) and decreased superoxide dismutase (SOD) activity (P < 0.05). The activity of CAT and SOD in D21_APS and D0 were similar. The highest activities of acid phosphatase (ACP), lysozyme (LZM) and alkaline phosphatase (AKP) were found in D21_APS group. The expression of proinflammatory factors IL-1β and TNF-α in D21_APS and D21 were significantly down-regulated compared to that of D7, while anti-inflammatory factor IL-10 was up-regulated (P < 0.05). Compared with D7 group, quinolone resistance gene (qnrB) in D21 and D21_APS groups were significantly down-regulated, and in contrast to D21 group, qnrB and qnrS genes in D21_APS group were significantly down-regulated (P < 0.05).High-throughput 16SrRNA gene sequencing revealed proportion of Cyanobacteria in intestinal microbiota increased from 8.23% to 52.66%, while Firmicutes decreased from 28.54% to 2.03% after ENR treatment. In D21 group, Proteobacteria was notable decrease compared to D0, while Firmicutes increased. In D21_APS, the dominant bacteria were Proteobacteria, Fusobacteriota and Firmicutes, and Acinetobacter, Cetobacterium and Aeromonas were the predominant genera. Cluster analysis indicated that bacterial community structure in D21_APS has a similar level to D0 at phylum level. Feeding APS increased abundance of genes related to styrene, isoleucine and lysine degradation; propanoate, butanoate phenylalanine, and tryptophan metabolism; lipopolysaccharide biosynthesis; bacterial secretion system; cell motility and secretion at KEGG pathway Level 3 compared to the basal diet. Taken together, APS can repair the damage of intestinal structure and intestinal microbiota caused by ENR.

Comparative study of the quick action effect of multiple enzyme-based nano-emulsified oils in enhancing nitrate contamination remediation in groundwater

Emulsified vegetable oil (EVO), as a novel green slow-releasing substrate, has performed great potential in subsurface bioremediation due to its slow release and longevity. Nevertheless, the long time it takes to initiate this process still exposed some limitations. Herein, multiple enzyme-based EVOs (EN-EVOs) were developed to enhance the quick-acting effect in nitrate-contaminated bioremediation. This study demonstrated that EN-EVOs loaded with cellulose (c-EVO) and protein enzymes (p-EVO) performed best, not only did not change the advantages of traditional EVO, but also optimized the stability and particle size to the level of 0.8–0.9 and 247.95–252.25 nm, respectively. Nitrate (NO3–N) degradation further confirmed the superiority of c-EVO in rapidly initiating degradation and achieving stable denitrification. Compared with traditional EVO, the maximum start-up efficiency and the rapid achieving stable denitrification efficiency were improved by 37.6% and 1.71 times, respectively. In such situation, the corresponding NO3–N removal efficiency, kinetics rate constant (k1), and half-life period (t1/2) reached as high as 85.39%, as quick as 1.079 d−1, and as short as 0.64 d after 30-day cultivation. Meanwhile, the rapid conversion efficiency of NO2–N was observed (k2 = 0.083 d−1). High-throughput 16S rRNA gene sequencing indicated that the quick-acting process of NO3–N reduction coupled to c-EVO was mediated by microbial reducers (e.g., Ralstonia, Gulbenkiania, and Sphingobacterium) with regulations of narG, nirS and norB genes. Microorganisms with these genes could achieve quick-acting not only by enhancing microbial activity and the synthesis and metabolism of volatile fatty acids, but also by reducing the production and accumulation of loosely bound-extracellular polymeric substances (LB-EPS). These findings advance our understanding on fast-acting of NO3–N degradation supported by c-EVO and also offer a promising direction for groundwater remediation.

Impact of earthworms on antibiotic resistance genes removal in ampicillin-contaminated soil through bacterial community alteration.

The emergence of antibiotic resistance genes (ARGs) as contaminants in soil poses a significant threat to public health. Earthworms (Eisenia foetida), which are common inhabitants of soil, have been extensively studied for their influence on ARGs. However, the specific impact of earthworms on penicillin-related ARGs remains unclear. In this study, we investigate the role of earthworms in mitigating ARGs, specifically penicillin-related ARGs, in ampicillin-contaminated soil. Utilizing high-throughput quantitative PCR (HT-qPCR), we quantified a significant reduction in the relative abundance of penicillin-related ARGs in soil treated with earthworms, showing a decrease with a p-value of <0.01. Furthermore, high-throughput 16S rRNA gene sequencing revealed that earthworm intervention markedly alters the microbial community structure, notably enhancing the prevalence of specific bacterial phyla such as Proteobacteria, Firmicutes, Chloroflexi, and Tenericutes. Our findings not only demonstrate the effectiveness of earthworms in reducing the environmental load of penicillin-related ARGs but also provide insight into the alteration of microbial communities as a potential mechanism. This research contributes to our understanding of the role of earthworms in mitigating the spread of antibiotic resistance and provides valuable insights for the development of strategies to combat this global health issue.

Expanding oxygen minimum zones in the northern Indian Ocean predicted by hypoxia-related bacteria

Oxygen minimum zones (OMZs) in the ocean are areas with dissolved oxygen (DO) concentrations below critical thresholds that impact marine ecosystems and biogeochemical cycling. In the northern Indian Ocean (NIO), OMZs exhibit a tendency to expand in mesopelagic waters and contribute significantly to global nitrogen loss and climate change. However, the microbial drivers of OMZ expansion in the NIO remain understudied. Here, we characterized bacterial communities across DO gradients in the NIO using high-throughput 16S rRNA gene sequencing. We found that Marinimicrobia, Chloroflexi, and the SAR324 clade were enriched in both oxygen-deficient and low oxygen mesopelagic waters. Furthermore, Marinimicrobia, Chloroflexi, and the SAR324 clade exhibited a significant negative correlation with DO (P &amp;lt; 0.01), suggesting that they were well-adapted to the oxygen-deficient OMZ habitat. Functional predictions revealed heightened nitrogen metabolism in OMZs, particularly nitrate reduction, suggesting its pivotal role in nitrogen loss. These findings underscore the importance of microbial communities in driving OMZ expansion in the NIO and highlight their implications in global biogeochemical cycles and climate change.

Influences of the Integrated Rice-Crayfish Farming System with Different Stocking Densities on the Paddy Soil Microbiomes.

Integrated rice-fish farming has emerged as a novel agricultural production pattern to address global food security challenges. Aiming to determine the optimal, scientifically sound, and sustainable stocking density of red claw crayfish (Cherax quadricarinatus) in an integrated rice-crayfish farming system, we employed Illumina high-throughput 16S rRNA gene sequencing to evaluate the impact of different stocking densities of red claw crayfish on the composition, diversity, function, and co-occurrence network patterns of soil bacterial communities. The high stocking density of red claw crayfish reduced the diversity and evenness of the soil bacterial community during the mid-culture stage. Proteobacteria, Actinobacteria, and Chloroflexi emerged as the most prevalent phyla throughout the experimental period. Low stocking densities initially boosted the relative abundance of Actinobacteria in the paddy soil, while high densities did so during the middle and final stages. There were 90 distinct functional groups identified across all the paddy soil samples, with chemoheterotrophy and aerobic chemoheterotrophy being the most abundant. Low stocking densities initially favored these functional groups, whereas high densities enhanced their relative abundances in the later stages of cultivation. Medium stocking density of red claw crayfish led to a more complex bacterial community during the mid- and final culture stages. The experimental period showed significant correlations with soil bacterial communities, with total nitrogen (TN) and total phosphorus (TP) concentrations emerging as primary factors contributing to the alterations in soil bacterial communities. In summary, our findings demonstrated that integrated rice-crayfish farming significantly impacted the soil microbiomes and environmental factors at varying stocking densities. Our study contributed to theoretical insights into the profound impact of integrated rice-crayfish farming with various stocking densities on bacterial communities in paddy soils.

Dietary Galacto-oligosaccharides Ameliorate Atopic Dermatitis-like Skin Inflammation and Behavioral Deficits by Modulating Gut Microbiota-Brain-Skin Axis.

Atopic dermatitis (AD), a chronic, highly pruritic, and inflammatory skin disorder, often coexists with psychiatric comorbidities including anxiety and depression, posing considerable challenges for treatment. The current research aims at evaluating the efficacy and potential therapeutic mechanism of galacto-oligosaccharides (GOS) on AD-like skin lesions and comorbid anxiety/depressive disorders. Macroscopical and histopathological examination showed that GOS could markedly relieve skin inflammation by decreasing the production of IgE, IL-4, IL-13, IFN-γ, and TNF-α and regulating the PPAR-γ/NF-κB signaling in DNFB-induced AD mice. Moreover, GOS significantly improved the anxiety- and depressive-like symptoms as mirrored by the behavior tests including FST, TST, OFT, and EZM through normalizing the neurotransmitter levels of 5-HT, DA, NE, and CORT in the brain. Mechanistically, by virtue of the high-throughput 16S rRNA gene sequencing and GC-MS techniques, GOS restructured the gut microbiota and specifically induced the proliferation of Lactobacillus and Alloprevotella, leading to an increase in the total content of fecal SCFAs, in particular acetate and butyrate. Pearson correlation analysis found a marked correlation among the altered gut microbiota/SCFAs, AD-associated skin manifestations, and comorbid behavioral phenotypes. Collectively, this work highlights that GOS is a promising strategy against both AD and associated depressive symptoms by modulating the gut microbiota-brain-skin axis.

Effects of Bacillus coagulans TBC169 on gut microbiota and metabolites in gynecological laparoscopy patients.

The primary objective of this study is to investigate the mechanism by which Bacillus coagulans TBC169 accelerates intestinal function recovery in patients who have undergone gynecological laparoscopic surgery, using metabolomics and gut microbiota analysis. A total of 20 subjects were selected and randomly divided into two groups: the intervention group (n = 10) receiving Bacillus coagulans TBC169 Tablets (6 pills, 1.05 × 108 CFU), and the control group (n = 10) receiving placebos (6 pills). After the initial postoperative defecation, fecal samples were collected from each subject to analyze their gut microbiota and metabolic profiles by high-throughput 16S rRNA gene sequencing analysis and untargeted metabonomic. There were no statistically significant differences observed in the α-diversity and β-diversity between the two groups; however, in the intervention group, there was a significant reduction in the relative abundance of unclassified_Enterobacteriaceae at the genus level. Furthermore, the control group showed increased levels of Holdemanella and Enterobacter, whereas the intervention group exhibited elevated levels of Intestinimonas. And administration of Bacillus coagulans TBC169 led to variations in 2 metabolic pathways: D-glutamine and D-glutamate metabolism, and arginine biosynthesis. This study demonstrated that consuming Bacillus coagulans TBC169 after gynecological laparoscopic surgery might inhibit the proliferation of harmful Enterobacteriaceae; mainly influence 2 pathways including D-glutamine and D-glutamate metabolism, and arginine biosynthesis; and regulate metabolites related to immunity and intestinal motility; which can help regulate immune function, maintain intestinal balance, promote intestinal peristalsis, and thus accelerate the recovery of intestinal function.

487 - Adult atopic dermatitis is associated with impaired oral health and oral dysbiosis - a case-control study

Abstract Background Previous studies linked chronic oral diseases to skin disorders such as psoriasis. However, data about oral health and oral microbiota in atopic dermatitis (AD) is sparse. Objectives To compare the oral health status and oral microbiota of AD patients and healthy controls. Methods This was a prospective sex and age- matched case-control study comparing adult participants with and without dermatologist-verified AD. Exclusion criteria included recent use of oral, topical, or systemic medication that could affect oral health or microbiome assessment. Oral health indices including Gingival Index, Plaque Index, Oral Hygiene Index, Caries Severity Index and prosthodontics status, were assessed by a dentist. Samples of oral flora were collected and subjected to high-throughput 16S rRNA gene sequencing analysis for microbiome analysis. Results Forty-five AD participants and 41 non-AD controls were recruited. The two groups had no significant differences in terms of their demographic and clinical characteristics, except for the higher rate of atopic co-morbidities in the AD group (p&amp;lt;.001). Compared to the control group, participants with AD had significantly poorer plaque (p=0.04) and oral hygiene indices (p=0.04) and a trend towards higher gingival index (p=0.05). The results of the Faith phylogenetic diversity (FDR) test indicated that the oral microbial diversity in the AD group was significantly higher (α-diversity, FDR-adjusted p=0.0007) when compared with the control group. Characterization of the similarities and differences in the composition of the microbial communities between the samples (β-diversity) from the AD patients and controls indicated that they clustered separately. The groups showed significant dissimilarity and distinct clustering of microbial abundance (FDR-adjusted p=0.001). Importantly, higher community diversity was previously linked to periodontitis and gingival disease. Furthermore, AD patients had a significantly increased abundance of taxa correlated with oral diseases and decreased abundance of oral health-associated bacteria. Conclusion AD appears to be associated with poorer oral health and oral dysbiosis, and thus, there is a need to increase the awareness of both patients and physicians about oral health.

Rutaecarpine ameliorates imiquimod-induced psoriasis-like dermatitis in mice associated with alterations in the gut microbiota.

Psoriasis is accepted as a chronic, inflammatory, immune-mediated skin disease triggered by complex environmental and genetic factors. For a long time, disease recurrence, drug rejection, and high treatment costs have remained enormous challenges and burdens to patients and clinicians. Natural products with effective immunomodulatory and anti-inflammatory activities from medicinal plants have the potential to combat psoriasis and complications. Herein, an imiquimod (IMQ)-induced psoriasis-like dermatitis model is established in mice. The model mice are treated with 1% rutaecarpine (RUT) (external use) or the oral administration of RUT at different concentrations. Furthermore, high-throughput 16S rRNA gene sequencing is applied to analyze the changes in the diversity and composition of the gut microbiota. Based on the observation of mouse dorsal skin changes, RUT can protect against inflammation to improve psoriasis-like skin damage in mice. Additionally, RUT could suppress the expression levels of proinflammatory cytokines (IL-23, IL-17A, IL-22, IL-6, and IFN-α) within skin tissue samples. Concerning gut microbiota, we find obvious variations within the composition of gut microflora between IMQ-induced psoriasis mice and RUT-treated psoriasis mice. RUT effectively mediates the recovery of gut microbiota in mice induced by IMQ application. Psoriasis is linked to the production of several inflammatory cytokines and gut microbiome alterations. This research shows that RUT might restore gut microbiota homeostasis, reduce inflammatory cytokine production, and ameliorate psoriasis symptoms. In conclusion, the gut microbiota might be a therapeutic target or biomarker for psoriasis that aids in clinical diagnosis and therapy.