Optimizing taxonomic classification of marker-gene amplicon sequences with QIIME 2's q2-feature-classifier plugin

Gut microbiota analysis in cirrhosis and non-cirrhotic portal hypertension suggests that portal hypertension can be main factor of cirrhosis-specific dysbiosis

Gut dysbiosis plays an important role in cirrhosis, but the mechanism of its development was not established. The aim of the study was to test the hypothesis that portal hypertension can be the main factor in the development of gut dysbiosis in cirrhosis. This cross-sectional study included 25 patients with chronic non-cirrhotic portal hypertension due to extrahepatic portal vein obstruction after portal vein thrombosis (PVT) (NCPVT group), 29 cirrhotic patients without PVT (CirNoPVT), 15 cirrhotic patients with chronic PVT (CPVT), and 22 healthy controls. The fecal microbiota was assessed using 16S rRNA gene sequencing. The CirNoPVT and CPVT groups had largely similar differences in gut microbiota composition from the control group. Patients with NCPVT, as well as patients with cirrhosis, had a higher abundance of Streptococcus, Escherichia, Enterococcus, Enterobacteriaceae, Enterococcaceae, Streptococcaceae, Bacilli, Gammaproteobacteria, Proteobacteria, and a lower abundance of Roseburia, Faecalibacterium, Methanobrevibacter, Ruminococcaceae, Methanobacteriaceae, Clostridia, Methanobacteria, and Euryarchaeota as they were compared with healthy individuals. Patients with NCPVT had a higher abundance of Bifidobacterium, Bifidobacteriaceae, Actinobacteria, and a lower abundance of Gemmiger and Catenibacterium compared to healthy individuals, which was not observed in the cirrhosis groups. The abundance of Porphyromonadaceae with the genus Parabacteroides was reduced in both groups with PVT, but not in CirNoPVT. There were no significant differences in gut microbiota beta-diversity among the CirNoPVT, CPVT and NCPVT groups. All these groups had significant differences in beta-diversity from the control group. Portal hypertension seems be the main factor in the development of gut dysbiosis in cirrhosis.

Urinary microbiota changes among NMIBC patients during BCG therapy: comparing BCG responders and non-responders

The gold standard for treating high-risk non-muscle-invasive bladder cancer involves the transurethral removal of cancerous tissue followed by BCG immunotherapy. So far, there is no reliable biomarker for predicting BCG efficacy and identifying patients who will or will not respond to BCG treatment. Emerging evidence suggests that urinary microbiota may play a crucial role in BCG efficacy. This study aimed to explore (i) changes in urinary microbiota during the six induction cycles of BCG and (ii) its potential predictive role in determining the outcome of BCG treatment. To this end, catheterized urine samples were collected before each of the six BCG doses and bacterial composition was analyzed using 16S rRNA gene sequencing. Patient inclusion criteria were male gender, no previous history of urothelial cancer, no other malignancies, no active infection, and no antibiotic usage for at least 20 days before the first BCG dose. We observed a significant decrease in biodiversity, measured by the Shannon Index, during the first week of therapy in 10 out of 12 patients (p=0.021). Additionally, differences in microbiota composition before the start of BCG therapy were noted between responders and non-responders to BCG therapy. Non-responders exhibited a 12 times higher abundance of genus Aureispira (p<0.001), and, at the species level, a 27-fold lower abundance of Negativicoccus succinivorans (p<0.001). Throughout the treatment, the abundance of the genus Aureispira decreased, showing an eightfold reduction by the end of therapy among non-responders (p<0.001). Our findings suggest that urinary microbiota plays an active role before and during the course of BCG therapy. However, this is a preliminary study, and further research involving larger patient cohorts is needed.

Native polymer degradation capacity of microorganisms in agricultural soils

With a growing global population increasing demand for food production, fertilisers are of paramount importance in the agricultural industry. New fertiliser coating candidates may reduce environmental harm but it is critical that they are evaluated for their native biodegradation potential within agricultural soils and their effects on microbial communities. Four of the seven compounds tested, poly(1,4-butylene adipate) (PBA), polyethylene adipate (PEA), polycaprolactone (PCL) and poly(3-hydroxybutyrate-co-3-hydroxyvalerate) (PHBV), showed degradation by indigenous soil microorganisms with headspace CO2 concentrations increasing between 14 to 98 % compared to the soil only control. Surprisingly, two previously characterised biodegradable polymers, polyethylene succinate (PES) and poly(1,4-butylene succinate) (PBS), showed minimal biodegradation in our study. Polymer degradation was confirmed visually using scanning electron microscopy and occurred in conjunction with shifts in the bacterial and fungal community composition of the soils. Soils with PBA, PEA, PCL and PHBV were enriched with polymer degrading microorganisms, such as Streptomyces spp., Bacillus spp., Exophiala spp. and Talaromyces spp. Using whole soil microcosms under ambient conditions to investigate indigenous degradation potential of polymers for fertiliser coatings provides an initial holistic picture of their degradation potential compared with using axenic cultures alone, and provides crucial new insights into the future of eco-friendly controlled release fertilisers.

Choline metabolism disorder induced by Prevotella is a risk factor for endometrial cancer in women with polycystic ovary syndrome

BACKGROUND

Polycystic ovary syndrome (PCOS) is an endocrine disorder associated with an increased risk of endometrial cancer, potentially mediated by vaginal microbiota dysbiosis and hormonal disturbances. This study investigates how hormonal imbalances in PCOS patients affect the vaginal microbiome and choline metabolism, thereby influencing endometrial cancer risk.

METHODS

In this observational study, 70 women were enrolled, including 36 with PCOS and 34 controls. We analyzed their vaginal microbiota, lipid metabolism, and endometrial transcriptome using 16S rRNA sequencing, untargeted lipidomics, and transcriptomic sequencing.

RESULTS

The PCOS group showed significant differences in vaginal microbiota composition, notably an increase in LPS-producing Prevotella spp. Functional analyses indicated activation of LPS biosynthesis and inflammatory signaling pathways. Lipidomics revealed disrupted choline metabolism, with alterations in phosphocholine and total choline levels. Transcriptomic data highlighted the up-regulation of inflammatory and metabolic dysregulation pathways.

CONCLUSIONS

Hormonal imbalances in PCOS contribute to significant changes in the vaginal microbiome and metabolic pathways, increasing the risk of endometrial cancer. These findings suggest potential therapeutic targets for reducing cancer risk in this population.

Microbial ecosystems and ecological driving forces in the deepest ocean sediments

Systematic exploration of the hadal zone, Earth's deepest oceanic realm, has historically faced technical limitations. Here, we collected 1,648 sediment samples at 6-11 km in the Mariana Trench, Yap Trench, and Philippine Basin for the Mariana Trench Environment and Ecology Research (MEER) project. Metagenomic and 16S rRNA gene amplicon sequencing generated the 92-Tbp MEER dataset, comprising 7,564 species (89.4% unreported), indicating high taxonomic novelty. Unlike in reported environments, neutral drift played a minimal role, while homogeneous selection (HoS, 50.5%) and dispersal limitation (DL, 43.8%) emerged as dominant ecological drivers. HoS favored streamlined genomes with key functions for hadal adaptation, e.g., aromatic compound utilization (oligotrophic adaptation) and antioxidation (high-pressure adaptation). Conversely, DL promoted versatile metabolism with larger genomes. These findings indicated that environmental factors drive the high taxonomic novelty in the hadal zone, advancing our understanding of the ecological mechanisms governing microbial ecosystems in such an extreme oceanic environment.

Recent genetic drift in the co-diversified gut bacterial symbionts of laboratory mice

Laboratory mice (Mus musculus domesticus) harbor gut bacterial strains that are distinct from those of wild mice but whose evolutionary histories are unclear. Here, we show that laboratory mice have retained gut bacterial lineages that diversified in parallel (co-diversified) with rodent species for > 25 million years, but that laboratory-mouse gut microbiota (LGM) strains of these ancestral symbionts have experienced accelerated accumulation of genetic load during the past ~ 120 years of captivity. Compared to closely related wild-mouse gut microbiota (WGM) strains, co-diversified LGM strains displayed significantly faster genome-wide rates of nonsynonymous substitutions, indicating elevated genetic drift-a difference that was absent in non-co-diversified symbiont clades. Competition experiments in germ-free mice further indicated that LGM strains within co-diversified clades displayed significantly reduced fitness in vivo compared to WGM relatives to an extent not observed within non-co-diversified clades. Thus, stochastic processes (e.g., bottlenecks), not natural selection in the laboratory, have been the predominant evolutionary forces underlying divergence of co-diversified symbiont strains between laboratory and wild house mice. Our results show that gut bacterial lineages conserved in diverse rodent species have acquired novel mutational burdens in laboratory mice, providing an evolutionary rationale for restoring laboratory mice with wild gut bacterial strain diversity.

Variation and assembly mechanisms of Rhinolophus ferrumequinum skin and cave environmental fungal communities during hibernation periods

Animal skin acts as the barrier against invasion by pathogens and microbial colonizers. Environmental microbiota plays a significant role in shaping these microbial communities, which, in turn, have profound implications for host health. Previous research has focused on characterizing microorganisms on bats' skin and in their roosting environments, particularly bacterial communities. The emergence of white-nose syndrome, caused by the fungal-pathogen Pseudogymnoascus destructans, highlights the importance of understanding fungal dynamics in cave ecosystems and on bats' skin. In this study, we employed ITS amplicon sequencing to investigate the fungal community associated with the skin of Rhinolophus ferrumequinum and surfaces within hibernacula. In addition, we utilized neutral community and null models to assess the relative importance of stochastic and deterministic processes in fungal community assembly. The infection status of P. destructans did not significantly impact fungal community composition either on bat skin or cave environments. However, fungal diversity was significantly higher in cave environments compared to bat skin. Notably, potentially inhibitory genera of fungal pathogens were present in both bats and cave environments during hibernation. Furthermore, the composition and structure of fungal communities on both bat skin and cave environments varied across hibernation periods. Our findings suggest neutral processes primarily drive the assembly of fungal communities associated with hibernating R. ferrumequinum and cave environments, with dispersal limitation exerting a significant influence. This study provides insights into the fungal communities associated with hibernating R. ferrumequinum and cave environments.IMPORTANCEAnimal habitats provide sources and reservoirs for host microorganisms, making it critical to understand changes in microbial communities between habitats and hosts. While most studies have focused on bacterial microorganisms, research on fungal communities is lacking. This study investigated how community dynamics and assembly processes differ between the skin of hibernating Rhinolophus ferrumequinum and the cave environments under pathogen stress. We found significant differences in the composition and structure of the fungal communities between bat skin and roosting cave environments. Fungal genera with potential inhibitory effects on pathogens were found in all bat skin and cave environments. In addition, dispersal limitations during stochastic processes were a key factor in the formation of environmental fungal communities on bat skin and in caves. These findings offer new insights for exploring pathogen-host-environment-microbe interactions.

Concordance of Helicobacter pylori Detection Methods in Symptomatic Children and Adolescents

BACKGROUND

Helicobacter pylori is the most prevalent chronic bacterial infection globally, acquired mostly during childhood. It is associated with chronic gastritis, peptic ulcer disease, and gastric cancer. Due to challenges in culturing H. pylori, diagnostic reference standards often rely on combining ≥2 non-culture, biopsy-based methods. Histology with Giemsa staining is widely used in clinical settings due to its low cost and reliable performance.

METHODS

This study evaluated the concordance between histology with Giemsa staining as the reference standard and other diagnostic methods, including the rapid urease test (RUT), ureA RT-PCR, 16S sequencing, and anti-H. pylori serum IgG. Positive percent of agreement (PPA), negative percent of agreement (NPA) and concordance kappa index were calculated.

RESULTS

A total of 120 patients (41 positive and 79 negative by Giemsa staining) were analyzed. Among the methods tested, RT-PCR for ureA showed the best performance (PPA = 94.7%, NPA = 98.6%, kappa = 0.939), while RUT underperformed compared with expectations (PPA = 65.9%, NPA = 97.5%, kappa = 0.681). Serology had the lowest performance (PPA = 53.7%, NPA = 96.1%, kappa = 0.548).

CONCLUSIONS

The combination of histology with Giemsa staining and ureA RT-PCR achieved the highest detection rate and strongest agreement.

Assembly and maturation of calf gut microbiome from neonate to post-puberty

With the help of rumen bacteria, ruminants can feed on indigestible plant materials and produce over 70% of their energy as fatty acids. However, during lactation, ruminants exhibit characteristics of monogastric animals due to an undeveloped rumen; therefore, understanding gut microbiome changes in growing calves is essential. Our understanding of the gut microbiome in growing calves remains limited in large populations with the same diet, breed, and period. Here, we describe 16S rRNA gene amplicon sequencing data from 420 faecal samples, 20 rumen contents, 17 small intestine contents, and 18 large intestine contents collected from 57 healthy, antibiotic-free Korean beef cattle from neonatal to post-pubertal age. Eight 16S rRNA gene amplicon datasets from the host diet samples were obtained. Approximately 148 million raw reads, averaging 153,352 ± 96,050 (mean ± SD) reads per sample, and 51,596 unique amplicon sequence variants (381-368 per sample) were identified in the 483 samples. These shareable datasets can be reused by researchers to assess gut microbiome-related functions in growing calves and improve ruminant production and health.

Probiotic Potential of Yeast, Mold, and Intermediate Morphotypes of Geotrichum candidum in Modulating Gut Microbiota and Body Physiology in Mice

Geotrichum candidum, a polymorphic fungus, exists in yeast, mold, and intermediate morphotypes, each with varying genome sizes and phenotypic traits. While G. candidum has been studied as a probiotic in dairy cattle and aquaculture, the differential probiotic potential of its morphotypes has not been fully investigated; therefore, the current study was designed to investigate their impact on the modulation of physiological and gut microbial diversity in BALB/c male mice. In this study, four strains of G. candidum were used, comprising two yeast morphotypes (QAUGC01 and UCMA3730), one mold morphotype (UCMA103), and one intermediate morphotype (UCMA91). BALB/c male mice were administered G. candidum yeast, intermediate, and mold morphotypes via drinking water for 4 weeks. After 4 weeks of experimentation, the yeast morphotype (QAUGC01) notably facilitated healthy weight gain compared to other groups. This was accompanied by significant increases in red blood cell count (p = 0.01). Importantly, QAUGC01 showed no detrimental effects on kidney function, as evidenced by significantly reduced CPK levels (77.25 ± 4.87 U/L) and low cholesterol levels (64.75 ± 0.83 mg/dL). Metagenomic analysis revealed that Firmicutes, Bacteroidetes, and Proteobacteria were predominant bacterial phyla, while Ascomycota and Basidiomycota dominated the fungal populations. Lactobacillus and Bifidobacterium were prominent in the gastrointestinal tract of QAUGC01-treated mice, while Lactococcus correlated with intermediate and mold morphotypes. Predictive functional annotation (PICRUSt2) has revealed the maximum relative abundance of metabolic pathways in mold and intermediate-supplemented mice gut. In contrast, the yeast morphotype (UCMA3730) exhibited a higher metabolic pathway activity in the large intestine. Conclusively, yeast morphotypes increase beneficial bacterial diversity, including Brevibacillus and Bacillus, particularly lactic acid bacteria throughout the gastrointestinal tract. These findings suggest that different G. candidum morphotypes have distinct probiotic potentials, with implications for enhancing gut health in food and feed applications.

Continuous Cropping of Tussilago farfara L. Has a Significant Impact on the Yield and Quality of Its Flower Buds, and Physicochemical Properties and the Microbial Communities of Rhizosphere Soil

Continuous cropping obstacles pose significant constraints and urgent challenges in the production of Tussilago farfara L. This experiment investigated the effects of consecutive cropping on T. farfara over periods of 1, 2, and 3 years. It assessed the yield and quality of T. farfara flower buds, in addition to the physicochemical properties of the rhizosphere soil. The microbial community in the rhizosphere was analyzed through 16S rDNA and ITS sequencing using Illumina Novaseq high-throughput sequencing technology, while also examining the correlations among these factors. The results reveal that as the duration of continuous cropping increases, the yield of T. farfara flower buds, along with the contents of extract, tussilagone, and total flavonoids, steadily decreased; soil pH, organic matter, available phosphorus, available potassium, alkaline nitrogen, and the activities of sucrose, catalase, and alkaline phosphatase markedly decreased. As the duration of consecutive cropping increases, the quantity and diversity of bacteria in the rhizosphere soil initially increase and then decrease, while the number of fungal species increases by 22.5%. Meanwhile, continuous cropping of T. farfara contributes to a gradual reduction in the relative abundance of beneficial genera such as Ralstonia, Nitrospira, and Trichoderma in the rhizosphere soil, while harmful genera such as Mortierella, Fusarium, and Tricharina accumulate significantly. Correlation analysis shows that changes in microbial communities notably influence the growth of T. farfara and soil quality. This study elucidates the impacts of continuous cropping on the yield and quality of T. farfara flower buds, soil physicochemical properties, and the microbial communities in the rhizosphere, providing a scientific basis for further research on continuous cropping barriers and the selection of beneficial microbial genera for the growth of T. farfara.

Modulating effects of mycotoxin and oxidized oil on intestinal microbiota in broiler chickens

Climatic change and increased use of alternative sources of feed ingredients could influence poultry production. Mycotoxin and oxidized oil are two contaminations that may occur in chicken feed as a result of climate change and use of alternative feed ingredients, and these factors may have differential and potentially additive effects on birds' intestinal microbiota. The study objective was to determine the main effects of corn, oil quality, and their interaction on ileal content, ileal scrapings, cecal content, and whole cecum (content and tissue) microbiota in broiler chickens. Broiler chickens were raised for 21 days post-hatch and fed diet made with regular or mycotoxin-contaminated corn (7,959 ppb of deoxynivalenol, 2.1 ppm of aflatoxin, 23,200 ppb of fumonisin, and 1,403 ppb of zearalenone), and regular or oxidized (148 meq/kg) oil. Bacterial genomic DNA was extracted and sequenced targeting the variable (V3-V4) region of the 16S gene. The bioinformatic and statistical analysis of the microbiota data showed mycotoxin and mycotoxin by oxidized oil interaction increased the richness and evenness in the ileal content and only evenness in the cecal content. Mycotoxin and mycotoxin by oxidized oil interaction also increased beta diversity based on the variability in microbial community in the ileal content while increasing the abundance of bacterial taxa, including Streptomyces and Escherichia-Shigella, and predicted pathways related to RNA and DNA synthesis (Mycothiol and pyrimidine deoxyribonucleotides synthesis) and redox regulation (ergothioneine biosynthesis) in ileal content and pathways related to glycol metabolism and degradation and amino acids degradation were increased in the cecal content. Streptomyces has been associated with mycotoxin detoxication, and its increase could reduce the negative effects of mycotoxins contrary to Escherichia-Shigella, which has been negatively correlated with weight gain in chickens. These results show that mycotoxin alone and its combination with oxidized oil affect bacterial diversity and abundance mostly in the ileum content and predicted metabolic pathways across intestinal sections.

Bentonite sterilization methods in relation to geological disposal of radioactive waste: comparative efficiency of dry heat and gamma radiation

AIMS

This study evaluates the effectiveness of two standard sterilization methods on microorganisms in bentonite, which is proposed as a buffer around metal canisters containing long-lived radioactive waste. Bentonite, as a natural clay, contains microorganisms with enhanced resistance to harsh conditions and the ability to reactivate upon decompaction. Sterile controls are crucial in experiments estimating the impact of microorganisms on nuclear waste repositories. Yet, the effectiveness of common sterilization methods on bentonite microorganisms has not been fully evaluated.

METHODS AND RESULTS

Two methods were compared: dry heat (nine cycles at 121°C for 4 h) and gamma irradiation (10-140 kGy at 147 Gy·min-1). Molecular-genetic, microscopic, and cultivation techniques were used to assess sterilization. Heat sterilization did not eliminate heat-resistant microorganisms, such as Bacillus, Paenibacillus, and Terribacillus, from bentonite powder even after nine heat cycles. However, bentonite suspended in deionized water was sterile after four heat cycles. In contrast, gamma irradiation effectively reduced microbial survivability above a dose of 10 kGy, with the highest doses (100-140 kGy) potentially degrading DNA.

CONCLUSIONS

Gamma irradiation at 30 kGy effectively sterilized bentonite powder. The findings of our experiments emphasize the importance of using appropriate sterilization methods to maintain sterile controls in experiments that evaluate the microbial impacts in nuclear waste repositories. However, further assessment is needed to determine the effects of potential alterations induced by gamma radiation on bentonite properties.

Deaminase inhibitor and casein hydrolysates drive microbial shifts favoring Campylobacter jejuni in an in vitro poultry cecal model

AIM

The dietary proteins in poultry feeds, including the polypeptide chain size, influence gut microbial composition and function. This study assessed the microbial preference for peptide size using the same protein source in three polypeptide forms.

METHODS AND RESULTS

We investigated the effects of diphenyliodonium chloride (DIC) on poultry cecal microbiota inoculated with Campylobacter jejuni and supplemented with various casein hydrolysates (intact casein, enzyme hydrolysate, acid hydrolysate, and a mix of all three) using an in vitro cecal model. The incubation occurred over 18 h at 42°C under microaerophilic conditions. We hypothesized a decrease in C. jejuni abundance by limiting nitrogenous metabolites while promoting the growth of protein fermentative bacteria. Additionally, we speculated that the response to DIC would vary with different polypeptides. Genomic DNA was extracted, amplified, and sequenced on an Illumina MiSeq platform. Analysis within QIIME2-2021.11 showed that DIC treatments did not significantly affect C. jejuni abundance but drastically decreased Enterobacteriaceae abundance (ANCOM, P < 0.05). DIC-treated groups exhibited a more stable community structure, especially in the peptide-amended group. Microbial interactions likely aided C. jejuni survival in DIC groups with casein hydrolysates. Methanocorpusculum, Phascolarctobacterium, and Campylobacter formed a core microbial community in both DIC-treated and non-treated groups. DIC altered co-occurrence patterns among core members and differentiated taxa in abundance in acid and peptide-DIC treated groups, changing negative relationships to positive ones (Spearman's Correlation, P < 0.05). Variations in polypeptide composition affected metabolite abundance, notably impacting the urea cycle in Campylobacter and Clostridiaceae. DIC shifted communal energy metabolism in microbiota on casein sources.

CONCLUSION

Campylobacter's adaptability to the deaminase inhibitor indicates reliance on the microbial community and their metabolic products, showcasing its metabolic versatility.

Exploring the interplay of under-deposit corrosion and microbiologically influenced corrosion in the presence of deposits with varied electrical conductivities

In oil and gas pipelines, the coexistence of native microorganisms with various solid compounds, such as corrosion products, scales, and reservoir sand, is well-established. However, research focused on understanding the collective impact of these components on carbon steel corrosion has been limited, with most studies concentrating on inert deposits like clay and sand. This study assessed the impact of electrically conductive deposits - magnetite (Fe3O4) and troilite (FeS) - on UDC and UDMC of carbon steel, employing silica (SiO2) as an inert control. A multifaceted approach, combining international corrosion standards, microscopy, and molecular microbiology techniques demonstrated that abiotic corrosion rates correlated with the electrical conductivity of the deposits. Magnetite, the deposit with the highest electrical conductivity, led to the highest uniform corrosion rate (0.110 mm/year). The troilite-containing reactor exhibited a corrosion rate of 0.017 mm/year, while the lowest rate was observed in the presence of sand (0.006 mm/year), the deposit with the lowest electrical conductivity. In biotic conditions, the highest average corrosion and pitting rates were also associated with magnetite, identifying UDC and UDMC in the presence of magnetite as the most corrosive scenario among the three deposits. Nevertheless, the average corrosion and pitting rates did not follow the same trend as in abiotic conditions, where electrical conductivity properties governed the behaviour. In biotic conditions, the heightened pitting corrosion observed in the presence of silica over troilite was attributed to higher metabolic activity and increased cell concentrations in the microbial consortium under this scenario. These findings underscore the complexity of UDMC, suggesting that an active microbial consortium does not solely drive severe corrosion but is influenced by multiple factors. This study offers insights into the role of different deposits and native microbial communities, paving the way for more targeted corrosion mitigation strategies to improve infrastructure longevity in oil and gas systems.

The fungal diversity in the lungs of children with cystic fibrosis captured by sputum-induction and bronchoalveolar lavage

BACKGROUND

The prevalence of fungi in cystic fibrosis (CF) lung infections is poorly understood and studies have focused on adult patients. We investigated the fungal diversity in children with CF using bronchoalveolar lavage (BAL) and induced sputum (IS) samples to capture multiple lung niches.

METHODS

Sequencing of the fungal ITS2 region and molecular mycobiota diversity analysis was performed on 25 matched sets of BAL-IS samples from 23 children collected as part of the CF-SpIT study (UKCRN14615; ISRCTNR12473810).

RESULTS

Aspergillus and Candida were detected in all samples and were the most abundant and prevalent genera, followed by Dipodascus, Lecanicillium and Simplicillium. The presumptive CF pathogens Exophiala, Lomentospora and Scedosporium were identified at variable abundances in 100 %, 64 %, and 24 % of sample sets, respectively. Fungal pathogens observed at high relative abundance (≥40 %) were not accurately diagnosed by routine culture microbiology in over 50 % of the cohort. The fungal communities captured by BAL and IS samples were similar in diversity and composition, with exception to C. albicans being significantly increased in IS samples. The respiratory mycobiota varied greatly between individuals, with only 13 of 25 sample sets containing a dominant fungal taxon. In 11/25 BAL sample sets, airway compartmentalisation was observed with diverse mycobiota detected from different lobes of the lung.

CONCLUSIONS

The paediatric mycobiota is diverse, complex and inadequately diagnosed by conventional microbiology. Overlapping fungal communities were identified in BAL and IS samples, showing that IS can capture fungal genera associated with the lower airway. Compartmentalisation of the lower airway presents difficulties for consistent mycobiota sampling.

Lack of significant effect of gut microbiota on weight gain in newly emerged worker honeybee

The western honeybee, Apis mellifera, harbours a simple and distinct microbiota that has been linked to various positive outcomes for the host. Among these cited benefits is improved weight gain for bees that have been inoculated with their native microbes. This result has been challenged by recent studies which investigated the impact of the gut microbiota on behavioural maturation and associated physiological changes and revealed no effect of the gut microbiota on weight gain. Therefore, we re-examined the role of the microbiota in weight gain by comparing microbiota-deprived bees with those inoculated with gut homogenate or defined communities composed of isolates representing the major bacterial taxa inhabiting the bee gut. We observed no differences in weight gain of adult bees or of their gut tissues across these groups. Further analysis based on nurse/forager cuticular hydrocarbon status and bacterial composition also revealed no significant changes. These results suggest the need for more nuanced investigations aimed at exploring factors such as the conditions in the hive of origin, including larval nutrition.

Microplastic induces microbial nitrogen limitation further alters microbial nitrogentransformation: Insights from metagenomic analysis

Microplastic has a significant impact on soil microbial communities, which play crucial roles in soil nitrogen (N) cycles. However, there is a limited understanding of their influences on genes associated with the entire N cycling pathways. Through a 120-day soil incubation using conventional (PE and PET) and biodegradable microplastics (PLA and PBAT), coupled with 16S rRNA and metagenomic sequencing, we investigated the responses of N-cycling genes to microplastics in two contrasting soils (i.e. black soil and loess soil). We found that biodegradable microplastics strongly altered microbial N functional profiles, and enhanced the abundance of numerous key genes involved in N fixation, organic N mineralization, N reduction, and denitrification. Furthermore, biodegradable microplastics significantly decreased net N mineralization (Nm) compared to control and conventional microplastic treatments, suggesting microbial N immobilization outweighed N mineralization. Analysis of the function-taxon bipartite network showed that the Nm was well predicted for the abundances and diversity of bacteria within specific modules, with Nm decreasing, the abundances of specific taxa in a given network modules increasing. These results indicated that biodegradable microplastics act as a carbon source to select specific taxa involved in enhancing N bioavailability (e.g., N fixation and organic N mineralization) to meet microbial N demand, which in turn filtered the bacterial community (decreased diversity but increased abundances) and gradually formed specific function-taxon modules. Comparing the two soils, microbes in the less fertile alkaline loess soil were more sensitive to biodegradable microplastics than those in the nutrient-rich acid black soil. Our study indicated that increasing usage of biodegradable plastics in the future may lead to accelerated soil microbial N limitation and transformation.

Habitat-Dependent DNA viral communities in atmospheric aerosols: Insights from terrestrial and marine ecosystems in East Asia

The transmission of viruses through aerosols is of growing public health concern, yet research on aerosol-associated viral communities lags behind that of terrestrial and aquatic ecosystems. Here, DNA viral diversity in natural aerosols from both over land and ocean in the East Asia region was examined. The results showed that atmospheric environments harbor a distinct viral community that differs from those present in terrestrial and aquatic ecosystems. A comparison of aerosol samples from different locations revealed that aerosol viruses are strongly influenced by altitude and their sources. Fragments of viruses that can infect pathogenic bacteria, as well as pathogenic viruses (such as herpesviruses, Inoviruses, and Iridovirus) were detected. Anthropogenically-influenced land aerosol samples contained viral communities with greater richness and diversity as well as a higher relative abundance of pathogenic and lytic viruses compared to pristine marine airborne samples. Furthermore, habitat-specific auxiliary metabolic genes (AMGs) were observed, such as the phosphate regulon (phoH), which was more prevalent in ocean aerosol samples and regulates phosphate uptake under low-phosphate conditions, thereby assisting viral hosts in overcoming metabolic challenges in different environmental conditions. This study highlights the ecological distinctness of the airborne viral community and the interconnectedness between those from land, sea, and atmosphere, underscoring the importance of evaluating their potential pathogenicity in future research.

Using gut microbiome metagenomic hypervariable features for diabetes screening and typing through supervised machine learning

Diabetes mellitus is a complex metabolic disorder and one of the fastest-growing global public health concerns. The gut microbiota is implicated in the pathophysiology of various diseases, including diabetes. This study utilized 16S rRNA metagenomic data from a volunteer citizen science initiative to investigate microbial markers associated with diabetes status (positive or negative) and type (type 1 or type 2 diabetes mellitus) using supervised machine learning (ML) models. The diversity of the microbiome varied according to diabetes status and type. Differential microbial signatures between diabetes types and negative group revealed an increased presence of Brucellaceae, Ruminococcaceae, Clostridiaceae, Micrococcaceae, Barnesiellaceae and Fusobacteriaceae in subjects with diabetes type 1, and Veillonellaceae, Streptococcaceae and the order Gammaproteobacteria in subjects with diabetes type 2. The decision tree, elastic net, random forest (RF) and support vector machine with radial kernel ML algorithms were trained to screen and type diabetes based on microbial profiles of 76 subjects with type 1 diabetes, 366 subjects with type 2 diabetes and 250 subjects without diabetes. Using the 1000 most variable features, tree-based models were the highest-performing algorithms. The RF screening models achieved the best performance, with an average area under the receiver operating characteristic curve (AUC) of 0.76, although all models lacked sensitivity. Reducing the dataset to 500 features produced an AUC of 0.77 with sensitivity increasing by 74% from 0.46 to 0.80. Model performance improved for the classification of negative-status and type 2 diabetes. Diabetes type models performed best with 500 features, but the metric performed poorly across all model iterations. ML has the potential to facilitate early diagnosis of diabetes based on microbial profiles of the gut microbiome.

Exploration and application of microorganisms related to the inference of the time since deposition (TsD) in semen and blood stains

Determining the time since deposition (TsD) of body fluid stains can provide crucial criminal information to forensic researchers. Although there are studies on inferring residual time through DNA and RNA markers, this requires high sample quality, and microorganisms, as a new type of marker with individual and tissue identification capabilities, have the potential for body fluid recognition and TsD inference. Blood and semen are the most common types of bodily fluid stains at crime scenes, but research on the inference of the TsD of these two types of stains through microorganisms still needs to be explored. Thus, this study collected samples of body fluid stains exposed indoors for up to 56 days and selected several microorganisms that were both liquid specific and related to residual time inference in blood (Methylobacterium and Sphingomonas) and semen (Gardnerella) stains via 16 S rRNA high-throughput sequencing. Furthermore, the microorganisms' ability to infer TsD was verified using qPCR in validation group samples stored under the same conditions, and two multiple logistic regression models were constructed. The average absolute deviation of differences between the predicted and actual retention times of the three types of body fluids in the test set using two estimation methods was 2.15 and 2.06 days, respectively. In conclusion, this study has discovered four novel microorganisms related to the retention time of blood and semen and has preliminarily constructed the TsD prediction models, providing a new direction for future forensic research on the inference of TsD in blood and semen stains.

Gut Microbiota-Derived Hyocholic Acid Enhances Type 3 Immunity and Protects Against Salmonella enterica Serovar Typhimurium in Neonatal Rats

This study investigates how microbiome colonization influences the development of intestinal type 3 immunity in neonates. The results showed that reduced oxygen levels in the small intestine of neonatal rats induced by Saccharomyces boulardii accelerated microbiome colonization and type 3 immunity development, which protected against Salmonella enterica serovar Typhimurium infection. Microbiome maturation increased the abundance of microbiome-encoded bile salt hydrolase (BSH) genes and hyocholic acid (HCA) levels. Furthermore, reducing oxygen levels in the intestine increased the abundance of Limosilactobacillus reuteri, a bacterium encoding BSH, and promoted intestinal type 3 immunity. However, inhibition of BSH blocked the L. reuteri-induced development of intestinal type 3 immunity. Mechanistically, HCA promoted the development of gamma-delta T cells and type 3 innate lymphoid cells by stabilizing the mRNA expression of RAR-related orphan receptor C via the farnesoid X receptor-WT1-associated protein-N6-methyl-adenosine axis. These results reveal that gut microbiota-derived HCA plays a crucial role in promoting the development of intestinal type 3 immunity in neonates. This discovery introduces potential therapeutic avenues for strengthening intestinal immunity in early life or treating bacterial infections by targeting microbial metabolites.

Intraduodenal administration of Reg3g improves gut barrier function and mitigates hepatic steatosis in mice

Regenerating islet-derived protein 3 gamma (Reg3g), a gut peptide has been implicated in host defense and various physiological functions including metabolic regulation. Emerging evidence has demonstrated that peripheral administration of Reg3g results in improved glucose regulation as a gut hormone. In this study, we explored the therapeutic potential of Reg3g through intraduodenal infusion in mouse models of metabolic disorders. The objective of this study was to test the hypothesis that administered Reg3g into the intestinal lumen contributes to metabolic improvements by enhancing gut barrier function. Our mouse studies revealed that duodenal infusion of Reg3g reduces gut permeability and systemic endotoxemia. Studies with intestinal organoids supported the role of Reg3g in preserving cellular integrity and antioxidant gene expression under fructose-induced stress. Although Reg3g treatment results in little change to body weight, food intake, or glucose tolerance, Reg3g-treated mice exhibited reduced hepatic lipid accumulation along with the downregulation of lipogenic pathway genes. These data point toward the positive impact of Reg3g administration through intraduodenal infusion to regulate the intricate cross talk between gut barrier function and hepatic steatosis with the gut-liver axis.NEW & NOTEWORTHY This study shows that intraduodenal administration of the gut peptide, regenerating islet-derived protein 3 g (Reg3g), reduces hepatic lipid accumulation, improves gut barrier function, and lowers systemic endotoxemia in mouse models of metabolic disorders. These findings elucidate the therapeutic benefits of Reg3g administration into the gut.

Synergistic effect of Alnus glutinosa saplings and rhizosphere microorganisms on organochlorine pesticides remediation in contaminated soil

The widespread use of hexachlorocyclohexanes (HCH) as pesticides has raised environmental concerns due to their persistence and toxicity. Addressing the pressing need for effective bioremediation strategies, this study explores the effects of α-, β-, δ-, and ε-HCH isomers on the growth, hormonal changes, physiological parameters and bioaccumulation in Alnus glutinosa saplings (1-year-old and 2-year-old) and bacterial communities in polluted soil. A. glutinosa saplings not only withstanded HCH exposure but also enhanced the remediation efficiency by 6.8-24.4%, suggesting an acceleration of pollutant breakdown likely mediated by root exudates positively affecting the soil microbiome. Interestingly, 1-year-old saplings demonstrated greater remediation efficiency post-pruning than unpruned 2-year-old saplings, despite the latter having a larger root biomass. The hormonal analysis indicated that HCH presence led to a reduction in abscisic acid (ABA) and an increase in jasmonic acid (JA), with the magnitude of changes being age-dependent. Salicylic acid (SA) levels increased 1-year-old and decreased in 2-year-old saplings under HCH stress. Moreover, a higher presence of lin-degrading genes in the rhizosphere of treated saplings compared to controls confirmed ongoing biodegradation processes. The outcomes help to better understand the processes involved in degradation of persistent pesticides in soil. The mechanism of in-plant isomerization and the identification of metabolites should be the focus of future research.

Oral vancomycin treatment alters levels of indole derivatives and secondary bile acids modulating the expression of mTOR pathway genes in astrocytes during EAE

Astrocytes play important roles in the central nervous system (CNS) during health and disease. Prior studies have shown that gut commensal-derived indole derivatives as well as secondary bile acids modulate astrocyte function during the late stage of EAE (recovery phase). Here we showed that administering vancomycin to mice starting during the early stage of EAE improved disease recovery, an effect that is mediated by the gut microbiota. We observed that 6 taxa within the Clostridia vadin BB60 group were enriched in vancomycin-treated mice compared to untreated EAE mice. Vancomycin-treated EAE mice also had elevated serum levels of the anti-inflammatory tryptophan-derived metabolite, indole-3-lactic acid and decreased levels of deoxycholic acid, a pro-inflammatory secondary bile acid. RNA sequencing revealed altered expression of several genes belonging to the mammalian target of rapamycin (mTOR) pathway in astrocytes obtained during the late stage of EAE from vancomycin-treated EAE mice. Furthermore, we observed a link between serum levels of indole derivatives and bile acids and expression of several genes belonging to the mTOR pathway. Interestingly, the mTOR signaling cascades have been implicated in several key biological processes including innate (e.g., astrocyte) immune responses as well as neuronal toxicity/degeneration. In addition, rapamycin, a specific inhibitor of mTOR, has been shown to inhibit the induction and progression of established EAE. Collectively, our findings suggest that the neuroprotective effect of vancomycin is at least partially mediated by indole derivatives and secondary bile acids modulating the expression of mTOR pathway genes in astrocytes.

Mapping the microbial landscape and variations based on biological sex, age, and biopsy location in the shoulder skin microbiome

BACKGROUND

The organisms responsible for periprosthetic joint infections (PJIs) of the shoulder are often skin pathogens originating from the patient's own skin flora at the time of surgery. Understanding the normal skin flora around the shoulder is an important step to identify the range of organisms that could be responsible for PJI and to ensure optimization of culture mediums to identify them. This study aimed to provide the first description of the shoulder skin microbiome using high-throughput next-generation sequencing methodology and explore variations by age, biological sex, and biopsy location.

METHODS

Patients undergoing arthroscopic surgery were approached for informed consent to have punch biopsies taken from anterior, lateral, and posterior arthroscopy portal sites. DNA extraction was undertaken followed by illumina sequencing, focusing on the V3-V4 regions of the 16S rRNA gene. Amplicon sequence variants (ASVs) were generated using Deblur workflow and used for taxonomic assignment. Variation in the microbiota community based on age, biological sex, and biopsy location was assessed through alpha and beta diversity metric calculations using phyloseq R package.

RESULTS

Sixty-two patients (24 female, 38 male) aged 18-80 years were recruited, resulting in 186 punch biopsy samples for analysis. Following removal of low-prevalence taxa, 606 ASVs were aggregated at the genus level, resulting in 214 genera across 13 phyla. The top 20 most abundant genera accounted for 73.5% of the overall sequence count. Cutibacterium was the most abundant genus within the study population, followed by Ralstonia, Staphylococcus, Bacteroides, and Streptococcus. Significant differences were observed in beta diversity metrics when comparing by biological sex, which accounted for 3.9%-5.3% of the variation in the microbial community, but not age or biopsy location. Males displayed a greater proportion of gram-positive and aerobic bacteria, whereas females exhibited a greater proportion of gram-negative and stress-tolerant bacteria.

CONCLUSION

This is the first study to look specifically at the microbiome of the cutaneous shoulder and describe the most abundant genera and compositional differences based on age, biological sex, and biopsy location. Biological sex was the only host covariant studied that reached significance in explaining microbiota variation. The top 20 most abundant genera, accounting for 74% of the overall sequence count, would be isolated with standard microbiological culture. As such, this study does not highlight a need to change current culture investigation practice for shoulder PJI, but it serves as an important catalog of skin commensals around the operative site in shoulder surgery.

Development of a flavor-oriented synthetic microbial community for pour-over rice wine: A comprehensive microbial community analysis

Huangjiu, a traditional Chinese alcoholic beverage, varies widely in quality and consistency when brewed using the traditional pour-over rice wine technique, largely due to the variability in its microbial community in an open fermentation environment. This study streamlined the microbial complexity using amplicon sequencing and culture-dependent methods, leading to the identification of a set of core microbial species instrumental in flavor development. A synthetic microbial community was crafted from these key species and employed in fermentation experiments. In this study, we demonstrated that the synthetic microbial community not only replicated the major flavor profiles of traditional pour-over rice wine but also it is further proved that the core species directly determines the main flavor of pour-over rice wine, these findings are supported by our quantitative analysis of volatile compounds and sensory evaluation data. This research underscores the potential of synthetic microbial communities in standardizing production processes and improving the sensory quality of traditional beverages like Huangjiu.

Unraveling phase-dependent variations of viral community, virus-host linkage, and functional potential during manure composting process

The temporal dynamics of bacterial and fungal communities significantly impact the manure composting process, yet viral communities are often underexplored. Bulk metagenomes, viromes, metatranscriptomes, and metabolomes were integrated to investigate dynamics of double-stranded DNA (dsDNA) virus and virus-host interactions throughout a 63-day composting process. A total of 473 viral operational taxonomic units (vOTUs), predominantly Caudoviricetes, showed distinct phase-dependent differentiation. In phase I (initial-mesophilic), viruses targeted Gammaproteobacteria and Firmicutes, utilizing restriction-modification (RM) systems. In phase II (thermophilic-maturing), viruses infected Alphaproteobacteria, Chloroflexi, and Planctomycetes, employing CRISPR-Cas systems. Lysogenic and lytic viruses exerting differential effects on bacterial pathogens across phases. Additionally, six types of auxiliary metabolic genes (AMGs) related to galactose and cysteine metabolisms were identified. The homologous lineages of AMGs with bacterial genes, along with the significant temporal correlation observed between virus-host-metabolite interactions, underscore the critical yet often overlooked role of viral communities in modulating microbial metabolisms and pathogenesis within composting ecosystems.

Symbiotic bacteria play crucial roles in a herbivorous mite host suitability

BACKGROUND

The tomato russet mite (TRM), Aculops lycopersici, is a strictly herbivorous and economically significant pest that infests Solanaceae plants, but its host suitability varies, showing high performance on tomatoes. Although symbiotic bacteria have been suggested to play crucial roles in the host adaptation of herbivores, their effects on TRM remain unclear.

RESULTS

In this study, using next generation high-throughput sequencing of the bacterial 16S rRNA data, we identified the bacterial diversity and community composition of TRM feeding on tomato, eggplant, and chili. Our results show no significant difference in the bacterial community composition of TRM across three host plants. However, the relative density of Escherichia coli (TRM_Escherichia) showed 9.36-fold higher on tomato than on eggplant and chili. These results align with the observed TRM performance among three host plants. When TRM_Escherichia was reduced using antibiotics, the treated TRM decreased the population density on tomato. However, when we transferred TRM from eggplant to tomato, the population density of TRM increased, coinciding with an increase of the TRM_Escherichia density. These results indicate that TRM_Escherichia may affect the host suitability of TRM. Our fluorescence in situ hybridization (FISH) results further showed that TRM_Escherichia is primarily distributed in the salivary glands. Metagenomic data results suggest that TRM_Escherichia functions in food digestion and energy metabolism.

CONCLUSION

We provided the first comprehensive analysis of TRM bacterial communities. Our findings demonstrate that the symbiotic bacterium TRM_Escherichia may play crucial roles in the suitability of TRM feeding on different Solanaceae hosts. © 2024 Society of Chemical Industry.

Environmental exposure to single and combined ZnO and TiO2 nanoparticles: Implications for rainbow trout gill immune functions and microbiota

ZnO and TiO2 nanoparticles (NPs) are widely employed for their antibacterial properties, but their potential environmental impact is raising concerns. This study aimed to assess their single and combined effects at environmentally relevant concentrations (210 μg L-1) on rainbow trout (Oncorhynchus mykiss) gills microbiota and immune functions. 16S rRNA gene sequencing performed after 5 and 28 days of exposure suggests that TiO2 NPs had a more immediate impact on bacterial diversity, while prolonged exposure to the mixture altered community composition. Changes in the relative abundance of potential pathogenic genera such as Candidatus Piscichlamydia and Flavobacterium were observed. Additionally, while the expression of the pro-inflammatory cytokine il1β, and antibacterial compounds (c3) was downregulated by TiO2 NPs and the mixture, ZnO NPs affected immune (mpo) and tight junction proteins (zo1). These results highlight the differences in the toxicity mechanisms existing between the single NPs and their combination, which showed higher toxicity to the gill bacterial community, but not to immune mechanisms. Furthermore, they suggest that exposure to environmental concentrations of NPs could potentially affect fish mucosal immunity and associated microbiota, highlighting the need for further research on the toxicity of NP mixtures.

Enhanced pharmaceutical removal from building wastewater by the novel integrated system of anaerobic baffled biofilm-membrane bioreactor and UV/O3: Microbial community, occurrence of bio-intermediates and post-treatment

This research aimed to develop the novel integrated system of anaerobic baffled biofilm-membrane bioreactor (AnBB-MBR) (with and without microaeration) and UV/O3 for removal of target pharmaceuticals (ciprofloxacin (CIP), caffeine (CAF), sulfamethoxazole (SMX) and diclofenac (DCF)) from building wastewater. The investigation was performed to elucidate how microaeration affected the removal performances, degradation kinetics and pathways of bio-intermediates of the AnBB-MBR. Two AnBB-MBR reactors - R1: AnBB-MBR (without microaeration) and R2: AnBB-MBR with microaeration at 0.93 LO2/LFeed - were operated at the same hydraulic retention time (HRT) of 30 h. The UV/O3 was selected as the post-treatment system. While UV alone slightly removed CIP without the removal of other compounds. After 150 min of the UV/O3, the R1 with UV/O3 achieved 97.31-100% removal efficiency of targeted pharmaceuticals and increased to 99.47-100% with the R2 integrated with UV/O3. The obtained pseudo-first order kinetic rate constants of the UV/O3 in treating the permeate of R1 were 0.0235, 0.004, 0.0423 and 0.097 min-1 for CIP, CAF, SMX and DCF, respectively. Whereas the obtained pseudo-first order kinetic rate constants of the UV/O3 in treating the permeate of R2 were 0.021, 0.0338, 0.0511 and 0.0527 min-1 for CIP, CAF, SMX and DCF, respectively. For the major microorganisms involved in targeted pharmaceutical removal in the R2 under microaerobic conditions included ammonia oxidizing bacteria (AOB) and methanotrophs, while Bacillus, Longilinea, Clostridium and Lactivibrio were possibly responsible for pharmaceutical removal in the R1 under anaerobic conditions. The differences of bio-intermediates between anaerobic and microaerobic conditions were exclusively identified. In addition, the integration of AnBB-MBR with microaeration and UV/O3 was more effective in removing a wide variety of bio-intermediates than the case of the integrated system without microaeration. Therefore, the integrated system of AnBB-MBR with microaeration and UV/O3 can be a promising technology for pharmaceutical removal from building wastewater.

Integrated use of electrochemical anaerobic reactors and genomic based modeling for characterizing methanogenic activity in microbial communities exposed to BTEX contamination

In soil polluted with benzene, toluene, ethylbenzene, and xylenes (BTEX), oxygen is rapidly depleted by aerobic respiration, creating a redox gradient across the plume. Under anaerobic conditions, BTEX biodegradation is then coupled with fermentation and methanogenesis. This study aimed to characterize this multi-step process, focusing on the interactions and functional roles of key microbial groups involved. A reactor system, comprising an Anaerobic Bioreactor (AB) and two Microbial Electrolysis Cell (MEC) chambers, designed to represent different spatial zones along the redox gradient, operated for 160 days with intermittent exposure to BTEX. The functional differentiation of each chamber was reflected by the gas emission profiles: 50%, 12% and 84% methane in the AB, anode and cathode chambers, respectively. The taxonomic profiling, assessed using 16S amplicon sequencing, led to the identification chamber-characteristic taxonomic groups. To translate the taxonomic shift into a functional shift, community dynamics was transformed into a simulative platform based on genome scale metabolic models constructed for 21 species that capture both key functionalities and taxonomies. Representatives include BTEX degraders, fermenters, iron reducers acetoclastic and hydrogenotrophic methanogens. Functionality was inferred according to the identification of the functional gene bamA as a biomarker for anaerobic BTEX degradation, taxonomy and literature support. Comparison of the predicted performances of the reactor-specific communities confirmed that the simulation successfully captured the experimentally recorded functional variation. Variations in the predicted exchange profiles between chambers capture reported and novel competitive and cooperative interactions between methanogens and non-methanogens. Examples include the exchange profiles of hypoxanthine (HYXN) and acetate between fermenters and methanogens, suggesting mechanisms underlying the supportive/repressive effect of taxonomic divergence on methanogenesis. Hence, the platform represents a pioneering attempt to capture the full spectrum of community activity in methanogenic hydrocarbon biodegradation while supporting the future design of optimization strategies.

Activation of Sirt1 by acetate alleviates silicofibrosis: Contribution of the gut microbiota

Silicosis is a prevalent occupational disease marked by progressive pulmonary fibrosis. Despite its significant health burden, the pathogenesis of silicosis remains unclear, and no specific therapeutic drugs are available. In this study, we developed a novel intervention strategy targeting gut microbiota and investigated its underlying mechanisms. Using 16S rRNA gene sequencing, we observed significant gut microbiota dysbiosis in silicosis rats at different times (1-8 weeks), notably characterized by altered relative abundance of Ruminococcus and Lactobacillus. Fecal microbiota transplantation altered the gut microbiota structure of silicosis rats, alleviated silica-induced lung histopathological injury, with LEfSe analysis identifying Bifidobacterium as a potential biomarker. Treatment with Bifidobacterium reduced the level of pro-inflammatory cytokines (IL-1β, IL-6 and TNF-α) and fibrosis markers (collagen III, α-SMA and vimentin) in the lungs of silicosis rats, accompanied with increased serum acetic acid levels. Acetate, a major metabolite of Bifidobacterium, demonstrated similar protective effects against silicosis in this study, suggesting its role as a key mediator of Bifidobacterium action in the lungs. Both Bifidobacterium and acetate significantly upregulated Sirt1 in intestinal and lung tissues, while Sirt1 inhibition diminished their benefits to silicosis. As a widely studied histone deacetylase, Sirt1 was proven to be markedly reduced in the lungs of silicosis rats in this study. EX-527, a potent Sirt1 inhibitor, could worsen silicosis damage by upregulating the level of TGF-β1 and the degree of Smad2/3 acetylation. Our study highlights the efficacy of postbiotics, such as Bifidobacterium and acetate, and identifies Sirt1 as a promising target for silicosis treatment.

The impact of coffee on gut microbial structure based on in vitro fecal incubation system

Coffee is globally popular beverage, renowned for its taste and stimulating properties. This study aims to explore the impact of two different types of coffee, depending on extraction methods, on the gut microbiota. Fecal samples from healthy donors (n = 20) were cultured with or without coffee using in vitro fecal incubation. Both coffee-treated groups exhibited lower microbial diversity and greater structural differences in their communities compared to the control. Notably, the Bifidobacterium genus was overrepresented in the instant coffee (IC)-treated groups, whereas the Blautia genus was underrepresented in both coffee-treated groups. Additionally, genes for TCA cycle and vitamin B6 metabolism were more prevalent in coffee-treated groups than in the control. However, the precursor pathways leading to the TCA cycle differed between the DC- and IC-treated groups, reflecting the distinct chemical compositions of each coffee type. These findings demonstrate that extraction method of coffee significantly affects its impacts on gut microbial structure.

Supplementary Information

The online version contains supplementary material available at 10.1007/s10068-024-01717-7.

Effects of transient change in temperature by daki warm treatment on the growth of bacteria during kimoto-style seed mash preparation

Daki warm treatment (daki-ire) is performed during the process of seed mash preparation in the brewing of Japanese sake in order to promote the saccharification of rice by koji enzyme and to enhance the growth of Saccharomyces cerevisiae. Although it is important to control the growth of lactic acid bacteria in the preparation of kimoto-style seed mash (traditional sake-brewing method), it has not been known whether the transient increase in the temperature and/or appropriate temperature zone produced by daki-ire influences the growth of bacteria. A temperature increase generally helps bacterial growth, but we have found no published investigation of the influence of temperature changes in daki-ire on bacterial growth during the kimoto-style seed mash preparation process. In this first comprehensive evaluation of the effects of the temperature change by daki-ire on bacterial communities, we investigated the bacterial community in three batches that were brewed by the same brewery using identical ingredients. The results demonstrated that the bacterial community or its transition during lactic acid fermentation was diverse despite the use of the same brewing conditions. We observed that (i) some lactic acid bacteria were carried over to the subsequent batches, and (ii) the increase in the initial amount of lactic acid bacteria plays an important role in the formation of the bacterial community. Our analysis of the bacterial growth activity before and after daki-ire indicated that the transient increase in temperature and/or local appropriate temperature by daki-ire, in and of itself, has relatively little direct impact on bacterial growth.

Microbial mechanisms of mixed planting in regulating soil phosphorus availability across different stand ages in Chinese fir plantations

The mixed planting of Chinese fir with broadleaf species to increase soil phosphorus (P) availability has been widely adopted in subtropical China. As soil P availability is significantly influenced by tree growth, the microbial mechanisms underlying the effects of mixed planting on soil P availability across different stand ages are not fully understood. In this study, we collected soil samples from mixed-species plantations of Chinese fir and Schima superba (MCP) and pure Chinese fir plantations (PCP) at young (5 years), middle-aged (20 years), and mature (32 years) stages in southeastern China. We determined the soil P fractions, organic P (Po) mineralizing ability, and dynamics of the microbial community associated with Po mineralization in the samples. We hypothesized that the influence of mixed planting on soil P availability is modulated by stand age. Compared with the PCP stands, the young and mature MCP stands exhibited significantly greater contents of labile and moderately labile P, with increases of 13.22% and 8.18%, respectively, in the young stands and 22.20% and 30.52%, respectively, in the mature stands. Conversely, the middle-aged MCP stands exhibited lower contents of labile and moderately labile P, with decreases of 20.93% and 18.16%, respectively. The communities of Po-mineralizing fungi (Pmin-F) and bacteria (Pmin-B) changed not only among the different plantation types but also across the various stand ages. The Pmin-F community contributed mainly to labile P, whereas the Pmin-B community was the primary driver of moderately labile P. Additionally, mixed planting mediated labile P availability through soil pH, accounting for 71% of the variation in this P fraction. Conversely, stand age affected the availability of moderately labile P through soil nitrogen availability and the Pmin-F community, explaining 81% of the variation in this P fraction. Overall, we revealed that the impact of mixed planting on soil P availability is modulated by stand age, with fungi and bacteria fulfilling distinct ecological roles in the process. Our results are highly important for maintaining soil P availability for the sustainable management of Chinese fir plantations.

The protist symbionts of Reticulitermes tibialis: Unexpected diversity enables a new taxonomic framework

Wood-feeding termites harbor specialized protists in their hindguts in a classic nutritional mutualism. The protists are vertically inherited, which has generated a broad-scale pattern of codiversification over ∼150 million years, but there are many incongruences due to lineage-specific loss and transfer of symbionts. Despite the evolutionary and economic importance of this symbiosis, the symbiont communities of most termite species are incompletely characterized or entirely unstudied. Here, we have investigated the protist symbiont community of Reticulitermes tibialis, using single-cell PCR to link morphology to 18S rRNA gene sequences. The protists belong to at least 41 species in 3 major lineages within Metamonada: Spirotrichonymphida, Pyrsonymphidae, and Trichonympha. The Spirotrichonymphida symbionts belong to 6 genera, including Pseudospironympha, which has not been found in Reticulitermes until now, and Dexiohelix, a new genus. Pyrsonymphidae traditionally include just Pyrsonympha and Dinenympha, but our morphology-linked 18S phylogeny indicates that both genera are polyphyletic. We accordingly restrict the definitions of Pyrsonympha and Dinenympha to the clades that include their type species, and we propose 5 new genera to accommodate the remaining clades. Short-read 18S amplicon sequencing revealed considerable variation in community composition across R. tibialis colonies in Arizona, suggestive of a symbiont metacommunity. Symbiont species varied in their prevalence across colonies, with a core set of about 12 highly prevalent symbiont species, 11 species with intermediate prevalence, and 18 rare species. This pattern contrasts with the traditional paradigm of consistent symbiont community composition across colonies of a termite species.

Effects of fecal microbiota transplantation on behavioral abnormality in attention deficit hyperactivity disorder-like model rats

Attention deficit/hyperactivity disorder (ADHD) is a neurodevelopmental disorder characterized by inattention, hyperactivity, and impulsivity. ADHD symptoms not only impact patients and their families but also impose societal costs. Current treatments for ADHD, including environmental adjustments and medication, are symptomatic and require long-term management. Recently, the link between gut microbiota dysbiosis and various psychiatric and neurological disorders has become evident. The effectiveness of fecal microbiota transplantation (FMT) from healthy individuals in treating autism spectrum disorder, a neurodevelopmental disorder related to ADHD, has been demonstrated. However, despite suggestions of a relationship between ADHD and gut microbiota, few studies have explored the efficacy of FMT for ADHD. In the current study, we used 16S rDNA analysis to show that ADHD-like model rats possess a gut microbiota that is distinct from that of healthy rats, and we demonstrated that FMT from healthy rats improved hyperactivity in ADHD-like model rats. Our findings suggest that differences in gut microbiota underlie ADHD-like behaviors and that FMT may be an effective treatment for ADHD.

Microbiome analysis of gut microbiota in patients with colorectal polyps and healthy individuals

Colorectal polyps serve as the primary precursors for colorectal cancer. A close relationship has been observed between colorectal polyps and gut microbiota. However, the composition and role of the microbiome associated with tubular adenoma are not well understood. In this study, we prospectively evaluated alterations in gut microbiota among patients with colorectal polyps. A total of 60 subjects were enrolled in this study, including 30 patients with colorectal polyps (CP group) and 30 healthy controls (control group). The 16S rRNA sequencing was employed to characterize the gut microbiome in fecal samples. The results revealed that the beta diversity of the gut microbiota in the CP group significantly differs from that of the control group (p = 0.001). At the phylum level, the relative abundance of Bacteroides, Fusobacteria, and Proteobacteria was higher in the CP group compared to the control group (p < 0.05), whereas the relative abundance of Actinobacteria was higher in the control group in comparison to the CP group (p < 0.05). At the genus level, the abundance of Bacteroides increased in the CP group (p < 0.05), while Bifidobacterium declined in the CP group (p < 0.05). At the species level, the abundance of Clostridium perfringens, unidentified_Bacteroides, unidentified_Dorea, Escherichia coli, Clostridium ramosum, and Ruminococcus gnavus was higher (p < 0.05), whereas the abundance of Bifidobacterium adolescentis, unclassified_Bifidobacterium, Bifidobacterium longum, Faecalibacterium prausnitzii, and unidentified_Bifidobacterium is lower in CP group compared to the control group (p < 0.05). There was a structural imbalance in the composition of intestinal colonization flora for CP patients, characterized by a decrease in beneficial bacteria and an increase in harmful bacteria. Escherichia, Shigella, and Bacteroides may serve as promising biomarkers for early detection of colorectal polyps.

Anthropogenic reverberations on the gut microbiome of dwarf chameleons (Bradypodion)

Exploration of the microbiome has been referred to as a final frontier in biological research. This is due to its precedence for generating insights on the holistic functioning of organismal biology by exploring the interactions between hosts and their associated symbiotic organisms. The microbiomes of many vertebrate groups still require exploration to advance current knowledge and fill previous knowledge gaps. This study generated initial descriptions of the bacterial microbiomes of three species of dwarf chameleon (Bradypodion) from the 16S rRNA gene region targeting the V3 and V4 hypervariable regions. This led to the successful identification of 1,073 and 4,502 independent amplicon sequence variants from buccal swab and faecal material samples, respectively. This newly acquired information is intended as a baseline for future work incorporating holobiont information. The diversity of microbial taxa suggests that the total dwarf chameleon microbiome is similar to other squamates investigated to date, as well as chelonians (Testudines). Microbial frequency differences were noted in comparison to crocodilians (Archosauria) and mammalian groups. Furthermore, this study aimed to examine the influence of habitat transformation on the composition of the microbiome in dwarf chameleons as each of the study species occupy both urban and natural habitats. Given that most urban habitats are highly transformed, the expectation was that microbial assemblages of the gastro-intestinal tracts of all three Bradypodion species would show significant differences between populations (i.e., natural, or urban). It was found, however, that the level of effect was contingent on species: B. melanocephalum populations showed noticeable microbiome differences between urban and natural populations; B. thamnobates showed variations in microbial community dispersions between populations; and B. setaroi showed no significant microbiome differences based on diversity metrics although some frequency differences, in microbiome composition, were observed between populations. We suggest that the magnitude of difference between the habitats occupied by the populations is a factor, given the apparent disparity between the natural and urban habitats for B. melanocephalum as compared to the other two species.

Age, sex, and mitochondrial-haplotype influence gut microbiome composition and metabolites in a genetically diverse rat model

We evaluated the impact of sex and mitochondrial-haplotype on the age-related changes in the fecal gut microbiome of the genetically heterogeneous rodent model, the OKC-HETB/W rat. The age-related changes in the microbiome differed markedly between male and female rats. Five microbial species changed significantly with age in male rats compared to nine microbial species in female rats. Only three of these microbes changed with age in both male and female rats. The mitochondrial-haplotype of the rats also affected how aging altered the microbiome. Interestingly, most of the microbial species that changed significantly with age were mitochondrial-haplotype and sex specific, i.e., changing in one sex and not the other. We also discovered that sex and mitochondrial-haplotype significantly affected the age-related variations in content of fecal short-chain fatty acids and plasma metabolites that influence or are regulated by the microbiome, e.g., tryptophan derived metabolites and bile acids. This study demonstrates that the host's sex plays a significant role in how the gut microbiome evolves with age, even within a genetically diverse background. Importantly, this is the first study to show that the mitochondrial-haplotype of a host impacts the age-related changes in the microbiome.

The Gut Microbiota of the Greater Horseshoe Bat Confers Rapidly Corresponding Immune Cells in Mice

BACKGROUND

Emerging infectious diseases threaten human and animal health, with most pathogens originating from wildlife. Bats are natural hosts for many infectious agents. Previous studies have demonstrated that changes in some specific genes in bats may contribute to resistance to viral infections, but they have mostly overlooked the immune function of the bat gut microbiota.

AIMS

In this study, we used fecal transplants to transfer the gut microbiota from the Greater Horseshoe Bat (Rhinolophus ferrumequinum) into mice treated with antibiotics. The gut microbiota changes in mice were detected using 16S rRNA high-throughput sequencing technology. Flow cytometry was used to detect changes in associated immune cells in the spleen and mesenteric lymph nodes of the mice.

RESULTS

The results showed that the gut microbiota of mice showed characteristics of some bat gut microbiota. The Greater Horseshoe Bat's gut microbiota changed some immune cells' composition in the spleen and mesenteric lymph nodes of mice and also conferred a faster and higher proportion of natural killer cell activation.

CONCLUSION

This result provides new evidence for the regulatory immune function of bat gut microbiota and contributes to a deeper insight into the unique immune system of bats.

Gut microbiota in chronic obstructive pulmonary disease varies by CT-verified emphysema status

Background and aim

The association of the gut microbiota to chronic obstructive pulmonary disease (COPD) phenotypes is underexplored. We aimed to compare stool samples from patients with COPD and subjects without COPD and relate findings to emphysema status, exacerbation rate, blood eosinophil levels, symptom score, and lung function.

Methods

We report findings from a single-centre case-control study with 62 current and former smoking patients with COPD and 49 subjects without COPD. DNA was extracted from stool samples, and the V3V4-region of the bacterial 16S-rRNA gene was sequenced. Emphysema was defined based on thoracic computed tomography (CT thorax) low attenuating areas ≥/<10% at threshold -950 and -910 hounsfield units, respectively. Differential abundance of taxa was evaluated using Analysis of Composition of Microbes with Bias Correction (ANCOM-BC). Beta diversity was compared using a distance-based permanova-test.

Results

The genus Veillonella was decreased and a genus belonging to class Clostridia was increased in COPD compared with controls without COPD. The composition of microbes (beta diversity) differed in emphysema compared to controls, and 27 genera were differentially abundant in emphysema vs. controls. Nine of these genera belonged to the family Lachnospiraceae. Lung function, blood counts and COPD assessment test score correlated with several genera's relative abundance. Of the genera showing significant correlation to lung function, nine belonged to the family Lachnospiraceae.

Conclusion

The gut microbiota in COPD differs from that in healthy individuals, even more so in emphysema. In particular, future studies should look into the mechanisms and therapeutic potential of dysbiosis affecting the family Lachnospiraceae.

Homogeneity Between Cervical and Vaginal Microbiomes and the Diagnostic Limitations of 16S Sequencing for STI Pathogens at Higher Ct Values

Understanding the interactions between the cervico-vaginal microbiome, immune responses, and sexually transmitted infections (STIs) is crucial for developing targeted diagnostic and therapeutic strategies. Although microbiome analyses are not yet standard practice, integrating them into routine diagnostics could enhance personalized medicine and therapies. We investigated the extent to which partial 16S short-read amplicon microbiome analyses could inform on the presence of six commonly encountered STI-causing pathogens in a patient cohort referred for colposcopy, and whether relevant taxonomic or diagnostic discrepancies occur when using vaginal rather than cervical swabs. The study cohort included cervical and vaginal samples collected from women referred for colposcopy at the University Hospital Bonn between November 2021 and February 2022, due to an abnormal PAP smear or positive hrHPV results. 16S rRNA gene sequencing libraries were prepared targeting the V1-V2 and V4 regions of the 16S RNA gene and sequenced on the Illumina MiSeq. PCR diagnostics for common STI-causing pathogens were conducted using the Allplex STI Essential Assay Kit (Seegene, Seoul, Republic of Korea). Concerning the bacterial microbiome, no significant differences were found between vaginal and cervical samples in terms of prevalence of taxa present or diversity. A total of 95 patients and 171 samples tested positive for at least one among Ureaplasma parvum, Ureaplasma urealyticum, Mycoplasma hominis, Mycoplasma genitalium, Chlamydophila trachomatis or Neisseria gonorrhoeae. Sequencing the V1-V2 region enabled detection of one-third to half of the PCR-positive samples, with the detection likelihood increasing at lower cycle threshold (Ct) values. In contrast, sequencing the V4 region was less effective overall, yielding fewer species-level identifications and a higher proportion of undetermined taxa. We demonstrate that the vaginal microbiome closely mirrors the cervical microbiome, a relationship that has not been explored previously, but which broadens the possibilities for microbiome analysis and pathogen detection and establishes vaginal swabs as a reliable method for detecting the investigated pathogens, with sensitivities comparable with or superior to endocervical swabs. On the other hand, the sensitivity of partial 16S amplicon sequencing appears insufficient for effective STI diagnostics, as it fails to reliably identify or even detect pathogens at higher Ct values.

Nutraceutical Blends Promote Weight Loss, Inflammation Reduction, and Better Sleep: The Role of Faecalibacterium prausnitzii in Overweight Adults-A Double-Blind Trial

This study explores the effects of a nutraceutical blend with prebiotics, β-glucans, essential minerals, and silymarin on gut microbiota, inflammation, and sleep quality in obesity through microbiota reshaping and metabolic improvements over 90 days. A double-blind, randomized trial was conducted on 77 participants divided into two groups receiving either a standard nutraceutical blend (NSupple) or a silymarin-enriched blend (NSupple_Silybum). Fecal and plasma samples were collected at baseline and post-supplementation for gut microbiota, metabolic, and inflammatory marker analysis. The results showed a reduction in body weight, waist-to-height ratio, total cholesterol, and fractions in the NSupple_Silybum group. There was a dysbiosis recovery shown by the increase in beneficial gut bacteria, such as Lentisphaerae phylum, Lactobacillus and Faecalibacterium genera, and Faecalibacterium prausnitzii in the NSupple group, with a concurrent reduction in Adlercreutzia and Sutterella in the NSupple_Silybum group. Both groups demonstrated improved inflammatory profiles by the reduced TNF-α/IL-10 ratio, reduced cortisol levels, and reduced Firmicutes/Bacteroides ratio. Additionally, improvements in sleep quality were associated with reductions in pro-inflammatory cytokines and improved microbiota composition. The nutraceutical blend reshaped gut microbiota, enhanced anti-inflammatory species, and improved metabolic and sleep parameters, highlighting its potential as a nutritional strategy for managing obesity and reducing inflammation.

Gut microbial predictors of first-line immunotherapy efficacy in advanced NSCLC patients

The composition of the gut microbiome of patients with advanced non-small cell lung cancer is currently considered a factor influencing the effectiveness of treatment with immune checkpoint inhibitors. We aimed to evaluate the baseline gut microbiome composition in patients before receiving first-line immunotherapy alone or combined with chemoimmunotherapy. We performed 16S rRNA sequencing based on hypervariable regions. Stool samples were collected from 52 patients with advanced NSCLC treated with immunotherapy or chemoimmunotherapy before treatment. We found that the Ruminococcaceae family, species Alistipes sp. genus Eubacterium ventriosum group and genus Marvinbryantia may be intestinal, microbiological predictors of response to treatment. Genus Akkermansia and species from the [Clostridum] leptum group predicted the length of PFS (progression-free survival). Longer OS (overall survival) is associated with bacteria from the Ruminococcaceae family genera [Eubacterium] ventriosum group, Marvinbryantia, Colidextribacter and species [Clostridum] leptum. Bacteria that have an adverse effect (shortening of PFS or OS) on the response to treatment using immune checkpoint inhibitors are Rothia genus, Streptococus salivarius, Streptococus, Family XIII AD3011 group and Family XIII AD3011 group, s. uncultured bacterium. The composition of intestinal flora can be a predictive factor for immunotherapy in NSCLC patients. Specific bacteria can be positively or negatively associated with response to treatment, progression-free survival, and overall survival. They can be potentially used as predictive markers in NSCLC patients treated with immunotherapy.

Assembly Mechanisms and Functional Adaptations of Soil Fungal Communities of Different Plant Rhizospheres in Ilmenite Mining Area

This study investigated the mechanisms of structural assembly and functional adaptations of fungal communities in the rhizosphere soils of seven different plants grown in the ilmenite zone. We analyzed changes in the rhizosphere soil fungal communities using ITS sequencing. The results revealed that different plants affected the properties of the rhizosphere soil. The contents of organic matter, total nitrogen, and total potassium in the rhizosphere soil exhibited significant variations compared to the soil that was not occupied by plants. Soil fungal composition analysis revealed that Ascomycota and Basidiomycota were the dominant phyla in the soil of this mining area. At the genus level, compared to the mineral soil without plants, the proportion of Epicoccum increased in the rhizosphere soils of different plants, while the proportion of Fusarium decreased. Alpha diversity studies revealed that fungal diversity in the rhizospheres of different plants changed significantly. Beta diversity studies showed a significant differentiation in the fungal community structure of different plant rhizosphere soils compared to the KB group. The FunGuild predictions indicated that different plant rhizosphere soils are enriched with different guilds and trophic patterns of fungi. In addition, we found that soil physical and chemical properties were significantly correlated with the abundance and diversity of fungal communities. The above results indicate that plant species and soil physicochemical properties are important factors influencing the assembly of soil fungal communities in the rhizosphere. This research provides insights into the assembly mechanisms and functional adaptations of fungal community structures in the rhizosphere soils of seven plant species in ilmenite iron mining areas. This helps us to screen plant and fungal community assemblages that can promote soil restoration in ilmenite mining areas and provide a theoretical basis for future ecological restoration in ilmenite areas.

Effects of Live and Peptide-Based Antimicrobiota Vaccines on Ixodes ricinus Fitness, Microbiota, and Acquisition of Tick-Borne Pathogens

This study explored the effects of antimicrobiota vaccines on the acquisition of Borrelia and Rickettsia, and on the microbiota composition of Ixodes ricinus ticks. Using a murine model, we investigated the immunological responses to live Staphylococcus epidermidis and multi-antigenic peptide (MAP) vaccines. Immunized mice were infected with either Borrelia afzelii or Rickettsia helvetica, and subsequently infested with pathogen-free I. ricinus nymphs. We monitored the tick feeding behavior, survival rates, and infection levels. Additionally, we employed comprehensive microbiota analyses, including the alpha and beta diversity assessments and microbial co-occurrence network construction. Our results indicate that both live S. epidermidis and MAP vaccines elicited significant antibody responses in mice, with notable bactericidal effects against S. epidermidis. The vaccination altered the feeding patterns and fitness of the ticks, with the Live vaccine group showing a higher weight and faster feeding time. Microbiota analysis revealed significant shifts in the beta diversity between vaccine groups, with distinct microbial networks and taxa abundances observed. Notably, the MAP vaccine group exhibited a more robust and complex network structure, while the Live vaccine group demonstrated resilience to microbial perturbations. However, the effects of antimicrobiota vaccination on Borrelia acquisition appeared taxon-dependent, as inferred from our results and previous findings on microbiota-driven pathogen refractoriness. Staphylococcus-based vaccines altered the microbiota composition but had no effect on B. afzelii infection, and yielded inconclusive results for R. helvetica. In contrast, previous studies suggest that E. coli-based microbiota modulation can induce a pathogen-refractory state, highlighting the importance of both bacterial species and peptide selection in shaping microbiota-driven pathogen susceptibility. However, a direct comparison under identical experimental conditions across multiple taxa is required to confirm this taxon-specific effect. These findings suggest that antimicrobiota vaccination influences tick fitness and microbiota assembly, but its effects on pathogen transmission depend on the bacterial taxon targeted and the selected peptide epitopes. This research provides insights into the need for strategic bacterial taxon selection to enhance vaccine efficacy in controlling tick-borne diseases.

Bacteria invade the brain following intracortical microelectrode implantation, inducing gut-brain axis disruption and contributing to reduced microelectrode performance

Brain-machine interface performance can be affected by neuroinflammatory responses due to blood-brain barrier (BBB) damage following intracortical microelectrode implantation. Recent findings suggest that certain gut bacterial constituents might enter the brain through damaged BBB. Therefore, we hypothesized that damage to the BBB caused by microelectrode implantation could facilitate microbiome entry into the brain. In our study, we found bacterial sequences, including gut-related ones, in the brains of mice with implanted microelectrodes. These sequences changed over time. Mice treated with antibiotics showed a reduced presence of these bacteria and had a different inflammatory response, which temporarily improved microelectrode recording performance. However, long-term antibiotic use worsened performance and disrupted neurodegenerative pathways. Many bacterial sequences found were not present in the gut or in unimplanted brains. Together, the current study established a paradigm-shifting mechanism that may contribute to chronic intracortical microelectrode recording performance and affect overall brain health following intracortical microelectrode implantation.

Orally Administrated Precision Nanomedicine for Restoring the Intestinal Barrier and Alleviating Inflammation in Treatment of Inflammatory Bowel Disease

Inflammatory bowel disease (IBD) presents a significant challenge in healthcare, characterized by its chronicity and complex pathogenesis involving genetic, immune, and environmental factors. Current treatment modalities, including anti-inflammatory drugs, immunomodulators, and biologics, often lack sufficient efficacy and are accompanied by adverse effects, necessitating the urgent search for therapeutic approaches targeting mucosal barrier restoration and inflammation modulation. Precision nanomedicine emerges as a promising solution to directly address these challenges. This study introduces the development of a targeted sequential nanomedicine for precise IBD treatment. This innovative formulation combines a prodrug carrier containing quercetin to restore intestinal barrier integrity through the regulation of tight junctions and an anti-inflammatory agent dexamethasone acetate to alleviate inflammation. Surface modification with pectin enables colon-specific drug delivery, facilitated by degradation by colon-specific microbiota. Responsive drug release, controlled by reactive oxygen species-sensitive chemical bonds within the carrier, ensures both spatial and temporal accuracy. In vitro and in vivo investigations confirm the nanomedicine's favorable physicochemical properties, release kinetics, and therapeutic efficacy, elucidating potential underlying mechanisms. Oral administration of the nanomedicine shows promising results in restoring intestinal barrier function, reducing inflammation, and modulating the gut microbiota. Consequently, this study presents a promising nanomedicine candidate for advancing IBD treatment paradigms.