DADA2: High-resolution sample inference from Illumina amplicon data

Mycorrhizal Fungi Influence on Mature Tree Growth: Stronger in High-Nitrogen Soils for an EMF-Associated Tree and in Low-Nitrogen Soils for Two AMF-Associated Trees

The plant-mycorrhizal fungi relationship can range from mutualistic to parasitic as a function of the fungal taxa involved, plant ontogeny, as well as the availability of resources. Despite the implications this relationship may have on forest carbon cycling and storage, we know little about how mature trees may be impacted by mycorrhizae and how this impact may vary across the landscape. We collected growth data of two arbuscular mycorrhizal fungi (AMF)-associated tree species, Acer rubrum and A. saccharum, and one ectomycorrhizal fungi (EMF)-associated tree species, Quercus rubra, to assess how the mycorrhizal fungi-plant association may vary along a gradient of nitrogen (N) availability. Individual assessments of fungal taxa relative abundances showed non-linear associations with tree growth; positive associations for the two AMF-associated trees were mostly under low N, whereas positive to neutral associations for the EMF-associated tree mainly took place at high N. Only A. rubrum exhibited greater tree growth with its tree soil-specific mycorrhizal community when compared with predictions under a random mycorrhizal soil community. Because mycorrhizal fungi are likely to mediate how plants respond to warming, increasing levels of N deposition and of atmospheric CO2, understanding these relationships is critical to accurately forecasting tree growth.

Earthworms attenuate antibiotic resistance genes and mobile genetic elements during vermicomposting of sewage sludge

Sewage sludge is among the richest reservoirs of antibiotic resistance genes (ARGs) that may spread to urban environment. Further investigation is warranted for removal of sludge-borne ARGs in large-scale vermicomposting systems. Under this scenario, there is the necessity to unveil the role of the widely-used earthworm species Eisenia andrei, since the current body of literature mostly focuses on E. fetida. The present study sought to evaluate the changes in sludge-borne ARGs and mobile genetic elements in a pilot-scale vermireactor in the presence of E. andrei in response to both gut- and cast-associated processes (GAPs and CAPs, respectively), by coupling high-throughput quantitative PCR and Illumina sequencing. After gut transit, large decreases in the relative abundances and number of the genes conferring resistance to major antibiotic classes, including some specific genes classified as of potentially high risk to human health, were recorded in the fresh casts. Likewise, genes encoding resistance to heavy metals were about nine-times lower in the egested materials than in the initial sludge. Genes coding for integrases or insertional sequences also exhibited reduced abundance as a result of GAP and CAP processes, suggesting that vermicompost appears to be less prone to horizontal gene transfer than untreated sludge. These findings provide evidence about the capacity of the earthworm E. andrei to diminish the risk of ARG spread during vermicomposting, reinforcing its potential for bioremediation purposes by transforming large quantities of waste into an improved fertiliser. This is crucial to propel vermicomposting technology forward and achieve transition toward net zero-waste process.

The Prostate Microbiome Is Associated With Prostate Size and PSA Level, Independent of Age, in BPH Patients

BACKGROUND

The etiology of benign prostatic hyperplasia (BPH) is not well understood, though recent literature suggests that the urinary tract microbiome may play a role. We aimed to examine the prostatic microbiome in BPH and its associations with patient characteristics.

METHODS

Men undergoing Holmium Laser Enucleation of the Prostate (HoLEP) were recruited if they were over 18 years old and had no history of prostate cancer, prostate surgery, or pelvic radiation. Exclusion criteria included positive preoperative urine culture, bladder stones, or catheter-dependence. Patient characteristics including age, prostate-specific antigen (PSA), American Urological Association symptom score (AUASS), and history of biopsy were recorded. Intraoperatively, prostate tissue was collected from each patient, as well as catheterized urine, urethral swabs, and swabs of the specimen container. Samples underwent DNA extraction, 16S sequencing, and analysis using R statistical software. Associations between bacterial taxonomic diversity and patient characteristics were quantified through Sparcc correlations.

RESULTS

Fifty patients were recruited. Mean age, PSA, prostate size, and AUASS were 67.8 years, 4.0 ng/mL, 108.6 g, and 19.4, respectively. After bioinformatic decontamination of prostate samples, alpha and beta diversity analyses indicated that microbiomes from the prostate, urethra, and urine were all distinct (p = 0.001); microbiota from the urine and urethra had higher similarity to each other than that of the prostate. Campylobacter, Caryophanaceae, Enterobacter, and Senegalimassilia positively correlated with prostate size or PSA.

CONCLUSIONS

The prostatic microbiome is unique and distinct from that of urine and urethra, with several known pathogens positively correlating with prostate size and PSA.

Distinct gut microbiota signatures in older people with sarcopenic obesity and sarcopenia without obesity

BACKGROUND

Previous evidence suggests that gut dysbiosis plays an important role in the development and progression of sarcopenia and sarcopenic obesity (SO), but evidence supporting this association is lacking. Thus, this study aimed to investigate the characteristics of gut microbiota in older people with sarcopenia and SO.

METHODS

A total of 1558 older adults (age ≥65 years) from a community-based cohort in Shanghai, China, underwent sarcopenia screening using the SARC-F questionnaire, with 351 participants completing further assessment. On the basis of the Asian Working Group for Sarcopenia 2019 and the World Health Organization obesity criteria, 60 participants were categorized into three groups: SO (n = 20), sarcopenia without obesity (Sar, n = 18), and controls (Con, n = 22). Gut microbiota composition was analyzed using 16S rRNA sequencing (V3-V4 regions).

RESULTS

Significant differences in the diversity and composition of the gut microbiota were observed in the Sar and SO groups. A reduction in alpha diversity (Chao1 and ACE indices) was found in the SO group. Beta diversity based on unweighted Unifrac PCoA was significantly different among the three groups. LEfSe analysis identified 39 taxa with significant differential abundances across groups. The Sar group exhibited enrichment of Christensenellaceae_R-7_group, Alistipes, Ruminococcus, Odoribacter, Prevotellaceae_UCG-001, Hungatella, Family_XIII_AD3011_group, Anaerotruncus, Ruminiclostridium, and Oxalobacter, along with their high taxonomic classifications. Meanwhile, Enterobacteriaceae, Allisonella, and Peptoclostridium were enriched in the SO group. Feature selection via Boruta algorithm identified five and four discriminatory taxa to construct random forest models, effectively distinguishing individuals with Sar and SO from Con. Key predictors for Sar included reduced Enterococcus, Enterobacter, and Hungatella and increased Odoribacter and Christensenellaceae_R-7_group. Conversely, SO was characterized by decreased Enterobacter, Alloprevotella, and Enterococcus and increased Allisonella. Five-fold cross-validation confirmed robust diagnostic efficacy, achieving AUCs of 0.860 (95 % CI: 0.786-0.996) for Sar and 0.826 (95 % CI: 0.735-0.970) for SO.

CONCLUSION

This study demonstrated that the gut microbiota of SO and Sar have distinct diversity and composition profiles. The results provide new insights into the role of gut microbiota in SO, highlighting its potential as a therapeutic target in this condition.

Partial mycoheterotrophy in Apostasia wallichii, an early-diverging Asian tropical orchid

All orchids exhibit mycoheterotrophy during their early development stages, which predisposes certain species to retain this nutritional mode into adulthood. Consequently, many orchids adopt partial mycoheterotrophy, a mixotrophic strategy combining carbon acquisition through both autotrophy and mycoheterotrophy. However, whether this strategy represents an ancestral trait remains contested. This study examines the fungal symbionts and nutritional strategies of the early-diverging orchid Apostasia wallichii and a sympatric, photosynthetic orchid, Cystorchis variegata, in tropical Asia (Sabah, Malaysian Borneo). Specifically, we explored their potential nutritional modes and mycobionts by analysing δ13C and δ15N isotopic profiles and employing high-throughput DNA sequencing. Community profiling via metabarcoding revealed that the A. wallichii individuals investigated were predominantly associated with putatively saprotrophic Botryobasidium fungi, while C. variegata was simultaneously associated with non-ectomycorrhizal rhizoctonias, saprotrophic non-rhizoctonia fungi, and ectomycorrhizal fungi. Additionally, stable isotope analysis showed that both A. wallichii and C. variegata were significantly enriched in 13C and 15N compared to co-occurring autotrophic plants, indicating partial mycoheterotrophy. Our findings, particularly the discovery of partial mycoheterotrophy associated with non-ectomycorrhizal fungi in A. wallichii, suggest that partial mycoheterotrophy in green orchids may be more widespread than previously believed and could represent an ancestral trait intrinsic to orchids.

Green, variegated, and albino Cremastra variabilis provide insight into mycoheterotrophic evolution associated with wood-decaying fungi

With approximately 31,000 species, orchids begin life as mycoheterotrophs, relying on fungi to meet their carbon demands. Notably, some green orchids retain the ability to acquire carbon through fungal associations (partial mycoheterotrophy) and occasionally produce albino or, more rarely, variegated phenotypes. A linear relationship has been observed between leaf chlorophyll content and dependence on fungal-derived carbon, particularly in orchids associated with ectomycorrhizal (ECM) fungi, but whether such plasticity is similarly robust among orchids associated with non-ECM fungi remains underexplored. Here, we focused on the green, variegated, and albino forms of Cremastra variabilis, which likely lack ECM associations, to investigate (i) whether the degree of mycoheterotrophy, indicated by 13C enrichment, correlates with chlorophyll content, and (ii) whether nutritional shifts align with changes in plant structure and mycorrhizal communities. Our results show that rhizoctonia fungi were dominant in green individuals with high chlorophyll levels and lacking coralloid rhizomes, whereas albino and most variegated individuals possessing coralloid rhizomes primarily associate with Psathyrellaceae fungi. Chlorophyll content and carbon stable isotope abundances were negatively correlated, indicating a gradient of increasing mycoheterotrophy from green to albino forms in individuals with coralloid rhizomes. In conclusion, C. variabilis maintains a flexible balance between photosynthesis and mycoheterotrophy, likely shaped by its subterranean morphology and fungal associations, with wood-decaying Psathyrellaceae fungi providing greater support for mycoheterotrophic nutrition than rhizoctonia fungi.

Microbiological, Inflammatory and Clinical Outcome of Citric Acid Passivated Definitive Abutments: Interim 12-Month Results From a Randomised Controlled Clinical Trial

AIM

To assess the efficacy of citric acid passivation on implant abutments by evaluating their impact on bacterial load, microbiome composition, inflammatory response, and clinical and radiographic outcomes compared with control abutments over a 12-month follow-up period.

METHODS

Implants were placed subcrestally in the posterior sextants and randomly assigned to receive a 2-mm high definitive abutment, either with citric acid passivation (CA group) or without (CTR group). Final restorations were delivered after 12 weeks. Samples of the peri-implant crevicular fluid were collected at 3, 6 and 12 months for microbiological and inflammatory analysis. Clinical and radiographic measurements were also performed at these intervals. The primary outcome was total bacterial quantification (log CFU/mL).

RESULTS

Data from 17 patients in the CA group and 16 in the CTR group were analysed. At 12 months, there were no significant differences in total bacterial load between groups (p = 0.689). The biofilm was predominantly composed of commensal bacterial genera in both groups throughout the study period. Although no significant differences were observed in the microbiome alpha- and beta-diversity (p > 0.05), the microbiome within study time points showed an increased beta-diversity in the CA group at 12 months (p = 0.019). CA abutments also showed a higher differential abundance of peri-implant pathogenic bacterial genera at 12 months. At the 6-month mark, the CA group exhibited a trend toward lower IL-1β levels compared with the CTR group (p = 0.072). No significant differences were noted in other clinical or radiographic parameters.

CONCLUSIONS

Citric acid passivation of definitive abutments does not enhance the microbiological or inflammatory profiles in the short term. Further studies are needed to explore the potential benefits of citric acid passivation on implant abutments.

TRIAL REGISTRATION

Initially registered on clinicatrials.gov (NCT05592327).

Effect of a 24-week supervised concurrent exercise intervention on fecal microbiota diversity and composition in young sedentary adults: The ACTIBATE randomized controlled trial

BACKGROUND

Numerous physiological responses to exercise are observed in humans, yet the effects of long-term exercise and varying intensities on the diversity and composition of human fecal microbiota remain unclear. We investigated the effect of a 24-week supervised concurrent exercise intervention, at moderate and vigorous intensities, on fecal microbiota diversity and composition in young adults.

METHODS

This ancillary study was based on data from the ACTIBATE randomized controlled trial (ClinicalTrials.gov ID: NCT02365129), and included adults (aged 18-25 years, 70 % female) that were randomized to (i) a control group (CON: no exercise, n = 20), (ii) a moderate-intensity exercise group (MOD-EX, n = 21), and (iii) a vigorous-intensity exercise group (VIG-EX, n = 20). Fecal samples were collected before and after the 24-week exercise intervention, and the diversity and composition of the fecal microbiota were analyzed by 16S rRNA sequencing. Inferential functional profiling of the fecal microbiota was performed and correlations between microbial changes and cardiometabolic outcomes were assessed.

RESULTS

Exercise did not modify beta or alpha diversities regardless of the intensity (all P ≥ 0.062). The relative abundance of the Erysipelotrichaceae family (Bacillota phylum) (-0.3 ± 1.2 %; P = 0.031) was however reduced in the VIG-EX group. Coprococcus was the only genus showed a significant difference between MOD-EX and VIG-EX after the intervention, with its relative abundance increasing in MOD-EX (+0.4 ± 0.6 %; P = 0.005). None of these changes were related to the exercise-induced cardiometabolic benefits (all P ≥ 0.05).

CONCLUSIONS

In young adults, a 24-week supervised concurrent exercise program, at moderate and vigorous intensities, resulted in minor changes in fecal microbiota composition, while neither alpha nor beta diversities were affected.

CLINICAL TRIAL REGISTRATION

ClinicalTrials.gov ID: NCT02365129.

Bidirectional interactions between St. John´s wort and gut microbiome: Potential implications on gut-brain-axis

Emerging evidence highlights the role of gut microbiome in mental health disorders, including depression, raising the question whether the action of antidepressants could be mediated, at least in part, via the microbiome-gut-brain axis. To explore this, we subjected a St. John's wort extract (STW 3-VI), clinically proven to be effective in mild to moderate depression, to a model of the upper and lower intestinal tract, including static in vitro predigestion followed by ex vivo incubation with human microbiota samples. To cover the interindividual diversity of gut microbiome composition, fecal samples from ten healthy volunteers were used. Although unchanged levels of most annotated compounds were observed during simulated upper intestinal tract digestion, incubation with fecal microbiota led to a significant change of the chemical profile of the extract. While hyperforins remained stable, flavonoids and hypericins were rapidly biotransformed, suggesting that they may act as prodrugs. Several metabolites were formed, many of which are known to be involved in gut-brain communication. Differential abundance analysis revealed significant changes in microbiome composition, particularly for taxa known to be potentially associated with depression. Among others, the Firmicutes/Bacteroidetes ratio, known to be lowered in depressive patients, was increased. Functional profiling revealed modulation of pathways involved in gut-brain communication, such as tyrosine and tryptophan metabolism. These bidirectional interactions suggest for the first time the gut microbiome as a potential mediator of the pharmacological effects of St. John's wort extracts via the microbiome-gut-brain axis.

Gut microbiota promotes cholesterol gallstone formation through the gut-metabolism-gene axis

BACKGROUND

Gallstone disease, arising from the interplay between host metabolism and gut microbiota, represents a significant health concern. Dysbiosis of the gut microbiome and disruptions in circadian rhythm contribute to the pathogenesis of gallstones. This study conducted a comprehensive analysis of gut microbiota and metabolites derived from stool and serum samples of 28 patients with cholesterol gallstones (CGS) and 19 healthy controls, employing methodologies such as 16S rRNA sequencing, metaproteomics, metabolomics, and host genetic analysis. Additionally, a retrospective cohort study was utilized to assess the efficacy of probiotics or ursodeoxycholic acid (UDCA) in preventing CGS formation post-bariatric surgery.

RESULTS

In CGS patients, gut microbiota diversity shifted, with harmful bacteria rising and beneficial ones declining. The altered microbiota primarily affected amino acid, lipid, nucleotide, and carbohydrate metabolism. Metabolic abnormalities were noted in amino acids, glucose, lipids, and bile acids with decreased levels of ursodeoxycholic, glycosodeoxycholic, and glycolithocholic acids, and increased glycohyodeoxycholic and allocholic acids. Glutamine and alanine levels dropped, while phenylalanine and tyrosine rosed. Animal studies confirmed gene changes in gallbladder tissues related to bile acid, energy, glucose, and lipid metabolism. Importantly, UDCA and probiotics effectively reduced CGS risk post-bariatric surgery, especially when combined.

CONCLUSIONS

Multi-omics can clarify CGS pathology, by focusing on the gut-metabolism-gene axis, paving the way for future studies on CGS prevention and treatment through gut microbiota or metabolic interventions.

Overwintering Does Not Affect Microbiota Diversity in Halyomorpha halys: Implications for Its Ecology and Management

Host-associated microbial communities play an important role in regulating many aspects of insect biology, but changes in this microbiota during diapause and overwintering are still largely unknown. Halyomorpha halys is an invasive agricultural pest characterised by a unique overwintering strategy where individuals aggregate and enter a state of dormancy, making it an excellent model to study the relationship between microbiota and diapause. We investigated the bacterial diversity of wild H. halys specimens before and after dormancy using 16S rRNA gene amplicon-sequencing. We found that microbiota varies between geographically neighbouring sampling locations, but there were no significant differences in microbial diversity or composition between populations sampled before and after diapause, despite stressful overwintering conditions. Such stability may relate to the highly specific taxa that dominate the stinkbug-associated microbial community. In addition, we did not detect any strong association of stink bugs with phytopathogens, but we found that two populations harboured Nosema maddoxi, a microsporidian pathogen of stink bugs. Our results are relevant to the assessment of accidental spillovers of microorganisms in newly invaded areas and to the implementation of the sterile insect technique based on mass trapping, irradiation, shipping and release after diapause of wild individuals.

Analysis of gill and skin microbiota in Larimichthys crocea reveals bacteria associated with cryptocaryoniasis resistance potential

Cryptocaryoniasis, caused by the ciliate parasite Cryptocaryon irritans, poses a significant threat to the large yellow croaker (Larimichthys crocea) in intensive marine aquaculture. This study explores the interaction between skin and gill microbiota and C. irritans infection, focusing on the role of commensal microbes in disease resistance. Fish were challenged with 100 theronts per gram of body weight, leading to substantial microbial dysbiosis, characterized by decreased alpha diversity and disrupted co-occurrence networks, particularly on the skin. Post-infection, Vibrio abundance significantly increased in both gills and skin, suggesting potential for secondary infections. Conversely, lower Vibrio levels correlated with higher populations of Bdellovibrio-like organisms (BALOs), which may play a beneficial role in microbial balance. Fish showed varying susceptibility, with mildly infected individuals exhibiting less histopathological damage and a stronger immune response, indicated by elevated interleukin-1β (IL-1β) and interleukin-8 (IL-8) levels. Correlation analyses revealed significant relationships between relative infection intensity (RII) and microbial composition, with certain bacteria known for anti-eukaryotic microbial properties showing negative correlations with RII. Additionally, the abundance of nitrogen-metabolizing bacteria also correlated negatively with RII. Functional predictions indicated increased bacterial genes related to denitrification and vitamin biosynthesis post-infection. Notably, Candidatus Midichloria was identified as a potential biomarker for C. irritans infection and is thought to be an endosymbiont of C. irritans, with its presence validated through PCR analysis. These findings illuminate microbial dynamics during C. irritans infection and suggest probiotic candidates for managing cryptocaryoniasis.

Composition of cercozoan diversity: Unravelling leaf, root, and soil specificity in crop plants

Protists are integral components of the plant holobiome, influencing plant growth and pathogenic pressure through their predatory activities. Wheat (Triticum aestivum), one of the most important crops globally, depends on favorable environmental conditions and effective pathogen management to achieve high yields. This study investigates the natural compositions of cercozoan diversity in winter wheat across various developmental stages (before sowing, at flowering, at ripening, and after harvesting) and plant compartments (leaves, roots, rhizosphere, and bulk soil) over two field seasons. The results revealed a pronounced dominance of the families Sandonidae, Allapsidae, Cercomonadidae, and Rhogostomidae across all samples. A strong enrichment of Sandonidae in leaf samples and Allapsidae in root samples was particularly notable. Importantly, no significant differences in cercozoan composition were observed across the different developmental stages of the plant. A comparative analysis between Triticum aestivum and Hordeum vulgare (barley) showed substantial similarity in cercozoan diversity across soil, leaf, and root compartments, with the only notable difference occurring in leaf samples during the ripening stage. The study concludes that cercozoan diversity in winter wheat is compartment-specific and remain stable across developmental stages. Further research is needed to explore cercozoan communities in greater taxonomic depth and to elucidate their ecological roles. Future studies should also assess whether similar patterns of compartmental variation and developmental consistency are observed in other major agricultural crops.

Invasive apple snails with their core microbes are underestimated hotspots for disseminating antibiotic resistance genes and virulence factors in aquatic habitats

Antibiotic resistance in pathogens is a threat to human health. The invasive apple snail (Pomacea canaliculata), widely distributed and linked to human activities, is a potential vector for human pathogens. However, its role in spreading antibiotic resistance genes (ARGs) is poorly understood. This study assessed the microbiological risk of this snail by sampling from five interconnected habitats: feces of invasive apple snails and native snails, ditch water, sediment, and soil. Using metagenomic and 16S rRNA sequencing, we analyzed the microbial communities and quantified the ARGs and virulence factors (VFs). Results showed that invasive apple snails carried significantly higher levels of ARGs and VFs compared with the native snails and environmental samples. ARGs and VFs were primarily found co-occurring in Aeromonas and Citrobacter freundii, with Aeromonas identified as the core microbe selected by invasive apple snails. Furthermore, the abundance and community dissimilarity of Aeromonas positively correlated with those of ARGs and VFs, both directly and indirectly through mobile genetic elements. This suggests Aeromonas may play a key role in disseminating ARGs and VFs across habitats. Overall, this study highlights the invasive apple snail as a significant vector for ARGs and virulent pathogens, providing critical insights for risk assessment and targeted management within the One Health framework.

Diversity and composition of ocular microbiota in contact lens wearers: Efficacy of liposomal ozonated oil

PURPOSE

To characterize the ocular surface microbiota in regular contact lens wearers with dry eyes and assess the effectiveness of reducing bacterial load using a liposomal ozonated oil solution.

METHODS

This prospective, longitudinal, controlled study randomized subjects into two groups. Group A (45 subjects) received hydroxypropylmethylcellulose (HPMC, Artific®), while Group B (41 subjects) received ozonated sunflower seed oil with soybean phospholipids (OSSO, Ozonest®). Microbial communities were analyzed via DNA metabarcoding of the 16S rRNA gene, and statistical analyses (alpha and beta diversity) were performed in R.

RESULTS

Both groups predominantly harbored Staphylococcus caprae, Streptococcus oralis, and Corynebacterium spp., with OSSO and HPMC users showing distinct bacterial profiles. Alpha diversity showed no significant differences, but beta diversity revealed differences in bacterial composition between the groups.

CONCLUSIONS

The results seem to indicate that the use of ozonized oil reduces the bacterial load compared to the solution used as a control.

Hand eczema and changes in the skin microbiome after 2 weeks of topical corticosteroid treatment

BACKGROUND

More than 50% of patients with hand eczema (HE) are colonized with Staphylococcus aureus. Comprehensive knowledge of the skin microbiome and its changes in patients with HE may provide insights into future potential therapeutical targets.

OBJECTIVE

To describe the skin microbiome in patients with moderate-to-severe chronic HE and assess its changes following treatment with topical corticosteroids (TCS).

METHODS

Bacterial samples were collected from lesional and nonlesional skin before and after 2 weeks of TCS treatment using ESwabs and analysed by 16S rRNA and tuf gene sequencing. Clinically, the disease severity was assessed by the Hand Eczema Severity Index (HECSI).

RESULTS

A cohort of 31 patients with HE were included and followed up. Compared to nonlesional skin, lesional skin differed in overall bacterial community composition (p = 0.02), displayed higher relative abundance of Staphylococcus, in particular S. aureus (p = 0.01) and lower abundance of Micrococcus (p = 0.02). As disease severity improved with treatment, these microbial characteristics on lesional skin shifted towards that of nonlesional skin on the hands.

CONCLUSIONS

The bacterial skin microbiome was altered in lesions of HE and partly driven by S. aureus colonization, however, shifted towards nonlesional skin following treatment. Our results emphasize the future possibilities for anti-S. aureus treatment strategies.

Gut microbiota and microbial metabolites are associated with body composition in 5-year-old children: A cross-sectional study in the Gen3G cohort

OBJECTIVE

To examine gut microbiota diversity, composition and metabolites in relation to overall mass (OM), fat mass (FM) and lean soft tissue mass (LSTM) measured by dual x-ray absorptiometry (DXA) in 5-year-old children.

METHODS

Mothers of the Gen3G cohort were enrolled prenatally in 2010-2013 in Quebec, Canada; 153 children from the cohort had data on gut microbiota and DXA scans at 5-6.4 years of age, and 140 also had plasma metabolite data. We characterized gut microbiota by 16S rRNA Illumina sequencing and metabolites by untargeted multiplatform mass spectrometry. We examined associations of microbial alpha diversity, beta diversity, composition (amplicon sequence variants; ASVs) and metabolites (microbial metabolites) with DXA measures, adjusting for age, sex, diet and drinking water.

RESULTS

Of the 153 children, 43.1% were female, and 96.1% self-identified as white. The median BMI was the 52nd percentile. Microbial richness (alpha diversity) was positively associated with OM, FM and LSTM. Of the 542 ASVs tested, 7 were associated with OM, 5 with FM and 4 with LSTM. One Veillonella ASV and two Blautia ASVs were significantly associated with all outcomes. Among 278 microbial metabolites, no metabolites were associated with FM, while glycoursodeoxycholate was associated with OM, and glycoursodeoxycholate, 3-hydroxybutyrate and gamma-glutamylalanine were associated with LSTM.

CONCLUSIONS

In 5-year-old children, gut microbiota alpha diversity, richness and specific gut microbes were associated with OM, FM and LSTM. Many of the associations followed a similar pattern for FM and LSTM, suggesting they may not be specific to adiposity but rather reflect overall growth.

Indole-3-propionic acid protects medium-diversity colitic mice via barrier enhancement preferentially over anti-inflammatory effects

Metabolites generated from the intestinal microbiota regulate local and distant tissues. One important metabolite generated from l-tryptophan is indole-3-propionic acid (IPA), which has been shown previously to regulate intestinal mucosal homeostasis in specific pathogen-free (SPF)-colonized animals through distinct receptor-mediated events. Interestingly, IPA levels are reduced in patients with inflammatory bowel disease (IBD). In the current study, we assessed whether IPA could improve colitis outcomes in the absence of its production by the microbiota. To do this, colitis was induced by dextran sulfate sodium (DSS) in gnotobiotic mice colonized with the 12-member stable defined moderately diverse microbiota mouse 2 (sDMDMm2) microbial consortium, which lacks the genes required for IPA generation. We found that these mice were exquisitely sensitive to DSS compared with SPF-colonized mice. However, IPA treatment significantly increased survival. Infiltrating immune cells in the colon were not altered by IPA treatment nor were there any remarkable changes in local and systemic inflammatory mediator levels. Nevertheless, IPA treatment changed the composition of the fecal microbiota and enhanced intestinal barrier function, demonstrated by a reduction in FITC-dextran flux and retainment of a bioluminescent Escherichia coli within the lumen of colitic mice. Together, our data suggest that IPA treatment in the context of its systemic depletion enhances barrier function and enhances survival in the presence of established inflammation. These data support continued assessment of IPA as a potential treatment for IBD.NEW & NOTEWORTHY Indole-3-propionic acid (IPA) is a metabolite produced by the intestinal microbiota that has been shown to elicit beneficial effects in the gastrointestinal (GI) tract that include regulating intestinal barrier function, reducing inflammation, and controlling immune responses that lead to fibrosis. In patients with inflammatory bowel disease (IBD), IPA levels are reduced. In the current study, we found that treating mice with IPA at the peak of intestinal inflammation improved clinical outcomes and disease.

Microbial communities and fatty acid markers across acidification and eutrophication extremes in a river influenced by mining activities

Microbial communities in combination with fatty acid and isotopic markers were studied seasonally to assess the effects of acid mine drainage (AMD) and nutrient loads in the Spree river. Negative values of δ15N, the bacterial and detrital markers 18: 1(n-7) and 18:1(n-9), pH values ∼3 and bacteria of the genera Ferrovum, Thiomonas, Acidocella, Acidiphilum, Syderoxydans and Galionella were characteristic of the AMD extreme. Potential iron-oxidizers may produce ferric ions and their precipitates may influence biogeochemical processes, while potential sulfur-oxidizers may contribute to elevated sulphate concentrations and challenge drinking water production in the Spree catchment. In this river, eutrophication was linked with polyunsaturated fatty acids (PUFA) enrichment and not with PUFA depletion as occurs in other freshwater systems. Elevated concentrations and proportions of PUFA as well as higher relative sequence abundance of cyanobacteria were characteristic of the highly eutrophic station, particularly during the phytoplankton bloom. The 18:5(n-3) from flagellates or dinoflagellates may indicate lipid anabolism and trophic upgrading processes. The dominance of the classes Bacteroidia, Gammaproteobacteria and Actinobacteria suggested eutrophic and changing hydrological conditions in the river. The microbial communities were better markers of seasonality than the biogeochemical markers and their combination offers an excellent resolution for the study of the ecology and biogeochemistry of water courses. The expected decreased runoff under climate-driven scenarios may worsen the AMD pollution and eutrophication problems and signify a considerable challenge for water management.

More Than a Stick in the Mud: Eelgrass Leaf and Root Bacterial Communities Are Distinct From Those on Physical Mimics

We examine the role of physical structure versus biotic interactions in structuring host-associated microbial communities on a marine angiosperm, Zostera marina, eelgrass. Across several months and sites, we compared microbiomes on physical mimics of eelgrass roots and leaves to those on intact plants. We find large, consistent differences in the microbiome of mimics and plants, especially on roots, but also on leaves. Key taxa that are more abundant on leaves have been associated with microalgal and macroalgal disease and merit further investigation to determine their role in mediating plant-microalgal-pathogen interactions. Root associated taxa were associated with sulphur and nitrogen cycling, potentially ameliorating environmental stresses for the plant. Our work identifies targets for future work on the functional role of the seagrass microbiome in promoting the success of these angiosperms in the sea through identifying components of microbial communities that are specific to seagrasses.

Microbial volatile organic compounds produced during the anaerobic digestion process can serve as potential indicators of microbial community stability

The principal challenge in monitoring anaerobic digestion (AD) processes lies in the fact that conventional operational parameters (pH, volatile fatty acids, etc.) frequently lag behind the actual microbial performance. This study proposes microbial volatile organic compounds (mVOCs) as a novel indicator reflecting the species-specific characteristics of microorganisms and evaluates their ability to indicate the stability of AD processes in response to organic loading rate (OLR) perturbations. Both gradual and pulsed increases in OLR concentration resulted in an instantaneous change in production, which was also reflected in the variation of mVOCs. Furthermore, alkanes, alkenes, alcohols, aldehydes, ketones, and aromatic compounds exhibited a more pronounced response to OLR perturbations. Additionally, these mVOCs presented a strong co-occurrence with specific bacterial genera (Syntrophomonas, Defluviitoga, and Fastidiosipila) and archaeal genera (Methanobacterium, Methanoculleus, and Methanosarcina), thus positioning them as crucial producers of mVOCs. This suggests that mVOCs could function as biochemical indicators of AD performance and facilitate the understanding of what mVOCs are produced, and who the contributing microorganisms are. Further research is required to elucidate the resolution of mVOCs regarding other AD process perturbations, as well as to establish the optimal measurement frequencies and reference values.

Young maize plants impact the bacterial community in Australian cotton-sown vertisol more than agricultural practices

Changes in soil characteristics due to varying farming practices can modify the structure of bacterial communities. However, it remains uncertain whether bacterial groups that break down organic material are similarly impacted. We examined changes in the bacterial community by pyrosequencing the 16S rRNA gene when young maize plants, their neutral detergent fibre fraction, or urea were applied to an Australian Vertisol. This soil was managed with either conventional tillage with continuous cotton, minimum tillage with continuous cotton, or a wheat-cotton rotation. The soil organic carbon content was 1.4 times higher in the wheat-cotton rotation than in the conventional tillage with continuous cotton treatment. Approximately 41.6% of the organic carbon was added with maize plants, and 13.1% of the neutral detergent fibre fraction was mineralized after 28 days. The application of young maize plants and the neutral detergent fibre fraction significantly altered the bacterial community and the presumed metabolic functional structure, but urea did not. Many bacterial groups, such as Streptomyces, Nocardioides, and Kribbella, and presumed metabolic functions were enriched by the application of organic material, but less so by urea. We found that a limited number of bacterial groups and presumed metabolic functions were affected in an irrigated Vertisol by the different cotton farming systems, but many were strongly affected by the application of maize plants or its neutral detergent fibre.

New insights into Peniophora crassitunicata and its co-inoculation with commercial microbial inoculant accelerating lignocellulose degradation and compost maturation during orchard wastes composting

Lignocellulosic composting has been widely promoted in the utilization of agricultural wastes, while few focus on orchard lignocellulosic wastes in the fruit industry. Peniophora is a laccase hyper-producer highly efficient in lignin degradation, yet its application in lignocellulosic composting has not been investigated. Here, an aerobic composting experiment was conducted to investigate the effects of inoculation with Peniophora crassitunicata and a commercial microbial inoculant (mainly Bacillus and Aspergillus) on grape (Vitis Vinifera L.) orchard lignocellulosic wastes degradation and the underlying mechanisms. The inoculation with P. crassitunicata, both individually (H) and in combination with the commercial microbial inoculant (HS), enhanced lignocellulose degradation efficiency. Notably, the co-inoculation exhibited higher lignocellulose degradation ratios and higher lignocellulosic enzyme activities compared to other treatments. The compost piles with co-inoculation experienced a more rapid temperature rise, a longer duration (15 days) of high temperatures, lower pH, and lower electrical conductivity (EC). Firmicutes (e.g. Bacillus, Paenibacillus) and Ascomycota (e.g. Aspergillus) along with Bacteroidota, Actinobacteriota, and Basidiomycota (e.g. Peniophora) dominated the microbial community in compost; carbohydrate metabolism dominated microbial metabolic pathways at the thermophilic phase, highlighting an active microbial community. As compost processed, highly mature and non-toxic compost products were finally obtained for the co-inoculation, with a pH of 7.87, C/N ratio of 13.5, NH4+-N/NO3‾-N ratio of 0.21-0.41, EC of 0.90 mS cm-1, and germination index of 149 %. The co-inoculation of P. crassitunicata with the commercial microbial inoculant effectively accelerated lignocellulose degradation and compost maturation, producing a friendly and non-toxic organic fertilizer for agricultural applications and thereby providing a new strategy for orchard wastes management and agricultural applications.

Freshwater fish community assessment using eDNA metabarcoding vs. capture-based methods: Differences in efficiency and resolution coupled to habitat and ecology

Environmental DNA (eDNA) metabarcoding has revolutionized ecological and environmental research by describing communities without relying on direct observations, making it a powerful, non-invasive, and cost-effective tool in biodiversity monitoring. However, the adoption of eDNA as a standard protocol in long-term monitoring programs, which have traditionally relied on capture-based methods, presents challenges in terms of data comparability. Here, we compared freshwater fish communities assessed through eDNA metabarcoding and electrofishing, across 35 sampling sites in the lower Tagus River basin, Portugal. For the majority of species or species-groups analysed individually (13 out of 17), a significant correspondence was observed between electrofishing and eDNA metabarcoding detections. A weaker correspondence was found between the number of specimens captured by electrofishing with the number of eDNA metabarcoding reads, with seven out of 13 taxa showing significant relationships. Species richness estimates based on the two methods were very similar at the basin level. The methods yielded significantly different species compositions, although these differences were driven by samples collected in the Tagus main channel, which is wider and has higher flow rates than tributaries. Benthic and shoreline fish communities showed similar species composition in the two methods, but this was not the case for pelagic communities, probably due to the higher water turnover of the pelagic zone and electrofishing inefficiency. Our results highlight the high potential of eDNA metabarcoding as a complementary method to electrofishing for freshwater fish monitoring, though further validation is needed to assess biases related to site-specific hydrological conditions and the ecology of the target species.

Molecular assessment of oyster microbiomes and viromes reveals their potential as pathogen and ecological sentinels

Oyster aquaculture world-wide is a booming industry that can provide many benefits to coastal habitats, including economic, ecosystem-level, and cultural benefits. Oysters present several risks for human consumption, including transmission of parasites, and bacterial and viral pathogens. Oyster microbiomes are well-defined, but their connection to the incidence of pathogens, humans or others, is unclear. Furthermore, viruses associated with oysters are largely unknown, and their connection to humans, animals, and ecosystem health has not been explored. Here, we employed a One Health framework and modern molecular techniques, including 16S rRNA amplicon and metagenomic sequencing, to identify links between changes in the microbial and viral communities associated with oysters and the incidence of pathogens detected in oyster tissues and their surrounding environments. In addition, we adapted the BioFire® FilmArray®, commonly used in hospitals, to determine the presence of human pathogens within the sampled oysters. We detected known human pathogens in 50 % of the oysters tested. Within the genomic datasets, we noted that pathogens of humans, animals, and plants in oysters were shared with the nearby water and sediments, suggesting a sink-source dynamic between the oysters and their surroundings. 16S rRNA gene analysis revealed that while oysters share common microbial constituents with their surrounding environments, they enrich for certain bacteria such as Mycoplasmatales, Fusobacteriales, and Spirochaetales. On the contrary, we found that oyster viromes harbored the same viruses in near equal relative abundances as their surrounding environments. Our results show how oysters could be used not only to determine the risk of human pathogens within coastal estuaries but also how oyster viruses could be used as ecosystem-level sentinels.

Comprehensive Analysis of Orthodontic Treatment Effects on the Oral Microbiome, Metabolome, and Associated Health Indicators

INTRODUCTION AND AIMS

Effects of orthodontic treatments on oral health, particularly on the microbiome and metabolome, are not well understood, and this study aims to clarify these influences using multi-omics approaches.

METHODS

We used 16SrRNA sequencing to analyze oral microbiota and untargeted metabolomics for metabolic profiling, comparing clear aligners (CAs) and fixed appliances (FAs) in healthy and unhealthy oral environments.

RESULTS

We found CAs significantly improve oral health markers-including reduced plaque accumulation, enamel demineralization, microbiome alpha diversity, and microbial heterogeneity, especially in unhealthy oral environments. Orthodontic treatment type and overall oral health status significantly altered the oral microbiota structure and metabolite composition. Notably, the effect of orthodontic methods was more pronounced on metabolome than on microbiome. There's a strong link between changes in oral microbiome, health status, and hygiene habits. For example, Prevotella and Treponema were linked to poor oral health indicators, whereas Rothia, Granulicatella, and Streptococcus were associated with good oral hygiene indicators. Machine learning analysis identified 13 key metabolites, including cholylarginine, alpha-CEHC glucuronide, 2-hydroxypentanoic acid, Cer (d17:1/6 keto-PGF1alpha), and LysoPE (15:0/0:0), which were associated with inflammatory responses and served as predictive markers for poor oral health. These metabolites were closely correlated with specific microbial species enriched in oral environment, including Rothia, Prevotella, and Anaeroglobus, suggesting their potential as biomarkers for oral health monitoring. KEGG enrichment revealed differential metabolites were significantly enriched in alkaloid biosynthesis pathways, particularly map01064, which is crucial for polyamine synthesis related to bacterial activities.

CONCLUSION

CAs significantly improve oral health markers, particularly affecting the metabolome more than the microbiome, with key metabolites and microbial species serving as potential biomarkers for oral health monitoring.

CLINICAL RELEVANCE

This study provides comprehensive insights into interactions among orthodontic treatments, oral health status, microbial, and metabolic dynamics, offering foundation for developing personalized strategies in oral health management and orthodontic care.

Effects of a high-fiber, high-fruit and high-vegetable, low-fat dietary intervention on the rectal tissue microbiome

BACKGROUND

Emerging evidence suggests that bacteria residing in colorectal tissue are plausibly associated with colorectal cancer. Prior studies investigated the effects of dietary interventions on the fecal microbiome, but few assessed colorectal tissue microbiome endpoints. We investigated the effects of a high-fiber, high-fruit, high-vegetable, and low-fat dietary intervention on the rectal tissue microbiome in the Polyp Prevention Trial (PPT).

METHODS

PPT is a 4-year randomized clinical trial with intervention goals of consuming (1) at least 18 g of fiber per 1000 kcal/day; (2) at least 3.5 servings of fruits and vegetables per 1000 kcal/day; and (3) no more than 20% of kcal/day from fat. Using 16S ribosomal RNA gene sequencing, we characterized bacteria in rectal biopsies collected at baseline and the end of years 1 and 4 (n = 233 in intervention arm and n = 222 in control arm). We estimated effects of the intervention on alpha and beta diversity and relative abundance of a priori-selected bacteria using repeated-measures linear mixed-effects models.

RESULTS

The intervention did not statistically significantly modify rectal tissue alpha diversity. Compared with the control arm, relative abundance of a priori-selected Porphyromonas (absolute intervention effects [standard errors] at T1 vs T0 = -0.24 [0.07] and T4 vs T0 = -0.12 [0.07]; P = .004) and Prevotella (absolute intervention effects at T1 vs T0 = -0.40 [0.14] and at T4 vs T0 = -0.32 [0.15]; P = .01) were more strongly decreased in the intervention arm.

CONCLUSION

The PPT intervention did not influence rectal tissue microbiome diversity or the relative abundance of most bacteria, except for 2 oral-originating bacteria that were previously associated with colorectal cancer presence.

Comparative analysis of deep dentinal caries microbiota in teeth with normal pulp, reversible pulpitis, symptomatic and asymptomatic irreversible pulpitis

AIM

To characterize the deep dentinal caries microbiota in teeth diagnosed with normal pulp with deep caries (NP), reversible pulpitis (RP), symptomatic irreversible pulpitis (SIP), and asymptomatic irreversible pulpitis (AIP), and to identify potential key pathogens associated with pulpitis progression, exploring their roles in disease advancement.

METHODOLOGY

In this cross-sectional study, we collected 108 dentinal caries samples, categorized into NP (n = 27), RP (n = 27), SIP (n = 27), and AIP (n = 27), according to the American Association of Endodontists' diagnostic criteria. 2 NP samples and 2 RP samples were excluded due to contamination. Samples were processed using Illumina MiSeq high-throughput sequencing. Alpha and beta diversity, taxa abundance differences, co-occurrence network analysis, and functional prediction were evaluated. Correlation analysis between the abundance of bacteria associated with clinical diagnosis, clinical signs, and pulp exposure status was performed with Spearman analysis and the Mantel test.

RESULTS

The bacteriome of deep dentinal caries exhibited statistically significant differences among NP, RP, SIP, and AIP groups. NP and RP showed similar microbial community structures, with comparable alpha diversity, beta diversity, bacterial phenotypes, functions, and network structures. In contrast, AIP and SIP displayed distinct microbial community profiles. AIP was characterized by higher alpha diversity and a greater abundance of gram-negative bacteria, with Propionibacterium and Prevotella_7 identified as bacteria associated with AIP pathogenesis. On the other hand, SIP showed lower alpha diversity and a higher abundance of facultative anaerobes, with Lactobacillus and Limosilactobacillus identified as bacteria associated with SIP pathogenesis. Fusobacterium, Prevotella, Treponema, and Selenomonas were identified as bacteria associated with both AIP and SIP. Compared to NP and RP, the microbial networks in AIP and SIP are more complex and contain more gram-negative endodontic pathogens. These pathogens form complex positive correlations with each other and numerous negative correlations with lactic acid bacteria.

CONCLUSIONS

The bacteriome of deep dentinal caries differs significantly across teeth diagnosed with NP, RP, AIP, and SIP. NP and RP exhibit similar microbial communities, whereas SIP and AIP display distinct microbial profiles.

Comprehensive profiling of smoked cheese from raw goat's milk handcrafted in Lower Silesia (Poland)

This study aimed to explore the distinctive characteristics of smoked cheese made from raw goat's milk, labelled "Produkt polski" and crafted in the Lower Silesia region of Poland. A comprehensive range of analyses was performed, including physico-chemical and morpho-textural evaluations, microbial counts, and a metataxonomic investigation to uncover the microbial diversity occurring in the cheese. The volatile organic compounds (VOCs) and the total fatty acid composition were also determined. Additionally, a consumer test based on a hedonic scale was conducted to capture the subjective experience of the product's appeal. The cheese samples revealed water activity (aw) ranging between 0.901 ± 0.003 and 0.926 ± 0.001, with pH levels between 5.08 ± 0.15 and 5.44 ± 0.01. Regarding fatty acid composition, all of the smoked cheeses displayed a similar profile, with saturated fatty acids dominating (SFA, ∼75 %), followed by monounsaturated (MUFA, ∼22 %) and polyunsaturated fatty acids (PUFA, ∼3 %). Microbial analysis revealed thriving populations, including lactococci (up to 8.63 ± 0.07 log colony-forming units g-1), thermophilic cocci (up to 6.85 ± 0.08 log cfu g-1), lactobacilli (up to 9.50 ± 0.04 log cfu g-1), enterococci (up to 5.93 ± 0.00 log cfu g-1), and eumycetes (up to 2.68 ± 0.48 log cfu g-1). Metataxonomic analysis identified dominant bacterial taxa such as Lactobacillus, Lactococcus, and Leuconostoc, as well as Carnobacterium and Lacticaseibacillus. Among the 24 lactic acid bacteria cultures isolated, the closest relatives to Enterococcus, Lacticaseibacillus, Lactococcus, and Leuconostoc were identified. Some isolates demonstrated promising pro-technological traits, positioning them as potential adjunct cultures for improving fermented dairy products. The volatile profile of the smoked cheese was particularly intriguing, with a total of 87 VOCs detected, categorized as esters (18), ketones (14), hydrocarbons (11), acids (10), phenols (11), alcohols (8), furans (5), lactones (4), aldehydes (3), and other compounds (3). Sensory evaluation revealed a moderate appreciation for the cheese's appearance, whereas the smoked flavor elicited the most varied scores, highlighting its strong impact on consumer preference.

Prospective Comparative Study of an Oral Synbiotic and a Myoinositol-Based Herbal Supplement in Modifying Hormone Levels and the Gut Microbiome in Non-cystic Acne

INTRODUCTION

Acne pathogenesis is multifactorial, involving systemic factors including gut dysbiosis, hormones, and chronic inflammation. Probiotics, myoinositol, and plant-derived molecules may modulate acne by targeting these factors. The objective is to compare a synbiotic containing herbs against a myoinositol-based herbal supplement on how they influence acne, the gut microbiome, short chain fatty acids (SCFAs), and hormonal profiles.

METHODS

This was an 8-week, randomized study involving 36 male and female patients aged 12 to 45 years with non-cystic acne. Subjects received either a synbiotic or a myoinositol-based herbal supplement (MBHS). Acne lesions were counted, stool samples were collected for gut microbiome and SCFA analyses, and hormone collections were performed at baseline, 4, and 8 weeks.

RESULTS

Several gut bacteria increased by at least threefold at both week 4 and 8 in the synbiotic (Erysipelatoclostridium merdavium, Blautia argi, Faecalibacterium prausnitzii, Prevotella copri, Streptococcus sp001556435, Blautia sp900541955) and MBHS group (Megamonas funiformis, Ligilactobacillus ruminis, Prevotella ssp015074785, Prevotella copri, Gca-900199835 sp900176495). Acne lesion counts decreased significantly in both groups at week 4 (p < 0.0001) and week 8 (synbiotic, p < 0.0001; MBHS, p < 0.0001). There were significant and trending increases in stool and plasma SCFAs in both cohorts at week 4 and 8. After 8 weeks of MBHS, 17-OHP and androstenedione significantly decreased from 27.3 to 11.3 pg/ml (p = 0.001) and 94.9 to 68.0 pg/ml (p = 0.04), respectively.

CONCLUSION

Both the synbiotic and MBHS improved gut health, augmented SCFAs, and reduced lesion counts in those with non-cystic acne. The MBHS may act by reducing hormone levels of 17-OHP and androstenedione.

CLINICAL TRIAL REGISTRATION

www.

CLINICALTRIALS

gov (NCT05919810).

Inhibitory control is related to fecal short-chain fatty acid concentrations in adults with overweight and obesity

Obesity is a pro-inflammatory condition with negative effects on executive functioning. Increased inflammation dysregulates gastrointestinal homeostasis and alters microbiota community composition. The gut microbiota produce immunomodulatory short-chain fatty acids (SCFA) that have been related to cognition in obesity, but the neural effects are not explored. Here, we hypothesized that greater fecal SCFA would be positively related to neuroelectric markers of inhibitory control and conflict monitoring in obesity. A cross-sectional cohort of 87 adults (35 ± 6 years, 53 females) with overweight and obesity (BMI = 32 ± 6 kg/m2) provided fresh fecal samples and participated in cognitive testing to assess response inhibition and conflict monitoring with electroencephalographic recording. Linear regressions, controlling for age, sex, BMI, and energy-adjusted dietary fiber intake, revealed positive relationships between NoGo N2 mean amplitude and fecal SCFA concentrations. Linear discriminant analysis effect size (LEfSe) revealed 16 amplicon sequence variants differentially abundant between high and low butyrate groups with Roseburia and Adlercreutzia individually related to NoGo N2 mean amplitude in MaAsLin2 modeling. Thus, greater fecal SCFA concentrations and SCFA producing microbiota (i.e., Roseburia) were related to markers of superior conflict monitoring in the NoGo task when adjusting for key covariates. These data highlight key associations between bacterial derived gut signaling molecules and neural regulation in cognitive domains particularly relevant to weight status that warrant further investigation.

Ecological outcomes of seagrass restoration in the Bohai Sea: Five-year shifts in sediment carbon, microbial diversity, and macrobenthic communities underscore the need for long-term monitoring

Seagrass meadow restoration is essential for bolstering ecosystem functions, including biodiversity and carbon sequestration. This study evaluates the ecological impacts of a five-year seagrass restoration effort in the Bohai Sea, with a focus on sediment organic carbon (SOC) storage, microbial diversity, and macrobenthic communities. Using sediment analysis, microbial DNA sequencing, and macrobenthic assessments, we explored how restoration influenced these key parameters. While no statistically significant increases in SOC were observed, trends suggest a gradual rise in carbon accumulation in restored areas. Microbial diversity in the restored site more closely resembled that of natural seagrass meadows, and macrobenthic species number and Margalef richness showed improvement compared to those in bare sediments. These findings indicate that although immediate, significant shifts may be subtle, seagrass restoration contributes to incremental gains in carbon storage and biodiversity. The study underscores the importance of long-term monitoring to fully capture the delayed ecological benefits of restoration efforts.

High-resolution DNA metabarcoding of modern surface sediments uncovers a diverse assemblage of dinoflagellate cysts in the Pacific and Arctic Oceans

Resting cysts of dinoflagellates can persist in sediments, seeding harmful algal blooms (HABs). A DNA metabarcoding approach was employed, targeting the large subunit ribosomal (LSU D1-D2) and the internal transcribed spacer (ITS1) to investigate the diversity and biogeography of dinoflagellate cysts from the South China Sea to the Chukchi Sea. The LSU and ITS1 datasets identified 196 and 118 species, respectively, with only 59 dinoflagellate cyst species revealed by both approaches. Eleven cyst species of potentially toxic dinoflagellates and 82 species previously unknown as cyst producers were detected. Cysts of Heterocapsa cf. horiguchii, Heterocapsa minima, Heterocapsa iwatakii, Heterocapsa rotundata, and Heterocapsa steinii were documented through germination for the first time, with the latter three species also detected via metabarcoding. This study provides critical insights into the diversity and biogeography of dinoflagellate cysts by highlighting the complementary detection capabilities of LSU and ITS1 molecular markers and their trans-latitudinal distribution patterns. The identification of potentially toxic cysts and their ecological distributions offers crucial information on the ecology of harmful dinoflagellates. These findings underscore the importance of molecular techniques in monitoring dinoflagellate cysts.

Host-Microbiome Associations of Native and Invasive Small Mammals Across a Tropical Urban-Rural Ecotone

Global change and urbanisation profoundly alter wildlife habitats, driving native animals into novel habitats while increasing the co-occurrence between native and invasive species. Host-microbiome associations are shaped by host traits and environmental features, but little is known about their plasticity in co-occurring native and invasive species across urban-rural gradients. Here, we explored gut microbiomes of four sympatric small mammal species along an urban-rural ecotone in Borneo, one of the planet's oldest rainforest regions experiencing recent urban expansion. Host species identity was the strongest determinant of microbiome composition, while land use and spatial proximity shaped microbiome similarity within and among the three rat species. The urban-dwelling rat Rattus rattus had a microbiome composition more similar to that of the native, urban-adapted rat Sundamys muelleri (R. rattus' strongest environmental niche overlap), than to the closely related urban-dwelling R. norvegicus. The urban-dwelling shrew Suncus murinus presented the most distinct microbiome. The microbiome of R. norvegicus was the most sensitive to land use intensity, exhibiting significant alterations in composition and bacterial abundance across the ecotone. Our findings suggest that environmental niche overlap among native and invasive species promotes similar gut microbiomes. Even for omnivorous urban-dwellers with a worldwide distribution like R. norvegicus, gut microbiomes may change across fine-scale environmental gradients. Future research needs to confirm whether land use intensity can be a strong selective force on mammalian gut microbiomes, influencing the way in which native and invasive species are able to exploit novel environments.

Urbanisation Affects Millipede Gut Microbiota Communities by Impeding Host Gene Flow

Urbanisation leads to the alteration of the living environment of soil fauna and isolates them, significantly influencing the evolutionary processes of soil fauna. Faunal gut microbiota serves to bridge hosts with changing environments; thus, they are viable indicators of host adaptation. For this study, we investigated how urbanisation affects the gut microbiota and population genetics of Spirobolus bungii. The results revealed that urbanisation did not affect the genetic diversity of S. bungii populations but acted as a barrier, which hindered its gene flow. Genetic differentiation was associated with the compositional similarity of gut microbiota among populations; however, environmental distinctions had no impact. Our findings highlighted that gene flow between populations was a critical factor, which supported the premise that urbanisation influences the gut microbiota compositions of species. This study contributes to a deeper understanding of the mechanisms that underlie changes in faunal gut microbiota driven by gene flow in the context of urbanisation.

Insight into endophytic microbiota-driven geographical and bioactive signatures toward a novel quality assessment model for Codonopsis Radix

Codonopsis Radix, a medicinal and dietary herb in traditional Chinese medicine, largely owes its pharmacological efficacy to both intrinsic phytochemistry and symbiotic interactions with plant-associated microbes. Here, we deciphered the geo-environmental regulation of Codonopsis Radix's endophytic microbiota across four major production regions using 16S rRNA/ITS sequencing and bioactive compound profiling. Results demonstrated that the planting environment significantly shaped the endophytic community of Codonopsis Radix, where Bifidobacteriaceae and Muribaculaceae exhibited the strongest correlations with its bioactive components. Monolobus and Bradyrhizobium not only exhibit distinct associations with Lobetyolin and Atractylenolide III respectively, but also demonstrate significant correlations with the key biosynthetic pathways of these compounds. Leveraging machine learning, we developed the first microbiota-driven quality assessment model, achieving 100.0% and 85.7% prediction accuracies for Lobetyolin and Atractylenolide III respectively, using Random Forest algorithms. This dual-metric framework-integrating microbial signatures with chemical profiles-establishes a novel paradigm for Codonopsis Radix quality control, bridging ecological insights with precision agriculture. Our findings illuminate the microbiota's role as a biosynthetic orchestrator in geoherbalism, offering actionable strategies for sustainable cultivation and standardized production of Codonopsis Radix.

Nutritional status reshapes gut microbiota composition in adolescent Afghan refugees in Peshawar, Pakistan

Although the human gut microbiome, and its role in health and disease, have been extensively studied in different populations, a comprehensive assessment of gut microbiome composition has not been performed in vulnerable refugee populations. In this study, we hypothesized that overall nutritional status, as indicated by serum micronutrients concentrations, is an important driver of variations in gut microbiome composition. Therefore, gut-microbiome diversity and associated demographic, health and nutritional factors were assessed in adolescent Afghan refugees (n=206). Blood and faecal samples were collected and analysed for nutrition status markers and 16S rRNA gene amplicon-based community profiling, respectively. Bioinformatics and statistical analysis were performed using SPSS, QIIME and R. Overall, 56 distinct phyla, 117 families and 252 genera were identified in the faecal samples. Bacterial diversity (alpha and beta diversity) and the Firmicutes:Bacteroidetes (F/B) ratio were significantly higher in the 15 to 19 year old age group (cf. the 10-14 age group) but were lower in the underweight and vitamin D deficient groups. Furthermore, LEfSe analysis identified significant differences in the relative abundance of bacterial genera based on age, BMI and micronutrient (vitamins and minerals) status. These results were further scrutinised by correlation analysis which confirmed that age, BMI and micronutrient status show significant correlations with F/B ratio and the relative abundance of specific bacterial taxa. Collectively, our study provides the first indication of how the gut-microbiota profile of adolescent Afghan refugees is associated with a range of nutrition-status factors. These findings can thus provide a basis for translational microbiota research aimed at improving the health of such understudied and vulnerable populations.

Testing the Effectiveness of a Commercially Sold Probiotic on Restoring the Gut Microbiota of Honey Bees: a Field Study

Antibiotic use in apiculture is often necessary to ensure the survival of honey bee colonies. However, beekeepers are faced with the dilemma of needing to combat bacterial brood infections while also knowing that antibiotics kill beneficial bacteria important for bee health. In recent years, bee probiotics have become increasingly purchased by beekeepers because of product claims like being able to "replenish the microbes lost due to agricultural modifications of honey bees' environment" or "promote optimal gut health." Unfortunately, these products have little scientific evidence to support their efficacy, and previous lab experiments have refuted some of their claims. Here, we performed hive-level field experiments to test the effectiveness of SuperDFM-HoneyBee™ - the most commonly purchased honey bee probiotic in the United States - on restoring the honey bee gut microbiota after antibiotic treatment. We found slight but significant changes in the microbiota composition of bees following oxytetracycline (TerraPro) treatment and no difference between the microbiota of antibiotic treated bees with or without subsequent probiotic supplementation. Moreover, the microorganisms in the probiotic supplement were never found in the guts of the worker bee samples. These results highlight that more research is needed to test the efficacy and outcomes of currently available commercial honey bee probiotic supplements.

Effects of probiotic treatment on the intestinal microbial community of Haliotis diversicolor

Probiotic treatment is an effective method for enhancing growth performance and improving intestinal flora in aquaculture species. This study examined the effects of three candidate-probiotics (Bacillus, photosynthetic bacteria, and Lactobacillus) on the rate of weight gain and the intestinal flora of abalone juveniles. Haliotis diversicolor was fed a probiotic-supplemented diet for 30 days. The abalones fed with Lactobacillus showed a more significant weight gain rate than those in the Bacillus, photosynthetic bacteria, and control groups. Through 16S rRNA high-throughput sequencing, 12,490 amplicon sequence variants (ASVs) were obtained from the abalone intestinal tract microbiome. After a short feeding period (5 days), the Bacillus and photosynthetic bacteria-treated groups showed an increased abundance of Proteobacteria in the abalone digestive tract. In the Lactobacillus-treated group, the quantity of Proteobacteria decreased, and the abundance of Bacteroidota increased. After 30 days of feeding, the abundance of Proteobacteria and Bacteroidetes at the phylum level was more significant in the Bacillus-treated group and photosynthetic bacteria-treated group than in the controls. The Lactobacillus-treated group showed an increase in the quantity of Proteobacteria and Chloroflexi. The dominant flora of the three probiotic treated groups changed slightly with respect to the control group. After a short period of feeding (5 days), the abundance of Rhodobacteraceae (at the genus level) in the abalone digestive tract increased in the Bacillus- and photosynthetic bacteria-treated groups, whereas in the Lactobacillus-treated group, Rhodobacteraceae decreased, and Maribacter increased in abundance. After 30 days of feeding, Bacteroidetes and Ruegeria were higher in the Bacillus-treated group than in the control group. Marinirhabdus and Bacteroidetes increased in the photosynthetic bacteria-treated group, and Roseivivax and Ruegeria increased in the Lactobacillus-treated group. The three probiotic-treated groups had higher microbial diversity than the control group. Therefore, our findings confirmed that adding Bacillus, photosynthetic bacteria, and Lactobacillus to the abalone diet increased abalones' weight gain rate and altered their intestinal microbiome composition.

Soil microbial responses to multiple global change factors as assessed by metagenomics

Anthropogenic activities impose multiple concurrent pressures on soils globally, but responses of soil microbes to multiple global change factors are poorly understood. Here, we apply 10 treatments (warming, drought, nitrogen deposition, salinity, heavy metal, microplastics, antibiotics, fungicides, herbicides and insecticides) individually and in combinations of 8 factors to soil samples, and monitor their bacterial and viral composition by metagenomic analysis. We recover 742 mostly unknown bacterial and 1865 viral Metagenome-Assembled Genomes (MAGs), and leverage them to describe microbial populations under different treatment conditions. The application of multiple factors selects for prokaryotic and viral communities different from any individual factor, favouring the proliferation of potentially pathogenic mycobacteria and novel phages, which apparently play a role in shaping prokaryote communities. We also build a 25 M gene catalog to show that multiple factors select for metabolically diverse, sessile and non-biofilm-forming bacteria with a high load of antibiotic resistance genes. Finally, we show that novel genes are relevant for understanding microbial response to global change. Our study indicates that multiple factors impose selective pressures on soil prokaryotes and viruses not observed at the individual factor level, and emphasizes the need of studying the effect of concurrent global change treatments.

Dysbiotic Microbiome-Metabolome Axis in Childhood Obesity and Metabolic Syndrome

The prevalence of childhood metabolic syndrome (MetS) and obesity is rising, with emerging evidence suggesting these conditions negatively affect oral health. However, the underlying molecular determinants are unclear. This study investigated the oral microbiome, inflammatory markers, and metabolites in children with obesity and MetS to explore the interrelationships between systemic disease and oral health. We recruited 76 periodontally healthy, caries-free individuals aged 10 to 17 y into 3 groups: MetS (29), metabolically healthy obesity (MHO) (30), and normal-weight healthy (NWH) controls (17). Unstimulated saliva was collected. Bacterial DNA was isolated, V3-V4 regions amplified, and 16S sequencing performed on the Illumina MiSeq platform. Sequences were annotated against the HOMD database. Multiplex assays quantified adipokines and cytokines, with significance determined by Tukey honestly significant difference. Gas chromatography/mass spectrometry identified metabolite peaks that were annotated against the Small Molecule Pathway Database, with enrichment analysis determining significance. Integrated multiomics analysis was performed using multiblock sparse partial least squares regression discriminant analysis. The MHO and MetS groups demonstrated lower abundances of Streptococcus, Actinomyces, and Schaalia and higher levels of Aggregatibacter, Campylobacter, Alloprevotella, Prevotella, Leptotrichia, and Porphyromonas compared with NWH, despite similar clinical oral status in all cohorts. MetS and MHO also had increased leptin, tumor necrosis factor-α, interleukin (IL)-1β, and IL-15 and decreased adiponectin levels versus NWH. Disease-associated metabolites, including glutamate, cholesterol, isoleucine, tyrosine, phenylalanine, serine, and indoleacetic acid, were significantly enriched in the MetS and MHO groups. Integrated multiomic analysis identified key correlations in the saliva of subjects with metabolic health or disease. Decreases in health-associated species and increases in proinflammatory cytokines and disease-associated metabolites in the saliva of MetS and obese adolescents with clinical oral health indicate an "at-risk" environment, potentially explaining their elevated risk for oral diseases. Increased salivary leptin and decreased adiponectin levels highlight the potential of saliva as a noninvasive biomarker source for childhood MetS.

Drinking Water Temperature Impacts the Pathogenesis of DSS-Induced Ulcerative Colitis by Regulating Intestinal Barrier Function and Remodeling the Gut Microbiota Composition

Environmental factors, including poor dietary habits and unhealthy drinking patterns, contribute to ulcerative colitis (UC). While the relationship between diet-related malnutrition and UC has been extensively explored, the impact of drinking water temperature remains largely overlooked, prompting us to investigate its influence on UC pathogenesis and explore the underlying mechanisms. In the present study, we observed that, unlike external thermal and cold therapy, varying drinking water temperatures transiently altered the internal body temperature of the digestive tract. Specifically, chronic drinking of 0°C water had significant anti-inflammatory effects and preserved the integrity of the mucosal barrier in a colitis mouse model. Mechanistically, this temperature spectrum changed the composition of the gut microbiota from inflammation-prone (25°C drinking water) to a resting pattern similar to that of the negative control. Specifically, the abundances of Blautia and Parasutterella, two beneficial genera, were strongly increased in response to 0°C water, accompanied by elevated levels of short-chain fatty acids. In contrast, drinking 40°C water had opposite effects on all the examined parameters and generally aggravated the development of colitis. This study is the first to demonstrate how modifying the temperature of habitual drinking water can modulate colitis progression, providing a novel and noninvasive approach to UC management. Specifically, chronic consumption of 0°C water alleviated the severity of colitis, whereas 40°C water aggravated the disease. Therefore, by focusing on commonly consumed drinking water temperatures, our findings suggest that this simple intervention could be a safe, convenient, and effective therapeutic strategy.

An Attempted Correlation Between the Fecal Microbial Community of Chinese Forest Musk Deer (Moschus berezovskii) and Differences in Musk Production and Quality

Musk, a dried secretion from the sac gland near the urethral foramen of adult male forest musk deer (Moschus berezovskii), has significant economic value and is extensively utilized as a valuable component in traditional Chinese medicine. In the practice of forest musk deer breeding, musk with different colors and varying moisture contents is observed during the season when the musk reaches maturity. For many years, researchers have focused mainly on musk composition and symbiotic bacteria. However, the influence of fecal fungi on the production and quality of musk is unknown. In this study, internal transcribed spacer (ITS) analysis was employed to explore the relationships between the fungal composition of musk deer fecal and the quality and production of musk produced by each individual. The results indicate that fungal genera known to cause diseases, such as Colletotrichum and Apiotrichum, are prevalent in the feces of musk deer that produce abnormal musk. Furthermore, the fecal microbiota health index (GMHI) is lower and the intestinal microbiota dysbiosis index (MDI) is greater in musk deer producing white musk than in normal individuals. Additionally, by correlating musk production with fecal fungi, we also found that Dolichousnea and Scolecoleotia were significantly positively correlated with musk production. Moreover, Metschnikowia, Ganodermataceae_gen_Incertae_sedis, Hypoxylon, Neovaginatispora, Didymella, Dothidea, and Trichoderma were negatively correlated with musk production. This study is the first to investigate gut fungi in relation to musk production/quality, establish gut health and fungal dysbiosis links, and identify candidate fungi tightly associated with musk traits. This exploratory approach is critical for exploring uncharted territories like gut fungi in musk deer and musk traits.

Study on the pathogenesis of idiopathic pediatric acute pancreatitis by combining intestinal microbiome and metabolome

Background

Idiopathic pediatric acute pancreatitis (IPAP) represents a significant health threat to children and adolescents, yet its underlying pathogenesis remains poorly understood, necessitating further research to elucidate its mechanisms. This study aims to explore the roles of intestinal microbiota, short-chain fatty acids (SCFAs), and serum metabolites in the pathogenesis of IPAP, as well as to assess the therapeutic potential of acetic acid intervention in this condition.

Methods

Fecal and serum samples from 22 cases of IPAP (excluding biliary origin) and 10 healthy controls were collected and analyzed. Intestinal microbial was characterized using 16S ribosomal RNA (16S rRNA) sequencing, while SCFAs and serum metabolites were quantified by liquid chromatography-tandem mass spectrometry (LC-MS/MS). Omics analysis was employed to identify microbial-metabolite regulation and regulatory networks and potential disease biomarkers. To evaluate the therapeutic efficacy of acetic acid in acute pancreatitis (AP), AP was induced in animal models by intraperitoneal injection of caerulein (50 µg/kg; once daily for seven days), followed by oral administration of acetic acid (10 mL/kg, once daily) in 4-, 6-, and 8-week models. Pancreatic and ileum tissues were examined for histopathological changes, serum enzymes levels, and intestinal barrier integrity.

Results

The results of 16S rRNA sequencing revealed significant differences in the composition and abundance of intestinal microbial communities between the control (Con) and IPAP groups. Pathogenic bacteria, such as f_Tannerellaceae and c_Bacteroidia, as well as certain symbiotic bacteria, were significantly enriched in the IPAP group. SCFAs metabolome analysis indicated that acetic acid, as a key intermediate metabolite, may play a regulatory role in the pathogenesis of IPAP. The construction of a microbial-metabolite regulatory network demonstrated that microorganisms such as g_Monoglobus and g_Morganella were closely associated with SCFAs, including acetic acid, suggesting that the development of IPAP is influenced by upstream and downstream regulatory mechanisms. Furthermore, significant associations were identified between serum metabolites and gut microbes. For instance, (4E,15E)-bilirubin and creatinine showed significant positive correlations with g_Bacteroides (P<0.01). Similarly, 1,2-ethanediol monoricinoleate was significantly positively correlated with g_Hungatella (P<0.01), while pubescenol and tecastemizole were significantly positively correlated with g_Parabacteroides (P<0.01). Animal experiments demonstrated that pancreatic and intestinal tissue damage was alleviated to varying degrees following treatment. Compared to the disease model group, the acetic acid treatment group exhibited significantly reduced serum levels of D-lactic acid, amylase, and lipase, along with a significantly increased positive staining surface density of intestinal barrier proteins (occludin, claudin-1, and ZO-1).

Conclusions

Intestinal flora, SCFAs and serum metabolites were significantly altered in IPAP, and the interaction regulated the development of IPAP. Acetic acid can effectively intervene the occurrence of IPAP.

Schistosoma mansoni infection causes consistent changes to the fecal bacterial microbiota of mice across and within sites

Eggs of Schistosoma mansoni are produced by adult female worms in mesenteries of infected hosts. Eggs can cross the intestinal barrier and form granulomas in the tissue or breach and exit the host through fecal excretion. These interactions may affect the host microbiome assemblages. Given the potential for schistosomal alteration of host gut microbiome and subsequent effects on the fecal bacterial composition, it is important to conduct controlled microbiome studies on model animals. While pursuing these studies, it is important to take into account the different conditions in which microbiome studies are conducted and their consequent impacts on variability and reproducibility of results. In particular, we are interested in inter-institutional effects on controlled microbiome studies, in which the study location itself may impact study outcomes. In this work, we report global changes caused by acute and chronic schistosomiasis on the fecal microbiome of mice at two different institutions and three timepoints.

Metabarcoding insights into microbial drivers of flavor development and quality stability in traditional Chinese red pepper sauce: impacts of varietal selection and solar/shade fermentation

BACKGROUND

Red pepper sauce is a traditional Chinese condiment, which is rich in nutrients and popular worldwide. However, the changes in the microbial community of red pepper sauce during fermentation and the effects of such changes on quality stability have been under studied. In this study, we systematically analyzed the relationship between the microbial community composition of multiple red pepper sauces and the biochemical indexes. Moreover, we also explored the dynamics of changes in the microbial community composition using metabarcoding sequencing.

RESULTS

Our analysis revealed significant differences in amino acids (AA), lactate, pectin, reducing sugar, flavonoids, phenolics, pigments, and alcohol dehydrogenase (ADH) activity among the six red pepper sauces. Moreover, the relative abundance of bacteria and fungi showed significant differences among multiple red pepper sauces. Among these biochemical indexes, water content, pigment, and capsaicin showed a significant negative correlation with the abundance of multiple bacterial genera. ADH activity showed a significant positive correlation with the abundance of multiple bacterial genera. The content of AA, flavonoid, pectin, and gamma-aminobutyric acid (GABA) was significantly correlated with the relative abundance of multiple fungi such as Rhodotorula, Dipodascus, Leucosporidium, Hannaella, and Coniochaeta.

CONCLUSIONS

These results provide a basis for revealing the biological basis of the quality stability and flavor characteristics of red pepper sauce, which are of great significance for further investigation of the fermentation mechanism and control of the product quality of red pepper sauce.

Gut microbiota dynamics and their impact on body condition in nestlings of the yellow-rumped flycatchers, Ficedula zanthopygia

Investigating the gut microbiome during host development is essential for understanding its influence on host health and fitness. While host body condition is a crucial fitness-related trait and a strong predictor of viability in numerous animal species, its relationship with gut bacteria remains underexplored, particularly in non-model organisms. This study examines the gut microbiome of the altricial wild bird species, yellow-rumped flycatchers (Ficedula zanthopygia), by analyzing nestling feces through 16S rRNA sequencing at four developmental stages: Day 3, Day 6, Day 9 and Day 12 post-hatching. We explored the temporal dynamics of the gut microbiome and its correlation with body condition, a key indicator of fitness. Our results demonstrate signinficant shifts in microbial community composition and diversity throughout development. Notably, Day 3 nestlings displayed lower alpha diversity compared to later stages, while microbial diversity stabilized from Days 6 to 12. Both the age of the nestlings and the environmental conditions of the nest box significantly shaped the gut microbial community structure. A contemporaneous relationship was observed, where the scaled-mass index (SMI) at Day 6 positively correlating with microbial diversity at that time. Additionally, a time-lagged effect emerged, linking SMI at Day 9 to microbial diversity at Day 6. These findings highlight the vital role of the gut microbiome in the development of nestlings, particularly emphasizing Day 6 as a critical period due to its stable microbial diversity and association with SMI. This study underscores the influence of gut bacteria on host fitness in developing birds.

Oral dysbiosis initiates periodontal disease in experimental kidney disease

BACKGROUND AND HYPOTHESIS

It is presently unclear why there is a high prevalence of periodontal disease in individuals living with chronic kidney disease. Whilst some have argued that periodontal disease causes chronic kidney disease, we hypothesized that alterations in saliva and the oral microenvironment in organisms with kidney disease may initiate periodontal disease by causing dysbiosis of the oral microbiota.

METHODS

Experimental kidney disease was created using adenine feeding and subtotal nephrectomy in rats, and by adenine feeding in mice. Loss of periodontal bone height was assessed using a dissecting microscope supported by micro-CT, light, confocal and electron microscopy, and immunohistochemistry. Salivary biochemistry was assessed using NMR spectroscopy. The oral microbiome was evaluated using culture-based and molecular methods, and the transmissibility of dysbiosis was assessed using co-caging and microbial transfer experiments into previously germ-free recipient mice.

RESULTS

We demonstrate that experimental kidney disease causes a reproducible reduction of alveolar bone height, without gingival inflammation or overt hyperparathyroidism but with evidence of failure of bone formation at the periodontal crest. We show that kidney disease alters the biochemical composition of saliva and induces progressive dysbiosis of the oral microbiota, with microbial samples from animals with kidney disease displaying reduced overall bacterial growth, increased alpha diversity, reduced abundance of key components of the healthy oral microbiota such as Streptococcus and Rothia, and an increase in minor taxa including those from gram-negative phyla Proteobacteria and Bacteroidetes. Co-housing diseased rats with healthy ones ameliorates the periodontal disease phenotype, whilst transfer of oral microbiota from mice with kidney disease causes periodontal disease in germ-free animals with normal kidney function.

CONCLUSIONS

We advocate that periodontal disease should be regarded as a complication of kidney disease, initiated by oral dysbiosis through mechanisms independent of overt inflammation or hyperparathyroidism.

Microbiological colonization of the pancreatic tumor affects postoperative complications and outcome after pancreatic surgery

Background

The patient´s microbiome has become a focal point in cancer research. Even for pancreatic cancer, alterations in the microbiome appear to influence cancer formation and progression. The aim of our single-center analysis was the examination of microbiological colonization of pancreas tissue at the time of surgery and its potential influence on complications and outcome.

Methods

We prospectively evaluated patients undergoing pancreatic surgery over a three-year period from June 2018 to June 2021. We focused on the microbiological colonization of pancreatic tissue which was acquired during pancreatic surgery. Tissue samples were cultivated at our institute of microbiology. Patients´ characteristics, complications and postoperative outcome were analyzed using a prospectively maintained SPSS database.

Results

Between June 2018 and June 2021, we collected pancreatic tissue samples of a total of 178 patients undergoing pancreas resections, mostly due to ductal adenocarcinoma (PDAC; 50.6%). We could cultivate bacterial or fungal species in pancreatic tissue samples of 50 of our patients (28.1%). The majority of cases were characterized by the presence of a single microbial species, but 20 patients (11.2%) showed colonization with up to four different species. Among the bacterial species detected were Enterococcus faecium, Enterococcus faecalis, Escherichia coli, Staphylococcus aureus, Enterobacter cloacae and Klebsiella pneumonia. We found significantly more microbiological culture growth in patients with a preoperative biliary stent (74.0% vs. 15.6%, p < 0.001). Concerning postoperative complications, we found no difference concerning pancreatic fistula, but colonization with E. coli was associated with a significantly higher rate of postpancreatectomy hemorrhage (30.0% vs. 8.9%, p = 0.032). Interestingly, survival of PDAC patients seems to be negatively affected by positive microbiological findings at the time of surgery, but without reaching statistical significance (p = 0.770).

Conclusion

In this first analysis of our patient cohort, we could show a microbiological colonization of pancreatic tumor tissue in almost a third of our patients. There seems to be only a minor impact on postoperative complications, but long-term outcome seems to be worse in patients with a positive pancreas microbiome. Further observation is needed to evaluate the influence of the tumor microbiome on the long-term oncological outcome in PDAC patients.

A suite of selective pressures supports the maintenance of alleles of a Drosophila immune peptide

The innate immune system provides hosts with a crucial first line of defense against pathogens. While immune genes are often among the fastest evolving genes in the genome, in Drosophila, antimicrobial peptides (AMPs) are notable exceptions. Instead, AMPs may be under balancing selection, such that over evolutionary timescales, multiple alleles are maintained in populations. In this study, we focus on the Drosophila AMP Diptericin A, which has a segregating amino acid polymorphism associated with differential survival after infection with the Gram-negative bacteria Providencia rettgeri. Diptericin A also helps control opportunistic gut infections by common Drosophila gut microbes, especially those of Lactobacillus plantarum. In addition to genotypic effects on gut immunity, we also see strong sex-specific effects that are most prominent in flies without functional diptericin A. To further characterize differences in microbiomes between different diptericin genotypes, we used 16S metagenomics to look at the microbiome composition. We used both lab-reared and wild-caught flies for our sequencing and looked at overall composition as well as the differential abundance of individual bacterial families. Overall, we find flies that are homozygous for one allele of diptericin A are better equipped to survive a systemic infection from P. rettgeri, but in general have a shorter lifespans after being fed common gut commensals. Our results suggest a possible mechanism for the maintenance of genetic variation of diptericin A through the complex interactions of sex, systemic immunity, and the maintenance of the gut microbiome.