Abundance Of Bacterial Taxa Research Articles

Taxonomic and metabolic characterisation of biofilms colonising Roman stuccoes at Baia’s thermal baths and restoration strategies

Stuccoes are very delicate decorative elements of Roman age. Very few of them survived almost intact to present days and, for this reason, they are of great interest to restorers and conservators. In this study, we combined metabarcoding and untargeted metabolomics to characterise the taxonomic and metabolic profiles of the microorganisms forming biofilms on the stuccoes located on the ceiling of the laconicum, a small thermal environment in the archaeological park of Baia (southern Italy). We found that some samples were dominated by bacteria while others by eukaryotes. Additionally, we observed high heterogeneity in the type and abundance of bacterial taxa, while the eukaryotic communities, except in one sample (at prevalence of fungi), were dominated by green algae. The metabolic profiles were comparable across samples, with lipids, lipid-like molecules and carbohydrates accounting for roughly the 50% of metabolites. In vitro and in vivo tests to remove biofilms on stuccoes using essential oils blends were successful at a 50% dilution for one hour and half. This integrative study advanced our knowledge on taxonomic and metabolic profiles of biofilms on ancient stuccoes and highlighted the potential impacts of these techniques in the field of cultural heritage conservation.

The Impact of Milk on Gut Permeability, Fecal 16S rRNA Gene Microbiota Profiling, and Fecal Metabolomics in Children with Moderate Malnutrition in Sierra Leone: A Double-Blind, Randomized Controlled Trial

Background. ObjectivesOur objectives were to determine the effect of dietary milk protein and milk carbohydrate on the intestinal permeability, fecal 16S rRNA gene configuration, and fecal metabolomics of children with moderate malnutrition. MethodsThis was a randomized, double-blind, controlled trial among 413 children with wasting in rural Sierra Leone who received 1 of the following 4 supplementary foods, which differed in sources of protein and carbohydrate: milk protein and milk carbohydrate (MPMC), milk protein and vegetable carbohydrate (MPVC), vegetable protein and milk carbohydrate (VPMC), or a control group consuming entirely vegetable-based food (VPVC). After 4 wk, urine and stool were collected from participants enrolled with mid-upper arm circumference of <12.1 cm. Urine was analyzed for lactulose excretion (%L). Stool samples were subjected to both 16S rRNA gene analysis to assess β-diversity and untargeted metabolomic abundance. ResultsAmong the 386 children who completed permeability testing, the mean difference (95% CI) in %L excretion as compared with VPVC was 0.01 (−0.05, 0.07) for MPMC, 0.05 (−0.01, 0.11) for MPVC, and 0.01 (−0.05, 0.07) for VPMC. Of the 374 children who provided a stool sample that was analyzed, the β-diversity among bacterial taxa was similar between dietary groups (P > 0.05 for all comparisons). No significant differences between dietary groups were seen among the 20 most abundant bacterial taxa. Among the 5769 unique metabolomic features identified, greater flavonoid levels in VPVC were seen. ConclusionsAbnormal intestinal permeability do not improve with 4 wk of supplementary feeding. Fecal rRNA do not differ with consumption of different diets.This trial was registered at clinicaltrials.gov as NCT04216043.

Link between bacterial communities and contrasted loads in ectoparasitic monogeneans from the external mucus of two wild sparid species (Teleostei)

BackgroundWhile teleost fishes represent two thirds of marine vertebrates, the role of their external microbiota in relationship with their environment remains poorly studied, especially in wild populations. Hence, the interaction of their microbiota with ectoparasites is largely unknown. Microbiota can act as a protective barrier against pathogens, and/or be involved in host recognition by parasites. Thus, host-parasite associations should now be considered as a tripartite interplay where the microbiota shapes the host phenotype and its relation to parasites. Monogeneans (Platyhelminthes) are direct life cycle ectoparasites commonly found on teleost skin and gills. The role of bacterial communities within skin and gill mucus which either pre-exist monogeneans infestation or follow it remain unclear. This is investigated in this study using the association between Sparidae (Teleostei) and their specific monogenean ectoparasites of the Lamellodiscus genus. We are exploring specificity mechanisms through the characterization of the external mucus microbiota of two wild sparid species using 16s rRNA amplicon sequencing. We investigated how these bacterial communities are related to constrated Lamellodiscus monogeneans parasitic load.ResultsOur results revealed that the increase in Lamellodiscus load is linked to an increase in bacterial diversity in the skin mucus of D. annularis specimens. The date of capture of D. annularis individuals appears to influence the Lamellodiscus load. Correlations between the abundance of bacterial taxa and Lamellodiscus load were found in gill mucus of both species. Abundance of Flavobacteriaceae family was strongly correlated with the Lamellodiscus load in gill mucus of both species, as well as the potentially pathogenic bacterial genus Tenacibaculum in D. annularis gill mucus. Negative correlations were observed between Lamellodiscus load and the abundance in Vibrionaceae in gill mucus of D. annularis, and the abundance in Fusobacteria in gill mucus of P. acarne specimens, suggesting potential applications of these bacteria in mitigating parasitic infections in fish.ConclusionsOur findings highlight the dynamic nature of fish microbiota, in particular in relation with monogeneans infestations in two wild sparid species. More generally, this study emphasizes the links between hosts, bacterial communities and parasites, spanning from the dynamics of co-infection to the potential protective role of the host’s microbiota.

O-276 Implantation failure is not associated with seven different vaginal bacterial community-state types; however, a distinct signature, including Ureaplasma parvum, is strongly linked to treatment failure

Abstract Study question Is microbial diversity or vaginal bacterial composition associated with embryonic implantation in women undergoing frozen-thawed embryo transfer? Summary answer While global diversity measures of microbial composition do not correlate with positive implantation, specific taxa may serve as predictors of treatment outcomes. What is known already Clinical studies have indicated a reduced likelihood of embryo implantation in women diagnosed with microbial dysbiosis. The application of Next-Generation Sequencing for microbiota analysis has significantly advanced our understanding of vaginal microbiome composition. Recent studies have proposed distinct vaginal microbiome patterns as potential predictors of IVF treatment success or failure. However, the evidence regarding the biological basis of test algorithms (such as the independent association of distinct community state types with outcomes) and the reliability of diagnostic test performance (including replicability and external validity) in predicting implantation success or failure in women undergoing embryo transfer remains less robust. Study design, size, duration In a prospective, single-centre observational cohort study (05/2017-03/2019, NCT03507673, local ethical approval reference no.18-005), conducted at a university-affiliated centre for reproductive medicine in Germany, vaginal swab samples were collected from infertile, asymptomatic female patients (n = 260), aged 18-45, undergoing frozen-thawed embryo transfer. Patients, each contributing a single treatment cycle, received sequential oral estradiol and oral estradiol/dydrogesterone in an HRT regimen for FET. Vaginal swabs were taken from baseline visit before transfer day and stored at –80 °C. Participants/materials, setting, methods 16S rRNA gene amplicon sequencing was performed targeting V3/V4 hypervariable region using Illumina MiSeq platform. Raw data assembly, filtering and taxonomic assignment were performed using mothur against EzBioCloud database. Statistical analyses, and visualization were conducted using R. Community structure via hierarchical clustering, alpha and beta diversity, and indicator species via LefSe analysis were assessed. Main results and the role of chance Based on a hierarchical clustering using the 25 most abundant bacterial taxa, seven separate community state types (CSTs) being either dominated by species of the genus Lactobacillus (CST-A, CST-B, CST-C, CST-E, CST-G) or Gardnerella (CST-F) or presenting a variable community composition (CST-D) were identified. A community state type dominated by Lactobacillus fornicalis was found in a small fraction of women and enhanced resolution among the Gardnerella genus impacts CST definitions in this sample. Embryonic implantation had no significant association to either alpha diversity measures or CST distribution; likewise, the previously suggested ratio of relative abundances of Lactobacillus iners vs. Lactobacillus crispatus was not associated with implantation. Lactobacillus fornicalis is positively linked to implantation, while Lactobacillus iners and Ureaplasma parvum were linked to implantation failure: above 50% relative abundance of Lactobacillus fornicalis, was associated with 75% positive implantation. Conversely, just 0.5% relative abundance of Ureaplasma parvum was associated with a decrease in implantation rate to approximately 20%. LefSe and binary regression analysis identified a relatively rare (6% in our sample) microbiome signature, mostly from CST-C (Lactobacillus iners dominated) with a very low likelihood of implantation, with Ureaplasma parvum as the common denominator. Limitations, reasons for caution Studies on the vaginal microbiome in IVF face issues such as study design variability, small sample-sizes, limited control for temporal dynamics, and patient heterogeneity. Attempts at establishing causal relationships through interventional studies in IVF have been limited and inconclusive. Understanding the microbiome’s functional aspects is crucial for reproductive outcome elucidation. Wider implications of the findings Current study findings don’t confirm previously reported associations between common vaginal bacterial CSTs and outcome. Therefore, screening for vaginal microbiome composition in asymptomatic women with subfertility is not recommended outside research. Signatures/taxae with an independent and strong negative association with implantation are likely to be rare yet deserve further attention. Trial registration number NCT03507673

Genome-wide association study identifies host genetic variants influencing oral microbiota diversity and metabolic health

The microbial communities of the oral cavity are important elements of oral and systemic health. With emerging evidence highlighting the heritability of oral bacterial microbiota, this study aimed to identify host genome variants that influence oral microbial traits. Using data from 16S rRNA gene amplicon sequencing, we performed genome-wide association studies with univariate and multivariate traits of the salivary microbiota from 610 unrelated adults from the Danish ADDITION-PRO cohort. We identified six single nucleotide polymorphisms (SNPs) in human genomes that showed associations with abundance of bacterial taxa at different taxonomical tiers (P < 5 × 10–8). Notably, SNP rs17793860 surpassed our study-wide significance threshold (P < 1.19 × 10–9). Additionally, rs4530093 was linked to bacterial beta diversity (P < 5 × 10–8). Out of these seven SNPs identified, six exerted effects on metabolic traits, including glycated hemoglobin A1c, triglyceride and high-density lipoprotein cholesterol levels, the risk of type 2 diabetes and stroke. Our findings highlight the impact of specific host SNPs on the composition and diversity of the oral bacterial community. Importantly, our results indicate an intricate interplay between host genetics, the oral microbiota, and metabolic health. We emphasize the need for integrative approaches considering genetic, microbial, and metabolic factors.

The gut-brain axis in individuals with alcohol use disorder: Anexploratory study of associations among clinical symptoms, brain morphometry, and the gut microbiome.

Alcohol use disorder (AUD) is commonly associated with distressing psychological symptoms. Pathologic changes associated with AUD have been described in both the gut microbiome and brain, but the mechanisms underlying gut-brain signaling in individuals with AUD are unknown. This study examined associations among the gut microbiome, brain morphometry, and clinical symptoms in treatment-seeking individuals with AUD. We performed a secondary analysis of data collected during inpatient treatment for AUD in subjects who provided gut microbiome samples and had structural brain magnetic resonance imaging (MRI; n = 16). Shotgun metagenomics sequencing was performed, and the morphometry of brain regions of interest was calculated. Clinical symptom severity was quantified using validated instruments. Gut-brain modules (GBMs) used to infer neuroactive signaling potential from the gut microbiome were generated in addition to microbiome features (e.g., alpha diversity and bacterial taxa abundance). Bivariate correlations were performed between MRI and clinical features, microbiome and clinical features, and MRI and microbiome features. Amygdala volume was significantly associated with alpha diversity and the abundance of several bacteria including taxa classified to Blautia, Ruminococcus, Bacteroides, and Phocaeicola. There were moderate associations between amygdala volume and GBMs, including butyrate synthesis I, glutamate synthesis I, and GABA synthesis I & II, but these relationships were not significant after false discovery rate (FDR) correction. Other bacterial taxa with shared associations to MRI features and clinical symptoms included Escherichia coli and Prevotella copri. We identified gut microbiome features associated with MRI morphometry and AUD-associated symptom severity. Given the small sample size and bivariate associations performed, these results require confirmation in larger samples and controls to provide meaningful clinical inferences. Nevertheless, these results will inform targeted future research on the role of the gut microbiome in gut-brain communication and how signaling may be altered in patients with AUD.

Differential Composition and Structure of the Microbiota from Active and Inactive Stages of HLA-B27-associated Uveitis by Paired Fecal Metagenomes

ABSTRACT Purpose To compare the diversities and abundances of bacterial taxa in the microbiome of patients with HLA B27-positive acute anterior uveitis (AAU) in the active and inactive phases. Methods An observational descriptive prospective and comparative study was conducted in ten HLA-B27-positive AAU patients (44.6 ± 13.4 years). The microbiome of the stool samples obtained in the active and inactive stages was analyzed by sequencing the V3 region of the 16S rRNA gene. Results The differences in the bacteria profile between active and inactive stages in each individual were confirmed (p < 0.0001). Ten OTUs were found exclusively in the active phase of 90% of the individuals, suggesting a proinflammatory association. Blautia OUT_4 and Faecalibacterium OUT_2 abundances showed a direct relationship between abundance and severity of ocular inflammation. Two OTUs were exclusive of the inactive stage, suggesting an anti-inflammatory role. Conclusion The metagenomic profile of the fecal microbiota differs in the acute phase of the AAU compared to when the inflammation subsides, despite being the same individual and a short time-lapse. AAU is a fertile field for studying the connection between subtle rapid changes in microbiota and their systemic consequences.

Exploring the potential effects of forest urbanization on the interplay between small mammal communities and their gut microbiota

Urbanization significantly impacts wild populations, favoring urban dweller species over those that are unable to adapt to rapid changes. These differential adaptative abilities could be mediated by the microbiome, which may modulate the host phenotype rapidly through a high degree of flexibility. Conversely, under anthropic perturbations, the microbiota of some species could be disrupted, resulting in dysbiosis and negative impacts on host fitness. The links between the impact of urbanization on host communities and their gut microbiota (GM) have only been scarcely explored. In this study, we tested the hypothesis that the bacterial composition of the GM could play a role in host adaptation to urban environments. We described the GM of several species of small terrestrial mammals sampled in forested areas along a gradient of urbanization, using a 16S metabarcoding approach. We tested whether urbanization led to changes in small mammal communities and in their GM, considering the presence and abundance of bacterial taxa and their putative functions. This enabled to decipher the processes underlying these changes. We found potential impacts of urbanization on small mammal communities and their GM. The urban dweller species had a lower bacterial taxonomic diversity but a higher functional diversity and a different composition compared to urban adapter species. Their GM assembly was mostly governed by stochastic effects, potentially indicating dysbiosis. Selection processes and an overabundance of functions were detected that could be associated with adaptation to urban environments despite dysbiosis. In urban adapter species, the GM functional diversity and composition remained relatively stable along the urbanization gradient. This observation can be explained by functional redundancy, where certain taxa express the same function. This could favor the adaptation of urban adapter species in various environments, including urban settings. We can therefore assume that there are feedbacks between the gut microbiota and host species within communities, enabling rapid adaptation.

Microbiome of Invasive Tick Species Haemaphysalis Longicornis in North Carolina, USA.

Ticks are one of the most important vectors of human and animal disease worldwide. In addition to pathogens, ticks carry a diverse microbiota of symbiotic and commensal microorganisms. In this study, we used next-generation sequencing (NGS) to survey the microbiomes of Haemaphysalis longicornis (Acari: Ixodidae) at different life stages collected from field populations in North Carolina (NC), USA. Sequence analyses were performed using QIIME2 with the DADA2 plugin and taxonomic assignments using the Greengenes database. Following quality filtering and rarefaction, the bacterial DNA sequences were assigned to 4795 amplicon sequence variants (ASVs) in 105 ticks. A core microbiome of H. longicornis was conserved across all ticks analyzed, and included bacterial taxa: Coxiella, Sphingomonas, Staphylococcus, Acinetobacter, Pseudomonas, Sphingomonadaceae, Actinomycetales, and Sphingobium. Less abundant bacterial taxa, including Rickettsia and Aeromonas, were also identified in some ticks. We discovered some ASVs that are associated with human and animal infections among the identified bacteria. Alpha diversity metrics revealed significant differences in bacterial diversity between life stages. Beta diversity metrics also revealed that bacterial communities across the three life stages were significantly different, suggesting dramatic changes in the microbiome as ticks mature. Based on these results, additional investigation is necessary to determine the significance of the Haemaphysalis longicornis microbiome for animal and human health.

Exploring the interplay between posttraumatic stress disorder, gut microbiota, and inflammatory biomarkers: a comprehensive meta-analysis.

Posttraumatic stress disorder (PTSD) is the most common mental health disorder to develop following exposure to trauma. Studies have reported conflicting results regarding changes in immune biomarkers and alterations in the abundance of bacterial taxa and microbial diversity in patients with PTSD. The purpose of this meta-analysis is to summarize existing studies examining gut microbiota characteristics and changes in immune biomarkers in patients with PTSD. Relevant studies were systematically searched in PubMed, Scopus, and Embase, published in English between January 1, 1960, and December 1, 2023. The outcomes included changes in abundance and diversity in gut microbiota (gut microbiota part) and changes in immune biomarkers (immune part). The meta-analysis included a total of 15 studies, with 9 focusing on changes in inflammatory biomarkers and 6 focusing on changes in gut microbiota composition in patients with PTSD. No differences were observed between groups for all inflammatory biomarkers (P≥0.05). Two of the six studies found that people with PTSD had less alpha diversity. However, the overall Standardized Mean Difference (SMD) for the Shannon Diversity Index was not significant (SMD 0.27, 95% CI -0.62-0.609, p = 0.110). Regarding changes in abundance, in two of the studies, a significant decrease in Lachnospiraceae bacteria was observed. This meta-analysis provides a comprehensive overview of gut microbiota characteristics in PTSD, suggesting potential associations with immune dysregulation. Future research should address study limitations, explore causal relationships, and consider additional factors influencing immune function in individuals with PTSD. https://www.crd.york.ac.uk, identifier CRD42023476590.

Calcium carbonate precipitating extremophilic bacteria in an Alpine ice cave

Extensive research has provided a wealth of data on prokaryotes in caves and their role in biogeochemical cycles. Ice caves in carbonate rocks, however, remain enigmatic environments with limited knowledge of their microbial taxonomic composition. In this study, bacterial and archaeal communities of the Obstans Ice Cave (Carnic Alps, Southern Austria) were analyzed by next-generation amplicon sequencing and by cultivation of bacterial strains at 10 °C and studying their metabolism. The most abundant bacterial taxa were uncultured Burkholderiaceae and Brevundimonas spp. in the drip water, Flavobacterium, Alkanindiges and Polaromonas spp. in the ice, Pseudonocardia, Blastocatella spp., uncultured Pyrinomonadaceae and Sphingomonadaceae in carbonate precipitates, and uncultured Gemmatimonadaceae and Longimicrobiaceae in clastic cave sediments. These taxa are psychrotolerant/psychrophilic and chemoorganotrophic bacteria. On a medium with Mg2+/Ca2+ = 1 at 21 °C and 10 °C, 65% and 35% of the cultivated strains precipitated carbonates, respectively. The first ~ 200 µm-size crystals appeared 2 and 6 weeks after the start of the cultivation experiments at 21 °C and 10 °C, respectively. The crystal structure of these microbially induced carbonate precipitates and their Mg-content are strongly influenced by the Mg2+/Ca2+ ratio of the culture medium. These results suggest that the high diversity of prokaryotic communities detected in cryogenic subsurface environments actively contributes to carbonate precipitation, despite living at the physical limit of the presence of liquid water.

Effects of extreme precipitation on bacterial communities and bioaerosol composition: Dispersion in urban outdoor environments and health risks

Concerns about contaminants dispersed by seasonal precipitation have grown due to their potential hazards to outdoor environments and human health. However, studies on the crucial environmental factors influencing dispersion changes in bacterial communities are limited. This research adopted four-season in situ monitoring and sequencing techniques to examine the regional distribution profiles of bioaerosols, bacterial communities, and risks associated with extreme snowfall versus rainfall events in two monsoon cities. In the early-hours of winter snowfall, airborne cultivable bioaerosol concentrations were 4.1 times higher than the reference exposure limit (500 CFU/m3). The concentration of ambient particles (2.5 μm) exceeded 24,910 particles/L (97 μg/m3), positively correlating with the prevalence of cultivable bioaerosols. These bioaerosols contained cultivable bacterial species such as pathogenic Staphylococcus aureus, Staphylococcus epidermidis, Streptococcus pneumoniae, and Escherichia coli. Bioaerosol concentrations increased by 53.0% during 50-mm snow extremes. Taxonomic analysis revealed that Pseudomonas, Staphylococcus, and Veillonella were the most abundant bacterial taxa in the initial snowmelt samples during winter precipitation. However, their abundance decreased by 87.6% as snowing continued (24 h). Reduced water base cation concentration also led to a 1.15-fold increase in the Shannon index, indicating a similar yet heightened bacterial diversity. Seasonally, Pedobacter and Massilia showed higher relative abundance (25% and 18%, respectively), presenting increased bacterial transmission to the soil. Furthermore, Pseudomonas was identified in 60% of spring snowstorm samples, suggesting long-distance dispersal of pathogenic bacteria. When these atmospheric aerosol particles carrying biological entities (0.65–1.1 μm) penetrated human alveoli, the calculated hazard ratio was 0.55, which as observed in inhalation exposures. Consequently, this study underscores the risk of seasonal precipitation-enhanced ambient bacterial transmission.

Effects of different foods and cooking methods on the gut microbiota: an in vitro approach.

To support personalized diets targeting the gut microbiota, we employed an in vitro digestion-fermentation model and 16S rRNA gene sequencing to analyze the microbiota growing on representative foods of the Mediterranean and Western diets, as well as the influence of cooking methods. Plant- and animal-derived foods had significantly different impacts on the abundances of bacterial taxa. Animal and vegetable fats, fish and dairy products led to increases in many taxa, mainly within the Lachnospiraceae. In particular, fats favored increases in the beneficial bacteria Faecalibacterium, Blautia, and Roseburia. However, butter, as well as gouda cheese and fish, also resulted in the increase of Lachnoclostridium, associated to several diseases. Frying and boiling produced the most distinct effects on the microbiota, with members of the Lachnospiraceae and Ruminococcaceae responding the most to the cooking method employed. Nevertheless, cooking effects were highly individualized and food-dependent, challenging the investigation of their role in personalized diets.

Niche-specific modulation of long-chain n-alkanes degrading bacterial community and their functionality in forest habitats across the leaf litter-soil compartments

Long-chain n-alkanes are vital constituents of plant-derived wax, however, their limited reactivity, life cycle in terms of biodegradation, and ecological impacts are not lucid in a niche-specific manner. Here, we provide an insight into the bacterial community and their functional variations associated with long-chain n-alkanes degradation across leaf litter-soil compartments in three rainforest habitats aiming to elucidate the microbial modulation linked to the long-chain n-alkanes concentration and composition. The ravine habitat showed significantly higher long-chain n-alkanes concentration, bacterial diversity and functional genes than the windward and leeward habitats. Among the statistically significant genera (p < 0.05) Intrasporangium, Virgisporangium, Micromonospora, and Planomicrobium were more abundant in the ravine habitat than in the other two habitats. Interestingly, three statistically significant genera including Sphingobium, Tepidisphaera, and Methylobacterium showed a decrease abundance with increasing soil depths compared to their abundance in leaf litter. The correlation analysis revealed that Rhizobium, Pseudorhodoferax, Micromonospora, Dongia, Actinoplanes, Bdellovibrio, Ohtaekwangia, Planctomicrobium, Opitutus, Actinokineospora, Novosphingobium, and Methylobacterium were significantly in a positive relationship with alkB gene and most of the long-chain n-alkanes (C27 to C34). The ordination analysis further unveiled a strong association among the long-chain n-alkanes concentration, potential degraders and alkB gene within the ravine habitat. Additionally, we observed a decreasing trend in the abundance of bacterial taxa and related functional genes with decreasing the long-chain n-alkane concentration, suggesting n-alkane specific taxa modulation. Fundamentally, this study provides niche-specific evidence that the concentration of long-chain n-alkanes could contribute to a shift in bacterial diversity, abundance and function in forest habitats.

Effects of multiple N, P, and K fertilizer combinations on strawberry growth and the microbial community.

Nitrogen (N), phosphorus (P), and potassium (K) exert various effects on strawberry (Fragaria ananassa Duchesne) yields. In this study, we employed an orthogonal experimental design (T1-T9) with three fertilization treatments (N, P, and K) at three levels to identify an optimal fertilization scheme for strawberry cultivation. The effects of fertilizer combinations the rhizosphere soil microbial community were also explored by using bacterial full-length 16S rRNA and fungal ITS (internal transcribed spacer) sequencing (30 samples for each analysis). The results showed that the average plant height and leaf area of the fertilized groups were 24.6% and 41.6% higher than those of the non-fertilized group (T0). After 60 d of planting, the sucrase activity in the T6 group increased by 76.67% compared to the T0 group, with phosphate fertilizer exerting a more significant impact on sucrase activity. The T6 treatment group had the highest alpha diversity index among bacterial and fungal microorganisms, and had a different microbial community structure compared with the control group. The most abundant bacterial taxa in the strawberry rhizosphere soil were Proteobacteria, Bacteroidota, and Acidobacteriota, and the most abundant fungal phyla were Monoblepharomycota, Glomeromycota, and Mucoromycota. Application of the optimal combined fertilizer treatment (T6) significantly increased the abundance of Proteobacteria and altered the abundance of Gemmatimonas compared to other treatment groups. Notably, Gemmatimonas abundance positively correlated with strawberry plant height and soil N, P, and K levels. These findings indicated that the relative abundance of beneficial bacteria could be enhanced by the application of an optimal fertilizer ratio, ultimately improving strawberry agronomic traits.

Amelioration of hyperuricemia by Lactobacillus acidophilus F02 with uric acid-lowering ability via modulation of NLRP3 inflammasome and gut microbiota homeostasis

Hyperuricemia is a metabolic disease caused by disturbances in purine metabolism and imbalances in the formation and excretion of uric acid. It is closely related to the gut microbiota, which is considered a therapeutic target. Some lactic acid bacteria with a uric acid lowering effect have the potential to ameliorate hyperuricemia in the host. However, the mechanism of action remains unclear. Here, we screened a strain of Lactobacillus acidophilus F02 that efficiently degrades uric acid precursors (inosine and guanosine) and further investigated its underlying mechanism on the alleviation of hyperuricemia in high fructose-adenine induced mice. Results showed that L. acidophilus F02 administration reduced serum uric acid levels in hyperuricemia mice by inhibiting xanthine oxidase and adenosine deaminase activity, while protecting hepatorenal injury and systemic inflammation by regulating the relative expression of NLRP3 inflammasome. Most importantly, it restored gut microbial homeostasis and the abundance of bacterial taxa (i.e., a balance in the relative abundance of Firmicutes and Actinobacteria and an increase in the abundance of Bacteroides, Ruminococcus and Lactobacillus). Furthermore, the ability of L. acidophilus F02 to lower uric acid and suppress NLRP3 inflammasome expression was confirmed in the HK-2 cell model, as well as the multiple immunomodulatory effects on RAW264.7 cells. Taken together, we speculate that fructose-adenine induced hyperuricemia triggers hepatorenal injury and gut microbiota dysbiosis, which is ameliorated by L. acidophilus F02. Collectively, the results suggest that lowering uric acid synthesis, increasing uric acid excretion and reducing NLRP3-related IL-1β levels are effective strategies to ameliorate hyperuricemia. Such information could inform future studies on the ecology of L. acidophilus and guide the use of this species for dietary applications in the food industry.

Explore the changes of intestinal flora in patients with coronavirus disease 2019 based on bioinformatics.

Studies have revealed that there were significant changes in intestinal flora composition in patients with coronavirus disease 2019 (COVID-19) compared to non-COVID-19 patients, regardless of whether they were treated with medication. Therefore, a comprehensive study of the intestinal flora of COVID-19 patients is needed to further understand the mechanisms of COVID-19 development. In total, 20 healthy samples and 20 COVID-19 samples were collected in this study. Firstly, alpha diversity and beta diversity were analyzed to assess whether there were difference in species richness and diversity as well as species composition between COVID-19 and control groups. The observed features index, Evenness index, PD index, and Shannon index were utilized to measure alpha diversity. The principal coordinates analysis (PCoA) and non-metric multidimensional scaling (NMDS) were performed to analyzed beta diversity. Linear discriminant analysis Effect Size (LEfSe) was utilized to analyze the variability in the abundance of bacterial taxa from different classification levels. The random forest (RF), Least absolute shrinkage and selection operator (LASSO), and univariate logistic regression were utilized to identify key Amplicon Sequence Variant (ASVs). Finally, the relevant networks of bacterial taxa were created in COVID-19 and control groups, separately. There were more species in the control group than in COVID-19 group. The observed features index, Shannon index, and Evenness index in the control groups were markedly higher than in the COVID-19 group. Therefore, there were marked variations in bacterial taxa composition between the COVID-19 and control groups. The nine bacterial taxa were significantly more abundant in the COVID-19 group, such as g-Streptococcus, f-Streptococcaceae, o-Lactobacillales, c-Bacilli and so on. In the control group, 26 bacterial taxa were significantly more abundant, such as c-Clostrjdia, o-Oscillospirales, f-Ruminococcaceae, etc. The 5 key ASVs were obtained through taking the intersection of the characteristic ASVs obtained by the three algorithms, namely ASV6, ASV53, ASV92, ASV96, and ASV105, which had diagnostic value for COVID-19. The relevance network in the control group was more complex compared to the COVID-19 group. Our findings provide five key ASVs for diagnosis of COVID-19, providing a scientific reference for further studies of COVID-19.

Ruminal bacterial communities differ in early-lactation dairy cows with differing risk of ruminal acidosis

IntroductionEarly-lactation Holstein cows (n= 261) from 32 herds in three regions (Australia, California, and Canada) were previously categorized using a discriminant analysis model as being at a high (26.1% of cows), medium (26.8% of cows), or low risk (47.1% of cows) of ruminal acidosis. We aimed to investigate if (1) risk of acidosis would be associated with ruminal bacterial taxa and dietary nutrient components, (2) there would be individual or combinations of bacterial taxa associated with acidosis-risk groups, and (3) the abundance of bacterial taxa would be associated with the intake of dietary nutrient components.MethodsDiets ranged from pasture supplemented with concentrates to total mixed rations. Bacteria 16S ribosomal DNA sequences from rumen samples collected &amp;lt; 3 hours after feeding via stomach tube were analyzed to determine bacterial presence. The relative abundance of each bacterial phylum and family was center log transformed and the transformed family data were subjected to two redundancy analysis biplots, one for acidosis risk group and one for region, to identify the 20 best-fit bacterial families from each respective redundancy analysis. A total of 29 unique families were identified when the lists of 20 families were combined from each redundancy analysis, and these 29 families were termed "influential" families." The association of acidosis-risk groups with the abundance of individual influential families was assessed by mixed models. Backward stepwise elimination mixed models were used to determine the bacterial taxa associated with each acidosis-risk group and the dietary nutrients associated with the abundance of the bacterial taxa.Results and discussionHigh-risk acidosis cows were associated with increased abundances of Anaerocella_f and Veillonellaceae and decreased abundances of several bacterial families with different characteristics. Five phyla: Firmicutes [odds ratio (OR) = 7.47 ± 7.43], Spirochaetes (OR = 1.28 ± 0.14), Lentisphaerae (OR = 0.70 ± 0.07), Planctomycetes (OR = 0.70 ± 0.09), and Tenericutes (OR = 0.44 ± 0.15), and nine families were associated with a higher risk of acidosis. Of the nine phyla identified to be of interest based on abundance and strength of association with acidosis-risk groups, all had one or more dietary nutrient that predicted their abundance. Sugar was the most frequently associated nutrient with the nine phyla, and was present in 78% (seven out of nine phyla) of the models; crude protein was present in 56% of models and crude fat was present in 44% of the models. Sugar and crude protein were most associated with the influential families and all but three families had one or more nutrient predictive of their abundance. Ruminal bacterial taxa are associated with ruminal acidosis; dietary sugar and crude protein are vital predictors of these and, thus, of ruminal acidosis risk.

Organic matter type and soil texture shape prokaryotic communities during early‐stage soil structure formation

AbstractBackgroundOrganic matter (OM) serves as substrate for heterotrophic microbial growth. Soil structure supports microbial life by providing various niches for colonization. Microorganisms in turn contribute to soil structure formation.AimsWe aim to understand how OM of different origin and soil texture affect prokaryotic community structure and the implications on early‐stage soil structure formation.MethodsAn artificial soil incubation experiment was conducted with different types of OM, including bacterial necromass and particulate organic matter (POM) of larger or smaller size (sPOM). The mineral composition was modified to obtain a clay loam, loam, and sandy loam texture. The abundance and composition of a natural microbial inoculum were determined after 30 days of incubation by real‐time PCR and 16S rRNA gene sequencing, respectively.ResultsThe different OM types had a stronger effect on the prokaryotic community structure and abundance than texture. The necromass treatment supported the most distinct prokaryotic community with the highest abundance and lowest diversity, as well as the most intense formation of water‐stable microaggregates in comparison to POM and sPOM treatments. Abundant bacterial taxa in all treatments are known to include extracellular polymeric substance producers, indicating that functional redundancy warrants aggregation by gluing agents. Texture‐related effects were most consistent in the POM treatment, where larger prokaryotic populations were observed in the coarser‐textured soils with fewer but larger soil pores and lower soil water content.ConclusionsDifferences in prokaryotic community structure and abundance due to OM source indicate that aggregation is dependent on different ecological strategists, a POM‐degrading population that promotes aggregation and contributes to necromass formation, and a necromass‐degrading consortium in which bacteria play a major role.

Municipal separate storm sewer system (MS4) dry weather flows and potential flow sources as assessed by conventional and advanced bacterial analyses

Municipal separate storm sewer systems (MS4s) function in urbanized areas to convey flows during both wet weather (i.e., stormwater) and dry weather (i.e., urban runoff as well as subsurface sources of flow) to receiving waters. While urban stormwater is known to contain microbial and chemical pollutants, MS4 dry weather flows, or non-stormwater discharges (NSWDs), are much less studied, although they are also known to contain pollutants, especially when these flows include raw sewage. In addition, some natural NSWDs (e.g., from groundwater infiltrating MS4 pipes) are critical for aquatic habitat protection. Thus, it is important to distinguish NSWD sources to prevent non-natural flows while retaining natural waters (i.e., groundwater). Here, MS4 dry weather flows were assessed by analyzing water samples from MS4 outfalls across multiple watersheds and water provider service areas in south Orange County, CA; potential NSWD sources including sewage, recycled water, potable water, and groundwater were sampled and analyzed for their likely contributions to overall NSWDs. Geochemical and microbiological water quality indicators, as well as bacterial communities, differed across NSWDs, yet water quality within most locations did not vary significantly diurnally or by sampling date. Meanwhile, NSWD source waters had distinctly different bacterial taxa abundances and specific bacterial genera. Shared geochemical and microbial characteristics of certain sources and outfall flows suggested the contributions of sources to outfall flows. The average proportions by sources contributing to MS4 outfalls were further estimated by SourceTracker and FEAST, respectively. The results of this study highlight the use of multiple tools when assessing chemical and microbiological water quality to predict sources of NSWDs contributing to urban MS4 flows during dry weather. This information can be used to support management actions to reduce unnatural and high risk sources of dry weather drainage while preserving natural sources important to environmental health in downstream receiving waters.