Changes In Microbial Structure Research Articles

Integrated Macrogenomics and Metabolomics Explore Alterations and Correlation between Gut Microbiota and Serum Metabolites in Adult Epileptic Patients: A Pilot Study.

Epilepsy (EP) is a complex brain disorder showing a lot of unknows reasons. Recent studies showed that gut microbiota can influence epilepsy via the brain-gut axis. Nevertheless, the mechanism by which gut microbiota affects adult epilepsy still remains unclear. In this study, fecal and serum samples were obtained from patients with epilepsy and normal controls. Using an integrated analysis, sequencing was performed by macrogenomics and high-throughput targeted metabolomics with various bioinformatics approaches. The macrogenomic sequencing revealed significant changes in microbial structure in patients suffering from epilepsy. For example, at the phylum level, the relative abundance of Actinobacteria, Bacteroidetes and Proteobacteria showed an increase in the patients with epilepsy, whereas that of Firmicutes decreased. In addition, the patients with epilepsy had significantly differential metabolite profiles compared to normal controls, and five clusters with 21 metabolites, mainly containing the upregulation of some fatty acids and downregulation of some amino acids. Tryptophan (AUC = 91.81, p < 0.0001), kynurenine (AUC = 79.09, p < 0.01) and 7Z,10Z,13Z,16Z-Docosatetraenoic acid (AUC = 80.95, p < 0.01) may be used as potential diagnostic markers for epilepsy. Differential serum metabolites have effects on tryptophan metabolism, iron death and other pathways. Furthermore, a multiomic joint analysis observed a statistically significant correlation between the differential flora and the differential serum metabolites. In our findings, a macrogenomic analysis revealed the presence of dysregulated intestinal flora species and function in adult epileptic patients. Deeper metabolomic analyses revealed differences in serum metabolites between patients with epilepsy and healthy populations. Meanwhile, the multiomic combination showed connection between the gut microbes and circulating metabolites in the EP patients, which may be potential therapeutic targets.

Effects of organic amendments on soil bacterial community structure and yield in a saline‐sodic soil cropped with rice

AbstractOrganic improvement measures play a crucial role in the reclamation of saline‐sodic soil. However, there is still a limited understanding regarding the relationships between soil microbes and soil properties and crop yield in response to the application of these organic materials to saline‐sodic soils. In a field trial, the following treatments were carried out: no modifier input (CK) and compound lignite organic modifier 30 t/ha (LOM) with 2 years of rice cultivation, no modifier input (RF) with 5 years of rice cultivation, and the full amount of straw was returned to the field with rice‐duck farming (SW). Compared with RF and CK, the SOM content in the 0–20 cm soil layer of SW and LOM was significantly increased by 4.600 and 5.020 g kg−1, respectively, while the total alkalinity and pH were significantly decreased. In the 20–40 cm soil layer, the LOM treatment resulted in decreased pH and total alkalinity compared with other treatments. Overall, changes in soil microbial structure changes were significantly associated with SOM and pH levels. In the 0–20 cm soil layer, the LOM treatment significantly increased the relative abundance of Proteobacteria, while SW treatment significantly increased the relative abundance of Bacteroidetes and Firmicutes compared with CK. Moreover，the relative abundances of Longobacteriaceae of Bacteroidetes, Hydrogenaceae, and Xanthomonas of Proteobacteria were positively correlated with crop yield. The yields of SW and LOM were 6985.587 and 7879.910 kg ha−1, respectively. These results demonstrate that implementing comprehensive organic improvement measures can enhance the properties of saline‐sodic soil and increase crop yield, with lignite composite organic amendments may be more suitable for sustainable agricultural development.

Bacterial Colonization in the Airways and Intestines of Twin and Singleton Preterm Neonates: A Single-Center Study.

Limited studies have investigated the microbial colonization of the airways and intestines in preterm neonates. We studied the composition of intestinal and airway bacterial colonies in several preterm twin pairs and singletons to explore the dominant bacteria, assess their variability, and predict their phenotypic and metabolic functions. In this descriptive study, we collected sputum and fetal stool specimens from 10 twin pairs (20 cases) and 20 singleton preterm neonates. These specimens were analyzed using 16S rRNA deep sequencing to study the alpha and beta diversities and community structures of airway and intestinal bacteria and predict their metabolic functions. Specimens from twins and singleton neonates had distinct aggregations of intestinal and airway bacteria but showed similarities and high microbial diversities during initial colonization. The top five phyla were Proteobacteria, Firmicutes, Actinobacteriota, Bacteroidota, and Cyanobacteria. The top ten genera were Streptococcus, Acinetobacter, Ralstonia, Staphylococcus, Comamonas, Enterococcus, Stenotrophomonas, Dechlorosoma, Sphingopyxis, and Rothia. Potentially pathogenic and highly stress-tolerant Gram-negative bacteria were predominant in the intestinal flora. A considerable proportion of colonies recovered from the airway and intestines of preterm neonates were functional bacteria. The richness of the intestinal and airway flora was not significantly different between twins and singletons, and the flora clustered together. Both intestinal and airway bacteria of twins and singletons were similar. The species involved in initial colonization were similar but different in proportions; therefore, changes in microbial structure and richness may not be attributed to these species.

Exploring the Feasibility of 16S rRNA Short Amplicon Sequencing-Based Microbiota Analysis for Microbiological Safety Assessment of Raw Oyster.

16S rRNA short amplicon sequencing-based microbiota profiling has been thought of and suggested as a feasible method to assess food safety. However, even if a comprehensive microbial information can be obtained by microbiota profiling, it would not be necessarily sufficient for all circumstances. To prove this, the feasibility of the most widely used V3-V4 amplicon sequencing method for food safety assessment was examined here. We designed a pathogen (Vibrio parahaemolyticus) contamination and/or V. parahaemolyticus-specific phage treatment model of raw oysters under improper storage temperature and monitored their microbial structure changes. The samples stored at refrigerator temperature (negative control, NC) and those that were stored at room temperature without any treatment (no treatment, NT) were included as control groups. The profiling results revealed that no statistical difference exists between the NT group and the pathogen spiked- and/or phage treated-groups even when the bacterial composition was compared at the possible lowest-rank taxa, family/genus level. In the beta-diversity analysis, all the samples except the NC group formed one distinct cluster. Notably, the samples with pathogen and/or phage addition did not form each cluster even though the enumerated number of V. parahaemolyticus in those samples were extremely different. These discrepant results indicate that the feasibility of 16S rRNA short amplicon sequencing should not be overgeneralized in microbiological safety assessment of food samples, such as raw oyster.

PH-responsive DMAEM Monomer for dental caries inhibition.

Previous research indicated that there is an aggregate of microorganism in oral cavity which takes part in promoting the occurrence of dental caries, but few studies on anticaries materials for these 'core microbiome' were developed. And We've found that DMAEM monomer has an obvious inhibitory effect on the growth of Streptococcus mutans and saliva biofilm, but the effect of that on the "core microbiome" of caries need further research. Thus, the objectives of this study were to explore the effect of DMAEM monomer on the core microbiota of dental caries, and to further study its anticaries effect. The changes of microbial structure and metabolic activity of the core microbiota biofilm were detected through measuring lactic acid yield, viable bacteria counts and demineralization depth, et al., and the anticaries potential in vivo of DMAEM monomer was evaluated by rat caries model. Meanwhile, high-throughput sequencing was used to analyze the microbial diversity change of saliva samples of rats. The results showed that DMAEM monomer could inhibit the growth of the core microbiota biofilm, decrease the metabolic activity and the acid production, as well as reduce the ability of demineralization under acidic conditions. Moreover, the degree of caries in the DMAEM group was significantly reduced, and the diversity and the evenness of oral microecology in the rats were statistically higher. In summary, DMAEM monomer could respond to acidic environment, significantly inhibit the cariogenic ability of the 'core microbiome' of caries, and help to maintain the microecological balance of oral cavity.

Effects of Variation in Tamarix chinensis Plantations on Soil Microbial Community Composition in the Middle Yellow River Floodplain

Floodplains have important ecological and hydrological functions in terrestrial ecosystems, experience severe soil erosion, and are vulnerable to losing soil fertility. Tamarix chinensis Lour. plantation is the main vegetation restoration measure for maintaining soil quality in floodplains. Soil microorganisms are essential for driving biogeochemical cycling processes. However, the effects of sampling location and shrub patch size on soil microbial community composition remain unclear. In this study, we characterized changes in microbial structure, as well as the factors driving them, in inside- and outside-canopy soils of three patch sizes (small, medium, large) of T. chinensis plants in the middle Yellow River floodplain. Compared with the outside-canopy soils, inside-canopy had higher microbial phospholipid fatty acids (PLFAs), including fungi, bacteria, Gram-positive bacteria (GP), Gram-negative bacteria (GN), and arbuscular mycorrhizal fungi. The ratio of fungi to bacteria and GP to GN gradually decreased as shrub patch size increased. Differences between inside-canopy and outside-canopy soils in soil nutrients (organic matter, total nitrogen, and available phosphorus) and soil salt content increased by 59.73%, 40.75%, 34.41%, and 110.08% from small to large shrub patch size. Changes in microbial community composition were mainly driven by variation in soil organic matter, which accounted for 61.90% of the variation in inside-canopy soils. Resource islands could alter microbial community structure, and this effect was stronger when shrub patch size was large. The results indicated that T. chinensis plantations enhanced the soil nutrient contents (organic matter, total nitrogen, and available phosphorus) and elevated soil microbial biomass and changed microbial community composition; T. chinensis plantations might thus provide a suitable approach for restoring degraded floodplain ecosystems.

Dose-dependent impact of compost on rhizosphere bacterial community in heavy metal-contaminated paddy soil

Different doses (1%, 5%, 10%, mass fraction) of animal manure compost were added into a multi-heavy metal contaminated paddy soil for 150 d, and the changes in microbial structure and composition were evaluated. Compost exhibited dose-dependent effects on the rhizosphere bacterial community. Low (1%) and middle (5%) additions of compost exerted more distinct influence on bacterial community structure in rhizosphere soil than in bulk soil. The bacterial diversity after addition of compost decreased in rhizosphere soils compared with that in bulk soil. Results of redundancy analysis (RDA) indicated that different responses of rhizosphere and non-rhizosphere bacterial community to the changed soil physicochemical properties (soil pH, Pb, Cd and Cu levels) might be one reason for the differences. Thus, in agricultural management practice, the influence of compost on rhizosphere microbes should be considered.

Reduced cadmium(Cd) accumulation in lettuce plants by applying KMnO4 modified water hyacinth biochar

In this study, water hyacinth was adopted to prepare biochar followed by modification using KMnO4. And the modified biochars were applied in Cd contaminated soil, exploring the effects of water hyacinth biochar on lettuce growth, Cd enrichment, soil enzyme activities and microbial changes by pot experiments. Modified biochar application significantly reduced the Cd accumulation in lettuce shoots and roots. Compared to the control, the application of water hyacinth biochar at 1% rate resulted in significant reduction of Cd contents by 40.7% and 33.7% in the shoots and roots of lettuce. Also, the reduction was 33.3% and 20.8% compared with the application rate of unmodified biochar. With the increase of biochar application, the amount of Cd was absorbed by lettuce shoots and roots showing significant reduction of plant Cd accumulation in response to the biochar application rate. Additionally, the lowest available Cd concentration in soil (1.34 mg kg−1) was obtained with the application of modified biochar at 1% rate, which might be the main reason for the lower Cd concentration in lettuce shoot and root parts. Furthermore, structural analysis showed that Cd was fixed on the modified biochar, in a passivated state, by larger specific surface area, more active sites and more stable covalent binding complexes leading to a strong decrease of the available Cd in the soil. Moreover, it was concluded that the increment of the enzyme activities in the soil was up to 2.51 times significantly following the application of modified water hyacinth biochar with 3% amount. Lastly, 16sRNA sequencing showed that biochar addition may lead to changes of microbial structure and abundance in soil.

Silicon Fertilizer and Microbial Agents Changed the Bacterial Community in the Consecutive Replant Soil of Lilies

Crop replanting leads to soil degradation and soil productivity reduction, which is a challenge for sustainable agricultural development. We previously found that silicon fertilizers combined with additional microbial agents are an effective means to alleviate problems that occur in a variety of Chinese lily during replanting, but little is known about the changes in microbial structure during this process. In the present study, we applied four treatments: CK (control), SF (silicon fertilizer), MF (microbial agents), and SMF (combination of silicon fertilizer and microbial agents). We treated the soil constantly for three years and investigated the bacterial community structure and some specific microbial groups in the soil of the lily root zone using 16S rRNA high-throughput sequencing analysis. The results showed that silicon fertilizer and microbial agent treatment significantly improved the growth status of the plants and changed the diversity and structure of the bacterial community in the soil. The genus Pseudomonas significantly increased in the SF treatment, and the phylum Actinobacteria and the genera Nordella, Devosia, and Rhodoplanes significantly increased in the SMF treatment. The genera Nordella, Pedomicrobium, and Chthoniobacter correlated with the seedling index or available silicon content. In addition, the two genera Gaiella and Nocardioides were the key species linking the bacterial community in the soil. The soil physicochemical properties played an important role in restoring the soil bacterial community structures. In conclusion, silicon fertilizer and microbial agents changed the diversity and structure of the bacterial community. Under the fertilizer supplement model, the enrichment of the phylum Actinobacteria and the genus Pseudomonas played an important role in improving soil health and alleviating CRPs in lilies. In addition, organic matter, available phosphorus, available potassium, and available silicon were found to be the most important factors that have a great impact on the restoration of bacterial community structures.

Effect of captivity and water salinity on culture-dependent frog skin microbiota and Batrachochytrium dendrobatidis (Bd) infection

ABSTRACT The world is undergoing a sixth mass extinction, and the drastic decline of amphibians in the last several decades is a major contributing factor. The spread of the deadly Batrachochytrium dendrobatidis (Bd) fungus is a major causative agent, and captive breeding programs are under way to try and save endangered populations. However, how captivity affects Bd infection and the skin microbiota is not clear. We identified the skin bacteria of the South Australian frog Crinia signifera and showed that their culture-dependent skin microbiota is moderately stable in cohorts sampled from the same location in subsequent years. Their microbiota was also structurally different to that of a sympatric frog species, Limnodynastes tasmaniensis, indicating a specific microbial signature. Twenty-four C. signifera were placed into captivity for four weeks, exposed to a range of water salinity levels, during which time there was a significant reduction in identifiable skin bacterial species diversity, richness, and a change in microbial structure. The infection intensity of Bd was also significantly reduced in captivity, with some frogs becoming completely clear of infection, whilst water salinity level was not a significant determinant of Bd infection or skin microbiota.

Insights into the effects of micro and nanoscale Fe0 on elimination of excessive acidification during anaerobic digestion of the organic fraction of municipal solid waste: Similarities and differences in reactor performance and syntrophic metabolism

Fe0 above the micro size (zero valent iron; ZVI) can effectively eliminate or inhibit excessive acidification during anaerobic digestion of the organic fraction of municipal solid waste, particularly at high organic loading rates. However, the role of nanoscale ZVI (NZVI) in anaerobic digestion remains controversial. In this study, the effect of NZVI at different dosages (0.4, 0.5, 0.6, 0.7, 0.8 g/g volatile solids [VS]) on the anaerobic digestion stability of the organic fraction of municipal solid waste was investigated and compared with the performance of ZVI, as were its effects on microbial syntrophism. Similarly to ZVI, NZVI recovered methane production from excessive acidification conditions, but the optimal NZVI dosage (0.4 g/gVS) was far lower than that for ZVI (0.8 g/gVS), and eventually the methane yield reached 324 mL/gVS. Microbial structure changes coupled with substance transformation revealed that NZVI enhanced the metabolism of hydrogenotrophic methanogens for interspecies hydrogen transfer and acetotrophic methanogens.

Long-term alkaline volatile fatty acids production from waste streams: Impact of pH and dominance of Dysgonomonadaceae

Alkaline co-fermentation of primary sludge and external organic waste (OW) was studied to elucidate the influence of substrate ratios and long-term system robustness and microbial community dynamics using batch and semi-continuous reactors. Volatile fatty acid (VFA) production increased with increasing OW fraction in the substrate due to synergistic effects of co-degradation. VFA production at pH 10 increased up to 30,300 mgCOD/L (yield of 630 mg COD/gVSfed) but reduced over time to ≈10,000 mgCOD/L. Lowering pH to 9 led to the restoration of VFA production with a maximum of 32,000 mg COD/L (676 mg COD/g VSfed) due to changes in microbial structure. VFA was composed mainly of acetic acid, but propionic acid increased at pH 9. The microbial community was dominated by Bacillaceae (34 ± 10%) and Proteinivoracales_uncultured (16 ± 11%) at pH 10, while Dysgonomonadaceae (52 ± 8%) was enriched at pH 9. The study demonstrated a zero-waste strategy that turns organic wastes into bio-based products.

Nitrogen addition promotes soil microbial beta diversity and the stochastic assembly

Nitrogen (N) deposition is one of major environmental concerns and alters the microbial communities in the pedosphere. A central debate in governing microbial community is on the relative importance of deterministic (ecological selection) vs. stochastic processes (dispersal, drift, diversification or speciation), which consequently limited our understanding of microbial assembly in response to N addition. Here, we conducted a global analysis of high-throughput sequencing data to reveal the mechanisms of N-addition effects on soil microbial communities. The results show that N addition significantly shifted the microbial community structure and promoted microbial beta diversity, particularly in the N-limited ecosystems. Changes in microbial structure and beta diversity increased significantly as the N addition rate, study duration, and the degree of soil acidification increased. The stochastic processes are more important than the deterministic processes for microbial community assembly, while N addition significantly increase the importance of stochastic processes whether the phylogenetic relationship is considered or not. Overall, the current study highlights the important of ecological stochasticity in regulating microbial assembly under N deposition scenarios.

Soil microbial community and network changes after long-term use of plastic mulch and nitrogen fertilization on semiarid farmland

Soil microbes are crucial for improving soil quality and productivity. Plastic film mulch (FM), in conjunction with fertilization, has significantly improved crop yields over vast areas of dryland production. However, how these practices affect soil microbial communities, especially as regards co-occurrence patterns within microbial taxa, is unclear. The objective of this study was to determine the effects of 10 years of FM and four nitrogen (N) fertilization rates [0 (N0), 100 (N100), 250 (N250), and 400 (N400) kg N ha−1] on soil bacterial and fungal diversity, community structure, composition, and the co-occurrence network in a rainfed maize (Zea mays L.) field on the Loess Plateau of China. Results showed that N fertilization and FM did not affect soil microbial biomass carbon, but these practices changed the soil bacterial and fungal community structures. The bacterial community structure was dominantly affected by N fertilization, owing to the increased soil N content and decreased soil pH, which reduced bacterial community diversity and altered the relative abundance of some copiotrophic/oligotrophic taxa (e.g., Gemmatimonadetes, Acidobacteria, Rokubacteria, and Planctomycetes). Plastic mulch played a greater role in regulating the fungal community structure, primarily because FM increased soil moisture and promoted soil organic matter decomposition, thereby reducing fungal richness and altered the relative abundance of Chytridiomycota, Mortierellomycota, Glomeromycota, and Mucoromycota. Moreover, FM mediated the effects of N fertilization by reducing soil N content, and then increased the N threshold that caused changes in microbial structure. Network analysis indicated that FM caused an unstable co-occurrence network with fewer positive and negative links, while N fertilization increased both positive and negative (except N400) links, indicating enhanced cooperation and competition among microbes. These results indicate that long-term plastic mulch and high N fertilization could result in risk for soil quality in terms of soil microbial community structure and stability, suggesting that developing new management strategies is necessary to sustain dryland productivity.

Integrated Fecal Microbiome and Serum Metabolomics Analysis Reveals Abnormal Changes in Rats with Immunoglobulin A Nephropathy and the Intervention Effect of Zhen Wu Tang

Immunoglobulin A nephropathy (IgAN), an autoimmune renal disease with complicated pathogenesis, is one of the principal reasons for end-stage renal disease in the clinic. Evidence has linked apparent alterations in the components of the microbiome and metabolome to renal disease in rats. However, thus far, there is insufficient evidence that supports the potential relationship between gut microbiome, circulating metabolites, and IgAN. This study was designed to probe the effects of IgAN on intestinal microecology and metabolic phenotypes and to understand the possible underlying mechanisms. Fecal and serum samples were collected from IgAN rats. Composition of the gut microbiota and biochemical changes in the metabolites was analyzed using 16S rDNA sequencing and untargeted metabolomics. The IgAN rats exhibited renal insufficiency and increased concentration of 24-h urine protein, in addition to deposition of IgA and IgG immune complexes in the kidney tissues. There was a disturbance in the balance of gut microbiota in IgAN rats, which was remarkably associated with renal damage. Marked changes in microbial structure and function were accompanied by apparent alterations in 1,403 serum metabolites, associated with the disorder of energy, carbohydrate, and nucleotide metabolisms. Administration of Zhen Wu Tang ameliorated microbial dysbiosis and attenuated the renal damage. Besides, treatment with Zhen Wu Tang modulated the metabolic phenotype perturbation in case of gut microbiota dysbiosis in IgAN rats. In conclusion, these findings provided a comprehensive understanding of the potential relationship between the intestinal microbiota and metabolic phenotypes in rats with IgAN. Elucidation of the intestinal microbiota composition and metabolic signature alterations could identify predictive biomarkers for disease diagnosis and progression, which might contribute to providing therapeutic strategies for IgAN.

Wine Terroir and the Soil Bacteria: An Amplicon Sequencing-Based Assessment of the Barossa Valley and Its Sub-Regions.

A wines’ terroir, represented as wine traits with regional distinctiveness, is a reflection of both the biophysical and human-driven conditions in which the grapes were grown and wine made. Soil is an important factor contributing to the uniqueness of a wine produced by vines grown in specific conditions. Here, we evaluated the impact of environmental variables on the soil bacteria of 22 Barossa Valley vineyard sites based on the 16S rRNA gene hypervariable region 4. In this study, we report that both dispersal isolation by geographic distance and environmental heterogeneity (soil plant-available P content, elevation, rainfall, temperature, spacing between row and spacing between vine) contribute to microbial community dissimilarity between vineyards. Vineyards located in cooler and wetter regions showed lower beta diversity and a higher ratio of dominant taxa. Differences in soil bacterial community composition were significantly associated with differences in fruit and wine composition. Our results suggest that environmental factors affecting wine terroir, may be mediated by changes in microbial structure, thus providing a basic understanding of how growing conditions affect interactions between plants and their soil bacteria.

Throat Microbial Community Structure and Functional Changes in Postsurgery Laryngeal Carcinoma Patients.

The microbial community structure in the throat and its shift after laryngectomy in laryngeal squamous cell carcinoma (LSCC) patients were investigated. Thirty swab samples taken prior to laryngectomy (SLC), 18 samples 1 week after laryngectomy (SLCA1w), and 30 samples 24 weeks after laryngectomy (SLCA24w) from 30 LSCC patients were examined. Microbial diversity was profiled through sequencing the V3-V4 variable region of the 16S rRNA gene. Quantitative real-time PCR (qPCR) was used to validate the 16S rRNA sequence data for the V3-V4 region. The community structure and function of throat microbiota were assessed by PICRUSt (phylogenetic investigation of communities by reconstruction of unobserved states) analysis. Both alpha and beta diversity results showed significant differences in the throat microbiota of LSCC patients before and after laryngectomy (P < 0.05). The drinking index of the SLC group was positively associated with the genus abundance of Prevotella (P < 0.05). The SLCA1w group had lower abundances of Fusobacterium, Leptotrichia, Lachnoanaerobaculum, and Veillonella than the SLC group (P < 0.05). The SLCA24w group had higher abundances of Streptococcus and Leptotrichia as well as lower abundances of Fusobacterium and Alloprevotella than the SLC group (P < 0.05). The throat microbiomes of the SLC group could be implicated in human cancer signaling pathways, as evidenced by PICRUSt analysis (P < 0.05). Our study clarifies alterations in throat microbial community structure and function in LSCC patients during the perioperative period and postoperative recovery period.IMPORTANCE Laryngeal squamous cell carcinoma greatly impacts patients' lives, and noninvasive means of prognostic assessment are valuable in determining the effectiveness of laryngectomy. We set out to study the microbial structure changes in the throat before and after laryngectomy and found the gene functions of several throat bacteria to be associated with human cancer signaling pathways. Our findings may offer insights into the disease management of patients with laryngeal squamous cell carcinoma. We hope to provide a means of using molecular mechanisms to improve the prognosis of laryngeal cancer treatment and to facilitate relevant research.

Soil Microbial Community Profiling and Bacterial Metabolic Activity of Technosols as an Effect of Soil Properties following Land Reclamation: A Case Study from the Abandoned Iron Sulphide and Uranium Mine in Rudki (South-Central Poland)

The aims of the study were (1) to recognize the structure of bacteria diversity in Technosols developed from mine spoils containing iron (Fe) sulphides with the use of culture-independent technique, and (2) to determine microbial metabolic activities, in the context of their potential to be an adequate indicators of soil properties being the consequence of land reclamation. The study site was located in the vicinity of the abandoned Fe sulphide and uranium mine in Rudki village (Holy Cross Mts., Poland). Three soil profiles with different chemical properties (pH, content of carbonates, soil salinity, content of total organic carbon and total nitrogen) were studied. Biodiversity was determined with the use of meta-barcoding of 16S rRNA community profiling analysis based on the hypervariable V3-V4 region of 16S rRNA gene (MiSeq, Illumina). The catabolic fingerprinting of soil microbial communities was evaluated with the use of Biolog®EcoPlates™ System. It was evidenced that changes in microbial structure and their metabolic activity were the consequence of a combined effect of both the soil depth and soil chemical properties being the final result of reclamation process. Consequently, microbial indicators (from phyla to genera level) indirectly testifying about success or ineffectiveness of reclamation in technogenic soils were recommended. To our best knowledge, the present study is the first insight into Polish Technosols biodiversity and catabolic activity.

The alteration of gut microbiome and metabolism in amyotrophic lateral sclerosis patients

Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disease accompanied with severe paralysis or even death, while the pathogenesis of ALS is still unclear and no effective therapy exists. The accumulating evidence has indicated the association between gut microbiota and various neurological diseases. Thus, to explore the potential role of gut microbiome in ALS, 20 patients diagnosed with probable or definite ALS and 20 healthy controls were enrolled and their fecal excrements were collected. The analysis of fecal community diversity with 16S rDNA sequencing showed an obvious change in microbial structure of ALS patients, where Bacteroidetes at the phylum level and several microbes at the genus level were up-regulated, while Firmicutes at the phylum level and Megamonas at the genus level were down-regulated compared to healthy controls. Additionally, decreased gene function associated with metabolic pathways was observed in ALS patients. The metagenomics further demonstrated the discrepancies in microflora at the species level and relevant metabolites thereof were also revealed when combined with metabolomics. In conclusion, the altered composition of the gut microbiota and metabolic products in ALS patients provided deeper insights into the pathogenesis of ALS, and these biomarkers might be established as potential therapeutic targets which deserve further exploration.

Microbial community profiles grown on 1020 carbon steel surfaces in seawater-isolated microcosm

Corrosion of metallic alloys is a concern worldwide, with impacts affecting different production sectors and consequent economic losses in the order of billions of dollars annually. Biocorrosion is a form of corrosion where the participation of microorganisms can induce, accelerate, or inhibit corrosive processes. In this study, it was evaluated that the changes in profile communities, by the sequencing of the 16S ribosomal gene, grown over steel coupons in a microcosm with no additional oxygen supplementation for 120 days. Analysis of abundance and diversity indices indicates marked changes in microbial structures throughout the 120-day period. Homology results of OTUs generated by Illumina sequencing indicated Proteobacteria phylum as the dominant group, comprising about 85.3% of the total OTUs, followed by Firmicutes and Bacteriodetes, both with 7.35%. Analyses at lower taxonomic levels suggested the presence of representatives described as corroders, such as Citreicella thiooxidans, Thalassospira sp., and Limnobacter thiooxidans. In conclusion, the results suggest that no additional oxygen supplementation profoundly altered the core of microbial communities, with a predominance of facultative anaerobic species.