Changes In Microbial Diversity Research Articles

An In Vitro Evaluation of the Antimicrobial Efficacy of a Novel Irrigant Using Next-Generation Sequencing

IntroductionTo evaluate the antimicrobial activity of Triton irrigation versus 4% sodium hypochlorite (NaOCl) utilizing a direct contact test and an extracted tooth model. MethodsIn the first experiment, a direct contact test was conducted to compare bacterial DNA removal and microbial diversity changes following irrigation with 4% NaOCl or Triton. Hydroxyapatite and dentin discs were inoculated with subgingival human-derived dental plaque for 2 weeks utilizing the Center for Disease Control biofilm reactor and subsequently challenged with the root canal irrigants for 5 minutes. In the second experiment, teeth contaminated with a multispecies biofilm (n = 24) were assigned into two treatment groups, NaOCl or Triton irrigation. Samples were obtained for quantitative real-time polymerase chain reaction and next-generation sequencing analysis before and after instrumentation. The Shannon and Chao1 indices were used to measure alpha diversity. The Bray–Curtis dissimilarity and ANOSIM was used to measure beta diversity. Differences in abundances of genera were evaluated using Kruskal–Wallis test with Bonferroni corrections. ResultsThe direct contact test revealed no significant differences in the bacterial load based on 16S rRNA gene molecules/μL, reads, or differences in the Shannon index among groups. In the extracted tooth model, a bacterial load reduction of log10 3.08 ± 0.69 and 2.76 ± 0.91 were found for NaOCl and Triton, respectively (P = .348). Next-generation sequencing showed fewer reads, lower Chao1, and beta diversity values when pretreatment and post-treatment samples were assessed in both experimental groups (P < .0001). The Kruskal–Wallis analysis found that 17 genera of bacteria were over-represented in minimal values in the Triton post-treatment group, 14 of these genera represented less than 1% of the microbial community. ConclusionsBoth irrigants had limited antimicrobial activity in the direct contact test. When used in conjunction with mechanical instrumentation both irrigants were able to reduce the bacterial DNA load and diversity in comparison with pretreatment communities. The NaOCl irrigation, followed by ethylenediaminetetraacetic acid flush, was more effective in decreasing DNA counts from low-abundance organisms.

Dynamic population changes during a bioaugmented sewage sludge composting process: Improvement of pharmaceutical active compounds degradation and conversion into an organic soil amendment

Bioaugmentation has resulted in an interesting tool to improve the remotion of emerging contaminants through composting technologies in sewage sludge, whose microbial population dynamics might play a critical role during degradation. It was hypothesized that the two-step bioaugmentation-composting technology can guarantee both, an effective addition of specific inoculants and the enhancement of the degradation activity in relation to their application and their interactions with indigenous communities. Following this hypothesis, this study aimed to define the changes of fungal and bacterial populations during microbial bioaugmentation of sewage sludge with two different inoculants (Penicillium oxalicum XD 3.1 and an enriched consortium) and throughout the composting process of the bioaugmented sludge. To do so, microbial DNA was obtained from the natural consortium and from the composite samples (at key stages of the process). The amplicon sequencing of 16S rRNA genes and internal transcribed spacer (ITS) region for bacteria and fungi was then performed using an Illumina Platform. The results highlighted the importance of the inoculation per se plays an important role in determining the success of microbial inoculation during the two-step composting. Thus, correctly addressing the degradation potential as well as the competitive ability of the inoculants to persist alongside native populations by enhancing the abundance, diversity and richness of fungi and bacterial taxa related with degradation processes. Moreover, various physicochemical parameters altered by the bioaugmentation equally explained the microbial diversity changes. Redundancy analyses of β-diversity revealed the asynchronous interaction with all physicochemical parameters that varied according to the composting stage.

The inflammatory immunity and gut microbiota are associated with fear response differences in laying hens

The fear response is a crucial adaptive mechanism for coping with environmental changes, and the individuals have different levels of fearfulness. The purpose of this study was to determine the status of the immune response and gut health in hens with different fear responses. A total of 80 healthy 75-week-old native Lindian chickens were individually housed in conventional cages and categorized into high (TH) and low (TL) levels of fearfulness using the tonic immobility (TI) test. The immunological status and intestinal health of the laying hens were assessed, and the intestinal microbial community was sequenced using 16S rRNA testing. The results showed that the immune-related genes of interleukin (IL)-1β, IL-4, IL-6, and IgG were significantly upregulated in the spleen of TH hens compared with hens in the TL group (P < 0.01). The inflammatory immune-related genes Toll-like receptor (TLR)2, TLR4, nuclear factor (NF)-κB, inducible nitric oxide synthase (iNOS), cyclooxygenase (COX)-2, IL-10, and IgG were significantly increased in the intestinal tract, whereas IL-4, IgA, and the intestinal barrier gene claudin-4 were significantly decreased in TH hens (P < 0.05). In addition, serum concentrations of IL-1β, IL-6, IL-10, interferon (IFN)-α and IgG were significantly higher in TH hens (P < 0.01). A high fear response also led to changes in gut microbial diversity, with a higher Simpson's index and lower β-diversity similarity than hens with a low-fear response (P < 0.05). The TH group showed an increase in eight genera, including Bacillaceae and Coprococcus, whereas the genus Anaerorhabdus decreased (P < 0.05). The gut microbiota has also been associated with gut barrier genes, and inflammatory cytokines. Bartonella stimulates IL-1β and IgG secretion, whereas Lactobacillus inhibits IL-6 secretion, and Coprococcus and Subdoligranulum are associated with the maintenance of intestinal barrier function. The results of this study suggest that laying hens with high fear response levels have a more sensitive immune response and a more enriched gut microbiota, which may have positive effects on adapting to a complex environment.

Effect of prednisolone in a kindling model of epileptic seizures in rats on cytokine and intestinal microbiota diversity

Epilepsy is a neurological disease characterized by spontaneous and recurrent seizures. Epileptic seizures can be initiated and facilitated by inflammatory mechanisms. As the dysregulation of the immune system would be involved in epileptogenesis, it is suggested that anti-inflammatory medications could impact epileptic seizures. These medications could potentially have a side effect by altering the structure and composition of the intestinal microbiota. These changes can disrupt microbial homeostasis, leading to dysbiosis and potentially exacerbating intestinal inflammation. We hypothesize that prednisolone may affect the development of epileptic seizures, potentially influencing the diversity of the intestinal microbiota and the regulation of pro-inflammatory cytokines in intestinal tissue. This study aimed to evaluate the effects of prednisolone treatment on epileptic seizures and investigate the effect of this drug on the bacterial diversity of the intestinal microbiota and markers of inflammatory processes in intestinal tissue. We used Male Wistar rat littermates (n = 31, 90-day-old) divided into four groups: positive control treated with 2 mg/kg of diazepam (n = 6), negative control treated with 0.9 g% sodium chloride (n = 6), and the remaining two groups were subjected to treatment with prednisolone, with one receiving 1 mg/kg (n = 9) and the other 5 mg/kg (n = 10). All administrations were performed intraperitoneally (i.p.) over 14 days. To induce the chronic model of epileptic seizures, we administered pentylenetetrazole (PTZ) 25 mg/kg i.p. on alternate days. Seizure latency (n = 6 – 10) and TNF-α and IL-1β concentrations from intestinal samples were measured by ELISA (n = 6 per group), and intestinal microbiota was evaluated with intergenic ribosomal RNA (rRNA) spacer (RISA) analysis (n = 6 per group). The prednisolone treatment demonstrated an increase in the latency time of epileptic seizures and TNF-α and IL-1β concentrations compared to controls. There was no statistically significant difference in intestinal microbiota diversity between the different treatments. However, there was a strong positive correlation between microbial diversity and TNF-α and IL-1β concentrations. The administration of prednisolone yields comparable results to diazepam on increasing latency between seizures, exhibiting promise for its use in clinical studies. Although there were no changes in intestinal microbial diversity, the increase in the TNF-α and IL-1β cytokines in intestinal tissue may be linked to immune system signaling pathways involving the intestinal microbiota. Additional research is necessary to unravel the intricacies of these pathways and to understand their implications for clinical practice.

Analysis of microbial community evolution, autolysis phenomena, and energy metabolism pathways in Pholiota nameko endophytes.

Pholiota nameko is a widely consumed edible fungus. This study focuses on two crucial developmental stages of Pholiota nameko, namely, mycelium and ascospores. The objectives of this research were to investigate changes in microbial diversity and community structure during the growth of Pholiota nameko and to analyze the adaptability of the dominant strains to their respective habitats through metabolic. Specifically, we conducted second-generation sequencing of the 16S rRNA gene (Illumina) on samples obtained from these stages. In addition, we isolated and characterized endophytes present in Pholiota nameko, focusing on examining the impact of dominant endophyte genera on autolysis. We also conducted a metabolic pathway analysis. The results unveiled 578,414 valid sequences of Pholiota nameko endophytic fungi. At the phylum level, the dominant taxa were Basidiomycota, Ascomycota, Zoopagomycota, and Mucoromycota. At the genus level, the dominant taxa observed were Pholiota, Inocybe, Fusarium, and Hortiboletus. For endophytic bacteria, we obtained 458,475 valid sequences. The dominant phyla were Proteobacteria, TM6, Firmicutes, and Bacteroidetes, while the dominant genera were Edaphobacter, Xanthomonas, Burkholderia, and Pseudomonas. Moreover, we identified the isolated strains in Pholiota nameko using 16S rDNA, and most of them were found to belong to the genus Pseudomonas, with Pseudomonas putida being the most prevalent strain. The findings revealed that the Pseudomonas putida strain has the ability to slow down the breakdown of soluble proteins and partially suppress the metabolic processes that generate superoxide anion radicals in Pholiota nameko, thereby reducing autolysis. Additionally, our results demonstrated that molybdenum enzyme-mediated anaerobic oxidative phosphorylation reactions were the primary energy metabolism pathway in the Pseudomonas putida strain. This suggests that the molybdenum cofactor synthesis pathway might be the main mechanism through which Pholiota nameko adapts to its complex and diverse habitats.

Biofabrication of Silver Nanoparticles by Azadirachta indica Rhizosphere Bacteria with Enhanced Antibacterial Properties

Microorganisms (MOs) are prominent in ecological functioning and balance. The rhizosphere is considered one of the most diverse ecosystems on Earth and serves as a breeding spot for many MOs. Rhizosphere microbial diversity changes according to plant species, genotype, and the nature of the soil. The current study reports the possible use of bacteria isolated from the rhizosphere of Azadirachta indica for synthesizing silver nanoparticles (AgNPs). The physicochemical characterization and antibacterial activity of these green synthesized AgNPs are also reported. The gene (16S rRNA) sequence of bacteria isolated from the rhizosphere showed a maximum similarity of 99.25% with Bacillus subtilis. After incubation, the colorless reaction mixture transformed to brown, which indicates the formation of AgNPs, and UV-vis spectral analysis also confirmed the biosynthesis of AgNPs. Compared to lower temperatures, the efficiency of AgNP synthesis was high at the higher temperature. The scanning electron microscope image demonstrated spherical-shaped AgNPs with sizes ranging from 18 to 21 nm. Energy-dispersive X-ray analysis established the elemental analysis of synthesized AgNPs. The synthesized AgNPs showed strong bactericidal properties against pathogenic bacteria Klebsiella pneumonia, Pseudomonas aeruginosa, Escherichia coli, and methicillin-resistant Staphylococcus aureus.

The Diversity and Composition of Soil Microbial Communities Differ in Three Land Use Types of the Sanjiang Plain, Northeastern China.

In recent years, the Sanjiang Plain has experienced drastic human activities, which have dramatically changed its ecological environment. Soil microorganisms can sensitively respond to changes in soil quality as well as ecosystem function. In this study, we investigated the changes in soil microbial community diversity and composition of three typical land use types (forest, wetland and cropland) in the Sanjiang Plain using phospholipid fatty acid analysis (PLFA) technology, and 114 different PLFA compounds were identified. The results showed that the soil physicochemical properties changed significantly (p < 0.05) among the different land use types; the microbial diversity and abundance in cropland soil were lower than those of the other two land use types. Soil pH, soil water content, total organic carbon and available nitrogen were the main soil physico-chemical properties driving the composition of the soil microbial community. Our results indicate that the soil microbial community response to the three different habitats is complex, and provide ideas for the mechanism by which land use changes in the Sanjiang Plain affect the structure of soil microbial communities, as well as a theoretical basis for the future management and sustainable use of the Sanjiang plain, in the northeast of China.

Effect of aerobic exercise and particulate matter exposure duration on the diversity of gut microbiota

ABSTRACT Inhalation of ambient particulate matter (PM) can disrupt the gut microbiome, while exercise independently influences the gut microbiome by promoting beneficial bacteria. In this study, we analyzed changes in gut microbial diversity and composition in response to combined interventions of PM exposure and aerobic exercise, extending up to 12 weeks. This investigation was conducted using mice, categorized into five groups: control group (Con), exercise group (EXE), exercise group followed by 3-day exposure to PM (EXE + 3-day PM), particulate matter exposure (PM), and PM exposure with concurrent treadmill exercise (PME). Notably, the PM group exhibited markedly lower alpha diversity and richness compared to the Con group and our analysis of beta diversity revealed significant variations among the intervention groups. Members of the Lachnospiraceae family showed significant enhancement in the exercise intervention groups (EXE and PME) compared to the Con and PM groups. The biomarker Lactobacillus, Coriobacteraceae, and Anaerofustis were enriched in the EXE group, while Desulfovibrionaceae, Mucispirillum schaedleri, Lactococcus and Anaeroplasma were highly enriched in the PM group. Differential abundance analysis revealed that Paraprevotella, Bacteroides, and Blautia were less abundant in the 12-week PM exposure group than in the 3-day PM exposure group. Moreover, both the 3-day and 12-week PM exposure groups exhibited a reduced relative abundance of Bacteroides uniformis, SMB53, and Staphylococcus compared to non-PM exposure groups. These findings will help delineate the possible roles and associations of altered microbiota resulting from the studied interventions, paving the way for future mechanistic research.

Microorganisms uniquely capture and predict stony coral tissue loss disease and hurricane disturbance impacts on US Virgin Island reefs.

Coral reef ecosystems are now commonly affected by major climate and disease disturbances. Disturbance impacts are typically recorded using reef benthic cover, but this may be less reflective of other ecosystem processes. To explore the potential for reef water-based disturbance indicators, we conducted a 7-year time series on US Virgin Island reefs where we examined benthic cover and reef water nutrients and microorganisms from 2016 to 2022, which included two major disturbances: hurricanes Irma and Maria in 2017 and the stony coral tissue loss disease outbreak starting in 2020. The disease outbreak coincided with the largest changes in the benthic habitat, with increases in the percent cover of turf algae and Ramicrusta, an invasive alga. While sampling timepoint contributed most to changes in reef water nutrient composition and microbial community beta diversity, both disturbances led to increases in ammonium concentration, a mechanism likely contributing to observed microbial community shifts. We identified 10 microbial taxa that were sensitive and predictive of increasing ammonium concentration. This included the decline of the oligotrophic and photoautotrophic Prochlorococcus and the enrichment of heterotrophic taxa. As disturbances impact reefs, the changing nutrient and microbial regimes may foster a type of microbialization, a process that hastens reef degradation.

Microbial response to Nature-Based Solutions in urban soils: A comprehensive analysis using Biolog® EcoPlates™

The study presents a comprehensive examination of changes in soil microbial functional diversity (hereafter called microbial activity) following the implementation of Nature-Based Solutions (NBS) in urban areas. Utilizing the Biolog® EcoPlates™ technique, the study explored variations in microbial diversity in urban soil under NBSs implementation across timespan of two years.Significant differences in microbial activity were observed between control location and those with NBS implementations, with seasonal variations playing a crucial role. NBS positively impacted soil microbial activity especially at two locations: infiltration basin and wild flower meadow showing the most substantial increase after NBS implementation. The study links rainfall levels to microbial functional diversity, highlighting the influence of climatic conditions on soil microbiome. The research investigates also the utilization of different carbon sources by soil microorganisms, shedding light on the specificity of substrate utilization across seasons and locations. The results demonstrate that NBSs implementations lead to changes in substrate utilization patterns, emphasizing the positive influence of NBS on soil microbial communities. Likewise, biodiversity indices, such as Shannon-Weaver diversity (H′), Shannon Evenness Index (E), and substrate richness index (S), exhibit significant variations in response to NBS. Notably, NBS implementation positively impacted H′ and E indexes, especially in infiltration basin and wild flower meadow, underlining the benefits of NBS for enhancing microbial diversity.The obtained results demonstrated valuable insight into the dynamic interactions between NBS implementation and soil microbial activity. The findings underscore the potential of NBS to positively influence soil microbial diversity in urban environments, contributing to urban sustainability and soil health. The study emphasizes the importance of monitoring soil microbial activity to assess the effectiveness of NBS interventions and guides sustainable urban development practices.

Oral microbiota imbalance: A predisposing factor for Henoch-Schönlein Purpura in children

Oral microecological dysregulation has been shown to be associated with various immune system disorders. Henoch-schonlein purpura (HSP) is an autoimmune small vessel inflammatory disease in children of uncertain etiology, and studies have suggested that streptococcal infection may be an influential factor in its development. However, the relationship between oral microecological dysregulation and HSP has not been clearly studied so far. In this study, an epidemiological survey on the oral health status of children with HSP was investigated in this paper, and collected dental plaque from four groups of children for 16SrDNA high-throughput sequencing to analyze the composition and changes of oral microbial diversity among different groups. The results showed that the oral health status of children with HSP was poor, except for the incidence of caries in the 5-year-old group, the caries rate and dmfs/DMFS in the 3,4 and 5-year-old groups were higher than the same age in the fourth Chinese Oral Health Epidemiological Survey. Moreover, the development of HSP is accompanied by disturbances in the oral microbiota; a decrease in the number of Firmicutes which producing butyric acid may be closely associated with the development of HSP; changes in the abundance of Streptococcus and Neisseria may be a risk factor for the development of HSP.

Intestinal microbial profiling and immune responses of hybrid snakehead (Channa maculata ♀ × Channa argus ♂) challenged with Nocardia seriolae strain

Nocardiosis in fish, caused by Nocardia seriolae (a kind of filamentous bacterium), is a severe disease in aquaculture, affecting over 40 species of marine and freshwater fish and causing great losses. To investigate the relationship between fish nocardiosis and the gut microbiota, we first artificially infected hybrid snakehead (female Channa maculata × male Channa argus) with N. seriolae (1.0 × 107 CFU/mL), then utilized techniques such as high-throughput sequencing of 16 S rRNA, histopathology, and quantitative reverse transcription-polymerase chain reaction (qRT-PCR) to analyze the changes in microbial community structure, intestinal histopathological characteristics, and related immune genes expression in hybrid snakehead. Changes in gut microbial community structure and diversity were observed starting from day 2, followed by fluctuations on day 4, and significant alterations on day 6. Four major phyla (Actinomycetes, Proteobacteria, Firmicutes, and Bacteroidetes), particularly Actinomycetes, reflected the temporal variations in the gut microbiota structure. The composition of the gut microbiota also underwent significant changes, with beneficial microorganisms such as Lactobacillus decreasing and harmful microorganisms such as Aeromonas and Nocardia increasing. The pathological sections showed that after N. seriolae injection, the fish intestinal villi became distorted and widely spaced, with increasing damage over time, leading to severe shrinkage and atrophy by the sixth day. Additionally, immune-related genes, such as TLR2 and IRF2, exhibited higher mRNA expression levels (P < 0.01) in the intestinal tissues of the infected fish. Overall, this study provides preliminary insights into the dynamic changes in gut microbial community, immune response, and intestinal pathogenic mechanisms during N. seriolae infection in hybrid snakehead, at both the levels of gut microbial composition and mRNA expression. These findings are important for better understanding and managing Nocardia infection in fish.

Abstract 2803: Identification of microbiome and predictive immune biomarkers in patients with advanced non-small lung cancer treated with pembrolizumab with or without chemotherapy

Abstract Background: Recent studies have shown that gut microbiota modulates antitumor immunity, and affect clinical efficacy of immune checkpoint inhibitors, including anti-programmed death-1 (PD-1) and programmed death-ligand 1 (PD-L1) inhibitors. We aimed to explore the metagenomic profiles of previously untreated, treatment naïve, stage IV non-small cell lung cancer (NSCLC) treated with pembrolizumab, an anti-PD1 agent with or without platinum-based chemotherapy and identify distinct ecological niche between responder and non-responder groups. Methods: We performed metagenome sequencing, whole exome sequencing (WES), and RNA sequencing (RNA-seq) on 50 patients with stage IV NSCLC, including adenocarcinoma (N=31) and squamous cell carcinoma (N=22). We employed Dirichlet Multinomial Mixtures (DMM) community typing to cluster microbial community profiling data at the genus level and analyzed the changes in microbial composition and diversity between enterotype 1 (E1, N=27) and enterotype 2 (E2, N=23). Mutation landscape including genomic alterations in relation to immune response was analyzed between responders and non-responders using WES data. Differentially expressed genes (DEGs), Gene Set Enrichment Analysis (GSEA), and immune deconvolution analysis were carried out using RNA-seq data to analyze molecular profiling of two enterotypes between the responder (N=15) and non-responder (N=35) groups. Results: The two enterotypes exhibited distinct microbial abundances and alpha diversity indices. Abundances of members of Bacteroidaceae (P=0.011) and Oscillospiraceae (P&amp;lt;0.001) were higher in E2 members, and enrichment of Lactobacillaceae (P=0.006) and Bifidobacteriaceae (P=0.041) were higher in E1. Compared to E1, the number of observed bacterial species (P&amp;lt;0.001) and Shannon index (P&amp;lt;0.001) was significantly higher in E2, indicating a healthier gut environment. The proportion of responders was higher in E2 than in E1 cluster. Comparison between responders and non-responder groups within each enterotype revealed that Lactobacillaceae showed an association with the response in E2 cluster. Mutation landscape revealed TP53 mutation as the most common mutation, more frequently observed in the E2 (100%) than in the E1 (56%) cluster. Conclusion: We explored the association between the gut microbiome and clinical response to pembrolizumab with or without combination with chemotherapy and found that E2 cluster enriched with Lactobacillaceae is associated with treatment response. Further analysis with larger cohort is ongoing. Citation Format: Jii Bum (Joy) Lee, Su-Jin Choi, Gang-Taik Lee, Junwon Yang, Hyun-Seok Oh, Arim Min, Bo-Eun Kwon, Seong-san Kang, Sujeong Baek, Dong Kwon Kim, Jae Hwan Kim, Sun Min Lim, Min Hee Hong, Kyoung-Ho Pyo, Byoung Chul Cho. Identification of microbiome and predictive immune biomarkers in patients with advanced non-small lung cancer treated with pembrolizumab with or without chemotherapy [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 2803.

Effects of ant nests on soil CH4 emissions from Syzygium oblatum communities of a secondary tropical forest.

Exploring the effects of ant nests on soil CH4 emissions in the secondary tropical forests is of great scientific significance to understand the contribution of soil faunal activities to greenhouse gas emissions. With static chamber-gas chromatography method, we measured the dry-wet seasonal dynamics of CH4 emissions from ant nests and control soils in the secondary forest of Syzygium oblatum communities in Xishuangbanna. We also examined the linkages of ant-mediated changes in functional microbial diversity and soil physicochemical properties with CH4 emissions. The results showed that: 1) Ant nests significantly accelerated soil CH4 emissions, with average CH4 emissions in the ant nests being 2.6-fold of that in the control soils. 2) The CH4 emissions had significant dry-wet seasonal variations, which was a carbon sink in the dry seasons (from -0.29±0.03 to -0.53±0.02 μg·m-2·h-1) and a carbon source in the wet seasons (from 0.098±0.02 to 0.041±0.009 μg·m-2·h-1). The CH4 emissions were significantly higher in ant nests than in control soils. The CH4 emissions from the ant nests had smaller dry-wet seasonal variation (from -0.38±0.01 to 0.12±0.02 μg·m-2·h-1) than those in the control soils (from -0.65±0.04 to 0.058±0.006 μg·m-2·h-1). 3) Ant nests significantly increased the values (6.2%-37.8%) of soil methanogen diversity (i.e., Ace and Shannon indices), temperature and humidity, carbon pools (i.e., total, easily oxidizable, and microbial carbon), and nitrogen pools (i.e., total, hydrolyzed, ammonium, and microbial biomass nitrogen), but decreased the diversity (i.e., Ace and Chao1 indices) of methane-oxidizing bacteria by 21.9%-23.8%. 4) Results of the structural equation modeling showed that CH4 emissions were promoted by soil methanogen diversity, temperature and humidity, and C and N pools, but inhibited by soil methane-oxidizing bacterial diversity. The explained extents of soil temperature, humidity, carbon pool, nitrogen pool, methanogen diversity, and methane-oxidizing bacterial diversity for the CH4 emission changes were 6.9%, 21.6%, 18.4%, 15.2%, 14.0%, and 10.8%, respectively. Therefore, ant nests regulated soil CH4 emission dynamics through altering soil functional bacterial diversities, micro-habitat, and carbon and nitrogen pools in the secondary tropical forests.

Rice straw ash and amphibian health: A deep dive into microbiota changes and potential ecological consequences

Rice straw is burned as a result of agricultural practices and technical limitations, generating significant volumes of ash that might have environmental and ecological consequences; however, the effects on organisms have not been researched. Amphibians depend on their gut and skin microbiomes. Ash exposure may cause inflammation and changes in microbial diversity and function in frogs' skin and gut microbiota due to its chemical composition and physical presence, but the implications remain unclear. Rana dybowskii were exposed to five aqueous extracts of ashes (AEA) concentrations for 30 days to study survival, metal concentrations, and microbial diversity, analyzing the microbiota of the cutaneous and gut microbiota using Illumina sequencing. Dominant elements in ash: K > Ca > Mg > Na > Al > Fe. In AEA, K > Na > Ca > Mg > As > Cu. Increased AEA concentrations significantly reduced frog survival. Skin microbiota alpha diversity varied significantly among all treatment groups, but not gut microbiota. Skin microbiota differed significantly across treatments via Bray-Curtis and weighted UniFrac; gut microbiota was only affected by Bray-Curtis. Skin microbiota varied significantly with AEA levels in Proteobacteria, Bacteroidetes, Actinobacteria, and Firmicutes, while the gut microbiota's dominant phyla, Firmicutes, Bacteroidetes, and Proteobacteria, remained consistent across all groups. Lastly, the functional prediction showed that the skin microbiota had big differences in how it worked and looked, which were linked to different health and environmental adaptation pathways. The gut microbiota, on the other hand, had smaller differences. In conclusion, AEA exposure affects R. dybowskii survival and skin microbiota diversity, indicating potential health and ecological impacts, with less effect on gut microbiota.

Aridity thresholds of microbiome-soil function relationship along a climatic aridity gradient in alpine ecosystem

Aridity is known to influence the structure and function of the soil microbiome and their connection with ecosystem functions, however, whether aridity leads to gradual (or abrupt) and systemic (or specific) changes in the microbiome-ecosystem functions relationships in alpine ecosystems is largely unknown. Here, we conducted a survey of 60 sites along an aridity-gradient transect across the Tibetan Plateau to investigate changes in microbial diversity and functions and to evaluate their relationship with soil functionality. We found that plant richness and biomass, soil microbial richness (e.g., bacteria, fungi, diazotrophs, saprotrophs, pathotrophs and symbiotrophs), the relative abundance of copiotrophs and soil functionality (e.g., C-, N-, and P cycling, multifunctionality) decreased along the aridity gradient, whereas the proportion of genes associated with organic matter decomposition and denitrification increased (obtained from metagenomic sequencing). Above an aridity threshold of ∼0.6, soil multifunctionality decreased slowly and supported a larger proportion of genes associated with cellulose, hemicellulose, chitin, lignin and pectin degradation as well as genes associated with denitrification (e.g., nosZ, nosZ atypical 2, norB-cNor and norB-qNor). In drier habitats (>0.6 aridity level), microbial diversity and genes involved in organic matter decomposition and N cycling were strongly correlated with soil multifunctionality, whereas plant diversity was closely associated with soil multifunctionality in wetter habitats (<0.6 aridity level). Plant biomass and soil organic C play a key role in regulating microbial compositional and functional diversity and further affect soil multifunctionality in drier habitats. These findings suggest that soil microbiomes may play a larger role in maintaining soil multifunctionality in more arid environments than in less arid environments. Our results highlight the threshold responses of microbial diversity and functions to aridity and provide novel insight into mechanisms by which climate change affects ecosystem functions.

Temperature drives microbial communities in anaerobic digestion during biogas production from food waste.

Resource depletion and climate changes due to human activities and excessive burning of fossil fuels are the driving forces to explore alternatives clean energy resources. The objective of this study was to investigate the potential of potato peel waste (PPW) at various temperatures T15 (15°C), T25 (25°C), and T35 (35°C) in anaerobic digestion (AD) for biogas generation. The highest biogas and CH4 production (117mL VS-g and 74mL VS-g) was observed by applying 35°C (T35) as compared with T25 (65mL VS-g and 22mL VS-g) on day 6. Changes in microbial diversity associated with different temperatures were also explored. The Shannon index of bacterial community was not significantly affected, while there was a positive correlation of archaeal community with the applied temperatures. The bacterial phyla Firmicutes were strongly affected by T35 (39%), whereas Lactobacillus was the dominant genera at T15 (27%). Methanobacterium and Methanosarcina, as archaeal genera, dominated in T35 temperature reactors. In brief, at T35, Proteiniphilum and Methanosarcina were positively correlated with volatile fatty acids (VFAs) concentration. Spearman correlation revealed dynamic interspecies interactions among bacterial and archaeal genera; facilitating the AD system. This study revealed that temperature variations can enhance the microbial community of the AD system, leading to increased biogas production. It is recommended for optimizing the AD of food wastes.

Golden bile powder prevents drunkenness and alcohol-induced liver injury in mice via the gut microbiota and metabolic modulation

BackgroundDrunkenness and alcoholic liver disease (ALD) are critical public health issues associated with significant morbidity and mortality due to chronic overconsumption of alcohol. Traditional remedies, such as bear bile powder, have been historically acclaimed for their hepatoprotective properties. This study assessed the efficacy of a biotransformed bear bile powder known as golden bile powder (GBP) in alleviating alcohol-induced drunkenness and ALD.MethodsA murine model was engineered to simulate alcohol drunkenness and acute hepatic injury through the administration of a 50% ethanol solution. Intervention with GBP and its effects on alcohol-related symptoms were scrutinized, by employing an integrative approach that encompasses serum metabolomics, network medicine, and gut microbiota profiling to elucidate the protective mechanisms of GBP.ResultsGBP administration significantly delayed the onset of drunkenness and decreased the duration of ethanol-induced inebriation in mice. Enhanced liver cell recovery was indicated by increased hepatic aldehyde dehydrogenase levels and superoxide dismutase activity, along with significant decreases in the serum alanine aminotransferase, aspartate aminotransferase, alkaline phosphatase, triglyceride, and total cholesterol levels (P < 0.05). These biochemical alterations suggest diminished hepatic damage and enhanced lipid homeostasis. Microbiota analysis via 16S rDNA sequencing revealed significant changes in gut microbial diversity and composition following alcohol exposure, and these changes were effectively reversed by GBP treatment. Metabolomic analyses demonstrated that GBP normalized the alcohol-induced perturbations in phospholipids, fatty acids, and bile acids. Correlation assessments linked distinct microbial genera to serum bile acid profiles, indicating that the protective efficacy of GBP may be attributable to modulatory effects on metabolism and the gut microbiota composition. Network medicine insights suggest the prominence of two active agents in GBP as critical for addressing drunkenness and ALD.ConclusionGBP is a potent intervention for alcohol-induced pathology and offers hepatoprotective benefits, at least in part, through the modulation of the gut microbiota and related metabolic cascades.

Analyzing microbial community and volatile compound profiles in the fermentation of cigar tobacco leaves

Variations in industrial fermentation techniques have a significant impact on the fermentation of cigar tobacco leaves (CTLs), consequently influencing the aromatic attributes of the resulting cigars. The entire fermentation process of CTLs can be categorized into three distinct phases: phase 1 (CTLs prior to moisture regain), phase 2 (CTLs post-moisture regain and pile fermentation), and phase 3 (CTLs after fermentation and drying). These phases were determined based on the dynamic changes in microbial community diversity. During phase 2, there was a rapid increase in moisture and total acid content, which facilitated the proliferation of Aerococcus, a bacterial genus capable of utilizing reducing sugars, malic acid, and citric acid present in tobacco leaves. In contrast, fungal microorganisms exhibited a relatively stable response to changes in moisture and total acid, with Aspergillus, Alternaria, and Cladosporium being the dominant fungal groups throughout the fermentation stages. Bacterial genera were found to be more closely associated with variations in volatile compounds during fermentation compared to fungal microorganisms. This association ultimately resulted in higher levels of aroma components in CTLs, thereby improving the overall quality of the cigars. These findings reinforce the significance of industrial fermentation in shaping CTL quality and provide valuable insights for future efforts in the artificial regulation of secondary fermentation in CTLs.Key points• Industrial fermentation processes impact CTLs microbial communities.• Moisture and total acid content influence microbial community succession in fermentation.• Bacterial microorganisms strongly influence CTLs’ aldehyde and ketone flavors over fungi.

Connection between gut microbiota and Anorexia Nervosa. Literature review

Introduction: Anorexia Nervosa (AN) stands as a severe mental disorder characterized by the highest mortality rate within the realm of psychiatric conditions. Its etiology encompasses genetic, neurobiological, environmental, and developmental factors. Recent investigations have shed light on the potential impact of the gut microbiota on the genesis and progression of AN.&#x0D; Aim of the Study: The aim of this paper is to provide a comprehensive review of the existing findings on relationship between gut dysbiosis and AN. The intention is to present new perspectives that contribute to a more detailed understanding of the multifaceted nature of this serious disorder.&#x0D; Description of the State of Knowledge: The gut microbiota takes a central role in modulating various physiological processes. Dysbiosis, which refers to an imbalance in gut microbiota composition, has recently drawn attention because of its association with several mental disorders. In the context of AN, studies have shown reduced microbial diversity and notable changes in specific bacterial populations. The influence of the gut microbiota on AN includes disturbances in the digestive system, changes in eating behaviours, and associations with related conditions such as anxiety and depression. Mechanisms such as the gut-brain axis, hormonal regulation and molecular mimicry contribute to these associations.&#x0D; Conclusions: Recognition of the pivotal role played by the gut microbiota in AN opens up avenues for potential therapeutic interventions. Pro- and prebiotics, along with fecal transplantation, emerge as promising modalities in the treatment of AN. Ongoing research is essential to further elucidate this evolving field, ultimately facilitating the development of targeted interventions for individuals with AN.