Changes In Microbial Composition Research Articles

Restoration of Intestinal Microbiota After Inulin Supplementation Halted: The Secondary Effect of Supplemented Inulin.

Consumption of inulin could affect the intestinal microbiota composition. Hereby, it is aimed to investigate the intestinal microbial community restoration process when the inulin supplementation is terminated (i.e., the secondary effect). The current study investigates the response and restoration of intestinal microbiota to/after high (Inulin-H) and low (Inulin-L) dosage of inulin supplementation or sequential antibiotics and inulin (Anti-Inulin-L) supplementation, based on analysis of 16S rRNA gene sequences in C57BL/6 mice. The number of significantly changed genera in response to inulin is highest in Anti-Inulin-L (n=66) group, followed by Inulin-H (n=51) and Inulin-L (n=38) group. After inulin supplementation stops, microbiota of all studied groups tend to recover to their original states, with highest percentage of inulin-responding microbes stay significantly different at Anti-Inulin-L (93.94%) group, followed by Inulin-H (74.51%) and Inulin-L (44.12%) groups. Of note, the relative abundance of some non-inulin-responding taxa significantly increases during restoration. Sequential antibiotics and inulin supplementation induce greatest changes in the intestinal microbial composition, followed by high and low dosage of inulin. Additionally, the changes induce by supplemented inulin in the intestinal microbial community, provide a chance for some microbes to outcompete the other microbes during the spontaneous restoration.

Early Succession of Community Structures and Biotic Interactions of Gut Microbes in Eriocheir sinensis Megalopa after Desalination.

As an enduring Chinese freshwater aquaculture product, the Eriocheir sinensis has a high economic value and is characterized by a catadromous life style that undergoes seawater-freshwater migration. However, little is known about their gut microbial status as they move from saltwater to freshwater acclimatization. Here, we sampled and cultivated Eriocheir sinensis megalopa from three aquaculture desalination ponds and investigated their gut microbiota diversity, community structures and biotic interactions from megalopa stage to the first juvenile stage after desalination for 9 days. Our results revealed that during the transition from megalopa to the first juvenile in Eriocheir sinensis, a significant change in gut microbial composition was observed (for instance, changes in relative abundance of dominant phyla), which was, however, not influenced by different sampling sites. The species diversity (such as the richness) of the gut microbiota showed a hump-shaped pattern along the succession. However, the compositional differences of the gut microbes showed constantly increasing patterns during the succession after freshwater adaption for all three sampling sites. Further co-occurrence analysis also showed that the complexity of the ecological networks in gut microbes was significantly enhanced during the development, such as increasing numbers of network links, connectivity and modularity, and was confirmed by decreasing average path length and proportions of negative links. Taken together, the differences in community structures and biological interactions of gut microorganisms were more pronounced in Eriocheir sinensis megalopa during desalination than in diversity and species compositions. This implies that the gut microbes of Eriocheir sinensis megalopa would become more robust and adaptive during the developmental process.

Consecutive Fertilization-Promoted Soil Nutrient Availability and Altered Rhizosphere Bacterial and Bulk Fungal Community Composition

Fertilization is an important measure to quickly supplement the soil nutrients required for plantation productivity. However, the response patterns of the microbial community and functional taxa in Larix plantation root, rhizosphere, and bulk soil to short-term and consecutive fertilization have rarely been reported. In this study, we assessed Larix root, rhizosphere, and bulk soil microbial community on days 0, 5, 15, and 30 after the first inorganic fertilization and after three consecutive years of fertilization. The bacterial 16S and fungal ITS high-throughput sequencing technology were used to monitor changes in microbial community composition and potential functional groups, as well as changes in soil nutrient content and enzyme activity to evaluate the status of plantation soil productivity. Consecutive fertilization treatment significantly increased the available nitrogen, phosphorus, and potassium (NPK) content and soil enzyme activity. The nonmetric multidimensional scaling (NMDS) and analysis of similarities (ANOSIM) results showed that there were significant differences in microbial community composition in root samples, rhizosphere soil, and bulk soil samples. The dominant microbial taxa were different between root and soil microbial community composition. Consecutive fertilization treatment had little effect on endophytic microbial community but significantly increased the abundance of Gaiellales in rhizosphere soil and Mortierella in bulk soil. The redundancy analysis (RDA) and co-occurrence network analyses showed that Gaiellales and Mortierellales had significant positive correlations with soil nutrient content and enzyme activity. The fungal functional group compositions were significantly affected by consecutive fertilization treatment and the proportions of ectomycorrhizal and saprotroph significantly decreased, but the proportion of endophyte significantly increased in bulk soil samples. Our results suggested that consecutive fertilization may promote soil nutrient availability by increasing the abundance of Gaiellales and Mortierella. Consecutive fertilization maintained the balance of the soil microbiota under Larix plantation and had a positive effect on promoting soil nutrient availability. This study provided a theoretical basis for consecutive fertilization to promote soil nutrient availability through specific microbial groups.

Eisenia fetida-driven vermitechnology for the eco-friendly transformation of steel waste slag into organic amendment: An insight through microbial diversity and multi-model approach

The processing of steel waste slag from the black metallurgical sector seriously threatened the ecology. To counter these dangers, appropriate detoxification methods were required. Vermitechnology was one such strategy that could successfully convert this industrial waste into nutrient-rich products suitable for use in agriculture. This research primarily focuses on employing vermitechnology for the transformation of waste steel slag into vermicompost and to determine changes in microbial composition, nutrient cycling, and metal detoxification facilitated by earthworms (Eisenia fetida). Earthworm populations in steel waste vermibeds (sw-vermibeds) increased by 2.87–3.07 folds. T1(SW + CD-1:1) comparatively showed increased levels of nutrients such as nitrogen, phosphorus, and potassium. Microbial and enzymatic parameters were more pronounced in treatment T1. The findings of phospholipid fatty acid (PLFA) diversity demonstrate microbial diversity and fatty acid composition. Based on PLFA Sobol Sensitivity Analysis (SSA), PUFA and cyclo were the most sensitive inputs to the presence of heavy metal (HMs) concentrations in SW. In accordance with Taylor-based modelling, R-tree, and Mars were the most trusted regression models for predicting HMs toxicity on microbes. The bioavailable metal fractions of HMs (Fe, Ni, Cd, Cu, Pb, and Cr) decreased by 61–83%. The correlation was performed for 0 and 90 days for metal microbial interactions r (0 days), [BSR vs Fe, Cd, Cu, Ni = −0.99, −0.82, −0.43, −0.99] and r (90 days), [FDA vs Fe, Cu, Ni = −0.97, −0.47, −0.95]. Overall, the results indicated that T1(1:1 SW + CD) provided more favorable conditions for the development of microbes and Eisenia fetida. This research presents a new perspective to the world community on the transformation of harmful steel waste slag into advantageous biological resources by introducing a novel method of employing Eisenia fetida to remediate hazardous steel waste slag.

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.

Hydrogeological controls on microbial activity and habitability in the Precambrian continental crust.

Earth's deep continental subsurface is a prime setting to study the limits of life's relationship with environmental conditions and habitability. In Precambrian crystalline rocks worldwide, deep ancient groundwaters in fracture networks are typically oligotrophic, highly saline, and locally inhabited by low-biomass communities in which chemolithotrophic microorganisms may dominate. Periodic opening of new fractures can lead to penetration of surface water and/or migration of fracture fluids, both of which may trigger changes in subsurface microbial composition and activity. These hydrogeological processes and their impacts on subsurface communities may play a significant role in global cycles of key elements in the crust. However, to date, considerable uncertainty remains on how subsurface microbial communities may respond to these changes in hydrogeochemical conditions. To address this uncertainty, the biogeochemistry of Thompson mine (Manitoba, Canada) was investigated. Compositional and isotopic analyses of fracture waters collected here at ~1 km below land surface revealed different extents of mixing between subsurface brine and (paleo)meteoric waters. To investigate the effects this mixing may have had on microbial communities, the Most Probable Number technique was applied to test community response for a total of 13 different metabolisms. The results showed that all fracture waters were dominated by viable heterotrophic microorganisms which can utilize organic materials associated with aerobic/facultative anaerobic processes, sulfate reduction, or fermentation. Where mixing between subsurface brines and (paleo)meteoric waters occurs, the communities demonstrate higher cell densities and increased viable functional potentials, compared to the most saline sample. This study therefore highlights the connection between hydrogeologic heterogeneity and the heterogeneity of subsurface ecosystems in the crystalline rocks, and suggests that hydrogeology can have a considerable impact on the scope and scale of subsurface microbial communities on Earth and potentially beyond.

Impact of dry density and incomplete saturation on microbial growth in bentonite clay for nuclear waste storage.

Many countries are in the process of designing a deep geological repository (DGR) for long-term storage of used nuclear fuel. For several designs, used fuel containers will be placed belowground, with emplacement tunnels being backfilled using a combination of highly compacted powdered bentonite clay buffer boxes surrounded by a granulated "gapfill" bentonite. To limit the potential for microbiologically influenced corrosion of used fuel containers, identifying conditions that suppress microbial growth is critical for sustainable DGR design. This study investigated microbial communities in powdered and gapfill bentonite clay incubated in oxic pressure vessels at dry densities between 1.1g cm-3 (i.e. below repository target) and 1.6g cm-3 (i.e. at or above repository target) as a 1-year time series. Our results showed an initial (i.e. 1 month) increase in the abundance of culturable heterotrophs associated with all dry densities <1.6g cm-3, which reveals growth during transient low-pressure conditions associated with the bentonite saturation process. Following saturation, culturable heterotroph abundances decreased to those of starting material by the 6-month time point for all 1.4 and 1.6g cm-3 pressure vessels, and the most probable numbers of culturable sulfate-reducing bacteria (SRB) remained constant for all vessels and time points. The 16S rRNA gene sequencing results showed a change in microbial community composition from the starting material to the 1-month time point, after which time most samples were dominated by sequences associated with Pseudomonas, Bacillus, Cupriavidus, and Streptomyces. Similar taxa were identified as dominant members of the culture-based community composition, demonstrating that the dominant members of the clay microbial communities are viable. Members of the spore-forming Desulfosporosinus genus were the dominant SRB for both clay and culture profiles. After initial microbial growth while bentonite was below target pressure in the early phases of saturation, microbial growth in pressure vessels with dry densities of at least 1.4g cm-3 was eventually suppressed as bentonite neared saturation.

Seasonality and longer-term development generate temporal dynamics in the Populus microbiome.

Temporal variation in community composition is central to our understanding of the assembly and functioning of microbial communities, yet the controls over temporal dynamics for microbiomes of long-lived plants, such as trees, remain unclear. Temporal variation in tree microbiomes could arise primarily from seasonal (i.e., intra-annual) fluctuations in community composition or from longer-term changes across years as host plants age. To test these alternatives, we experimentally isolated temporal variation in plant microbiome composition using a common garden and clonally propagated plants, and we used amplicon sequencing to characterize bacterial/archaeal and fungal communities in the leaf endosphere, root endosphere, and rhizosphere of two Populus spp. over four seasons across two consecutive years. Microbial community composition differed among seasons and years (which accounted for up to 21% of the variation in microbial community composition) and was correlated with seasonal dissimilarity in climatic conditions. However, microbial community dissimilarity was also positively correlated with time, reflecting longer-term compositional shifts as host trees aged. Together, our findings demonstrate that temporal patterns in tree microbiomes arise from both seasonal fluctuations and longer-term changes, which interact to generate unique seasonal patterns each year. In addition to shedding light on two important controls over the assembly of plant microbiomes, our results also suggest future studies of tree microbiomes should account for background temporal dynamics when testing the drivers of spatial patterns in microbial community composition and temporal responses of plant microbiomes to environmental change.IMPORTANCEMicrobiomes are integral to the health of host plants, but we have a limited understanding of the factors that control how the composition of plant microbiomes changes over time. Especially little is known about the microbiome of long-lived trees, relative to annual and non-woody plants. We tested how tree microbiomes changed between seasons and years in poplar (genus Populus), which are widespread and ecologically important tree species that also serve as important biofuel feedstocks. We found the composition of bacterial, archaeal, and fungal communities differed among seasons, but these seasonal differences depended on year. This dependence was driven by longer-term changes in microbial composition as host trees developed across consecutive years. Our findings suggest that temporal variation in tree microbiomes is driven by both seasonal fluctuations and longer-term (i.e., multiyear) development.

Influence of Decomposed Stubble Return on the Soil Microbial Community Under Perennial Crop Rotation

The aim of this study was to understand how the application of decomposed stubble return (DSR), a type of bio-organic fertilization, affects soil microbial communities under crop rotation. The changes in microbial composition and diversity related to DSR were investigated based on metagenomic sequencing and comparative analysis of two groups of soil samples after a 3-year tomato-pepper-papaya rotation: the DSR and no-DSR (i.e., without DSR) groups, with the soils before crop rotation as the control group. Inter-group comparisons of the crop performance (growth and yield) and physicochemical soil properties (pH value, nutrient elements, and heavy metals) were also conducted to reveal the effects of DSR application on the soil. The relative abundance of bacteria was higher than 90% in all soil samples. Proteobacteria and Actinobacteria in the DSR group and Proteobacteria and Firmicutes in the no-DSR group, whereas Acidobacteria and Proteobacteria in the control, were the two most abundant phyla. The abundance of Proteobacteria decreased, whereas that of Actinobacteria increased, in the DSR-amended soil compared to the no-DSR soil. At genus level, Acidobacterium dominated in the control and genera Pseudomonas, Burkholderia, and Bacillus in the no-DSR group, while Burkholderia, Pseudomonas, and Bacillus in the DSR-amended soil comprised the majority of their microbiomes. The DSR soil had higher microbial diversity and relative abundance of Ascomycota fungi than the no-DSR group after the crop rotation. Along with higher diversity of microbial community, more favorable soil pH, better crop growth, higher crop yields, higher abundance of soil nutrient elements, and lower accumulation of heavy metals in the soil were found in the DSR group compared to the no-DSR one. Furthermore, the DSR soil had more similarities with the control than with the No-DSR soil, in aspects of microbial composition and microbe-derived potential gene functions. It was indicated that decomposed stubble return may improve soil conditions or prevent them from degradation incurred by long-term crop cultivation. It was suggested that the application of the compost derived from fermented post-harvest plant residue may be a general strategy for developing more sustainable agricultural systems.

Ginger polysaccharide alleviates the effects of acute exposure to carbonate in crucian carp (Carassius auratus) by regulating immunity, intestinal microbiota, and intestinal metabolism

Alkaline stress poses a significant challenge to the healthy growth of fish. Ginger polysaccharide (GP) is one of the main active substances in ginger and has pharmacological effects, such as anti-oxidation and immune regulation. However, the physiological regulatory mechanism of GP addition to diet on alkalinity stress in crucian carp remains unclear. This study aimed to investigate the potential protective effects of dietary GP on antioxidant capacity, gene expression levels, intestinal microbiome, and metabolomics of crucian carp exposed to carbonate (NaHCO3). The CK group (no GP supplementation) and COG group (NaHCO3 stress and no GP supplementation) were set up. The GPCS group (NaHCO3 stress and 0.4% GP supplementation) was stressed for seven days. Based on these data, GP significantly increased the activities of total antioxidant capacity (T-AOC), superoxide dismutase (SOD), catalase (CAT), glutathione peroxidase (GSH-PX), acid phosphatase (ACP), and alkaline phosphatase (AKP) in carp under alkalinity stress (p < 0.05) and decreased the activity of malon dialdehyde (MDA) (p < 0.05). GP restored the activity of GSH-PX, ACP, and AKP to CK levels. The expression levels of tumor necrosis factor β (TGF-β), tumor necrosis factor-alpha (TNF-α), interferon-gamma (IFN-γ), and interleukin 8 (IL-8) genes were decreased, and the expression levels of determination factor kappa-B (NF-κB) and interleukin 10 (IL-10) genes were increased (p < 0.05). Based on 16 S rRNA high-throughput sequencing, GP improved the changes in the intestinal microbial diversity and structural composition of crucian carp caused by NaHCO3 exposure. In particular, GP increased the relative abundance of Proteobacteria and Bacteroidetes and decreased the relative abundance of Actinobacteria. The metabolic response of GP to NaHCO3 exposed crucian carp guts was studied using LC/MS. Compared to the COG group, the GPCS group had 64 different metabolites and enriched 10 metabolic pathways, including lipid metabolism, nucleotide metabolism, and carbohydrate metabolism. The addition of GP to feed can promote galactose metabolism and provide an energy supply to crucian carp, thus alleviating the damage induced by alkalinity stress. In conclusion, GP can mitigate the effects of NaHCO3 alkalinity stress by regulating immune function, intestinal flora, and intestinal metabolism in crucian carp. These findings provide a novel idea for studying the mechanism of salt-alkali tolerance in crucian carp by adding GP to feed.

MICROBIOTA TRANSPLANTATION AND ITS ROLE IN AUTOIMUNNE DISEASES: LITERATURE REVIEW

Introduction: Autoimmune diseases affect around 10% of the world population. Most of these are complex diseases caused by the interaction between genetic, epigenetic and environmental factors. Furthermore, autoimmune diseases have become the third largest chronic disease, after cardiovascular diseases and cancer. The human microbiome may play an important role in autoimmunity, as loss of immunological tolerance may be caused by changes in microbial composition. Microorganisms can provoke an immune response against the host if tolerance mechanisms fail for several reasons. Objective: To carry out a literature review evaluating the role of microbiota transplantation in patients with autoimmune diseases. Method: This is a bibliographic review, with a search for articles carried out through the Virtual Health Library (VHL), LILACS, PubMed and Scopus for all relevant articles that included in their theme the involvement of microbiota transplantation and its role in autoimmune diseases. Final considerations: Fecal microbiota transplantation (FMT) has a very important role for patients with autoimmune diseases (AD), especially individuals with type 1 diabetes mellitus, systemic sclerosis, systemic lupus erythematosus and rheumatoid arthritis, in which FMT has demonstrated promising results. for the treatment of these individuals. However, as the literature is still quite limited in relation to the type of donor and ideal dosage, in addition to the route of administration and treatment interval for each type of autoimmune disease, it is important to carry out targeted studies with the aim of evaluating the effects. benefits of FMT targeted to each AD, in addition to the possible adverse events and the particular characteristics of this procedure in the treatment of ADs associated with changes in intestinal flora.

Analysis of Vaginal Microbiota Variations in the Third Trimester of Pregnancy and Their Correlation with Preterm Birth: A Case-Control Study.

This study conducted a detailed analysis of the vaginal microbiota in pregnant women to explore its correlation with preterm birth (PTB) outcomes. The primary objective was to identify microbial variations associated with increased PTB risk. Secondary objectives included investigating how changes in microbial composition relate to the local immune environment and PTB. Utilizing a retrospective case-control design, the study involved pregnant women with liveborn infants between 2019 and 2023. In total, 89 women who delivered preterm and 106 term deliveries were included. Data collection focused on third-trimester vaginal cultures. Statistically significant differences were observed between the preterm and full-term groups in several areas. The median white blood cell count (10.2 × 103/mm3 vs. 7.6 × 103/mm3, p = 0.009) and neutrophil count (7.2 × 103/mm3 vs. 5.1 × 103/mm3, p < 0.001) were higher in the preterm group. Vaginal pH was also elevated in preterm births (5.6 vs. 4.4, p < 0.001), with a higher prevalence of bacterial vaginosis (29.2% vs. 12.3%, p = 0.001) as indicated by the Nugent Score. The study noted a significant association of PTB with the presence of Candida spp. (OR = 1.84, p = 0.018), Gardnerella vaginalis (OR = 2.29, p = 0.003), Mycoplasma hominis (OR = 1.97, p = 0.007), and Ureaplasma urealyticum (OR = 2.43, p = 0.001). Conversely, a reduction in Lactobacillus spp. correlated with a decreased PTB risk (OR = 0.46, p = 0.001). The study provides compelling evidence that specific vaginal microbiota components, particularly certain pathogenic bacteria and an altered Lactobacillus profile, are significantly associated with PTB risk. These findings highlight the potential of targeting microbial factors in strategies aimed at reducing PTB rates. Further research is necessary to fully understand the complex interplay between microbial dynamics, host immunity, and PTB outcomes.

Changes in Microbial Composition During the Succession of Biological Soil Crusts in Alpine Hulun Buir Sandy Land, China

Biological soil crusts (biocrusts) are considered “desert ecosystem engineers” because they play a vital role in the restoration and stability maintenance of deserts, including those cold sandy land ecosystems at high latitudes, which are especially understudied. Microorganisms participate in the formation and succession of biocrusts, contributing to soil properties’ improvement and the stability of soil aggregates, and thus vegetation development. Accordingly, understanding the composition and successional characteristics of microorganisms is a prerequisite for analyzing the ecological functions of biocrusts and related applications. Here, the Hulun Buir Sandy Land region in northeastern China—lying at the highest latitude of any sandy land in the country—was selected for study. Through a field investigation and next-generation sequencing (Illumina MiSeq PE300 Platform), our goal was to assess the shifts in diversity and community composition of soil bacteria and fungi across different stages during the succession of biocrusts in this region, and to uncover the main factors involved in shaping their soil microbial community. The results revealed that the nutrient enrichment capacity of biocrusts for available nitrogen, total nitrogen, total phosphorus, total content of water-soluble salt, available potassium, soil organic matter, and available phosphorus was progressively enhanced by the succession of cyanobacterial crusts to lichen crusts and then to moss crusts. In tandem, soil bacterial diversity increased as biocrust succession proceeded but fungal diversity decreased. A total of 32 bacterial phyla and 11 fungal phyla were identified, these also known to occur in other desert ecosystems. Among those taxa, the relative abundance of Proteobacteria and Cyanobacteria significantly increased and decreased, respectively, along the cyanobacterial crust–lichen–moss crust successional gradient. However, for Actinobacteria, Chloroflexi, and Acidobacteria their changed relative abundance was significantly hump-shaped, increasing in the shift from cyanobacterial crust to lichen crust, and then decreasing as lichen crust shifted to moss crust. In this process, the improved soil properties effectively enhanced soil bacterial and fungal community composition. Altogether, these findings broaden our understanding about how soil microbial properties can change during the succession of biocrusts in high-latitude, cold sandy land ecosystems.

A28 A SERUM REDOX STATUS-RELATED INDICATOR IS ASSOCIATED WITH THE RISK OF ONSET OF CROHN'S DISEASE

Abstract Background Crohn's disease (CD) is a gastrointestinal disorder characterized by chronic inflammation. While increased oxidative stress is observed in established CD patients, it remains unknown whether a shift in redox status is present before the diagnosis of CD and whether it is correlated with changes in immune response and microbial composition. Our hypothesis is that oxidative stress plays a role in the development of CD, and it could be detected before the diagnosis of CD. Furthermore, it is likely to be correlated with systemic inflammation and alterations in gut microbiota composition. Aims We aimed to assess the relationship between the serum redox status-related indicators, specifically amino acids ratios, with risk of CD onset and if this is further association with systemic inflammation marker, and gut microbiota composition. Methods In the Genetic Environment Microbial Project (CCC-GEM), a cohort of first-degree relatives (FDRs) of CD patients was prospectively followed. Among them, we identified subjects who later developed CD, defined as pre-CD (n=69), and matched them at a 1:4 ratio with FDRs who remained disease-free (n=276). Serum levels at enrollment of cysteineglycine (reduced form) and cystineglycine (oxidized form) were quantified by mass spectrometry, and the cysteineglycine/cystineglycine ratio was used as an indicator of redox status. Conditional logistic regression assessed the association with CD, while partial Spearman regression evaluated its correlation with systemic inflammation, as indicated by c-reactive protein (CRP), and gut microbiota composition (determined by fecal 16S rRNA sequencing). Results A decrease in the ratio indicates a shift in redox status toward oxidative stress. The cysteineglycine/cystineglycine ratio was negatively associated with the likelihood of developing CD (coefficient = -0.6188; p =0.0146), and it was also negatively correlated with CRP levels (coefficient = -0.177; p =0.00095). A list of taxa belonging to the phyla Firmicutes and Actinobacteriota were positively correlated with cysteineglycine/cystineglycine ratio (p≤0.05). Conclusions This study is the first to report that when redox status shifts towards oxidative stress, as indicated by the cysteineglycine/cystineglycine ratio, the likelihood of CD increases. Furthermore, these markers also correlate with CRP levels and gut microbiota composition, indicating a loss of various taxa when the redox status shifts towards oxidative stress. Submitted on behalf of the CCC-GEM consortium. Funding Agencies CCC, CIHRHCT

Reforestation of Cunninghamia lanceolata changes the relative abundances of important prokaryotic families in soil.

Over the past decades, many forests have been converted to monoculture plantations, which might affect the soil microbial communities that are responsible for governing the soil biogeochemical processes. Understanding how reforestation efforts alter soil prokaryotic microbial communities will therefore inform forest management. In this study, the prokaryotic communities were comparatively investigated in a secondary Chinese fir forest (original) and a reforested Chinese fir plantation (reforested from a secondary Chinese fir forest) in Southern China. The results showed that reforestation changed the structure of the prokaryotic community: the relative abundances of important prokaryotic families in soil. This might be caused by the altered soil pH and organic matter content after reforestation. Soil profile layer depth was an important factor as the upper layers had a higher diversity of prokaryotes than the lower ones (p < 0.05). The composition of the prokaryotic community presented a seasonality characteristic. In addition, the results showed that the dominant phylum was Acidobacteria (58.86%) with Koribacteraceae (15.38%) as the dominant family in the secondary Chinese fir forest and the reforested plantation. Furthermore, soil organic matter, total N, hydrolyzable N, and were positively correlated with prokaryotic diversity (p < 0.05). Also, organic matter and were positively correlated to prokaryotic abundance (p < 0.05). This study demonstrated that re-forest transformation altered soil properties, which lead to the changes in microbial composition. The changes in microbial community might in turn influence biogeochemical processes and the environmental variables. The study could contribute to forest management and policy-making.

Sex differences in colonic gene expression and fecal microbiota composition in a mouse model of obesity-associated colorectal cancer

This study investigated the sex-specific correlation between obesity and colorectal cancer emphasizing a more pronounced association in males. Estrogen, chromosomal genes, and gut bacteria were assessed in C57BL6/J male, female and ovariectomized (OVX) female mice, subjected to either a low-fat diet (LFD) or high-fat diet (HFD) for 14 weeks. Induction of colon tumor involved azoxymethane (10 mg/kg) administration, followed by three cycles of dextran sulfate sodium. Male mice on HFD exhibited higher final body weight and increased colon tumors compared to females. Colonic mucin 2 expression was significantly higher in females. HFD-modulated differentially expressed genes numbered 290 for males, 64 for females, and 137 for OVX females. Only one up-regulated gene (Gfra3) overlapped between females and OVX females, while two down-regulated genes (Thrsp and Gbp11) overlapped between males and OVX females. Genes up-regulated by HFD in males were linked to cytokine-cytokine interaction, HIF-1 signaling pathway, central carbon metabolism in cancer. Sex-specific changes in gut microbial composition in response to HFD were observed. These findings suggest a male-specific vulnerability to HFD-induced colon tumor formation, implicating key genes and colonic bacteria in colon tumorigenesis.

Differential effects of four laboratory animal control diets on gut microbiota in mice.

The gut microbiota is intricate and susceptible to multiple factors, with diet being a major contributor. The present study aimed to investigate the impact of four commonly used laboratory animal control diets, namely Keao Xieli's maintenance diet (KX), HFK's 1025 (HF), Research Diets' D12450B (RD), and Lab Diet's 5CC4 (LD), on the gut microbiota of mice. A total of 40 mice were randomly assigned to four groups, and each group was fed one of the four diets for a duration of 8 weeks. The assessment of gut microbiota was conducted using 16S rRNA sequencing both at the beginning of the study (week 0) and the end (week 8), which served as the baseline and endpoint samples, respectively. Following the 8-week feeding period, no significant differences were observed in physiological parameters, including body weight, visceral weight, and blood biochemical indices, across the four groups. Nonetheless, relative to the baseline, discernible alterations in the gut microbiota were observed in all groups, encompassing shifts in beta-diversity, hierarchical clustering, and key genera. Among the four diets, HF diet exhibited a significant influence on alpha-diversity, RD diet brought about notable changes in microbial composition at the phylum level, and LD diet demonstrated an interconnected co-occurrence network. Mantel analysis indicated no significant correlation between physiological parameters and gut microbiota in the four groups. Overall, our study demonstrated that the four control diets had a minimal impact on physiological parameters, while exerting a distinct influence on the gut microbiota after 8 weeks. © 2024 Society of Chemical Industry.

Fecal microbiome composition and diversity of cryopreserved canine stool at different duration and storage conditions.

Fresh-frozen stool banks intended for humans with gastrointestinal and metabolic disorders have been recently established and there are ongoing efforts to establish the first veterinary fresh-frozen stool bank. Fresh frozen stored feces provide an advantage of increased availability and accessibility to high-quality optimal donor fecal material. The stability of frozen canine feces regarding fecal microbiome composition and diversity has not been reported in dogs, providing the basis for this study. We hypothesized that fecal microbial composition and diversity of healthy dogs would remain stable when stored at -20°C and -80°C for up to 12 months compared to baseline samples evaluated before freezing. Stool samples were collected from 20 apparently healthy dogs, manually homogenized, cryopreserved in 20% glycerol and aliquoted, frozen in liquid nitrogen and stored at -20°C or -80°C for 3, 6, 9, and 12 months. At baseline and after period of storage, aliquots were thawed and treated with propidium monoazide before fecal DNA extraction. Following long-read 16S-rRNA amplicon sequencing, bacterial community composition and diversity were compared among treatment groups. We demonstrated that fresh-frozen canine stools collected from 20 apparently healthy dogs could be stored for up to 12 months at -80°C with minimal change in microbial community composition and diversity and that storage at -80°C is superior to storage at -20°C. We also found that differences between dogs had the largest effect on community composition and diversity. Relative abundances of certain bacterial taxa, including those known to be short-chain fatty acid producers, varied significantly with specific storage temperatures and duration. Further work is required to ascertain whether fecal donor material that differs in bacterial community composition and diversity across storage conditions and duration could lead to differences in clinical efficacy for specific clinical indications of fecal microbiota transplantation.

Could Adverse Effects of Antibiotics Due to Their Use/Misuse Be Linked to Some Mechanisms Related to Nonalcoholic Fatty Liver Disease?

Nonalcoholic fatty liver disease, recently re-named metabolic dysfunction-associated steatotic fatty liver disease, is considered the most prevalent liver disease worldwide. Its molecular initiation events are multiple and not always well-defined, comprising insulin resistance, chronic low-grade inflammation, gut dysbiosis, and mitochondrial dysfunction, all of them acting on genetic and epigenetic grounds. Nowadays, there is a growing public health threat, which is antibiotic excessive use and misuse. This widespread use of antibiotics not only in humans, but also in animals has led to the presence of residues in derived foods, such as milk and dairy products. Furthermore, antibiotics have been used for many decades to control certain bacterial diseases in high-value fruit and vegetables. Recently, it has been emphasised that antibiotic-induced changes in microbial composition reduce microbial diversity and alter the functional attributes of the microbiota. These antibiotic residues impact human gut flora, setting in motion a chain of events that leads straight to various metabolic alterations that can ultimately contribute to the onset and progression of NAFLD.

The beneficial endophytic microbes enhanced tobacco defense system to resist bacterial wilt disease

BackgroundThe vital role of rhizosphere microbiome in protecting plants against pathogen infection has been well characterized. By contrast, beneficial effects of the plant endophytic microbiome and interactions with plants remain poorly understood. Here, we integrated microbial community analysis, culture-based methods and plant defense gene quantification to systematically investigate the responses of endophytic root and stem microbiomes and the defense system of the tobacco plant to Ralstonia solanacearum, a bacterial pathogen causing bacterial wilt disease worldwide.ResultsAn obvious reduction of community diversity and changes of microbial composition were observed in tobacco root and stem compartments upon R. solanacearum infection. Beneficial endophytic microbes were enriched in both diseased root and stem compartments, and beneficial microbes enriched in roots were more diverse than those in stems. Several beneficial bacteria enriched in diseased roots showed positive correlations with the pathogen abundance and exhibited great antagonistic activities against R. solanacearum. At the same time, the expression of key genes participating in plant defense signaling pathways and activities of plant defense enzymes were activated with R. solanacearum infection. Inoculation of beneficial endophyte Burkholderia ASV_550 in soils could greatly enhance the tobacco defense system in the presence of pathogen and decrease the disease incidence.ConclusionsThe recruited beneficial microbes exhibited an enhancement of the defense system of host plants. This work provides endophyte evidence for the “cry for help” strategy in plants and advances the current understanding of plant–microbe interactions in resisting plant disease.Graphical