Experimental insights into the importance of aquatic bacterial community composition to the degradation of dissolved organic matter

Rice-crayfish farming system promote subsoil microbial residual carbon accumulation and stabilization by mediating microbial metabolism process

Rice-crayfish farming systems (RCs) can help mitigate climate change by enhancing soil organic carbon (SOC) sequestration. However, the mechanisms that govern the responses of microbial residues carbon (MRC), a key component of SOC, in RCs are not fully understood. We conducted a 6-year field experiment comparing RCs and rice monoculture systems (RMs). Specifically, we explored how MRC formation and stabilization differ between the two systems and how those differences are linked to changes in the metabolic processes of microbes. Results showed that MRC levels in RCs were 5.2 % and 40.0 % higher in the topsoil and subsoil, respectively, compared to RMs, indicating depth-dependent effects. Notably, MRC accumulation and stabilization in RCs were promoted through a cascade of processes of dissolved organic carbon (DOC) accessibility-microbial metabolism-mineral protection. In addition, the mechanism of MRC accumulation in subsoil differed between the two systems. Specifically, RMs improved accessibility of DOC by reducing humification and aromaticity of subsoil DOC, which helped microbes access to resources at lower cost. This decreased the respiration rate of microbes, thereby increasing microbial carbon pump (MCP) efficiency and thus promoting MRC accumulation. By contrast, the crayfish in RCs facilitated carbon exchange between topsoil and subsoil through their burrowing behaviors. This increased carbon allocation for microbial metabolism in the subsoil, supporting a larger microbial population and thus enhancing the MCP capacity, while reducing MRC re-decomposition via enhanced mineral protection, further increasing subsoil MRC accumulation. That is, MRC accumulation in the subsoil of RCs was predominantly driven by microbial population numbers (MCP capacity) whereas that of RMs was mostly driven by microbial anabolic efficacy (MCP efficiency). Our findings reveal a key mechanism by which RCs promoted soil MRC accumulation and stabilization, highlighting the potential role of DOC accessibility-microbial metabolism-mineral protection pathway in regulating MRC accumulation and stabilization.

Aberration of social behavior and gut microbiota induced by cross-fostering implicating the gut-brain axis

The gut microbiota and neurological development of neonatal mice are susceptible to environmental factors that may lead to altered behavior into adulthood. However, the role that changed gut microbiota and neurodevelopment early in life play in this needs to be clarified. In this study, by modeling early-life environmental changes by cross-fostering BALB/c mice, we revealed the effects of the environment during the critical period of postnatal development on adult social behavior and their relationship with the gut microbiota and the nervous system. The neural projections exist between the ascending colon and oxytocin neurons in the paraventricular nuclei (PVN), peripheral oxytocin levels and PVN neuron numbers decreased after cross-fostering, and sex-specific alteration in gut microbiota and its metabolites may be involved in social impairments and immune imbalances brought by cross-fostering via the gut-brain axis. Our findings also suggest that social cognitive impairment may result from a combination of PVN oxytocinergic neurons, gut microbiota, and metabolites.

Environmentally relevant concentrations of naphthenic acids initiate intestinal injury and gut microbiota dysbiosis in marine medaka (Oryzias melastigma)

Naphthenic acids (NAs) are important pollutants in marine crude oils and have obvious toxic effects on marine organisms. However, the effects of NAs on the intestine are largely unknown. Thus, we evaluated the effects of NAs exposure in the intestines of marine medaka. Fish were experimentally exposed to NAs (0.5 mg/L, 5 mg/L, and 10 mg/L) for 96 h and monitored for changes in intestinal histology, markers of oxidative stress, and intestinal microbiome responses. Significant mucosal damage, inflammation, and oxidative stress were observed in the intestines of marine medaka after exposure to NAs. In addition, significant changes in the gut microbiota were observed. Specifically, the relative abundance of Proteobacteria decreased, while that of Verrucomicrobiota increased in the high-concentration exposure group. In addition, nutrient synthesis and metabolism in the gut were affected. The results of this study contribute to a better understanding of the ecological risk of different concentrations of NAs to marine organisms. CAPSULE ABSTRACT: Changes in the gut microbial community of marine medaka (Oryzias melastigma) caused by naphthenic acids in the marine environment were investigated through the assessment of gut inflammatory factors and comprehensive analysis using 16S rDNA high-throughput sequencing. The results indicated the induction of intestinal inflammation and changes in the structural composition of the intestinal flora.

Altered gut microbe metabolites in patients with alcohol‑induced osteonecrosis of the femoral head: An integrated omics analysis

Excessive alcohol consumption is considered to be a major risk factor of alcohol-induced osteonecrosis of the femoral head (AONFH). The gut microbiota (GM) has been reported to aid in the regulation of human physiology and its composition can be altered by alcohol consumption. The aim of the present study was to improve the understanding of the GM and its metabolites in patients with AONFH. Metabolomic sequencing and 16S rDNA analysis of fecal samples were performed using liquid chromatography-mass spectrometry to characterize the GM of patients with AONFH and healthy normal controls (NCs). Metagenomic sequencing of fecal samples was performed to identify whether GM changes on the species level were associated with the expression of gut bacteria genes or their associated functions in patients with AONFH. The abundance of 58 genera was found to differ between the NC group and the AONFH group. Specifically, Klebsiella, Holdemanella, Citrobacter and Lentilactobacillus were significantly more abundant in the AONFH group compared with those in the NC group. Metagenomic sequencing demonstrated that the majority of the bacterial species that exhibited significantly different abundance in patients with AONFH belonged to the genus Pseudomonas. Fecal metabolomic analysis demonstrated that several metabolites were present at significantly different concentrations in the AONFH group compared with those in the NC group. These metabolites were products of vitamin B6 metabolism, retinol metabolism, pentose and glucuronate interconversions and glycerophospholipid metabolism. In addition, these changes in metabolite levels were observed to be associated with the altered abundance of specific bacterial species, such as Basidiobolus, Mortierella, Phanerochaete and Ceratobasidium. According to the results of the present study, a comprehensive landscape of the GM and metabolites in patients with AONFH was revealed, suggesting the existence of interplay between the gut microbiome and metabolome in AONFH pathogenesis.

Aquatic conditions & bacterial communities as drivers of the decomposition of submerged remains

Aquatic decomposition, as a forensic discipline, has been largely under-investigated as a consequence of the highly complex and influential variability of the water environment. The limitation to the adaptability of scenario specific results justifies the necessity for experimental research to increase our understanding of the aquatic environment and the development of post-mortem submersion interval (PMSI) methods of estimation. This preliminary research aims to address this contextual gap by assessing the variation in the bacterial composition of aquatic biofilms as explained by water parameter measurements over time, associated with clothed and bare decomposing remains. As part of three field investigations, a total of 9 still-born piglets (n = 3, per trial) were used as human analogues and were submerged bare or clothed in either natural cotton or synthetic nylon. Changes in the bacterial community composition of the water surrounding the submerged remains were assessed at 4 discrete time points post submersion (7, 14, 21 and 28 days) by 16 S rRNA gene Next Generation Sequencing analysis and compared to coinciding water parameter measurements (i.e. conductivity, total dissolved solids (TDS), salinity, pH, and dissolved oxygen (DO)). Bacterial diversity was found to change over time and relative to clothing type, where significant variation was observed between synthetic nylon samples and bare/cotton samples. Seasonality was a major driver of bacterial diversity, where substantial variation was found between samples collected in early winter to those collected in mid - late winter. Water parameter measures of pH, salinity and DO were identified to best explain the global bacterial community composition and their corresponding dynamic trajectory patterns overtime. Further investigation into bacterial community dynamics in accordance with varying environmental conditions could potentially lead to the determination of influential extrinsic factors that may drive bacterial activity in aquatic decomposition. Together with the identification of potential bacterial markers that complement the different stages of decomposition, this may provide a future approach to PMSI estimations.

The resting cyst of dinoflagellate Scrippsiella acuminata host bacterial microbiomes with more diverse trophic strategies under conditions typically observed in marine sediments

Variation in the condition of marine sediments provides selective preservation milieus, which act as a key determinant for the abundance and distribution of dinoflagellate resting cysts in natural sediments. Microbial degradation is an understudied biological factor of potential importance in the processes. However, gaps remain in our knowledge about the fundamental information of the bacterial consortia associated with dinoflagellate resting cysts both in laboratory cultures and in the field. Here we used Scrippsiella acuminata as a representative of cyst-producing dinoflagellates to delineate the diversity and composition of bacterial microbiomes co-existing with the laboratory-cultured resting cysts, and to explore possible impacts of low temperature, darkness, and anoxia (the mock conditions commonly observed in marine sediments) on the associated bacterial consortia. Bacterial microbiome with high diversity were revealed associated with S. acuminata at resting stage. The mock conditions could significantly shift bacterial community structure and exert notably inhibitory effects on growth-promoting bacteria. Resting cysts under conditions typically observed in marine sediments fostered bacterial microbiomes with more diverse trophic strategies, characteristic of prominently enriched anaerobic chemotrophic bacteria generating energy via respiration with several different terminal electron acceptors, which yielded more acidic milieu unfavorable for the preservation of calcareous resting cysts. Our findings suggest that there is complex and dynamic interaction between dinoflagellates resting cysts and the associated bacterial consortia in natural sediments. This intrinsic interaction may influence the maintenance and/or accumulation of dinoflagellate resting cysts with potential of germination and initiation blooms in the field.

Urban greenspace types and climate factors jointly drive the microbial community structure and co-occurrence network

The benefits of urban green space are socially widely recognized as a direct link between plant-microbe interactions and the maintenance of biodiversity, community stability, and ecosystem functioning. Nevertheless, there is a lack of knowledge about the factors influencing microbial communities in urban green spaces, especially those related to phyllosphere epiphytes and stem epiphytes. In this study, we analyzed the microbial community assembly in leaf and stem bark samples collected from Square, Road, Campus, and Park. Illumina sequecing of 16S amplicons was performed to characterize microbial diversity and composition. The α-diversity was significantly higher in the bark epiphytic community, compared to the phyllosphere. Moreover, urban greenspaces'type altered the way communities gathered. The main soil and air properties factors of the urban greenhouse (e.g. soil temperature, atmospheric moisture, air temperature) were shaping the characteristics of bacterial communities on the leaf surface and bark epiphytic. In addition, in the co-occurrence network analysis, keystone taxa were not mostly observed in abundant species, which may be necessary to maintain ecosystem functions. Finally, our findings provide a deeper understanding of the ecological dynamics and microbial interactions within plant phyllosphere and stem epiphytes microbiomes.

A systematic review of invasive non-native freshwater bivalves

The introduction of invasive species has become an increasing environmental problem in freshwater ecosystems due to the high economic and ecological impacts it has generated. This systematic review covers publications from 2010 to 2020, focusing on non-native invasive freshwater bivalves, a particularly relevant and widespread introduced taxonomic group in fresh waters. We collected information on the most studied species, the main objectives of the studies, their geographical location, study duration, and type of research. Furthermore, we focused on assessing the levels of ecological evidence presented, the type of interactions of non-native bivalves with other organisms and the classification of their impacts. A total of 397 publications were retrieved. The studies addressed a total of 17 species of non-native freshwater bivalves; however, most publications focused on the species Corbicula fluminea and Dreissena polymorpha, which are recognised for their widespread distribution and extensive negative impacts. Many other non-native invasive bivalve species have been poorly studied. A high geographical bias was also present, with a considerable lack of studies in developing countries. The most frequent studies had shorter temporal periods, smaller spatial extents, and more observational data, were field-based, and usually evaluated possible ecological impacts at the individual and population levels. There were 94 publications documenting discernible impacts according to the Environmental Impact Classification for Alien Taxa (EICAT). However, 41 of these publications did not provide sufficient data to determine an impact. The most common effects of invasive bivalves on ecosystems were structural alterations, and chemical and physical changes, which are anticipated due to their role as ecosystem engineers. Despite a considerable number of studies in the field and advances in our understanding of some species over the past decade, long-term data and large-scale studies are still needed to understand better the impacts, particularly at the community and ecosystem levels and in less-studied geographic regions. The widespread distribution of several non-native freshwater bivalves, their ongoing introductions, and high ecological and economic impacts demand continued research. Systematic reviews such as this are essential for identifying knowledge gaps and guiding future research to enable a more complete understanding of the ecological implications of invasive bivalves, and the development of effective management strategies.

Microbial stratification and DOM removal in drinking water biofilters: Implications for enhanced performance

Biofiltration is a low-cost, low-energy technology that employs a biologically activated bed of porous medium to reduce the biodegradable fraction of the dissolved organic matter (DOM) pool in source water, resulting in the production of drinking water. Microbial communities at different bed depths within the biofilter play crucial roles in the degradation and removal of dissolved organic carbon (DOC), ultimately impacting its performance. However, the relationships between the composition of microbial communities inhabiting different biofilter depths and their utilisation of various DOC fractions remain poorly understood. To address this knowledge gap, we conducted an experimental study where microbial communities from the upper (i.e., top 10 cm) and lower (i.e., bottom 10 cm) sections of a 30-cm long laboratory-scale biofilter were recovered. These communities were then individually incubated for 10 days using the same source water as the biofilter influent. Our study revealed that the bottom microbial community exhibited lower diversity yet had a co-occurrence network with a higher degree of interconnections among its members compared to the top microbial community. Moreover, we established a direct correlation between the composition and network structure of the microbial communities and their ability to utilise various DOM compounds within a DOM pool. Interestingly, although the bottom microbial community had only 20 % of the total cell abundance compared to the top community at the beginning of the incubation, it utilised and hence removed approximately 60 % more total DOC from the DOM pool than the top community. While both communities rapidly utilised labile carbon fractions, such as low-molecular-weight neutrals, the utilisation of more refractory carbon fractions, like high-molecular-weight humic substances with an average molecular weight of more than ca. 1451 g/mol, was exclusive to the bottom microbial community. By employing techniques that capture microbial diversity (i.e., flow cytometry and 16S rRNA amplicon sequencing) and considering the complexities of DOM (i.e., LCOCD), our study provides novel insights into how microbial community structure could influence the microbial-mediated processes of engineering significance in drinking water production. Finally, our findings could offer the opportunity to improve biofilter performances via engineering interventions that shape the compositions of biofilter microbial communities and enhance their utilisation and removal of DOM, most notably the more classically humified and refractory DOM compound groups.

Capabilities of Microbial Consortia from Disparate Environment Matrices in the Decomposition of Nature Organic Matter by Biofiltration

Dissolved organic matter (DOM) plays a pivotal role in drinking water treatment, influencing the performance of unit processes and final water quality (e.g. disinfection byproduct risk). Biofiltration is an effective method of reducing DOM, but currently lacks a comprehensive appreciation of the association between microbial profiles and biofiltration performance. In this study, bench-scale biofiltration units inoculated with microbial consortia from river and soil matrices were operated successively for comparing their efficacy in terms of DOM removal. The results showed that biofiltration units receiving soil microbes were significantly superior (p < 0.05) to those receiving river inoculated microbes in terms of decomposing DOM recalcitrant fractions and reducing DBP formation potential, resulting in DOC and DBP precursor removals of up to 58.4 % and 87.9 %, respectively. Characterization of the taxonomic composition revealed that differences in the microbial assembly of the two biofilter groups were subject to deterministic rather than stochastic factors. Furthermore, more complicated interspecific relationships and niche structures in soil inoculated biofilters were deciphered by co-occurrence network, providing a plausible profile on a taxonomic division of labor in DOM stepwise degradation. Accordingly, the contribution of microbial compositions was found to be of greater importance than the GAC mass and biomass attached to the media. Thus, this study has advanced the understanding of microbial-mediated DOM decomposition in biofiltration, and also provided a promising strategy for enhancing the process for water use via developing appropriate engineered consortia of bacteria.

The dual role of 20(S)-protopanaxadiol in alleviating pulmonary fibrosis through the gut-lung axis

BACKGROUND

Pulmonary Fibrosis (PF) is a progressive lung disease characterized by the diffuse interstitial tissue, leading to severe breathing difficulties. The existing treatment methods are primarily aimed at slowing the progression of the disease, underscoring the urgent need to discover new drug interventions targeting novel sites. The "gut-lung axis" represents a complex bidirectional communication system where the gut microbiota not only influences lung immunity but also responds to lung-derived signals. Recent advances have uncovered that alterations in gut microbiota composition can significantly impact respiratory diseases, offering new insights into their pathogenesis and potential therapeutic approaches.

METHODS

This study is based on the fundamental concepts of the lung-gut axis and our previous research, further exploring the potential mechanisms of 20(S)-Protopanaxadiol (PPD) in ginseng against PF. We utilized a bleomycin-induced mouse model of PF and employed metabolomics and 16S rRNA sequencing to investigate the pathways through which PPD regulates the pulmonary fibrosis process via the gut-lung axis. Finally, we employed strategies such as antibiotic-induced microbiota disruption and fecal microbiota transplantation (FMT) to provide a comprehensive perspective on how PPD regulates pulmonary fibrosis through gut microbiota.

RESULTS

The results of the bleomycin (BLM) mouse model of PF proved that PPD can directly act on the glycolysis- related metabolic reprogramming process in lung and the AMPK/STING pathway to improve PF. Combined the analysis of gut microbiota and related metabolites, we found that PPD can regulate the process of PF through the gut-lung axis target points G6PD and SPHK1. FMT and antibiotic-induced microbiota disruption further confirmed intermediate effect of gut microbiota in PF process and the treatment of PPD. Our study suggests that PPD can alleviate the process of pulmonary fibrosis either by directly acting on the lungs or by regulating the gut microbiota.

CONCLUSION

This study positions PPD as a vanguard in the therapeutic landscape for pulmonary fibrosis, offering a dual mechanism of action that encompasses both modulation of gut microbiota and direct intervention at molecular targets. These insights highlight the immense therapeutic potential of harnessing the gut-lung axis.

Interpretable machine learning reveals microbiome signatures strongly associated with dairy cow milk urea nitrogen

The gut microbiome plays an important role in the healthy and efficient farming of dairy cows. However, high-dimensional microbial information is difficult to interpret in a simplified manner. We collected fecal samples from 161 cows and performed 16S amplicon sequencing. We developed an interpretable machine learning framework to classify individuals based on their milk urea nitrogen (MUN) concentrations. In this framework, we address the challenge of handling high-dimensional microbial data imbalances and identify 9 microorganisms strongly correlated with MUN. We introduce the Shapley Additive Explanations (SHAP) method to provide insights into the machine learning predictions. The results of the study showed that the performance of the machine learning model improved (accuracy = 72.7%) after feature selection on high-dimensional data. Among the 9 microorganisms, g__Firmicutes_unclassified had the greatest impact in the model. This study provides a reference for precision animal husbandry.

Effect of dapagliflozin on ferroptosis through the gut microbiota metabolite TMAO during myocardial ischemia-reperfusion injury in diabetes mellitus rats

Dapagliflozin (DAPA) demonstrates promise in the management of diabetic mellitus (DM) and cardiomyopathy. Trimethylamine N-oxide (TMAO) is synthesized by the gut microbiota through the metabolic conversion of choline and phosphatidylcholine. Ferroptosis may offer novel therapeutic avenues for the management of diabetes and myocardial ischemia-reperfusion injury (IRI). However, the precise mechanism underlying ferroptosis in cardiomyocytes and the specific role of TMAO generated by gut microbiota in the therapeutic approach for DM and myocardial IRI utilizing DAPA need to be further explored. Nine male SD rats with specific pathogen-free (SPF) status were randomly divided equally into the normal group, the DM + IRI (DIR) group, and the DAPA group. The diversity of the gut microbiota was analyzed using 16S rRNA gene sequencing. Additionally, the Wekell technique was employed to measure the levels of TMAO in the three groups. Application of network pharmacology to search for intersection targets of DAPA, DIR, and ferroptosis, and RT-PCR experimental verification. Ultimately, the overlapping targets that were acquired were subjected to molecular docking analysis with TMAO. The changes of Bacteroidetes and Firmicutes in the gut microbiota of DIR rats were most significantly affected by DAPA. Escherichia-Shigella and Prevotella_9 within the phylum Bacteroidetes could be identified as the primary effects of DAPA on DIR. Compared with the normal group, the TMAO content in the DIR group was significantly increased, while the TMAO content in the DAPA group was decreased compared to the DIR group. For the network pharmacology analysis, DAPA and DIR generated 43 intersecting target genes, and then further intersected with ferroptosis-related genes, resulting in 11 overlapping target genes. The mRNA expression of ALB, HMOX1, PPARG, CBS, LCN2, and PPARA decreased in the DIR group through reverse transcription polymerase chain reaction (RT-PCR) validation, while the opposite trend was observed in the DAPA group. The docking score between TMAO and DPP4 was - 5.44, and the MM-GBSA result of - 22.02 kcal/mol. It epitomizes the finest docking performance among all the target genes with the lowest score. DAPA could reduce the levels of metabolite TMAO produced by gut microbiota, thereby regulating related target genes to decrease ferroptosis in DIR cardiomyocytes.

Temporal heterogeneity of the root microbiome in Panax ginseng soils across ecological compartments under mild soil disturbance

Introduction

Knowledge on spatiotemporal heterogeneity of plant root microbiomes is lacking. The diversity of the root microbiome must be revealed for understanding plant-microbe interactions and the regulation of functionally crucial microbial taxa.

Methods

We here investigated the dynamics of microbial group characteristics within each soil ecological compartment [rhizoplane (B), rhizosphere (J), and bulk soil (T)] across different cultivation years (year 4: F4 and year 5: F5) by using high-throughput sequencing (16S and ITS).

Results

According to the species diversity, microbiome diversity and the ASV (amplified sequence variant) number in the rhizoplane ecotone increased significantly with an increase in the planting years. By contrast, the microbiome diversity of the rhizosphere soil remained relatively stable. PCoA and PERMANOVA analyses revealed that microbial taxa among different planting years and ecological compartments varied significantly. Planting years exerted the least effect on the rhizosphere microbiome, but their impact on fungi in the rhizoplane and bacteria in the bulk soil was the most significant.

Discussion

Planting years influenced the microbial community composition in various ecological compartments of ginseng root soil. Potentially harmful fungi such as Cryptococcus (2.83%), Neonectria (0.89%), llyonectria (0.56%), Gibberella (0.41%), Piloderma (4.44%), and Plectosphaerella (3.88%) were enriched in F5B with an increase in planting years, whereas the abundance of potentially beneficial Mortierella increased. Correlation analysis indicated associations between bacterial taxa and soil pH/S-CAT, and between fungal taxa and soil moisture content/total potassium. Our study highlights the significance of changes in rhizoplane fungi and the stability of the rhizosphere microbial community in comprehending plant ecological sustainability.

Leucine Supplementation Modulates Lipid Metabolism and Inflammation in Early Weaning Piglets

Early weaning can induce the programmed dysregulation of glycolipid metabolism and inflammation in adult animals. The primary objective of this study was to evaluate the efficacy of leucine supplementation administered promptly after early weaning in mitigating these adverse effects in piglets. At day 21, 24 piglets were randomly selected and divided into 3 groups: EW group where the piglets were weaned at day 21 and fed basal diet, EWL group where the piglets were weaned at day 21 and fed the basal diet with supplementation of 1% leucine, and C group where the piglets were fed basal diet and weaned at 28 days. Each group contained eight replicates, with one piglet per replicate. The results indicated that early weaning had an impact on gut health and could activate the inhibitor of the kappa B kinase gamma/inhibitor kappa B alpha/NF-kappa-B (IKKγ/IκBα/NF-κB) signaling pathway to ameliorate pro-inflammatory factor and apoptosis levels. Furthermore, early weaning reduced the activity of fatty acid β oxidation (FAβO) and affected genes linked with lipid metabolism. Supplementing with leucine can improve the effects of these factors. In summary, leucine may alleviate the influences of early weaning on the lipid metabolism and inflammation in piglets.

Amelioration of the physicochemical properties enhanced the resilience of bacteria in bauxite residues

Bacteria-driven strategies have gained attention because of their effectiveness, viability, and cost-efficiency in the soil formation process of bauxite residues. However, further investigation is needed to enhance the extreme environment of bauxite residues and facilitate long-term sustainable development of bacteria. Here, soil, phosphogypsum, and leaf litter were selected as amendments, and soil and leaf litter were also used as bacterial inoculants in a 12-month microcosm experiment with bauxite residues. The results showed significant improvements in physicochemical properties, including alkalinity, organic carbon content, nutrient availability, and physical structure, when bauxite residue was mixed with amendments, particularly when different amendments were combined. The diversity, structure, and function of the bacterial community were significantly enhanced with the amelioration of the physicochemical properties. In the treated samples, especially those treated with a combination of different amendments, the relative abundance (RA) of alkali-resistant bacterial taxa decreased, whereas the RA of some common taxa found in normal soil increased, and the structure of the bacterial community gradually changed towards that of normal soil. A strong correlation between physicochemical and biological properties was found. These findings suggest that rational application of soil, phosphogypsum, and leaf litter effectively improves the environmental conditions of bauxite residues and facilitate long-term sustainable bacterial communities.

Dynamic alterations of flavor, functional nutrients, and microbial community during fermentation of different animal milk kefirs

Kefir is a traditional dairy beverage, usually made from cow or goat milk fermented with kefir grains, and has many health benefits. To elucidate the fermentation patterns of animal milk kefirs during the fermentation process and find the optimal milk types, cow, camel, goat, and donkey milk were fermented with kefir grains for 0, 1, 3, 5, and 7 days. Volatile and non-volatile metabolites and microbial changes were dynamically monitored. The results showed that volatile flavor substances were massively elevated in four kefirs on days 1-3. Lipids and carbohydrates gradually decreased, while amino acids, small peptides, and tryptophan derivatives accumulated during fermentation in four kefirs. Besides, four kefirs had similar alterations in Lactobacillus and Acetobacter, while some distinctions existed in low-abundance bacteria. Association analysis of microorganisms and volatile and non-volatile metabolites also revealed the underlying fermentation mechanism. This study found that appropriately extending the fermentation time contributed to the accumulation of some functional nutrients. Furthermore, goat and donkey milk could be the better matrices for kefir fermentation.

Upstream land use with microbial downstream consequences: Iron and humic substances link to Legionella spp

Intensified land use can disturb water quality, potentially increasing the abundance of bacterial pathogens, threatening public access to clean water. This threat involves both direct contamination of faecal bacteria as well as indirect factors, such as disturbed water chemistry and microbiota, which can lead to contamination. While direct contamination has been well described, the impact of indirect factors is less explored, despite the potential of severe downstream consequences on water supply. To assess direct and indirect downstream effects of buildings, farms, pastures and fields on potential water sources, we studied five Swedish lakes and their inflows. We analysed a total of 160 samples in a gradient of anthropogenic activity spanning four time points, including faecal and water-quality indicators. Through species distribution modelling, Random Forest and network analysis using 16S rRNA amplicon sequencing data, our findings highlight that land use indirectly impacts lakes via inflows. Land use impacted approximately one third of inflow microbiota taxa, in turn impacting ∼20-50 % of lake taxa. Indirect effects via inflows were also suggested by causal links between e.g. water colour and lake bacterial taxa, where this influenced the abundance of several freshwater bacteria, such as Polynucleobacter and Limnohabitans. However, it was not possible to identify direct effects on the lakes based on analysis of physiochemical- or microbial parameters. To avoid potential downstream consequences on water supply, it is thus important to consider possible indirect effects from upstream land use and inflows, even when no direct effects can be observed on lakes. Legionella (a genus containing bacterial pathogens) illustrated potential consequences, since the genus was particularly abundant in inflows and was shown to increase by the presence of pastures, fields, and farms. The approach presented here could be used to assess the suitability of lakes as alternative raw water sources or help to mitigate contaminations in important water catchments. Continued broad investigations of stressors on the microbial network can identify indirect effects, avoid enrichment of pathogens, and help secure water accessibility.

The Mediation/Moderation Effects of Gut Microbiota on Sleep Quality and Primary Liver Cancer: A Mendelian Randomization and Case-Control Study

Background

Primary liver cancer (PLC) is a fatal malignancy, sleep quality and gut microbiota were shown to be associated with PLC. However, the mechanism of how sleep quality affects PLC is unclear. This study aims to investigate the mediation/moderation effects of gut microbiota on sleep quality and the occurrence of PLC.

Methods

The causality of sleep quality and the occurrence of PLC was detected through the Mendelian randomization (MR) analysis based on the data including 305,359 individuals (Finland Database) and 456,348 participants (UK Biobank). The primary method used for MR analysis was inverse-variance weighted analysis. Gut microbiota' mediation/moderation effects were uncovered in the case-control study including 254 patients with PLC and 193 people with benign liver diseases through the mediation/moderation effect analyses. People's sleep quality was evaluated through the Pittsburgh sleep quality index (PSQI).

Results

Poor sleep quality could lead to PLC through the MR analysis (P = 0.026). The case-control study uncovered that Actinobacteria had mediation effects on the relationship between PSQI score, self-sleep quality, and the occurrence of PLC (P = 0.048, P = 0.046). Actinobacteria and Bifidobacterium could inhibit the development of PLC caused by short night sleep duration (P = 0.021, P = 0.022). Erysipelotrichales could weaken the influence of daytime dysfunction on PLC (P = 0.033). Roseburia modulated the contribution of nocturnal insomnia and poor sleep quality to PLC (P = 0.009, P = 0.017).

Conclusion

Poor sleep quality was associated with PLC. Gut microbiota' mediation/moderation effects on poor sleep quality and the occurrence of PLC prompted an insightful idea for the prevention of PLC.

Investigating oral microbiome profiles in patients with cleft lip and palate compared with the healthy control

BACKGROUND

Patients with cleft lip and palate (CLP) have an oronasal communication differed from the closed state in healthy individuals, leading to a unique oral microbiome. This study aimed to determine if variances in the oral microbiota persist among CLP patients who have received treatments for the closure of these fistulas compared to the microbiota of healthy individuals.

METHODS

Saliva samples were collected from a cohort comprising 28 CLP patients (CLP group) and 30 healthy controls (HC group). Utilizing 16S rRNA sequencing on the Illumina NovaSeq platform, we conducted a comprehensive analysis of the diversity and composition of the oral microbiota.

RESULTS

The analysis of the microbiota in the saliva samples revealed a total of 23 microbial phyla, 38 classes, 111 orders, 184 families, 327 genera and 612 species. The alpha diversity with microbial abundance and evenness indicated the significant difference between the CLP and HC groups. Principal coordinate analysis (PCoA) and the ADONIS test further supported the presence of distinct microorganisms between the two groups. The CLP group displayed elevated abundances of Neisseria, Haemophilus, Porphyromonas, and Granulicatella, as indicated by LefSe analysis. Conversely, Rothia, Veillonella, and Pauljensenia exhibited significant reductions in abundance in the CLP group. The results of the PICRUSt analysis indicated significant differences in the relative abundance of 25 KEGG pathways within the CLP group. Through Spearman correlation analysis, strong associations between Rothia, Veillonella, and Pauljensenia and 25 functional pathways linked to CLP were identified.

CONCLUSION

Findings of this study offer a thorough comprehension of the microbiome profiles of CLP patients after the restoration of oronasal structure and are anticipated to present innovative concepts for the treatment of CLP.

Extracellular vesicles of Bacteroides uniformis induce M1 macrophage polarization and aggravate gut inflammation during weaning

Weaning process is commonly associated with gastrointestinal inflammation and dysbiosis of the intestinal microbes. In particular, the impact of gut bacteria and of extracellular vesicles (EV) on the etiology of intestinal inflammation during weaning is not well understand. We have uncovered a potential link between gut inflammation and the corresponding variation of macrophage bacterial sensing and pro-inflammatory polarization during the weaning process of piglet through single-cell transcriptomic analyses. We conducted a comprehensive analysis of bacterial distribution across the gastrointestinal tract and pinpointed Bacteroides uniformis (B. uniformis) enriching in piglets undergoing weaning. Next, we found out that exposure to B. uniformis-derived EVs (BEVs) exacerbated gut inflammation in a murine colitis model while recruiting and polarizing intestinal macrophages towards a pro-inflammatory phenotype. BEVs modulated the function of macrophages cultured in vitro by suppressing the GM-CSF/STAT5/ARG1 pathway, thereby affecting polarization towards an M1-like state. The effects of BEVs were verified both in the macrophage-clearance murine model and by using an adoptive transfer assay. Our findings highlight the involvement of BEVs in facilitating the polarization of pro-inflammatory macrophages and promoting gut inflammation during weaning.

Paeoniflorin ameliorates oxaliplatin-induced peripheral neuropathy via inhibiting neuroinflammation through influence on gut microbiota

Oxaliplatin (OXA)-induced peripheral neuropathy (OIPN) is a severe side effect that greatly limits OXA clinical use and threatens patients' life and health. Paeoniflorin exhibits extensive anti-inflammatory and neuroprotective effects, but whether it can protect against OIPN and the underlying mechanisms remain unclear. This study aimed to investigate the effects of paeoniflorin on OIPN and probe into the underlying mechanisms. The OIPN model was established through oxaliplatin injection in rats. The ameliorative effects of paeoniflorin on OIPN was assessed by nociceptive hypersensitivities through pain behavioral methods. Neuroinflammation were examined by measuring the levels of inflammatory cytokines and immune cells infiltration. The signaling pathway of TLR4/MyD88/NF-κB was evaluated by Western blotting. Gut microbial changes were detected by 16S rDNA sequencing technology. In addition, antibiotics-induced microbiota eradication and fecal microbial transplantation (FMT) were applied for exploring the function of gut microbiota in the protective effects of paeoniflorin. The results revealed that paeoniflorin significantly alleviated mechanical and cold hypersensitivity, mitigated neuroinflammation and influenced gut microbial composition in OIPN rats. Fecal microbiota transplantation further verified that gut microbiota was required for paeoniflorin ameliorating OIPN and that the underlying mechanism involved downregulation of TLR4/MyD88/NF-κB signaling. Specifically, Akkermansia, Dubosiella and Corynebacterium might serve as crucial genera regulated by paeoniflorin in the treatment of OIPN. In summary, our investigations delineate paeoniflorin's ameliorative effects on OIPN by alleviating neuroinflammation through regulations of gut microbiota. This suggests that paeoniflorin may serve as a new potential strategy for treatment of OIPN in clinical practice.

Spatial distribution characteristics and interaction effects of DOM and microbial communities in kelp cultivation areas

The influence of macroalgae cultivation on aquaculture carbon sinks is significant, with microbial carbon (C) pumps contributing to a stable inert dissolved carbon pool in this context. Concurrently, dissolved organic matter (DOM) exchange at the marine sediment-water interface profoundly affects global ecosystem element cycling. However, the interactions between DOM and bacterial communities at the sediment-water interface in kelp cultivation areas, especially regarding microbial function prediction, have not been fully explored. This study analyzed the DOM characteristics, environmental factors, and bacterial community structure in the Tahewan kelp--Saccharina japonica cultivated area and compared them with those in non-cultivated areas. The results indicated significantly higher dissolved organic carbon (DOC) concentrations in the kelp culture area, particularly in surface seawater and overlying water. The dominant bacterial phyla in both regions included Pseudomonadota, Actinomycetota, and Bacteroidota in both regions, while Desulfobacterota was more prevalent in the sediment environment of the cultivated region. Parallel factor analysis (EEM-PARAFAC) was used to identify DOM components, among which component C2 (a microbial humic-like substance DOM) was highly resistant to microbial degradation. We infer that C2 has similar properties to recalcitrant dissolved organic matter (RDOM). Analysis of the predicted functional genes based on 16S rRNA gene data showed that methanol oxidation, methylotrophy, and methanotrophy were significant in the bottom seawater of the cultivation area. The carbon (C), nitrogen (N), and sulfur (S) cycle functional genes in the sediment environment of the kelp cultivation area were more active than those in other areas, especially in which sulfate reduction and denitrification were the two main processes. Furthermore, a DOM priming effect was identified in the cultivated sediment environment, where kelp-released labile dissolved organic matter (LDOM) stimulates rapid degradation of the original RDOM, potentially enhancing C sequestration.

Effects of sulfur nanoparticles on rhizosphere microbial community changes in oilseed rape plantation soil under mercury stress

In the present study, experiments were conducted to assess the influence of nanoscale sulfur in the microbial community structure of metallophytes in Hg-contaminated rhizosphere soil for planting rapeseed. The results showed that the richness and diversity of the rhizobacteria community decreased significantly under Hg stress, but increased slightly after SNPs addition, with a reduction in the loss of Hg-sensitive microorganisms. Moreover, all changes in the relative abundances of the top ten phyla influenced by Hg treatment were reverted when subjected to Hg + SNPs treatment, except for Myxococcota and Bacteroidota. Similarly, the top five genera, whose relative abundance decreased the most under Hg alone compared to CK, increased by 19.05%-54.66% under Hg + SNPs treatment compared with Hg alone. Furthermore, the relative abundance of Sphingomonas, as one of the dominant genera for both CK and Hg + SNPs treatment, was actively correlated with plant growth. Rhizobacteria, like Pedobacter and Massilia, were significantly decreased under Hg + SNPs and were positively linked to Hg accumulation in plants. This study suggested that SNPs could create a healthier soil microecological environment by reversing the effect of Hg on the relative abundance of microorganisms, thereby assisting microorganisms to remediate heavy metal-contaminated soil and reduce the stress of heavy metals on plants.

Effects of non-pelleted or pelleted low-native grass and pelleted high-native grass diets on meat quality by regulating the rumen microbiota in lambs

Diet modulates the rumen microbiota, which in turn can impact the animal performance. The rumen microbiota is increasingly recognized for its crucial role in regulating the growth and meat quality of the host. Nevertheless, the mechanism by which the rumen microbiome influences the fatty acid and amino acid profiles of lambs in the grass feeding system remains unclear. This study aimed to evaluate the effects of different native grass-based diets on animal performance, meat quality, fatty acid compositions, amino acid profiles, and rumen microbiota of lamb. Seventy-two Ujumqin lambs were randomly assigned into three treatments according to the initial body weight (27.39 ± 0.51 kg) and age (6 months ± 6 days). The lambs received three diets: (i) non-pelleted native grass hay with 40% concentrate diet; the native grass and concentrate were fed individually; (ii) pelleted native grass hay with 40% concentrate diet (PHLC); (iii) pelleted native grass hay with 60% concentrate diet (PHHC). The results showed that among the three groups, the PHHC and PHLC diets had markedly (P < 0.05) higher average daily gain and pH45 min, respectively. All amino acid levels were significantly (P < 0.05) decreased in the PHHC diet than in the PHLC diet. The principal coordinate analysis of the ruminal microbiota indicated the markedly distinct separation (P = 0.001) among the three groups. In addition, the correlation analysis showed that the Rikenellaceae_RC9_gut_group, Prevotellaceae_UCG-003, Succinivibrio, and Succiniclasticum were significantly (P < 0.05) associated with most of the fatty acid and amino acid profiles. The correlation analysis of the association of microbiome with the meat quality provides us with a comprehensive understanding of the composition and function of the rumen microbial community, and these findings will contribute to the direction of future research in lamb.

IMPORTANCE

Diet modulates the gut microbiome, which in turn impact the meat quality, yet few studies investigate the correlation between the rumen microbiome and the fatty acid profile of meat. Here, the current study develops an experiment to investigate the correlation of the rumen microbiome and fatty acid profile of meat: rumen microbiome responses to feed type and meat quality. The results indicated a unique microbiota in the rumen of lamb in response to diets and meat quality. Associations between utilization and production were widely identified among the affected microbiome and meat quality, and these findings will contribute to the direction of future research in lamb.

Excessive Ozonation Stress Triggers Severe Membrane Biofilm Accumulation and Fouling

The established benefits of ozone on microbial pathogen inactivation, natural organic matter degradation, and inorganic/organic contaminant oxidation have favored its application in drinking water treatment. However, viable bacteria are still present after the ozonation of raw water, bringing a potential risk to membrane filtration systems in terms of biofilm accumulation and fouling. In this study, we shed light on the role of the specific ozone dose (0.5 mg-O3/mg-C) in biofilm accumulation during long-term membrane ultrafiltration. Results demonstrated that ozonation transformed the molecular structure of influent dissolved organic matter (DOM), producing fractions that were highly bioavailable at a specific ozone dose of 0.5, which was inferred to be a turning point. With the increase of the specific ozone dose, the biofilm microbial consortium was substantially shifted, demonstrating a decrease in richness and diversity. Unexpectedly, the opportunistic pathogen Legionella was stimulated and occurred in approximately 40% relative abundance at the higher specific ozone dose of 1. Accordingly, the membrane filtration system with a specific ozone dose of 0.5 presented a lower biofilm thickness, a weaker fluorescence intensity, smaller concentrations of polysaccharides and proteins, and a lower Raman activity, leading to a lower hydraulic resistance, compared to that with a specific ozone dose of 1. Our findings highlight the interaction mechanism between molecular-level DOM composition, biofilm microbial consortium, and membrane filtration performance, which provides an in-depth understanding of the impact of ozonation on biofilm accumulation.

Quantitative characterization and dynamics of bacterial communities in ready-to-eat chicken using high-throughput sequencing combined with internal standard-based absolute quantification

Ready-to-eat (RTE) chicken products are prone to bacterial contamination, posing foodborne illness risks. High-throughput sequencing (HTS) has been widely used to study the distribution of pathogenic and spoilage bacteria in RTE chicken products but lacks quantitative data on taxa abundances. In this study, we employed a method combining HTS with absolute quantification, using Edwardsiella tarda as an internal standard strain, to achieve the relative and absolute abundances of microbiota in RTE chicken products stored at 4 and 25 °C. The results showed that the addition of appropriate concentration of internal standard strains exhibited no significant impact on the structure composition, relative abundance, and absolute abundance of bacterial communities in chicken meat, achieving comprehensive absolute quantification in RTE chicken products. Furthermore, the absolute abundance of bacterial genera at the end of storage followed a log-normal distribution, with most genera having an absolute abundance between 103 and 105 CFU/g. This study provides insights into the quantification of bacterial communities in RTE chicken products, laying a foundation for the development of strategies to extend the shelf life of RTE products.

Rainfall-induced changes in aquatic microbial communities and stability of dissolved organic matter: Insight from a Fen river analysis

Microbial communities are pivotal in aquatic ecosystems, as they affect water quality, energy dynamics, nutrient cycling, and hydrological stability. This study explored the effects of rainfall on hydrological and photosynthetic parameters, microbial composition, and functional gene profiles in the Fen River. Our results demonstrated that rainfall-induced decreases in stream temperature, dissolved oxygen, pH, total phosphorus, chemical oxygen demand, and dissolved organic carbon concentrations. In contrast, rainfall increased total dissolved solids, salinity, and ammonia-nitrogen concentrations. A detailed microbial community structure analysis revealed that Cyanobacteria was the dominant microbial taxon in the Fen River, accounting for approximately 75% and 25% of the microalgal and bacterial communities, respectively. The abundance of Chlorophyta and Bacillariophyta increased by 47.66% and 29.92%, respectively, whereas the relative abundance of Bacteroidetes decreased by 37.55% under rainfall conditions. Stochastic processes predominantly affected the assembly of the bacterial community on rainy days. Functional gene analysis revealed variations in bacterial functions between sunny (Sun) and rainy (Rain) conditions, particularly in genes associated with the carbon cycle. The 3-oxoacyl-[acyl-carrier-protein] reductase gene was more abundant in the Fen River bacterial community. Particular genes involved in metabolism and environmental information processing, including the acetyl-CoA C-acetyltransferase (atoB), enoyl-CoA hydratase (paaF), and branched-chain amino acid transport system gene (livK), which are integral to environmental information processing, were more abundant in Sun than the Rain conditions. In contrast, the phosphate transport system gene, the galactose metabolic gene, and the pyruvate metabolic gene were more abundant in Rain. The excitation-emission matrix analysis with parallel factor analysis identified four fluorescence components (C1-C4) in the river, which were predominantly protein- (C1) and humic-like (C2-C4) substances. Rainfall affected organic matter production and transport, leading to changes in the degradation and stability of dissolved organic matter. Overall, this study offers insight into how rainfall affects aquatic ecosystems.

Changes of characteristics and disinfection by-products formation potential of intracellular organic matter with different molecular weight in metalimnetic oxygen minimum

Metalimnetic oxygen minimum (MOM) occurs in reservoirs or lakes due to stratification and algal blooms, which has low dissolved oxygen (DO) levels and leads to the deterioration of water quality. The transformation mechanism and the impact on the water quality of intracellular organic matter (IOM) derived from algae are poorly understood under MOM conditions. In this study, IOM extracted by Microcystis aeruginosa was divided into five components according to molecular weight (MW), and the changes of characteristics and correlated disinfection by-products formation potential (DBPFP) were analyzed and compared under MOM conditions. The removal efficiency of dissolved organic carbon (DOC) in the <5 kDa fraction (66.6%) was higher than that in the >100 kDa fraction (41.8%) after a 14-day incubation under MOM conditions. The same tendency also occurred in Fmax and DBPFP. The decrease in Fmax was mainly due to the decline in tryptophan-like and tyrosine-like for all IOM fractions. The diversity of microorganisms degrading the MW > 100 kDa fraction was lower than others. Besides low MW fractions, these findings indicated that more attention should be paid to high MW fractions which were resistant to biodegradation under MOM conditions during water treatment.

Screening for potential warning biomarkers in cows with ketosis based on host-microbiota co-metabolism analysis

Introduction

The risk of ketosis is assessed by monitoring changes in plasma metabolites and cow behavior during the peripartum period. However, little is known about changes in the fecal bile acid and microbiota of cows before parturition. Therefore, this study clarified the bile acid profile and screened potential warning biomarkers in heifers 7 days before calving.

Methods

Ninety healthy cows were tracked in the transition period, and plasma and feces were collected 7 days before calving, on calving day, and 7 days after calving. The cows were divided into ketosis and healthy groups based on the blood β-hydroxybutyric acid levels from day 7 after calving. The levels of serum biochemical indices were measured at three time points using commercial kits. Ten cows in the ketosis group (KET-7) and 10 healthy cows (HEA-7) were randomly selected 7 days before calving for metabolome and 16S rRNA amplicon sequencing.

Results

No significant differences in serum energy-related indices were observed 7 days before calving. The major bile acids in the feces of the KET-7 group were non-conjugated secondary bile acids (UnconSBA). Differential bile acids were primarily derived from UnconSBA. The potential ketosis warning metabolite in feces for 7 days before delivery was isodeoxycholic acid. The abundance of Rikenellaaceae-RC9-gut-group in the KET-7 group increased, whereas the abundance of Oscillospiraceae UCG-010 bacteria significantly decreased. Lactobacillus and Prevotella-9 in feces were potential warning biomarkers for ketosis in dairy cows 7 days before calving. The variation in differential bile acids in the plasma, consistent with the feces, was mainly derived from UnconSBA. Lithocholic acid in the plasma was a potential ketosis warning metabolite 7 days before delivery.

Conclusion

Ketotic cows experienced bile acid metabolism disorders 7 days before calving, and the gut microbiota was closely related to bile acid metabolism disorders. Future studies should investigate the relationship between secondary bile acids and the development of ketosis.

Comparative analysis of the gut bacteria and fungi in migratory demoiselle cranes (Grus virgo) and common cranes (Grus grus) in the Yellow River Wetland, China

Introduction

Gut microbiota are closely related to the nutrition, immunity, and metabolism of the host and play important roles in maintaining the normal physiological activities of animals. Cranes are important protected avian species in China, and they are sensitive to changes in the ecological environment and are thus good environmental indicators. There have been no reports examining gut fungi or the correlation between bacteria and fungi in wild Demoiselle cranes (Grus virgo) and Common cranes (Grus grus). Related research can provide a foundation for the protection of rare wild animals.

Methods

16S rRNA and ITS high-throughput sequencing techniques were used to analyze the gut bacterial and fungal diversity of Common and Demoiselle cranes migrating to the Yellow River wetland in Inner Mongolia.

Results

The results revealed that for gut bacteria α diversity, Chao1 index in Demoiselle cranes was remarkably higher than that in Common cranes (411.07 ± 79.54 vs. 294.92 ± 22.38), while other index had no remarkably differences. There was no remarkable difference in fungal diversity. There were marked differences in the gut microbial composition between the two crane species. At the phylum level, the highest abundance of bacteria in the Common crane and Demoiselle crane samples was Firmicutes, accounting for 87.84% and 74.29%, respectively. The highest abundance of fungi in the guts of the Common and Demoiselle cranes was Ascomycota, accounting for 69.42% and 57.63%, respectively. At the genus level, the most abundant bacterial genus in the Common crane sample was Turicibacter (38.60%), and the most abundant bacterial genus in the Demoiselle crane sample was Catelicoccus (39.18%). The most abundant fungi in the Common crane sample was Penicillium (6.97%), and the most abundant fungi in the Demoiselle crane sample was Saccharomyces (8.59%). Correlation analysis indicated that there was a significant correlation between gut bacteria and fungi.

Discussion

This study provided a research basis for the protection of cranes. Indeed, a better understanding of the gut microbiota is very important for the conservation and management of wild birds, as it not only helps us to understand their life history and related mechanisms, but also can hinder the spread of pathogenic microorganisms.

Distinct compositions and functions of circulating microbial DNA in the peripheral blood compared to fecal microbial DNA in healthy individuals

The crucial function of circulating microbial DNA (cmDNA) in peripheral blood is gaining recognition because of its importance in normal physiology and immunity in healthy individuals. Evidence suggests that cmDNA in peripheral blood is derived from highly abundant, translocating gut microbes. However, the associations with and differences between cmDNA in peripheral blood and the gut microbiome remain unclear. We collected blood, urine, and fecal samples from volunteers to compare their microbial information via 16S rDNA sequencing. The results revealed that, compared with gut microbial DNA, cmDNA in peripheral blood was associated with reduced diversity and a distinct microbiota composition. The cmDNA in the blood reflects the biochemical processes of microorganisms, including synthesis, energy conversion, degradation, and adaptability, surpassing that of fecal samples. Interestingly, cmDNA in blood showed a limited presence of DNA from anaerobes and gram-positive bacteria, which contrast with the trend observed in fecal samples. Furthermore, analysis of cmDNA revealed traits associated with mobile elements and potential pathologies, among others, which were minimal in stool samples. Notably, cmDNA analysis indicated similarities between the microbial functions and phenotypes in blood and urine samples, although greater diversity was observed in urine samples. Source Tracker analysis suggests that gut microbes might not be the main source of blood cmDNA, or a selective mechanism allows only certain microbial DNA into the bloodstream. In conclusion, our study highlights the composition and potential functions associated with cmDNA in peripheral blood, emphasizing its selective presence; however, further research is required to elucidate the mechanisms involved.IMPORTANCEOur research provides novel insights into the unique characteristics and potential functional implications of circulating microbial DNA (cmDNA) in peripheral blood. Unlike other studies that analyzed sequencing data from fecal or blood microbiota in different study cohorts, our comparative analysis of cmDNA from blood, urine, and fecal samples from the same group of volunteers revealed a distinct blood-specific cmDNA composition. We discovered a decreased diversity of microbial DNA in blood samples compared to fecal samples as well as an increased presence of biochemical processes microbial DNA in blood. Notably, we add to the existing knowledge by documenting a reduced abundance of anaerobes and gram-positive bacteria in blood compared to fecal samples according to the analysis of cmDNA and gut microbial DNA, respectively. This observation suggested that a potential selective barrier or screening mechanism might filter microbial DNA molecules, indicating potential selectivity in the translocation process which contrasts with the traditional view that cmDNA primarily originates from random translocation from the gut and other regions. By highlighting these differences, our findings prompt a reconsideration of the origin and role of cmDNA in blood circulation and suggest that selective processes involving more complex biological mechanisms may be involved.

Modulating phyllosphere microbiome structure and function in Loropetalum chinense and Osmanthus fragrans: The impact of foliar dust and heavy metals

Trees can effectively capture airborne particles and improve air quality. However, the specific response of phyllosphere microbiome (PMo) in different plant species to particulate matter (PM) and the heavy metals it contains are not yet fully understood. In this study, we investigated the impact of PM on the diversity and function of PMo in Loropetalum chinense and Osmanthus fragrans trees grown in industrial and clean zones with varying levels of PM pollution. Our findings revealed that leaf dust had a significant negative effect on microbial richness, with O. fragrans exhibiting higher microbial diversity than L. chinense. The dominant phylum of phyllosphere bacteria in all samples was Proteobacteria, and the dominant genera were Stenotrophomonas and Delftia. The relative abundance of these genera varied significantly among plant species and regions. Our results showed that PM had a significant impact on the community composition of PMo, with the presence of heavy metals exerting a greater effect than particle size. Moreover, the foliar microbial community of plants grown in industrial zones exhibited significantly higher metabolic functions related to stress resistance and disease resistance compared to plants in control zones. These findings highlight the structural and functional responses of PMo to PM and indicate their potential for enhancing plant adaptation to environmental stress.

Wetlands as a potential multifunctioning tool to mitigate eutrophication and brownification

Eutrophication and brownification are ongoing environmental problems affecting aquatic ecosystems. Due to anthropogenic changes, increasing amounts of organic and inorganic compounds are entering aquatic systems from surrounding catchment areas, increasing both nutrients, total organic carbon (TOC), and water color with societal, as well as ecological consequences. Several studies have focused on the ability of wetlands to reduce nutrients, whereas data on their potential to reduce TOC and water color are scarce. Here we evaluate wetlands as a potential multifunctional tool for mitigating both eutrophication and brownification. Therefore, we performed a study for 18 months in nine wetlands allowing us to estimate the reduction in concentrations of total nitrogen (TN), total phosphorus (TP), TOC and water color. We show that wetland reduction efficiency with respect to these variables was generally higher during summer, but many of the wetlands were also efficient during winter. We also show that some, but not all, wetlands have the potential to reduce TOC, water color and nutrients simultaneously. However, the generalist wetlands that reduced all four parameters were less efficient in reducing each of them than the specialist wetlands that only reduced one or two parameters. In a broader context, generalist wetlands have the potential to function as multifunctional tools to mitigate both eutrophication and brownification of aquatic systems. However, further research is needed to assess the design of the generalist wetlands and to investigate the potential of using several specialist wetlands in the same catchment.

Chemical characteristics of dissolved organic matter in effluent from sludge alkaline fermentation liquid-fed sequencing batch reactors

Sludge alkaline fermentation liquid (SAFL) is a promising alternative to acetate for improving biological nitrogen removal (BNR) from wastewater. SAFL inevitably contains some refractory compounds, while the characteristics of dissolved organic matter (DOM) in effluent from SAFL-fed BNR process remain unclear. In this study, the molecular weight distribution, fluorescent composition and molecular profiles of DOM in effluent from SAFL and acetate-fed sequencing batch reactors (S-SBRs and A-SBRs, respectively) at different hydraulic retention time (12 h and 24 h) was comparatively investigated. Two carbon sources resulted in similar effluent TN, but a larger amount of DOM, which was bio-refractory or microorganisms-derived, was found in effluent of S-SBRs. Compared to acetate, SAFL increased the proportion of large molecular weight organics and humic-like substances in effluent DOM by 74.87%-101.3% and 37.52%-48.35%, respectively, suggesting their bio-refractory nature. Molecular profiles analysis revealed that effluent DOM of S-SBRs exhibited a more diverse composition and a higher proportion of lignin-like molecules. Microorganisms-derived molecules were found to be the dominant fraction (71.51%-72.70%) in effluent DOM (<800 Da) of S-SBRs. Additionally, a prolonged hydraulic retention time enriched Bacteroidota, Haliangium and unclassified_f_Comamonadaceae, which benefited the degradation of DOM in S-SBRs. The results help to develop strategies on reducing effluent DOM in SAFL-fed BNR process.

The gut microbiota regulates the depressive-type behaviors and inflammatory processes after severe burn injuries in mice

An emerging number of studies have recently revealed the correlation between burn injuries and psychological disorders. Gut microbiota and inflammatory factors may play a vital role in this process. Nevertheless, there are few studies conducted to disclose the potential mechanism of the gut microbiota between depression and burn injuries. In this study, we constructed a burn model of C57BL/6 mice, which showed that the symptom of depression became more and more severe with the burn of mice lasted longer. Meanwhile, there are significant differences of composition of gut microbiota among mice before and after burn. Then, we tested the inflammatory factors in the brain and peripheral blood, which showed an increased expression of Iba1, VWF, TNF-α and IL-6, and a decreased expression of IL-10 in burn mice. In addition, the expression of zonula occludens-1 (ZO-1) in cecum showed a down-regulation in burn mice, which indicated impaired intestinal barrier function. Lastly, the crossing fecal microbiota transplantation (FMT) and cohousing experiment were conducted to determine the functions of cross-transplantation of fecal microbiota on the depressive-type behaviours in burned mice. According to the score of Tail suspension test (TST), the burn mice were divided into two groups: Resilient mice (no-depressed mice) and Abnormal mice (depressed mice). After abnormal mice were transplanted with fecal microbiota of resilient mice, the symptom of depression was improved, and the expression of TNF-α, IL-6 and IL-10 return to normal levels (P < 0.05). On the contrary, after resilient mice were transplanted with fecal microbiota of abnormal mice both the TST scores and inflammatory factor developed depressive-type changes. In conclusion, our study demonstrated the changes of gut microbiota and inflammatory factors in depressed burn mice and non-depressed burn mice. The gut microbiota dysbiosis could impaired intestinal barrier function and lead to neuroinflammation, and this phenomenon could be significantly mitigated by FMT.

Exploring the diversity, bioactivity of endophytes, and metabolome in Synsepalum dulcificum

Synsepalum dulcificum exhibits high edible and medicinal value; however, there have been no reports on the exploration of its endophyte resources. Here, we conducted analyses encompassing plant metabolomics, microbial diversity, and the biological activities of endophytic metabolites in S. dulcificum. High-throughput sequencing identified 4,913 endophytic fungal amplicon sequence variants (ASVs) and 1,703 endophytic bacterial ASVs from the roots, stems, leaves, flowers, and fruits of S. dulcificum. Fungi were classified into 5 phyla, 24 classes, 75 orders, 170 families, and 313 genera, while bacteria belonged to 21 phyla, 47 classes, 93 orders, 145 families, and 232 genera. Furthermore, there were significant differences in the composition and content of metabolites in different tissues of S. dulcificum. Spearman's correlation analysis of the differential metabolites and endophytes revealed that the community composition of the endophytes correlated with plant-rich metabolites. The internal transcribed spacer sequences of 105 isolates were determined, and phylogenetic analyses revealed that these fungi were distributed into three phyla (Ascomycota, Basidiomycota, and Mucoromycota) and 20 genera. Moreover, 16S rDNA sequencing of 46 bacteria revealed they were distributed in 16 genera in three phyla: Actinobacteria, Proteobacteria, and Firmicutes. The antimicrobial activities (filter paper method) and antioxidant activity (DPPH and ABTS assays) of crude extracts obtained from 68 fungal and 20 bacterial strains cultured in different media were evaluated. Additionally, the α-glucosidase inhibitory activity of the fungal extracts was examined. The results showed that 88.6% of the strains exhibited antimicrobial activity, 55.7% exhibited antioxidant activity, and 85% of the fungi exhibited α-glucosidase inhibitory activity. The research suggested that the endophytes of S. dulcificum are highly diverse and have the potential to produce bioactive metabolites, providing abundant species resources for developing antibiotics, antioxidants and hypoglycemic drugs.

Towards (better) fluvial meta-ecosystem ecology: a research perspective

Rivers are an important component of the global carbon cycle and contribute to atmospheric carbon exchange disproportionately to their total surface area. Largely, this is because rivers efficiently mobilize, transport and metabolize terrigenous organic matter (OM). Notably, our knowledge about the magnitude of globally relevant carbon fluxes strongly contrasts with our lack of understanding of the underlying processes that transform OM. Ultimately, OM processing en route to the oceans results from a diverse assemblage of consumers interacting with an equally diverse pool of resources in a spatially complex network of heterogeneous riverine habitats. To understand this interaction between consumers and OM, we must therefore account for spatial configuration, connectivity, and landscape context at scales ranging from local ecosystems to entire networks. Building such a spatially explicit framework of fluvial OM processing across scales may also help us to better predict poorly understood anthropogenic impacts on fluvial carbon cycling, for instance human-induced fragmentation and changes to flow regimes, including intermittence. Moreover, this framework must also account for the current unprecedented human-driven loss of biodiversity. This loss is at least partly due to mechanisms operating across spatial scales, such as interference with migration and habitat homogenization, and comes with largely unknown functional consequences. We advocate here for a comprehensive framework for fluvial networks connecting two spatially aware but disparate lines of research on (i) riverine metacommunities and biodiversity, and (ii) the biogeochemistry of rivers and their contribution to the global carbon cycle. We argue for a research agenda focusing on the regional scale-that is, of the entire river network-to enable a deeper mechanistic understanding of naturally arising biodiversity-ecosystem functioning coupling as a major driver of biogeochemically relevant riverine carbon fluxes.

A hydrolyzed casein diet promotes Ngn3 controlling enteroendocrine cell differentiation to increase gastrointestinal motility in mice

Gut hormones are produced by enteroendocrine cells (EECs) found along the intestinal epithelium, and these cells play a crucial role in regulating intestinal function, nutrient absorption and food intake. A hydrolyzed casein diet has been reported to promote the secretion of gut hormones through the regulation of EEC development, but the underlying mechanism remains unclear. Therefore, this study was conducted to investigate whether the hydrolyzed casein diet can regulate EEC differentiation by employing mouse and organoid models. Mice were fed diets containing either casein (casein group) or hydrolyzed casein (hydrolyzed casein group) as the sole protein source. The hydrolyzed casein diet upregulated the expression of transcription factors, induced EEC differentiation, increased fasting serum ghrelin concentrations and promoted gastrointestinal (GI) motility in the duodenum compared to the casein diet. Interestingly, these differences could be abolished when there is addition of antibiotics to the drinking water, suggesting a significant role of gut microbiota in the hydrolyzed casein-mediated EEC function. Further investigation showed that the hydrolyzed casein diet led to reduced microbial diversity, especially the abundance of Akkermansia muciniphila (A. muciniphila) on the duodenal mucosa. In contrast, gavage with A. muciniphila impaired EEC differentiation through attenuated neurog3 transcription factor (Ngn3) expression, mediated through the promotion of Notch signaling. Moreover, pasteurized A. muciniphila showed similar effects to enter organoids in vitro. Overall, we found that a hydrolyzed casein diet reduced the abundance of A. muciniphila and promoted Ngn3 controlling EEC differentiation and this pathway is associated with increased GI motility in mice. The findings provide new insights into the role of hydrolyzed casein in gut transit and guidelines for using hydrolyzed casein in safe formula milk.

Coupling pathway prediction and fluorescence spectroscopy to assess the impact of auxiliary substrates on micropollutant biodegradation

Some bacteria can degrade organic micropollutants (OMPs) as primary carbon sources. Due to typically low OMP concentrations, these bacteria may benefit from supplemental assimilation of natural substrates present in the pool of dissolved organic matter (DOM). The biodegradability of such auxiliary substrates and the impacts on OMP removal are tightly linked to biotransformation pathways. Here, we aimed to elucidate the biodegradability and effect of different DOM constituents for the carbofuran degrader Novosphingobium sp. KN65.2, using a novel approach that combines pathway prediction, laboratory experiments, and fluorescence spectroscopy. Pathway prediction suggested that ring hydroxylation reactions catalysed by Rieske-type dioxygenases and flavin-dependent monooxygenases determine the transformability of the 11 aromatic compounds used as model DOM constituents. Our approach further identified two groups with distinct transformation mechanisms amongst the four growth-supporting compounds selected for mixed substrate biodegradation experiments with the pesticide carbofuran (Group 1: 4-hydroxybenzoic acid, 4-hydroxybenzaldehyde; Group 2: p-coumaric acid, ferulic acid). Carbofuran biodegradation kinetics were stable in the presence of both Group 1 and Group 2 auxiliary substrates. However, Group 2 substrates would be preferable for bioremediation processes, as they showed constant biodegradation kinetics under different experimental conditions (pre-growing KN65.2 on carbofuran vs. DOM constituent). Furthermore, Group 2 substrates were utilisable by KN65.2 in the presence of a competitor (Pseudomonas fluorescens sp. P17). Our study thus presents a simple and cost-efficient approach that reveals mechanistic insights into OMP-DOM biodegradation.

Terrestrial dissolved organic matter inputs drive the temporal dynamics of riverine bacterial ecological networks and assembly processes

Rivers receive, transport, and are reactors of terrestrial dissolved organic matter (DOM) and are highly influenced by changes in hydrological conditions and anthropogenic disturbances, but the effect of DOM composition on the dynamics of the bacterial community in rivers is poorly understood. We conducted a seasonal field sampling campaign at two eutrophic river mouth sites to examine how DOM composition influences the temporal dynamics of bacterial community networks, assembly processes, and DOM-bacteria associations. DOM composition and seasonal factors explained 34.7% of the variation in bacterial community composition, and 14.4% was explained purely by DOM composition where specific UV absorbance (SUVA254) as an indicator of aromaticity was the most important predictor. Significant correlations were observed between SUVA254 and the topological features of subnetworks of interspecies and DOM-bacteria associations, indicating that high DOM aromaticity results in more complex and connected networks of bacteria. The bipartite networks between bacterial taxa and DOM molecular formulae (identified by ultrahigh-resolution mass spectrometry) further revealed less specialized bacterial processing of DOM molecular formulae under the conditions of high water level and DOM aromaticity in summer than in winter. A shift in community assembly processes from stronger homogeneous selection in summer to higher stochasticity in winter correlated with changes in DOM composition, and more aromatic DOM was associated with greater similarity in bacterial community composition. Our results highlight the importance of DOM aromaticity as a predictor of the temporal dynamics of riverine bacterial community networks and assembly.

Changes in Intestinal Flora and Serum Metabolites Pre- and Post-Antitumor Drug Therapy in Patients with Non-Small Cell Lung Cancer

OBJECTIVE

this study aimed to identify the relationships between gut microbiota, metabolism, and non-small cell lung cancer (NSCLC) treatment outcomes, which are presently unclear.

METHODS

in this single-center prospective cohort study, we investigated changes in the gut microbiota and serum metabolite profile in 60 patients with NSCLC after four cycles of anticancer therapy.

RESULTS

The microbial landscape of the gut exhibited a surge in Proteobacteria and Verrucomicrobiota populations, alongside a decline in Firmicutes, Actinobacteriota, and Bacteroidota. Furthermore, a significant shift in the prevalence of certain bacterial genera was noted, with an increase in Escherichia/Shigella and Klebsiella, contrasted by a reduction in Bifidobacterium. Metabolomic analysis uncovered significant changes in lipid abundances, with certain metabolic pathways markedly altered post-treatment. Correlation assessments identified strong links between certain gut microbial genera and serum metabolite concentrations. Despite these findings, a subgroup analysis delineating patient responses to therapy revealed no significant shifts in the gut microbiome's composition after four cycles of treatment.

CONCLUSIONS

This study emphasizes the critical role of gut microbiota changes in NSCLC patients during anticancer treatment. These insights pave the way for managing treatment complications and inform future research to improve patient care by understanding and addressing these microbiota changes.

Divergent Fate and Roles of Dissolved Organic Matter from Spatially Varied Grassland Soils in China During Long-Term Biogeochemical Processes

Terrestrial dissolved organic matter (DOM) is critical to global carbon and nutrient cycling, climate change, and human health. However, how the spatial and compositional differences of soil DOM affect its dynamics and fate in water during the carbon cycle is largely unclear. Herein, the biodegradation of DOM from 14 spatially distributed grassland soils in China with diverse organic composition was investigated by 165 days of incubation experiments. The results showed that although the high humified fraction (high-HS) regions were featured by high humic-like fractions of 4-25 kDa molecular weight, especially the abundant condensed aromatics and tannins, they unexpectedly displayed greater DOM degradation during 45-165 days. In contrast, the unique proteinaceous and 25-100 kDa fractions enriched in the low humified fraction (low-HS) regions were drastically depleted and improved the decay of bulk DOM but only during 0-45 days. Together, DOM from the high-HS regions would cause lower CO2 outgassing to the atmosphere but higher organic loads for drinking water production in the short term than that from the low-HS regions. However, this would be reversed for the two regions during the long-term transformation processes. These findings highlight the importance of spatial and temporal variability of DOM biogeochemistry to mitigate the negative impacts of grassland soil DOM on climate, waters, and humans.

Danggui Shaoyao San: comprehensive modulation of the microbiota-gut-brain axis for attenuating Alzheimer's disease-related pathology

Background: Alzheimer's disease (AD), an age-associated neurodegenerative disorder, currently lacks effective clinical therapeutics. Traditional Chinese Medicine (TCM) holds promising potential in AD treatment, exemplified by Danggui Shaoyao San (DSS), a TCM formulation. The precise therapeutic mechanisms of DSS in AD remain to be fully elucidated. This study aims to uncover the therapeutic efficacy and underlying mechanisms of DSS in AD, employing an integrative approach encompassing gut microbiota and metabolomic analyses. Methods: Thirty Sprague-Dawley (SD) rats were allocated into three groups: Blank Control (Con), AD Model (M), and Danggui Shaoyao San (DSS). AD models were established via bilateral intracerebroventricular injections of streptozotocin (STZ). DSS was orally administered at 24 g·kg-1·d-1 (weight of raw herbal materials) for 14 days. Cognitive functions were evaluated using the Morris Water Maze (MWM) test. Pathological alterations were assessed through hematoxylin and eosin (HE) staining. Bloodstream metabolites were characterized, gut microbiota profiled through 16S rDNA sequencing, and cortical metabolomics analyzed. Hippocampal proinflammatory cytokines (IL-1β, IL-6, TNF-α) were quantified using RT-qPCR, and oxidative stress markers (SOD, CAT, GSH-PX, MDA) in brain tissues were measured with biochemical assays. Results: DSS identified a total of 1,625 bloodstream metabolites, predominantly Benzene derivatives, Carboxylic acids, and Fatty Acyls. DSS significantly improved learning and spatial memory in AD rats and ameliorated cerebral tissue pathology. The formulation enriched the probiotic Ligilactobacillus, modulating metabolites like Ophthalmic acid (OA), Phosphocreatine (PCr), Azacridone A, Inosine, and NAD. DSS regulated Purine and Nicotinate-nicotinamide metabolism, restoring balance in the Candidatus Saccharibacteria-OA interplay and stabilizing gut microbiota-metabolite homeostasis. Additionally, DSS reduced hippocampal IL-1β, IL-6, TNF-α expression, attenuating the inflammatory state. It elevated antioxidative enzymes (SOD, CAT, GSH-PX) while reducing MDA levels, indicating diminished oxidative stress in AD rat brains. Conclusion: DSS addresses AD pathology through multifaceted mechanisms, encompassing gut microbiome regulation, specific metabolite modulation, and the mitigation of inflammation and oxidative stress within the brain. This holistic intervention through the Microbial-Gut-Brain Axis (MGBA) underscores DSS's potential as an integrative therapeutic agent in combatting AD.

Influence of cultivation duration on microbial taxa aggregation in Panax ginseng soils across ecological niches

Introduction

Microbial communities are crucial for plant health and productivity. However, the influence of cultivation age on the ecological processes in assembling plant microbiomes at various ecological niches remains unclear.

Methods

We selected 12 samples from ginseng farmlands with different cultivation years (N4: 4 years old, N6: 6 years old). We used soil physicochemical properties, enzyme activities, and high-throughput sequencing (16S rDNA and ITS) to examine the rhizoplane (RP), rhizosphere (RS), and bulk soil (BS).

Results

Our results indicated that cultivation years significantly affect the soil microbiome's diversity and community composition across different ecological niches. The BS microbiome experienced the largest effect, while the RS experienced the smallest. N6 showed a greater impact than N4. This effect was more pronounced on the fungal communities than the bacterial communities of various ecological niches and can be closely related to the soil's physicochemical properties. In N4 soils, we observed an upward trend in both the number of ASVs (amplicon sequence variations) and the diversity of soil microbial taxa across various ecological niches. In N4RP, the bacteria Sphingomonas, known for degrading toxic soil compounds, was present. All ecological niches in N4 showed significant enrichment of Tetracladium fungi, positively associated with crop yield (N4RP at 6.41%, N4RS at 11.31%, and N4BS at 3.45%). In N6 soils, we noted a stark decline in fungal diversity within the BS, with a 57.5% reduction in ASVs. Moreover, Sphingomonas was abundantly present in N6RS and N6BS soils. The relative abundance of the pathogen-inhibiting fungus Exophiala in N6RP and N6RS reached 34.18% and 13.71%, respectively, marking increases of 4.9-fold and 7.7-fold. Additionally, another pathogeninhibiting fungus, Humicola, showed significant enrichment in N6BS, with a 7.5-fold increase. The phenolic acid-producing fungus Pseudogymnoascus in N6RP, N6RS, and N6BS showed increases of 2.41-fold, 2.55-fold, and 4.32-fold, respectively. We hypothesize that functional genes related to the metabolism of terpenoids and polyketides, as well as signaling molecules and interactions, regulate soil microbial taxa in ginseng from different cultivation years.

Discussion

In conclusion, our study enhances understanding of plant-microbe interactions and aids the sustainable development of medicinal plants, particularly by addressing ginseng succession disorder.

IgA-mediated control of host-microbial interaction during weaning reaction influences gut inflammation

The mechanisms of how host-microbe mutualistic relationships are established at weaning contingently upon B-cell surveillance remain inadequately elucidated. We found that CD138+ plasmacyte (PC)-mediated promotion of IgA response regulates the symbiosis between Bacteroides uniformis (B. uniformis) and the host during the weaning period. The IgA-skewed response of CD138+ PCs is essential for B. uniformis to occupy a defined gut luminal niche, thereby fostering stable colonization. Furthermore, B. uniformis within the natural gut niche was perturbed in the absence of IgA, resulting in exacerbated gut inflammation in IgA-deficient mice and weaned piglets. Thus, we propose that the priming and maintenance of intestinal IgA response from CD138+ PCs are required for host-microbial symbiosis, whereas the perturbation of which would enhance inflammation in weaning process.

Probiotic Bacillus licheniformis ZW3 Alleviates DSS-Induced Colitis and Enhances Gut Homeostasis

Despite Bacillus species having been extensively utilized in the food industry and biocontrol as part of probiotic preparations, limited knowledge exists regarding their impact on intestinal disorders. In this study, we investigated the effect of Bacillus licheniformis ZW3 (ZW3), a potential probiotic isolated from camel feces, on dextran sulfate sodium (DSS)-induced colitis. The results showed ZW3 partially mitigated body weight loss, disease activity index (DAI), colon shortening, and suppressed immune response in colitis mice, as evidenced by the reduction in the levels of the inflammatory markers IL-1β, TNF-α, and IL-6 (p < 0.05). ZW3 was found to ameliorate DSS-induced dysfunction of the colonic barrier by enhancing mucin 2 (MUC2), zonula occluden-1 (ZO-1), and occludin. Furthermore, enriched beneficial bacteria Lachnospiraceae_NK4A136_group and decreased harmful bacteria Escherichia-Shigella revealed that ZW3 improved the imbalanced gut microbiota. Abnormally elevated uric acid levels in colitis were further normalized upon ZW3 supplementation. Overall, this study emphasized the protective effects of ZW3 in colitis mice as well as some potential applications in the management of inflammation-related diseases.

Matrine Mediated Immune Protection in MS by Regulating Gut Microbiota and Production of SCFAs

There is clearly an unmet need for more effective and safer treatments for multiple sclerosis (MS). Our previous studies showed a significant therapeutic effect of matrine, a monomer of traditional herbal medicine, on experimental autoimmune encephalomyelitis (EAE) mice. To explore the mechanism of matrine action, we used 16S rRNA sequencing technology to determine the gut microbes in matrine-treated EAE mice and controls. The concentrations of short-chain fatty acids (SCFAs) were then tested by metabonomics. Finally, we established pseudo-sterile mice and transplanted into them fecal microbiota, which had been obtained from the high-dose matrine-treated EAE mice to test the effects of matrine. The results showed that matrine could restore the diversity of gut microbiota and promote the production of SCFAs in EAE mice. Transplantation of fecal microbiota from matrine-treated mice significantly alleviated EAE severity, reduced CNS inflammatory infiltration and demyelination, and decreased the level of IL-17 but increased IL-10 in sera of mice. In conclusion, matrine treatment can regulate gut microbiota and metabolites and halt the progression of MS.

Analysis of the microbial diversity in takin (Budorcas taxicolor) feces

Introduction

The intestinal tract of animals is a complex and dynamic microecosystem that is inextricably linked to the health of the host organism. Takin (Budorcas taxicolor) is a threatened species, and its gut microbiome is poorly understood. Therefore, this study aimed to analyze the microbial community structure and potential pathogens of takin.

Methods

Takin fecal samples were collected from five sites in a nature reserve to ensure the uniformity of sample collection, determine the effects of different geographical locations on gut microbes, and analyze the differences in microbial communities between sites. Subsequently, high-throughput 16S rDNA gene sequencing was performed to analyze the microbial diversity and potential pathogens in the gut; the findings were verified by isolating and culturing bacteria and metagenomic sequencing.

Results and discussion

The takin gut microflora consisted mainly of four phyla: Firmicutes (69.72%), Bacteroidota (13.55%), Proteobacteria (9.02%), and Verrucomicrobiota (3.77%), representing 96.07% of all microorganisms. The main genera were UCG-005 (20.25%), UCG-010_unclassified (12.35%), Firmicus_unclassified (4.03%), and Rumino coccsea_unclassified (3.49%), while the main species were assigned to Bacteria_unclassified. Potential pathogens were also detected, which could be used as a reference for the protection of takin. Pseudomonas presented the highest abundance at Shuichiping and may represent the main pathogen responsible for the death of takin at the site. This study provides an important reference for investigating the composition of the bacterial community in the intestine of takin.

Versatile, vigilance, and gut microbiome support the priority of high-ranking hens

Dominance hierarchy exists in social animals and shows profound impacts on animals' survival, physical and mental health, and reproductive success. Aggressive interaction, as the main indicator used to calculate social hierarchy, however, is not found in some female animals. In this study, we aimed to figure out the establishment of social hierarchy in hens that almost perform aggressive behaviors and investigated the interactions of social hierarchy with production performance and gut microbiome. Forty 49-day-old Qingyuan hens were randomly divided into four groups. The social hierarchy of hens was calculated by the relative position around the feeder. The rank 1 (R1), R2, R3, R4, R5, R6, R7, R8, R9, and R10 birds were determined in ascending order. Then, R1 and R2 birds (four duplicates, n = 8) were named as the high-ranking hens (HR) group, while R9 and R10 individuals were named as the low-ranking hens (LR) group (four duplicates, n = 8). The heart index (p = 0.01), number of visits per day, daily feed intake, and occupation time per day were higher in the HR group than LR group, but the LR group had a higher feed intake per visit than the HR group. The alpha diversity was significantly lower in the HR group than the LR group (p = 0.05). The relative abundance of phylum Firmicutes was higher while that of phylum Deferribacterota was lower in the HR group than LR group (p < 0.05). At the genus level, the relative abundance of Succinatimonas, Eubacterium hallii group, and Anaerostipes were higher in HR group than in LR group. The relative abundance of Bacteroides, Mucispirillum, Subdoligranulum, and Barnesiellaceae unclassified was higher in the LR group than HR group (p < 0.05). In conclusion, the rank of hens could be calculated by the relative position around the feeder when they compete for food. The dominant hens have a versatile. Moreover, they are more vigilant and have priority when foraging. Low-ranking hens adopt strategies to get enough food to sustain themselves. Hens of high-rank possess beneficial bacteria that use favorable substances to maintain the balance of the gut environment.