Microbial Function Research Articles

Maternal gastrointestinal microbiome shapes gut microbial function and resistome of newborns in a cow-to-calf model

BackgroundThe maternal gut microbiome is the direct and important source of early colonization and development of the neonatal gut microbiome. However, differences in unique and shared features between mothers with different physiological phenotypes and their newborns still lack exhaustive investigation. Here, using a cow-to-calf model, a comprehensive investigation was conducted to elucidate the pattern and characterization of microbial transfer from the maternal source to the offspring.ResultsThe microbiota in the rumen and feces of dairy cows were divided into two clusters via enterotype analysis. The cows from the enterotype distinguished by Prevotella in the rumen had better production performance, whereas no difference was observed in the cows classified by feces enterotype. Furthermore, through a pairwise combination of fecal and ruminal enterotypes, we screened a group of dairy cows with excellent phenotypes. The gastrointestinal microbiomes of cows with different phenotypes and their offspring differed significantly. The rumen was a more important microbial source for meconium than feces. Transmission of beneficial bacteria from mother to offspring was observed. Additionally, the meconium inherits advantageous metabolic functions of the rumen. The resistome features of the rumen, feces, and meconium were consistent, and resistome abundance from cows to calves showed an expanding trend. The interaction between antibiotic-resistance genes and mobile genetic elements from the rumen to meconium was the most remarkable. The diversity of core metabolites from cows to calves was stable and not affected by differences in phenotypes. However, the abundance of specific metabolites varied greatly.ConclusionsOur study demonstrates the microbial taxa, metabolic function, and resistome characteristics of maternal and neonatal microbiomes, and reveals the potential vertical transmission of the microbiome from a cow-to-calf model. These findings provide new insights into the transgenerational transmission pattern of the microbiome.2cueHjjtpyRzwmAWUdZ5oAVideo

The structure and function of rhizosphere bacterial communities: impact of chemical vs. bio-organic fertilizers on root disease, quality, and yield of Codonopsis pilosula.

Long-term use of chemical fertilizers (CFs) can cause soil compaction and acidification. In recent years, bio-organic fertilizers (BOFs) have begun to replace CFs in some vegetables and cash crops, but the application of CFs or BOFs has resulted in crop quality and disease occurrence. This study aimed to analyze the microbial mechanism of differences between CFs and BOFs in root disease, quality, and yield of tuber Chinese herbal medicine. We studied the effects of CFs, organic fertilizers, commercial BOFs, biocontrol bacteria BOFs, and biocontrol fungi BOFs on rhizosphere microbial community structure and function, root rot, quality, and yield of Codonopsis pilosula at different periods after application and analyzed the correlation. Compared to CFs, the emergence rate and yield in BOF treatments were increased by 21.12 and 33.65%, respectively, and the ash content, water content, and disease index in the BOF treatments were decreased by 17.87, 8.19, and 76.60%, respectively. The structural equation model showed that CFs promoted the quality and yield of C. pilosula by influencing soil environmental factors, while BOFs directly drove soil bacterial community to reduce disease index and improve the quality and yield of C. pilosula. There was a stronger interaction and stability of soil microbial networks after BOF treatments. Microlunatus, Rubrobacter, Luteitalea, Nakamurella, and Pedomicrobium were identified as effector bacteria, which were related to disease prevention and yield and quality increase of C. pilosula. Microbial functional analysis indicated that the signal transduction and amino acid metabolism of soil bacteria might play a major role in improving the quality and yield of C. pilosula in the early and middle growth stages. In conclusion, compared to CFs, BOFs obtained a lower disease index of root rot and a higher quality and yield of C. pilosula by changing the structure and function of the rhizosphere bacterial community.

Effects of the Radicle Sheath on the Rhizosphere Microbial Community Structure of Seedlings in Early Spring Desert Species Leontice incerta

Most research on plant–microbe interactions emphasize the effects of micronutrients on the rhizosphere microbial community structure. However, the influence of seed structures, particularly the radicle sheath, on microbial diversity at the seedling root tips under varying temperatures and humidity has been less explored. This study conducted controlled indoor experiments in the northern desert of Xinjiang to assess the radicle sheath’s impact on microbial community composition, diversity, and function. The results indicated no significant changes in the Chao1 index for bacteria and fungi, but notable differences were observed in the Shannon and Simpson indices (p < 0.05). Under drought conditions, the radicle sheath significantly reduced bacterial infections without affecting fungi. Genus-level analysis showed an increased abundance of specific dominant bacterial groups when the radicle sheath was retained. NMDS analysis confirmed its significant effect on both bacterial and fungal community structures. LEfSe analysis identified 34 bacterial and 15 fungal biomarkers, highlighting the treatment’s impacts on microbial taxonomic composition. Functional predictions using PICRUSt 2 revealed that the radicle sheath facilitated the conversion of CH4 to CH3OH and various nitrogen cycle processes under drought. Overall, the radicle sheath plays a crucial role in maintaining rhizosphere microbial community stability and enhancing the functions of both bacteria and fungi under drought conditions.

Winter Grazing, Not Fencing or Unicast, Promotes Stability of Microbial Community and Function in the Qilian Mountains of Qinghai‐Xizang Plateau

ABSTRACTIn alpine meadows, microorganisms are essential to sustain the stability of terrestrial geochemical processes and vegetation–soil–microbial systems. The present study in order investigate how various management measures impact the microbial communities' composition and functionality, we utilize metagenomic sequencing techniques to examinate the composition and function of soil microbial communities in the southern Qilian Mountains of the Qinghai‐Xizang Plateau in response to the management practices of fencing enclose (FE), winter grazing (WG), transition zone between natural and artificial grasslands (TZ), and artificial unicast oats (AU). Vegetation diversity and soil physicochemical characteristics were dramatically altered by the management measures. The prokaryotic community structure was considerably similar in FE and WG, as well as in TZ and AU. Near‐natural (FE) and artificial establishment (AU) disturbances changed the fungal community structure. Enzymes related to carbon metabolism did not respond significantly to the management measures, whereas those related to nitrogen metabolism did not respond significantly in TZ and AU. The relative abundance of enzymes participating in nitrogen metabolism was higher under TZ and AU than under FE and WG. We concluded that grassland management measures altered the structure of aboveground graminoid and leguminous vegetation communities and belowground biomass allocation, resulting in changes in K uptake, causing striking changes in the structure of fungal communities and nitrogen‐metabolizing enzymes; moderate disturbance (WG) was beneficial for maintaining the stability of microbial communities in alpine grasslands.

Biotic and abiotic properties mediating sediment microbial diversity and function in a river-lake continuum.

A river-lake system plays an important role in water management by providing long-term and frequent water diversions. However, hydrological connectivity in the system can have a profound effect on sediment microbial communities through pH, nutrient concentrations, and benthos invertebrates. Consequently, identifying the key environmental factors and their driving mechanisms is vital for microbial adaptation strategies to extreme environments. In this study, we analyzed the significant difference in sediment bacterial and fungal community structures and diversity indices among Dongting Lake and its tributary rivers, which worked as a typical river-connected lake ecosystem. There were significant differences in biotic and abiotic environments in the sediment habitats of Dongting Lake and its tributary rivers. Random forest analysis revealed that pH and Mollusca were found to be the most important abiotic and biotic variables for predicting both bacterial and fungal community structures, respectively. The beta diversity decomposition analyses showed that the bacterial and fungal community compositional dissimilarities among different sections were dominated by species replacement processes, with more than half of the OTUs in each section being unique. Notably, both biotic and abiotic factors affected the number and the relative abundance of these bacterial and fungal unique OTUs, leading to changes in community composition. Mollusca, pH, TP, NO3-N, and NH4-N were negatively related to the relative abundance of Actinobacteria, Acidobacteria, Gemmatimonadetes, Planctomycetes, and Ascomycota, while Annelida and ORP were positively related to the relative abundance of Actinobacteria and Gemmatimonadetes. Additionally, PICRUSt analysis revealed that the functional dissimilarity among lakes and rivers was strengthened in unique species compared to all species in bacterial and fungal communities, and the changes of functional types helped to improve the habitat environment in the main Dongting Lake and promote the process of microbial growth. From our results, the role of macrozoobenthos and physicochemical characteristics in driving the sediment microbial community spatial variations became clear, which contributed to further understanding of the river-lake ecosystem.

Adaptation of rhizobacterial and endophytic communities in Citrus Grandis Exocarpium to long-term organic and chemical fertilization.

Organic fertilizers (OF) are crucial for enhancing soil quality and fostering plant growth, offering a more eco-friendly and enduring solution compared to chemical fertilizers (CF). However, few studies have systematically analyzed the effects of OF/CF on root microbiome of medicinal plants, especially in combination with active ingredients. In this study, we investigated the composition and function of bacteria and fungi in the rhizosphere or within the root of traditional Chinese medicinal plants, Citri Grandis Exocarpium (Huajuhong), which were treated with OF or CF over 1, 3, and 5 years (starting from 2018). Additionally, we conducted metabolome analysis to evaluate the effects of different fertilizers on the medicinal properties of Huajuhong. The results indicated that extended fertilization could enhance the microbial population and function in plant roots. Notably, OF demonstrated a stronger influence on bacteria, whereas CF enhanced the cohesion of fungal networks and the number of fungal functional enzymes, and even potentially reduced the proliferation of harmful rhizosphere pathogens. By adopting distancebased redundancy analysis, we identified the key physicochemical characteristics that significantly influence the distribution of endophytes, particularly in the case of OF. In contrast, CF was found to exert a more pronounced impact on the composition of the rhizosphere microbiome. Although the application of OF resulted in a broader spectrum of compounds in Huajuhong peel, CF proved to be more efficacious in elevating the concentrations of flavonoids and polysaccharides in the fruit. Consequently, the effects of long-term application of OF or CF on medicinal plants is different in many ways. This research provides a guide for OF/CF selection from the perspective of soil microecology and aids us to critically assess and understand the effects of both fertilizers on the soil environment, and promotes sustainable development of organic agriculture.

Effects of Grafting on the Structure and Function of Coffee Rhizosphere Microbiome

Heterologous double-root grafting represents an effective strategy to mitigate challenges associated with continuous coffee cropping and reduce soil-borne diseases. However, its specific regulatory mechanism remains unclear. Therefore, a field experiment was conducted including six different grafting combinations for C. canephora cv. Robusta (Robusta) and Coffea Liberica (Liberica): Robusta scion with a homologous double root (R/RR), Liberica scion with a homologous double root (L/LL), Robusta scion with a heterologous double root (R/RL and L/RL), and Liberica scion with a heterologous double root (L/LR and R/LR); these combinations were conducted to clarify the effects of heterologous double-root grafting combinations on the root exudates and soil microbial diversity, structure, and function of Robusta and Liberica. The results demonstrated notable differences in root exudates, rhizosphere microbial structure, and function between Robusta and Liberica. Despite Liberica having lower diversity in its rhizosphere microbial communities and relatively higher levels of potential pathogenic bacteria, it showed stronger resistance to diseases. Roots of Robusta in heterologous double-root coffee seedlings significantly enhanced the secretion of resistance compounds, increased the relative abundance of potentially beneficial bacteria, and reduced the relative abundance of potential pathogenic fungi. This enhances the rhizosphere immunity of Robusta against soil-borne diseases. The results indicated that grafting onto Liberica roots can strengthen resistance mechanisms and enhance the rhizosphere immunity of Robusta, thereby mitigating challenges associated with continuous cropping.

Depth-dependent effects of forest diversification on soil functionality and microbial community characteristics in subtropical forests

Soil microbes are critical to the maintenance of forest ecosystem function and stability. Forest diversification, such as monocultures versus mixed forests stands, can strongly influence microbial community patterns and processes, as well as their role in soil ecosystem multifunctionality, such as in subtropical forest ecosystems. However, less is known about these patterns and processes vary with soil depth. Here, we investigated the results of an eight-year forest diversification field experiment comparing the soil ecosystem multifunctionality, bacterial and fungal community assembly, and network patterns in mixed versus monoculture plantations along vertical profiles (0–80 cm depth) in a subtropical region. We found that the introduction of broadleaf trees in coniferous monocultures led to enhanced synergies between multiple functions, thus improving soil multifunctionality. The effects of mixed plantations on the functional potential in top soils were greater than in deep soils, especially for carbon degradation genes (apu, xylA, cex, and glx). Microbial community assembly in the top layer, particularly in mixed plantations, was dominated by stochastic processes, whereas deterministic were more important in the deep layer. Soil microbial network complexity and stability were higher in the top layer of mixed plantations, but in the deep layer was monoculture. Interestingly, the changes in microbial communities and multifunctionality in the top layer were mainly related to variation in nutrients, whereas those in the deep were more influenced by soil moisture. Overall, we reveal positive effects of mixed forest stands on soil microbial characteristics and functionality compared to that of monocultures. Our findings highlighted the importance of enhancing functional diversity through the promotion of tree species diversity, and managers can better develop forest management strategies to promote soil health under global change scenarios.

Warm growing season activates microbial nutrient cycling to promote fertilizer nitrogen uptake by maize

The influence of nitrogen (N) inputs on soil microbial communities and N uptake by plants is well-documented. Seasonal variations further impact these microbial communities and their nutrient-cycling functions, particularly within multiple cropping systems. Nevertheless, the combined effects of N fertilization and growing seasons on soil microbial communities and plant N uptake remain ambiguous, thereby constraining our comprehension of the optimal growing season for maximizing crop production. In this study, we employed 15N isotope labeling, high-throughput sequencing, and quantitative polymerase chain reaction (qPCR) techniques to investigate the effects of two distinct growing seasons on microbial communities and maize 15N uptake ratios (15NUR). Our results showed that the warm growing season (26.6 °C) increased microbial diversity, reduced network complexity but enhanced stability, decreased microbial associations, and increased modularization compared to the cool growing season (23.1 °C). Additionally, the warm growing season favored oligotrophic species and increased the abundance of microbial guilds and functional genes related to N, phosphorus, and sulfur cycling. Furthermore, alterations in the characteristics of soil microbial keystone taxa were closely linked to variations in maize 15NUR. Overall, our findings demonstrate significant seasonal variations in soil microbial diversity and functioning, with maize exhibiting higher 15NUR during the warm growing season of the double cropping system.

Enrichment of marine microbes to remove nitrogen of urea wastewater under salinity stress

Salinity (NaCl) and urea concentration significantly affect the diversity, structural and physiological function of microbial communities in the biological treatment of wastewater. However, the responses of microbial in high salt and urea wastewater remain elusive. Here, we investigated microbial community function and assembly of four regions using gradient domestication experiment combined with 16S rRNA gene sequencing and statistical methods. The results showed that with the increase of salinity and urea concentration, the consortium Xiamen could still remove most urea, while the other three consortia could not. The alpha diversity of microbial community initially decreased and then increased, showing a recovery trend. After domestication, the consortium Xiamen exhibited high physiological activity and complex network structure, and the community assembly process changed from stochastic to deterministic during the domestication. Furthermore, the keystones with low abundance were associated with urea removal and important for maintain the complexity of the networks, while Arenibacter and Oceanimonas were found to be keystones in maintaining efficient urea removal in harsh environments. To sum up, environmental effects dominated by salinity and urea concentration stress drove the community assembly and species coexistence that underpinned the microbial differentiation pattern at a geographic scale. These results provided new sights for elucidate how microbial response to salinity and urea during wastewater treatment.

Exploring the potential role of microbiota and metabolites in acute exacerbation of chronic obstructive pulmonary disease.

The acute exacerbation of chronic obstructive pulmonary disease seriously affects the respiratory system function and quality of life of patients. This study employed 16S rRNA sequencing and metabolomics techniques to analyze the respiratory microbiota and serum metabolites of COPD and AECOPD patients. The results showed that the microbial diversity in the respiratory tract of AECOPD patients was significantly lower than that of COPD patients, and the relative abundance of Bacteroidetes, Prevotella and Neisseria in the respiratory tract of AECOPD patients was significantly lower than that of COPD patients. However, the relative abundance of Haemophilus_D, Veillonella_A and Pseudomonas_E, in AECOPD patients was significantly higher than that of COPD patients, and the ability of respiratory microbiota in AECOPD patients to participate in alanine metabolism was significantly lower than that of COPD patients. Metabolome results further revealed that the serum alanine levels in AECOPD patients were significantly lower than those in COPD patients, and these differential metabolites were mainly involved in linoleic acid metabolism, protein digestion and absorption and regulation of lipolysis in adipocytes. In summary, the structural characteristics of respiratory microbiota in COPD and AECOPD patients are different from those in healthy populations, and their microbiota diversity decreases and microbial community structure and function will also undergo changes when acute exacerbations occur. In addition, the predicted microbial community function and metabolomics results indicate that the onset of AECOPD is mainly related to energy and amino acid metabolism disorders, especially alanine metabolism.

Improving viral annotation with artificial intelligence.

Viruses of bacteria, "phages," are fundamental, poorly understood components of microbial community structure and function. Additionally, their dependence on hosts for replication positions phages as unique sensors of ecosystem features and environmental pressures. High-throughput sequencing approaches have begun to give us access to the diversity and range of phage populations in complex microbial community samples, and metagenomics is currently the primary tool with which we study phage populations. The study of phages by metagenomic sequencing, however, is fundamentally limited by viral diversity, which results in the vast majority of viral genomes and metagenome-annotated genomes lacking annotation. To harness bacteriophages for applications in human and environmental health and disease, we need new methods to organize and annotate viral sequence diversity. We recently demonstrated that methods that leverage self-supervised representation learning can supplement statistical sequence representations for remote viral protein homology detection in the ocean virome and propose that consideration of the functional content of viral sequences allows for the identification of similarity in otherwise sequence-diverse viruses and viral-like elements for biological discovery. In this review, we describe the potential and pitfalls of large language models for viral annotation. We describe the need for new approaches to annotate viral sequences in metagenomes, the fundamentals of what protein language models are and how one can use them for sequence annotation, the strengths and weaknesses of these models, and future directions toward developing better models for viral annotation more broadly.

Increasing tree phylogenetic diversity stimulates microbial functional potential in a subtropical forest

Abstract Soil microbial functions are closely related to ecosystem productivity, carbon sequestration and their responses to global change. Tree phylogenetic diversity has been found to impact microbial community composition, diversity, and functions, but how it modulates the linkage between microbial community facets and functions remains unclear. Here, 45 plots covering a natural gradient of tree phylogenetic diversity (TPD) were selected in a subtropical forest of southwest China to explore how increasing TPD impacts soil microbial community facets and microbial functional potential. The microbial functional potential was evaluated based on the abundances of carbon, nitrogen, and phosphorus cycling-related functional genes. Soil fungal alpha diversity increased significantly, but bacterial alpha diversity did not change as TPD increased. Both soil microbial network complexity and stability improved significantly with increasing TPD. Ultimately, increasing TPD promoted soil microbial functional potential by stimulating soil carbon and nitrogen availability, microbial keystone diversity, and network stability collectively. These findings emphasize the critical roles of keystone taxa and network stability as microbial factors in stimulating soil microbial function in response to increasing TPD. Therefore, it is strongly recommended to increase TPD in order to stimulate soil microbial functions and other ecosystem functions when implementing afforestation or ecological restoration projects.

Cow Dung Liquid Mulch Improves Maize Yields: Beneficial Microorganisms Are Enriched and Environmental Risks Are Reduced and Nutrient Cycling Is Promoted

Cow dung liquid mulch (CDLM), which uses cow dung as a raw material, has a good degradability and is a potential alternative to traditional plastic agricultural mulch, but there is a lack of research on the effects of CDLM on rhizosphere soil physicochemical properties, rhizosphere soil microbial functions, and crop yields. In this study, the link between maize yield, environmental factors, and functional genes as well as the responses of microbial community functions to CDLM and polyethylene mulch (PE) were studied using metagenomic sequencing. Functional annotation was also performed on clusters of orthologous groups of proteins, the Kyoto Encyclopedia of Genes and Genomes, and carbohydrate-active enzyme sequencing data. The results showed that CDLM significantly increased maize yield by 30.9% compared to CK while maintaining lower soil microplastic levels. CDLM promotes the enrichment of beneficial microorganisms such as Mycolicibacterium and Pseudomonas. The relative abundance of functional genes related to microbial metabolism, soil element cycling pathways, and organic matter degradation was significantly higher in CDLM than in CK. Microbial functional genes were positively correlated with maize yield and environmental factors such as soil nutrients. These results suggested that CDLM can improve maize yield by enriching beneficial microorganisms, reducing rhizosphere soil environmental risks, and enhancing rhizosphere soil microbial function. Rhizosphere soil nutrients and microbial functional genes together mediated the positive response of maize yield to CDLM. This study can provide a scientific basis and data support for the safe use of mulch in the future.

Anthropogenic impacts on the terrestrial subsurface biosphere.

The terrestrial subsurface is estimated to be the largest reservoir of microbial life on Earth. However, the subsurface also harbours economic, industrial and environmental resources, on which humans heavily rely, including diverse energy sources and formations for the storage of industrial waste and carbon dioxide for climate change mitigation. As a result of this anthropogenic activity, the subsurface landscape is transformed, including the subsurface biosphere. Through the creation of new environments and the introduction of substrates that fuel microbial life, the structure and function of subsurface microbiomes shift markedly. These microbial changes often have unintended effects on overall ecosystem function and are frequently challenging to manage from the surface of the Earth. In this Review, we highlight emerging research that investigates the impacts of anthropogenic activity on the terrestrial subsurface biosphere. We explore how humans alter the constraints on microbial life in the subsurface through drilling, mining, contamination and resource extraction, along with the resulting impacts of microorganisms on resource recovery and subsurface infrastructure.

Associations between maternal microbiome, metabolome and incidence of low-birth weight in Guatemalan participants from the Women First Trial.

Low birth weight (LBW; <2,500 g) affects approximately 15 to 20 percent of global births annually and is associated with suboptimal child development. Recent studies suggest a link between the maternal gut microbiome and poor obstetric and perinatal outcomes. The goal of this study was to examine relationships between maternal microbial taxa, fecal metabolites, and maternal anthropometry on incidence of LBW in resource-limited settings. This was a secondary analysis of the Women First trial conducted in a semi-rural region of Guatemala. Maternal weight was measured at 12 and 34 weeks (wk) of gestation. Infant anthropometry measures were collected within 48 h of delivery. Maternal fecal samples at 12 and 34 weeks were used for microbiome (16S rRNA gene amplicon sequencing) and metabolomics analysis (34 wk). Linear mixed models using the MaAslin2 package were utilized to assess changes in microbiome associated with LBW. Predictive models using gradient boosted machines (XGBoost) were developed using the H2o.ai engine. No differences in β-diversity were observed at either time point between mothers with LBW infants relative to normal weight (NW) infants. Simpson diversity at 12 and 34 weeks was lower in mothers with LBW infants. Notable differences in genus-level abundance between LBW and NW mothers (p < 0.05) were observed at 12 weeks with increasing abundances of Barnesiella, Faecalibacterium, Sutterella, and Bacterioides. At 34 weeks, there were lower abundances of Magasphaera, Phascolarctobacterium, and Turicibacter and higher abundances of Bacteriodes, and Fusobacterium in mothers with LBW infants. Fecal metabolites related to bile acids, tryptophan metabolism and fatty acid related metabolites changed in mothers with LBW infants. Classification models to predict LBW based on maternal anthropometry and predicted microbial functions showed moderate performance. Collectively, the findings indicate that alterations in the maternal microbiome and metabolome were associated with LBW. Future research should target functional and predictive roles of the maternal gut microbiome in infant birth outcomes including birthweight.

Integrated omics revealed the altered colonic microenvironment after inhibition of peripheral serotonin synthesis by LP533401

AbstractGut‐derived 5‐hydroxytryptamine (5‐HT), known as serotonin, plays a crucial role in regulating gastrointestinal functions. However, the impact of disruptions in gut‐derived 5‐HT synthesis on the early gut microbiome and intestinal microenvironment remains unclear. In this study, LP533401, an inhibitor targeting peripheral 5‐HT synthesis, was administered orally to neonatal rats starting at 4 days post‐birth. By day 11, inhibition of gut‐derived 5‐HT resulted in altered colonic morphology, characterized by increased crypt depth and reduced myenteric thickness. To investigate the mechanisms underlying these alterations, we employed a combination of metagenomics, mucosal transcriptome, and untargeted metabolomics on colonic samples. Metagenome profiling revealed an upregulation in the microbial two‐component system (ko02020) and tyrosine metabolism (ko00350), with minimal effects on taxa abundances. Transcriptome profiling analysis indicated the discriminant expression of genes enriched in pathogen infection‐responsive signaling (e.g., Salmonella and Yersinia infection) and the Wnt signaling pathway that affected stem cell proliferation. Consistent with increased crypt depth, marker genes related to cell proliferation were excessively activated. Metabolomics analysis indicated lower ascorbate level and higher succinic acid level, correlating with 5‐HT concentrations and increased crypt depth. Additionally, altered metabolic pathways (e.g., nucleotide metabolism, signal transduction, metabolism of cofactors and vitamins) suggested an impact on the colonic function. In summary, early inhibition of gut‐derived 5‐HT may unfavorably reshape the colonic microenvironment, affecting gut morphology, microbial function, stem cell proliferation, and mucosal metabolism.

Microbiota modulation by teriflunomide therapy in people with multiple sclerosis: An observational case-control study

Multiple sclerosis (MS) is a chronic immune-mediated and heterogeneous disease characterized by demyelination, axonal damage, and physical and cognitive impairment. Recent studies have highlighted alterations in the microbiota of people with MS (pwMS). However, the intricate nature of the disease and the wide range of treatments available make it challenging to identify specific microbial populations or functions associated with MS symptoms and disease progression. This study aimed to characterize the microbiota of pwMS treated with the oral drug teriflunomide (TF) and compare it with that of pwMS treated with beta interferons (IFNβ), pwMS treated with no previous disease modifying therapies (naïve), and healthy controls. Our findings demonstrate significant alterations in both the composition and function of the gut microbiota in pwMS that are further influenced by disease-modifying therapies. Specifically, oral treatment with TF had a notable impact on the gut microbiota of pwMS. Importantly, the dysregulated microbial environment within the gut was associated with symptoms commonly experienced by pwMS, including fatigue, anxiety, and depression.

Metagenomic insight into the soil microbial functions across land uses

Metagenomic insight into the soil microbial functions across land uses

Pseudogymnoascus destructans invasion stage impacts the skin microbial functions of highly vulnerable Myotis lucifugus.

The role of the skin microbiome in resistance and susceptibility of wildlife to fungal pathogens has been examined from a taxonomic perspective but skin microbial function, in the context of fungal infection, has yet to be studied. Our objective was to understand effects of a bat fungal pathogen site infection status and course of invasion on skin microbial function. We sampled seven hibernating colonies of Myotis lucifugus covering three-time points over the course of Pseudogymnoascus destructans (Pd) invasion and white nose syndrome (pre-invasion, epidemic and established). Our results support three new hypotheses about Pd and skin functional microbiome: 1) there is an important effect of Pd invasion stage, especially at the epidemic stage; 2) disruption by the fungus at the epidemic stage could decrease anti-fungal functions with potential negative effects on the microbiome and bat health; 3) the collection site might have a larger influence on microbiomes at the pre-invasion stage rather than at epidemic and established stages. Future studies with larger samples size and using meta-omics approaches will help confirm these hypotheses, and determine the influence of the microbiome on wildlife survival to fungal disease.