Altered Microbial Community Research Articles

Fecal microbiota transplant from long-living Ames dwarf mice alters the microbial composition and biomarkers of liver health in normal mice.

Aging is associated with intestinal dysbiosis, a condition characterized by diminished microbial biodiversity and inflammation. This leads to increased vulnerability to extraintestinal manifestations such as autoimmune, metabolic, and neurodegenerative conditions thereby accelerating mortality. As such, modulation of the gut microbiome is a promising way to extend healthspan. In this study, we explore the effects of fecal microbiota transplant (FMT) from long-living Ames dwarf donors to their normal littermates, and vice versa, on the recipient gut microbiota and liver transcriptome. Importantly, our previous studies highlight differences between the microbiome of Ames dwarf mice relative to their normal siblings, potentially contributing to their extended lifespan and remarkable healthspan. Our findings demonstrate that FMT from Ames dwarf mice to normal mice significantly alters the recipient's gut microbiota, potentially reprogramming bacterial functions related to healthy aging, and changes the liver transcriptome, indicating improved metabolic health. Particularly, the microbiome of Ames dwarf mice, characterized by a higher abundance of beneficial bacterial families such as Peptococcaceae, Oscillospiraceae, and Lachnospiraceae, appears to play a crucial role in modulating these effects. Alongside, our mRNA sequencing and RT-PCR validation reveals that FMT may contribute to the significant downregulation of p21, Elovl3, and Insig2, genes involved with cellular senescence and liver metabolic pathways. Our data suggest a regulatory axis exists between the gut and liver, highlighting the potential of microbiome-targeted therapies in promoting healthy aging. Future research should focus on functional validation of altered microbial communities and explore the underlying biomolecular pathways that confer geroprotection.

Aspartame affects methane yield and enhances transmission of antibiotic resistance genes during anaerobic digestion of sludge

Aspartame (ASP) is a widely used artificial sweetener, yet recent studies have shown that ASP have potential toxic effect. ASP is also detected in sludge, however, the influence of ASP on the performance of sludge anaerobic digestion and the fate of antibiotic resistance genes (ARGs) have not been thoroughly investigated. Under stress of 0, 0.5, 5 and 50mg/L ASP, cumulative methane production was 181.7, 167.0, 154.0 and 140.8 mlCH4/g VSS, respectively. ASP inhibited the dissolution and conversion of organic matter in sludge. Sequencing data revealed a decline in the abundance of functional microorganisms compared to control, such as hydrolytic-acidifying bacteria and methanogens, potentially attributed to increased intracellular reactive oxygen species and damaged cell membranes caused by ASP addition. Specifically, 50mg/L ASP reduced the total abundance of methanogens by 59.40% compared to control. Concurrently, alterations in microbial communities along with an increase in Tn916 and intI1 were observed, increasing the abundance of ARGs. The total abundance of five ARGs peaked at 1.43E+12 copies/g at 5mg/L ASP, representing 139% of the control. This research contributes valuable insights into the alterations in anaerobic digestion caused by ASP, emphasizing the potential risks in the overall environmental system.

Gut microbial communities and transcriptional profiles of black soldier fly (Hermitia illucens) larvae fed on fermented sericulture waste.

Sericulture waste poses significant challenges to industrial and environmental safety. Black soldier fly larvae (BSFL) offer a promising solution for organic waste management by converting it into insect protein. This study aimed to develop a microbial fermented method for utilizing sericulture waste to feed BSFL and explore the underlying mechanisms. Our results showed that all fermented sericulture waste groups had positive effects on body weight, survival rate, substrate consumption rate, and substrate conversion rate. Metagenomic analysis revealed a notable increase in the abundances of commensal genera, including Sedimentibacter, Clostridium, Enterococcus, Bacteroides, and Bacillus, in the gut of BSFL fed on sericulture waste fermented with the most effective combination of microbial strains (B. subtilis, B. licheniformis, and E. faecalis). In contrast, BSFL reared on unfermented sericulture waste exhibited higher abundances of potentially pathogenic and harmful genera, including Providencia, Klebsiella, Escherichia, Brucella, and Enterobacter. Clusters of orthologous genes (COG) analysis indicated that altered microbial communities in the fermented group mainly participated in metabolic pathways, defense mechanism, and signal transduction mechanism. Transcriptome analysis further revealed that the upregulated genes were functionally associated with key metabolic pathways and immune mechanisms in the fermented group. These findings underscore the pivotal role of selected microbial fermentation in utilizing sericulture waste as BSFL feed, providing a sustainable solution for organic waste management.

Periodontitis Exacerbates Colorectal Cancer by Altering Gut Microbiota-Derived Metabolomics in Mice.

The correlation between periodontitis and colorectal cancer (CRC) has drawn widespread attention. However, how periodontitis affects CRC progression remains unclear. C57BL/6 mice were used to establish experimental periodontitis and CRC model. Histological alterations of periodontium and colon were observed by hematoxylin and eosin staining. Micro-computed tomography (micro-CT) was applied to evaluate alveolar bone loss (ABL). Tumor growth was detected by immunofluorescence. Gut bacteria were analyzed using 16S rRNA sequencing. Gas chromatography-mass spectrometry (GC-MS) was performed to observe the alterations of gut microbial metabolites. The detection of associated pathways was carried out using quantitative real-time PCR (qRT-PCR). Experimental periodontitis significantly induced increases in tumor number in mice with CRC. Double immunofluorescence for Ki67 and β-catenin, as well as Cyclin D1 and β-catenin, indicated that experimental periodontitis observably promoted tumor growth. 16S rRNA sequencing and untargeted metabolomics analysis displayed that experimental periodontitis altered gut microbial community and metabolite profiles in CRC mice. Notably, we found that experimental periodontitis dramatically increased the level of three oncometabolites (serotonin, adenosine, and spermine) in mice with CRC. Alterations of gut microbial community and metabolites might be relevant in experimental periodontitis deteriorating CRC.

Microbial changing patterns across lateral and vertical horizons in recently formed permafrost after the outburst of Zonag Lake, Tibetan Plateau.

In polar and alpine regions, global warming and landform changes are draining lakes, transforming them into permafrost with altered microbial communities and element cycling. In this study, we investigated bacterial and archaeal (prokaryotic) community changes in the newly exposed sediment of Zonag Lake (Tibetan Plateau), focusing on prokaryotic diversity, community structure, and genes involved in carbon fixation and nitrogen cycling across lateral (up to 800m) and vertical (up to 80cm) horizons. The results showed that prokaryotic richness decreased across the lateral horizons, coinciding with reductions in carbon concentrations. Dramatic changes in community structure changes were also observed, primarily influenced by the distance from the lake and then by sediment depth, with environmental filtering and dispersal limitations shaping the lateral and vertical distributions, respectively. Based on PICRUSt2 results, the relative abundance of genes related to carbon fixation increased along the lateral horizon, suggesting that microbial carbon fixers are counteracting the carbon loss during permafrost formation. In contrast, the genes related to denitrification also increased, which may lead to nitrogen loss and contribute to global warming by releasing nitric oxide gas. This study highlights the resilience of prokaryotic communities in drained lake basins and their ecological implications under global warming.

Polyethylene microplastics distinctly affect soil microbial community and carbon and nitrogen cycling during plant litter decomposition

Plant litter is an important input source of carbon and nitrogen in soil. While microplastics (MPs) and plant litter are ubiquitously present in soil, their combined impact on soil biogeochemical processes remains poorly understood. To address this gap, we examined the soil changes resulting from the coexistence of plant litter (Alfalfa) and polyethylene microplastics (PE). The soil changes included physicochemical properties, composition of soil dissolved organic matter, and structure of the soil microbial community. The results showed that the addition of polyethylene (PE) inhibited the degradation of humus-like substances and decreased the quantity of humic acid-like compounds in soil dissolved organic matter (DOM). PE negatively impacted plant litter decomposition, disrupted soil organic carbon (SOC) breakdown, interfered with the nitrogen cycle, and significantly altered microbial community structures during the process. By day 35, SOC and total nitrogen (TN) levels were reduced by 39.8% and 10.1%, respectively, in the presence of PE. Furthermore, PE significantly decreased the abundance of nitrogen-fixing microbes, including Streptomyces (43.1%) and Bacillus (45.9%), which play key roles in nitrate reduction to ammonium. This study highlights the environmental effects of MPs on plant litter decomposition and their potential implications for soil biogeochemical processes.

Soil inoculation changed soil microbial communities, but did not accelerate the decomposition of European Beachgrass (Ammophila arenaria) in Point Reyes National Seashore

Legacy effects after the removal of invasive plants present significant challenges to restoration. The pivotal role of soil microbial communities in shaping these legacy effects is increasingly recognized, yet there is a lack of effective methods to mitigate altered microbial communities. In Point Reyes National Seashore (California), although the invaded European beachgrass (Ammophila arenaria [L.] Link) was successfully controlled by herbicide treatment, beachgrass litter remained undecomposed for over 5 years, leaving pronounced legacy effects on soil organic matter and microbial community composition. We hypothesized that soil inoculation from uninvaded dune scrub can accelerate the decomposition of beachgrass litter in herbicide‐treated sites by restoring the soil microbial communities and the abundance of microbial decomposers. Three litterbags containing European beachgrass litter or litter from two common shrubs at dune scrub were deployed into each plot to assess the impact of soil inoculation on litter decomposition rates. Our results revealed that soil inoculation, regardless of the inoculation level, did not accelerate the decomposition of European beachgrass. Only the decomposition of bush lupine litter, which had the highest litter quality among three types of litter, was accelerated at the highest inoculation level (approximately 11,880 g/m2). Additionally, soil inoculation increased the richness and compositional homogeneity of soil microbial communities, along with the relative abundances of wood saprotrophic fungi, soil saprotrophic fungi, and lichenized fungi. Although these findings demonstrate the potential of soil inoculation, the cost‐effectiveness of soil inoculation limits its feasibility in accelerating the delayed decomposition of European beachgrass litter in Point Reyes.

Decoupled fungal and bacterial functional responses to biochar amendment drive rhizosphere priming effect on soil organic carbon mineralization

The application of biochar to soil is widely recognized as a promising strategy for enhancing the accumulation and stability of soil organic carbon (SOC), which is crucial in mitigating climate change. However, the influence of interactions between plants and biochar on soil microbial communities and their involvement in SOC mineralization and stability remains unclear. This understanding is essential for optimizing carbon (C) sequestration in systems involving plants, soil, and biochar. In this study, employing a 13C natural abundance approach, we investigated the effect of biochar on the maize rhizosphere priming effect (RPE) in paddy soil. We also examined alterations in microbial communities and functional genes related to C degradation and fixation. Over the 99 days of maize growth, biochar application increased RPE and total SOC while decreasing dissolved organic C. It also elevated soil pH, resulting in shifts in fungal and bacterial community structure, favoring oligotrophic species. Fungal and bacterial assemblies were dominated by deterministic and stochastic processes, respectively. While the abundance of fungal guilds varied irregularly, bacterial guilds were uniformly enriched under biochar-plant interactions. Functional traits such as ecoenzymatic activities, bacterial guilds, and functional genes predominantly affected RPE under biochar application. Bacterial functional genes associated with C degradation and fixation were concurrently enhanced with biochar application. Our results indicate that interactions between plants and biochar can enhance native SOC mineralization and accumulation in a short timeframe by modulating functional traits of soil microorganisms, particularly the bacterial community involved in C degradation and fixation.Graphical

A population-scale analysis of 36 gut microbiome studies reveals universal species signatures for common diseases

The gut microbiome has been implicated in various human diseases, though findings across studies have shown considerable variability. In this study, we reanalyzed 6314 publicly available fecal metagenomes from 36 case-control studies on different diseases to investigate microbial diversity and disease-shared signatures. Using a unified analysis pipeline, we observed reduced microbial diversity in many diseases, while some exhibited increased diversity. Significant alterations in microbial communities were detected across most diseases. A meta-analysis identified 277 disease-associated gut species, including numerous opportunistic pathogens enriched in patients and a depletion of beneficial microbes. A random forest classifier based on these signatures achieved high accuracy in distinguishing diseased individuals from controls (AUC = 0.776) and high-risk patients from controls (AUC = 0.825), and it also performed well in external cohorts. These results offer insights into the gut microbiome’s role in common diseases in the Chinese population and will guide personalized disease management strategies.

435 Use of plant bioactives to improve the efficiency of rumen function

Abstract Plant bioactives, also known as phytogenics or phytobiotics, are secondary metabolites of plant origin that are deployed as host-defense mechanisms against predators or to enable them to be more competitive in their environment. These metabolites also regulate growth and reproductive functions in the plant. They can be grouped into three major classes: terpenoids, phenolic compounds, and alkaloids. Various studies have shown their worth in improving livestock production and health via insectifugal, organoleptic and enhanced rumen functions. Ruminants are critical to food security because they are able to convert poor-quality feed materials into nutritious products like meat. The rumen provides temporary storage of feed but serves the main function of digesting those complex materials through symbiotic relationships among prokaryotic and eukaryotic organisms within the rumen vat. Antimicrobial resistance and other health or social license challenges have led researchers to find acceptable replacements that will not exacerbate the health and social issues in animals and humans. Plant bioactives appeal to producers because of the ‘natural’ brand and because they are usually certified as generally recognized as safe (GRAS). Anecdotal reports from input companies show an increased demand for mineral supplements infused with phytogenics. The complex chemical compositions of these products appear to make them less prone to developing resistance by microorganisms. Phytogenics research has been further catalyzed by government legislation that has banned the use of medically important antibiotics to prevent the spread of antibiotic resistance. Potential improvements in livestock productivity are associated with mechanisms such as enhanced nutrient utilization, increased digestibility, modified digestive secretions or altered microbial communities. These benefits contribute to the increasing use of these phytogenics by livestock producers to keep their animals healthy and productive while enhancing the profitability of their operations. We will examine the different bioactives and their applications in improving the efficiency of the rumen function. Some commercial products in the Canadian market will be presented. Other research trials showcasing their potential benefits to rumen health and general animal productivity will also be discussed.

317 Microbial interventions to improve gut health in neonatal ruminants

Abstract Colonization and establishment of a balanced and healthy gut microbiome during the neonatal period can directly and indirectly influence animals by affecting the development and metabolism, nutrition absorption, barrier and immune functions, and endocrine and neuron transmitter secretions. Therefore, neonatal period represents a crucial window of time in animal’s life that induces long-term developmental and immune memory. Therefore, alterations in the early gut microbial composition and colonization trajectories lead to long-term negative effects on animals’ production and health. While the rapidly developing gut microbial community is affected by various external factors due to its instability, it provides a great opportunity for microbial intervention to alter microbial colonization trajectories and their subsequent impact on gut health. Recent advance research has been successful in restoring altered gut microbial communities by using microbial interventions such as vaginal seeding, fecal microbial transplantation, probiotics, and prebiotics. However, there is a lack of understanding on the long-term effects of these interventions on gut health in neonatal ruminants. Direct fed microbes (live naturally existing microbes that can improve health and production performance) with psychobiotic function (a type of probiotic that affect cognitive and behavioral functions of the host via the gut-brain axis) can be one of the novel microbiome solutions to target and alter the microbiome dysbiosis. The use of direct fed microbes, postbiotics and psychobiotics and their potential implications in improving calf health and productivity leads to a novel solution to the manipulation of the gut microbiome in calves.

Effects of Pre-Dehydration Treatments on Physicochemical Properties, Non-Volatile Flavor Characteristics, and Microbial Communities during Paocai Fermentation.

The paocai industry faces challenges related to the production of large volumes of high-salinity and acidic brine by-products. Maintaining paocai quality while reducing brine production is crucial. This study utilized high-throughput sequencing technology to analyze microbial changes throughout the fermentation process, along with the non-volatile flavor compounds and physicochemical properties, to assess the impact of hot-air and salt-pressing pre-dehydration treatments on paocai quality. The findings indicate that pre-dehydration of raw material slowed the fermentation process but enhanced the concentration of non-volatile flavor substances, including free amino acids and organic acids. Hot-air pre-dehydration effectively reduced initial salinity to levels comparable to those in high-salinity fermentation of fresh vegetables. Furthermore, pre-dehydration altered microbial community structures and simplified inter-microbial relationships during fermentation. However, the key microorganisms such as Lactobacillus, Weissella, Enterobacter, Wallemia, Aspergillus, and Kazachstania remained consistent across all groups. Additionally, this study found that biomarkers influenced non-volatile flavor formation differently depending on the treatment, but these substances had minimal impact on the biomarkers and showed no clear correlation with high-abundance microorganisms. Overall, fermenting pre-dehydrated raw materials presents an environmentally friendly alternative to traditional paocai production.

Novel pectin-carboxymethylcellulose-based double-layered mucin/chitosan microcomposites successfully protect the next-generation probiotic Akkermansia muciniphila through simulated gastrointestinal transit and alter microbial communities within colonic ex vivo bioreactors

The rapid acceleration of microbiome research has identified many potential Next Generation Probiotics (NGPs). Conventional formulation processing methods are non-compatible, leading to reduced viability and unconfirmed incorporation into intestinal microbial communities; consequently, demand for more bespoke formulation strategies of such NGPs is apparent. In this study, Akkermansia muciniphila (A.muciniphila) as a candidate NGP was investigated for its growth and metabolism properties, based on which a novel microcomposite-based oral formulation was formed. Initially, a chitosan-based microcomposite was coated with mucin to establish a surface culture of A.muciniphila. This was followed by ‘double encapsulation’ with pectin (PEC) using a novel Entrapment Deposition by Prilling method to create core–shell double-encapsulated microcapsules. The formulation of A.muciniphila was verified to require no oxygen-restriction properties, and additionally, biopolymers were selected, including carboxymethylcellulose (CMC), that support and enhance its growth; consequently, a high viability (6 log CFU/g) of A.muciniphila microencapsulated in PEC-CMC double-encapsulates was obtained. Subsequently, the high stability of the PEC-CMC double-encapsulates was verified in simulated gastric fluid, successfully protecting and then releasing the A.muciniphila under intestinal conditions. Finally, employing a model of gastrointestinal transit and faecal-inoculated colonic bioreactors, significant alterations in microbial communities following administration and successful establishment of A.muciniphila were demonstrated.

Soil Characteristics and Response Mechanism of the Microbial Community in a Coal–Grain Compound Area with High Groundwater Levels

Coal mining has led to escalating ecological and environmental issues in significant coal and grain production areas, posing a severe danger to food security. This study examines the disturbance patterns of soil factors and microbial communities in coal and grain production areas, and attempts to understand the impact of subsidence and water accumulation stress on soil characteristics and microbial communities in coal mining subsidence areas with high subsidence levels. Five specific regions of Zhao Gu Yi Mine, situated in Henan Province and under the ownership of Jiaozuo Coal Group, were chosen. Aside from the control group (CK), the study blocks situated in the coal mining subsidence zones consisted of perennial subsidence ponding (PSP), seasonal subsidence ponding (SSP), the neutral zone (NZ), and the horizontal deformation zone (HDZ). The soil nutrient indices and the stoichiometric properties of soil C, N, and P were assessed on the surface of each block. The organization of the soil microbial community was identified using high-throughput sequencing. The findings indicate that: 1. Substantial disparities exist in soil properties and microbial community structure between the subsidence and non-subsidence zones. The levels of soil organic mater (SOM), total nitrogen (TN), total phosphorus (TP), available nitrogen (AN), and available phosphorus (AP) all decrease to different extents in the subsidence area. Additionally, the coal mining subsidence waterlogged area exhibits higher levels compared to the coal mining subsidence non-waterlogged area. Conversely, the soil water content (SWC), C/N ratio, C/P ratio, and N/P ratio all increase to varying degrees. 2. Regarding the composition of the community, the presence of Proteobacteria is considerably greater in the non-water-logged area of coal mining subsidence (NZ, HDZ) compared to the water-logged area and control group (p < 0.05). The prevalence of Firmicutes in the subsidence water area was substantially greater compared to both the subsidence non-waterlogged area and the control group (p < 0.05). The prevalence of Gemmatimonadota is markedly greater in the waterlogged area of mining subsidence compared to the non-waterlogged area and CK (p < 0.05). The Ascomycota population reached its highest value in the neutral zone (NZ), which was significantly greater than the values observed in the seasonal subsidence ponding (SSP) and perennial subsidence ponding (PSP) regions (p < 0.05). On the other hand, the Rozellomycota population had its highest value in the SSP region, which was significantly greater than the values observed in the other regions (p < 0.05). 3. The abundance and variety of soil bacteria and fungi, as well as their important populations, are associated with different levels of soil characteristics. The primary elements that influence the alteration of microbial communities are soil nutrients and soil water content. The presence of coal mine subsidence and water accumulation has a notable impact on the properties of the soil in the surrounding area. This study offers a scientific foundation for reclaiming land affected by subsidence caused by coal mining in regions where coal and grain production are the dominant industries.

Bioturbation effect of high - Yield pyrazine strain on the microbial community and flavour metabolites of fortified Daqu

In order to comprehensively explore the regulatory effect of bioturbation on the assembly and overall metabolic characteristics of Daqu microbial community. This study used metatranscriptomics and metabolomics to investigate the composition of the microbial community, physicochemical properties, and overall metabolic profile of Daqu before and after bioturbation by Bacillus velezensis. The results demonstrated that the acidity, moisture, amino acid nitrogen, and starch content of Daqu exhibited a significant increase following bioturbation. The symbol microorganisms of Daqu have also changed significantly, from the original Aspergillus chevalieri, Rasamsonia emersonii, Aspergillus ruber, Aspergillus glaucus, Aspergillus wentii and Aspergillus cristatus to Paecilomyces varioti, Trichomonascus ciferrii and Staphylococcus gallinarum. Correlation analyses and integration pathways indicated that altered microbial community abundance also promoted the metabolism of starch, ethanol, fatty acids, and pyrazine, resulting in a significant enhancement of Daqu's saccharification and liquefaction power, as well as the content of some volatile and non-volatile metabolites, with pyrazines increased by 24.50%. The application of fortified Daqu to Baijiu fermentation can significantly enhance the content of various pyrazines in Baijiu. These results are helpful to elucidate the mechanism of biochemical changes, microbial assembly and flavor production of Daqu after biodisturbance.

Vaginal and endometrial microbiome dysbiosis associated with adverse embryo transfer outcomes

BackgroundAssisted reproductive technology (ART) is the most effective method to treat infertility and the pathogenesis of implantation failure after in vitro fertilization-embryo transfer (IVF-ET) is a challenging filed in infertility. Microbes in the female reproductive tract are considered to be associated with gynecological and obstetric diseases. However, its effects on embryo implantation failure are unsured.PurposeThis study aimed to investigate reproductive tract dysbiosis, identify different bacteria in reproductive tract as potential biomarkers of embryo implantation failure and demonstrate the pathogenesis through metabolites analysis.MethodsWe compared the data from 16S rRNA gene and metagenome in reproductive tracts through QIIME2 and HUMAnN2 by the times of embryo implantation failure on 239 infertile patients and 17 healthy women.ResultsOur study revealed a strong positive correlation between Lactobacillus abundance and embryo implantation success (IS) after IVF-ET. The microbial community composition and structure in reproductive tract showed substantially difference between the embryo implantation failure (IF) and healthy control. Moreover, we established a diagnostic model through receiver operating characteristic (ROC) with 0.913 area under curve (AUC) in IS and multiple implantation failures (MIF), verified its effectiveness with an AUC = 0.784 demonstrating microbial community alterations could efficiently discriminate MIF patients. Metagenome functional analyses of vaginal samples from another independent infertile patients after IVF-ET revealed the L-lysine synthesis pathway enriched in IF patients, along with ascended vaginal pH and decreased Lactobacillus abundance.ConclusionsThis study clarifies several independent relationships of bacteria in vagina and endometrial fluid on embryo implantation failure and undoubtedly broadens the understanding about female reproductive health.

Bacterial Insights: Unraveling the Ocular Microbiome in Glaucoma Pathogenesis.

This review explores the connection between the ocular surface microbiome and glaucoma, highlighting its impact on disease progression. Beginning with an overview of global glaucoma significance, it emphasizes the importance of understanding the cellular characteristics and microbiology of the ocular microbiome. A search was conducted on the PubMed and Cochrane Library databases using the phrase "ocular microbiome glaucoma". 0 records were returned from the Cochrane Library while 21 were returned from PubMed. A total of 21 results were retrieved from 2017 to 2024. This comprised one opinion paper, four original research articles, and 16 reviews. This review covered the anatomy of the ocular surface, advanced analysis methods, and the ocular microbiome. It also delved into dysbiosis in glaucoma, addressing altered microbial communities and their potential role in disease progression. The intricate interplay between the ocular microbiome and the host's immune system is explored, emphasizing crosstalk and inflammatory responses. The review concludes by discussing therapeutic implications, including modulating ocular microbiota and potential future treatment strategies. Understanding the microbiome in healthy and glaucomatous eyes can help researchers and clinicians in innovative approaches to ocular health.

Response of stream habitat and microbiomes to spruce budworm defoliation: New considerations for outbreak management.

Defoliation by eastern spruce budworm is one of the most important natural disturbances in Canadian boreal and hemi-boreal forests with annual area affected surpassing that of fire and harvest combined, and its impacts are projected to increase in frequency, severity, and range under future climate scenarios. Deciding on an active management strategy to control outbreaks and minimize broader economic, ecological, and social impacts is becoming increasingly important. These strategies differ in the degree to which defoliation is suppressed, but little is known about the downstream consequences of defoliation and, thus, the implications of management. Given the disproportionate role of headwater streams and their microbiomes on net riverine productivity across forested landscapes, we investigated the effects of defoliation by spruce budworm on headwater stream habitat and microbiome structure and function to inform management decisions. We experimentally manipulated a gradient of defoliation among 12 watersheds during a spruce budworm outbreak in the Gaspésie Peninsula, Québec, Canada. From May through October of 2019-2021, stream habitat (flow rates, dissolved organic matter [DOM], water chemistry, and nutrients), algal biomass, and water temperatures were assessed. Bacterial and fungal biofilm communities were examined by incubating six leaf packs for five weeks (mid-August to late September) in one stream reach per watershed. Microbiome community structure was determined using metabarcoding of 16S and ITS rRNA genes, and community functions were examined using extracellular enzyme assays, leaf litter decomposition rates, and taxonomic functional assignments. We found that cumulative defoliation was correlated with increased streamflow rates and temperatures, and more aromatic DOM (measured as specific ultraviolet absorbance at 254 nm), but was not correlated to nutrient concentrations. Cumulative defoliation was also associated with altered microbial community composition, an increase in carbohydrate biosynthesis, and a reduction in aromatic compound degradation, suggesting that microbes are shifting to the preferential use of simple carbohydrates rather than more complex aromatic compounds. These results demonstrate that high levels of defoliation can affect headwater stream microbiomes to the point of altering stream ecosystem productivity and carbon cycling potential, highlighting the importance of incorporating broader ecological processes into spruce budworm management decisions.

CD71 + erythroid cells promote intestinal symbiotic microbial communities in pregnancy and neonatal period

BackgroundThe establishment of microbial communities in neonatal mammals plays a pivotal role in shaping their immune responses to infections and other immune-related conditions. This process is influenced by a combination of endogenous and exogenous factors. Previously, we reported that depletion of CD71 + erythroid cells (CECs) results in an inflammatory response to microbial communities in newborn mice.ResultsHere, we systemically tested this hypothesis and observed that the small intestinal lamina propria of neonatal mice had the highest frequency of CECs during the early days of life. This high abundance of CECs was attributed to erythropoiesis niches within the small intestinal tissues. Notably, the removal of CECs from the intestinal tissues by the anti-CD71 antibody disrupted immune homeostasis. This disruption was evident by alteration in the expression of antimicrobial peptides (AMPs), toll-like receptors (TLRs), inflammatory cytokines/chemokines, and resulting in microbial dysbiosis. Intriguingly, these alterations in microbial communities persisted when tested 5 weeks post-treatment, with a more notable effect observed in female mice. This illustrates a sex-dependent association between CECs and neonatal microbiome modulation. Moreover, we extended our studies on pregnant mice, observing that modulating CECs substantially alters the frequency and diversity of their microbial communities. Finally, we found a significantly lower proportion of CECs in the cord blood of pre-term human newborns, suggesting a potential role in dysregulated immune responses to microbial communities in the gut.ConclusionsOur findings provide novel insights into pivotal role of CECs in immune homeostasis and swift adaptation of microbial communities in newborns. Despite the complexity of the cellular biology of the gut, our findings shed light on the previously unappreciated role of CECs in the dialogue between the microbiota and immune system. These findings have significant implications for human health.9S5HPFpJwLA9vyqyoAGSTRVideo

A history of repeated antibiotic usage leads to microbiota-dependent mucus defects

ABSTRACT Recent evidence indicates that repeated antibiotic usage lowers microbial diversity and ultimately changes the gut microbiota community. However, the physiological effects of repeated – but not recent – antibiotic usage on microbiota-mediated mucosal barrier function are largely unknown. By selecting human individuals from the deeply phenotyped Estonian Microbiome Cohort (EstMB), we here utilized human-to-mouse fecal microbiota transplantation to explore long-term impacts of repeated antibiotic use on intestinal mucus function. While a healthy mucus layer protects the intestinal epithelium against infection and inflammation, using ex vivo mucus function analyses of viable colonic tissue explants, we show that microbiota from humans with a history of repeated antibiotic use causes reduced mucus growth rate and increased mucus penetrability compared to healthy controls in the transplanted mice. Moreover, shotgun metagenomic sequencing identified a significantly altered microbiota composition in the antibiotic-shaped microbial community, with known mucus-utilizing bacteria, including Akkermansia muciniphila and Bacteroides fragilis, dominating in the gut. The altered microbiota composition was further characterized by a distinct metabolite profile, which may be caused by differential mucus degradation capacity. Consequently, our proof-of-concept study suggests that long-term antibiotic use in humans can result in an altered microbial community that has reduced capacity to maintain proper mucus function in the gut.