Changes In Microbial Composition Research Articles

Soil microbial community structure and soil fertility jointly regulate soil microbial residue carbon during the conversion from subtropical primary forest to plantations

Soil microbes mediate soil organic carbon (SOC) storage by affecting microbial residue carbon (C) in terrestrial ecosystems, a main source of SOC. However, how microbial residue C accumulation changes during the conversion of subtropical primary forest to plantations and the role of soil microbial community structure in regulating these changes remain unclear. Here, effects of conversion from forest on microbial residue C accumulation in three plantations, including tea (Camellia sinensis var. assamica), walnut (Juglans regia), and macadamia (Macadamia integrifolia). We assessed amino sugars content and the relative importance of soil microbial community structure, soil fertility, and aboveground biomass in four forest types in southwest Yunnan province, China. Our results show that total microbial residue C accounted for 27.8 % of SOC on average across all forest types, and fungal residue C contributed more to SOC than bacterial residue C across different forest types. Conversion from primary forest decreased fungal, bacterial, and total microbial residue C content in all plantation types except tea. Microbial residue C contents was significantly lower in the macadamia plantation than in the primary forest and the tea plantation. Fungal and total microbial residue C content increased with increasing soil microbial community composition, soil fungal abundance, and soil fertility. Soil fertility regulated fungal, bacterial, and total microbial residue C accumulation, which was major determinant of microbial residue C via its influence on soil fungal and bacterial abundance. Overall, we found that soil fungal abundance contributed more to microbial residue C accumulation than change in soil microbial community composition. We also found that soil bacterial abundance was negatively correlated with fungal and microbial residue C, while soil fungal abundance was positively related to microbial residue C accumulation. Ascomycota was most important phylum regulating microbial residue C. These findings suggest that soil fungal and bacterial abundance and soil fertility are the principal regulators of microbial residue C accumulation during the conversion from primary forest to different plantations.

贵州普定土壤酶活性和氮循环功能基因数据集

The karst ecosystem in southwest China is the most fragile ecological environment in China. To protect the ecological environment, the project of "Grain to Green Program" was initiated in the late 1990s for the vegetation restoration in this region. Changes in soil microbial abundance, community composition and functional activity are closely linked to soil nutrient supply and turnover, which are the critical factors influencing vegetation restoration processes. Soils were sampled from five different vegetation types at Chenqi catchment and Tianlong Mountain, and rhizosphere soils were sampled from the typical tree species at Tianlong Mountain. Through rigorous data quality control processes (including survey sampling, sample analysis, and data accuracy checks), we obtained a dataset of soil microbial enzyme activities and nitrogen cycling functional genes in different vegetation types from the karst ecosystem. This dataset consisted of one excel file with eight different sheets, which contains the data on soil microbial enzyme activities, nitrogen cycling functional gene abundance and nitrogen transformation rate, microbial living biomass, microbial residue carbon, and soil physicochemical properties along soil profile ranging from the surface to bedrock layer in various vegetation types of 2016. Furthermore, the dataset also includes the enzyme activity and physicochemical properties of the rhizosphere soils from typical tree species in the primary forest in 2018. The dataset serves as valuable reference data for better understanding the microbial regulation mechanism of soil nutrient cycling in karst areas, and it is also of great practical significance for soil nutrient management in ecologically fragile regions under the background of "Grain to Green Program" policy.

Effect of endogenous sodium and potassium ions in plants on the quality of alfalfa silage and bacterial community stability during fermentation.

This study investigated the impact of endogenous sodium and potassium ions in plants on the quality of alfalfa silage, as well as the stability of bacterial communities during fermentation. Silage was produced from the fermented alfalfa, and the chemical composition, fermentation characteristics, and microbiome were analyzed to understand their interplay and impact on silage fermentation quality. The alfalfa was cultivated under salt stress with the following: (a) soil content of <1‰ (CK); (b) 1‰-2‰ (LP); (c) 2‰-3‰ (MP); (d) 3‰-4‰ (HP). The results revealed that the pH of silage was negatively correlated with the lactic acid content. With the increase of lactic acid (LA) content increased (26.3-51.0 g/kg DM), the pH value decreased (4.9-5.3). With the increase of salt stress, the content of Na+ in silage increased (2.2-5.4 g/kg DM). The presence of endogenous Na+ and K+ ions in plants significantly affected the quality of alfalfa silage and the dynamics of bacterial communities during fermentation. Increased salt stress led to changes in microbial composition, with Lactococcus and Pantoea showing a gradual increase in abundance, especially under high salt stress. Low pH inhibited the growth of certain bacterial genera, such as Pantoea and Pediococcus. The abundance of Escherichia-Shigella and Comamonas negatively correlated with crude protein (CP) content, while Enterococcus and Lactococcus exhibited a positive correlation. Furthermore, the accumulation of endogenous Na+ in alfalfa under salt stress suppressed bacterial proliferation, thereby reducing protein degradation during fermentation. The pH of the silage was high, and the LA content was also high. Silages from alfalfa under higher salt stress had higher Na+ content. The alpha diversity of bacterial communities in alfalfa silages showed distinct patterns. Desirable genera like Lactococcus and Lactobacillus predominated in silages produced from alfalfa under salt stress, resulting in better fermentation quality.

Seasonal changes of soil microbiota and its association with environmental factors in coal mining subsidence area

As a special type of wetland, the new wetland in the coal mining subsidence area is highly sensitive to environmental changes. In recent years, more and more attention has been paid to the studies of soil microbial diversity in newly born wetlands in coal mining subsidence areas. However, there are few reports on the seasonal variation of soil microbial diversity and its relationship with soil physical and chemical properties. In this study, 16S rRNA gene sequencing technology was used to analyze the seasonal changes of soil microbial composition and functional diversity in newly formed wetlands in coal mining subsidence areas, and to determine the seasonal changes of soil nutrient elements and physical and chemical properties in coal mining subsidence areas, so as to analyze the correlation between soil microbial diversity and soil nutrient elements and physical and chemical properties in newly formed wetlands in coal mining subsidence areas. A total of 16,050 OTUs were obtained after sample gene noise reduction. Proteobacteria, Acidobacteriota and Bacteroidota were the highest abundance in the coal mining subsidence area of Jining. The two seasons gathered separately, and temperature (Temp), total phosphorus (TP), available phosphorus (AP), total organic carbon (TOC) and dry matter content (DMC) were the key factors for the seasonal change of soil microbial community in the wetland of the coal mining subsidence area of Jining. The contents of Temp, AP and TP were significantly correlated with the abundance of soil microorganisms in summer subsidence area, while the contents of DMC and TOC were significantly correlated with the abundance of soil microorganisms in winter subsidence area. Soil microbial diversity in coal mining subsidence area was correlated with the seasons. Temp, TP, AP, TOC and DMC were the key factors for the seasonal change of soil microbial community in the wetland of the coal mining subsidence area of Jining.

Gut microbiota affects the estrus return of sows by regulating the metabolism of sex steroid hormones

BackgroundSex hormones play important roles in the estrus return of post-weaning sows. Previous studies have demonstrated a complex and bi-directional regulation between sex hormones and gut microbiota. However, the extent to which the gut microbiota affects estrus return of post-weaning sows is largely unknown.ResultsIn this study, we first screened 207 fecal samples from well-phenotyped sows by 16S rRNA gene sequencing and identified significant associations between microbes and estrus return of post-weaning sows. Using metagenomic sequencing data from 85 fecal samples, we identified 37 bacterial species that were significantly associated with estrus return. Normally returning sows were characterized by increased abundances of L. reuteri and P. copri and decreased abundances of B. fragilis, S. suis, and B. pseudolongum. The changes in gut microbial composition significantly altered the functional capacity of steroid hormone biosynthesis in the gut microbiome. The results were confirmed in a validation cohort. Significant changes in sex steroid hormones and related compounds were found between normal and non-return sows via metabolome analysis. An integrated analysis of differential bacterial species, metagenome, and fecal metabolome provided evidence that normal return-associated bacterial species L. reuteri and Prevotella spp. participated in the degradation of pregnenolone, progesterone, and testosterone, thereby promoting estrogen biosynthesis. Furthermore, the microbial metabolites related to sow energy and nutrient supply or metabolic disorders also showed relationships with sow estrus return.ConclusionsAn integrated analysis of differentially abundant bacterial species, metagenome, and fecal metabolome revealed the involvement of L. reuteri and Prevotella spp. in sow estrus return. These findings provide deep insight into the role of gut microbiota in the estrus return of post-weaning sows and the complex cross-talk between gut microbiota and sex hormones, suggesting that the manipulation of the gut microbiota could be an effective strategy to improve sow estrus return after weaning.

An Insight on Gut Flora, Colorectal Cancer Mechanism, and Treatment Strategies

The microbiota in the stomach functions like an actual organ. To maintain gut homeostasis, the digestive tract’s symbiotic relationships with the local microorganisms are crucial. This symbiotic connection may be upset, and illnesses like inflammatory bowel disorders and cancer can be promoted. Infections, dietary changes, and lifestyle modifications are a few examples of environmental factors that might alter the microbiome. It is becoming increasingly clear that the microbiota plays a part in the development of colorectal cancer. The complex interplay of tumour cells, nonneoplastic cells, and a large variety of microbes results in colorectal cancer. About 10% of new cancer cases globally are colorectal cancer instances (CRC). The gut microflora, which is situated adjacent to the colorectal epithelium, is made up of a sizable population of bacteria that interact with host cells to control a variety of physiological functions, including energy production, metabolism, and immune response. Sequencing research has revealed microbial compositional and ecological changes in CRC patients, while functional research in animal models has identified several bacteria, including Fusobacterium nucleatum, specific strains of Escherichia coli, and Bacteroides fragilis, as key players in the development of colorectal cancer. In this review, we focus on dysbiosis and the potentially carcinogenic characteristics of bacteria to evaluate the possible connections between the bacterial microbiota and colorectal carcinogenesis. We also discuss pertinent mechanisms in microbiota-related carcinogenesis, the potential for using the microbiota as CRC biomarkers, and the possibility of manipulating the microbiota for CRC prevention or treatment.

Subtyping irritable bowel syndrome using cluster analysis: a systematic review

BackgroundIrritable bowel syndrome (IBS) is a common chronic functional gastrointestinal disorder associated with a wide range of clinical symptoms. Some researchers have used cluster analysis (CA), a group of non-supervised learning methods that identifies homogenous clusters within different entities based on their similarity.Objective and methodsThis literature review aims to identify published articles that apply CA to IBS patients. We searched relevant keywords in PubMed, Embase, Web of Science, and Scopus. We reviewed studies in terms of the selected variables, participants’ characteristics, data collection, methodology, number of clusters, clusters’ profiles, and results.ResultsAmong the 14 articles focused on the heterogeneity of IBS, eight of them utilized K-means Cluster Analysis (K-means CA), four employed Hierarchical Cluster Analysis, and only two studies utilized Latent Class Analysis. Seven studies focused on clinical symptoms, while four articles examined anocolorectal functions. Two studies were centered around immunological findings, and only one study explored microbial composition. The number of clusters obtained ranged from two to seven, showing variation across the studies. Males exhibited lower symptom severity and fewer psychological findings. The association between symptom severity and rectal perception suggests that altered rectal perception serves as a biological indicator of IBS. Ultra-slow waves observed in IBS patients are linked to increased activity of the anal sphincter, higher anal pressure, dystonia, and dyschezia.ConclusionIBS has different subgroups based on different factors. Most IBS patients have low clinical severity, good QoL, high rectal sensitivity, delayed left colon transit time, increased systemic cytokines, and changes in microbial composition, including increased Firmicutes-associated taxa and depleted Bacteroidetes-related taxa. However, the number of clusters is inconsistent across studies due to the methodological heterogeneity. CA, a valuable non-supervised learning method, is sensitive to hyperparameters like the number of clusters and random initialization of cluster centers. The random nature of these parameters leads to diverse outcomes even with the same algorithm. This has implications for future research and practical applications, necessitating further studies to improve our understanding of IBS and develop personalized treatments.

Gut microbiota and metabolites in estrus cycle and their changes in a menopausal transition rat model with typical neuroendocrine aging.

Neuroendocrine alterations in the mid-life hypothalamus coupled with reproductive decline herald the initiation of menopausal transition. The certain feature and contribution of gut microflora and metabolites to neuroendocrine changes in the menopausal transition remain largely unknown. Fecal samples of rats experiencing different reproductive stages were collected and processed for 16S rRNA and liquid chromatography-mass spectrometry sequencing. The differences of gut microbiota and metabolites between young and middle-aged rats during proestrus and diestrus were analyzed, and their relationships to neuroendocrine aging were then examined. At the genus level, Anaeroyorax, Rikenella, Tyzzerella_3, and Atopostipes were abundant at proestrus, while Romboutsia, Turicibacter, Clostridium_sensu_stricto_1, Ruminococcaceae_NK4A214_group, CHKCI002, Ruminococcaceae_UCG-010, Staphylococcus, Family_XII_AD3011_group, Ruminococcaceae UCG-011, and Christensenellaceae_R_7_group were enriched in the diestrus of middle-aged rats. DNF00809, Phocea, and Lachnospiraceae_UCG-006 were found abundant during proestrus instead, while Bacteroides, Lactobacillus, Erysipelatoclostridium, Anaeroplasma, Anaerofustis, Parasutterella, and Enterococcus were enriched at the diestrus of young female individuals. Discriminatory metabolites were identified involving 90 metabolic pathways among the animal sets, which were enriched for steroid hormone biosynthesis, arachidonic metabolism, primary bile acid synthesis, and ovarian steroidogenesis. A total of 21 metabolites lacking in hormone-associated changes in middle-aged female individuals presented positive or negative correlations with the circulating luteinizing hormone, bile acid, fibroblast growth factor 19, and gut hormones. Moreover, close correlations were detected between the intestinal bacteria and their metabolites. This study documents specific gut microbial composition changes and concomitant shifting trends of metabolites during menopausal transition, which may initiate the gut-brain dysfunction in neuroendocrine aging.

Change in the Gut Microbiota of Lactating Sows and Their Piglets by Inclusion of Dietary Spray-Dried Plasma in Sow Diets.

This study aimed to investigate the effects of dietary spray-dried plasma (SDP) on the gut microbiota of lactating sows and their piglets. A total of 12 sows were randomly assigned to one of two dietary treatment groups in a completely randomized design. The treatments were a sow diet based on corn and soybean meal (CON), and a CON diet with an added 1% SDP. The sows were fed the dietary treatments from d 30 before farrowing to weaning (d 28). The fecal samples of three sows from each treatment and two of their randomly selected piglets were collected to verify their fecal microbiota. There were no differences in the alpha diversity and distinct clustering of the microbial communities in the sows and their piglets when SDP was added to the sow diets from late gestation to weaning. The fecal microbiota of the lactating sows and their piglets showed a higher relative abundance of the phylum Bacteroidota and genus Lactobacillus and Ruminococcus and showed a lower relative abundance of the phylum Bacillota and genus Bacteroides, Escherichia/Shigella, and Clostridium in the sows fed the SDP diet than those fed the CON diet. Overall, these results show that the addition of SDP to the sow diet during lactation altered the gut environment with positive microbial composition changes. These results were similar in the nursing piglets, suggesting that the control of the sow diets during lactation may contribute to the intestinal health and growth in piglets after weaning.

Process conditions affect microbial diversity and activity in a haloalkaline biodesulfurization system.

Biodesulfurization (BD) systems that treat sour gas employ mixtures of haloalkaliphilic sulfur-oxidizing bacteria to convert sulfide to elemental sulfur. In the past years, these systems have seen major technical innovations that have led to changes in microbial community composition. Different studies have identified and discussed the microbial communities in both traditional and improved systems. However, these studies do not identify metabolically active community members and merely focus on members' presence/absence. Therefore, their results cannot confirm the activity and role of certain bacteria in the BD system. To investigate the active community members, we determined the microbial communities of six different runs of a pilot-scale BD system. 16S rRNA gene-based amplicon sequencing was performed using both DNA and RNA. A comparison of the DNA- and RNA-based sequencing results identified the active microbes in the BD system. Statistical analyses indicated that not all the existing microbes were actively involved in the system and that microbial communities continuously evolved during the operation. At the end of the run, strains affiliated with Alkalilimnicola ehrlichii and Thioalkalivibrio sulfidiphilus were confirmed as the most active key bacteria in the BD system. This study determined that microbial communities were shaped predominantly by the combination of hydraulic retention time (HRT) and sulfide concentration in the anoxic reactor and, to a lesser extent, by other operational parameters.IMPORTANCEHaloalkaliphilic sulfur-oxidizing bacteria are integral to biodesulfurization (BD) systems and are responsible for converting sulfide to sulfur. To understand the cause of conversions occurring in the BD systems, knowing which bacteria are present and active in the systems is essential. So far, only a few studies have investigated the BD system's microbial composition, but none have identified the active microbial community. Here, we reveal the metabolically active community, their succession, and their influence on product formation.

Bio-organic fertilizers from food wastes induce changes in soil microbial community composition and the development of bok-choy (&lt;i&gt;Brassica rapa&lt;/i&gt;)

Bio-organic fertilizers from food wastes induce changes in soil microbial community composition and the development of bok-choy (&lt;i&gt;Brassica rapa&lt;/i&gt;)

Wetland soil microbial responses to upland agricultural intensification and snail invasion

Wetland soils harbor diverse microorganisms including bacteria, archaea, and fungi, all of which play significant roles in maintaining soil health and ecosystem functions but are susceptible to influences from multiple environmental changes. Agricultural intensification and biological invasion are two fundamental drivers of environmental change for wetlands, but their interactive effects on soil microbial communities remain less well understood, particularly for seasonal subtropical wetlands. Yet such understanding is vital for wetland conservation and management. In this study, we conducted a 14-week field mesocosm experiment to investigate how agricultural intensification and invasive apple snail (Pomacea maculata) – an emerging and increasingly concerning threat to natural and agricultural systems in southeastern U.S. – altered wetland soil microbial communities and structures. We found that invasive P. maculata showed selective effects on relative abundance of specific microbial taxa (e.g., Proteobacteria, Nitrospirota), and interactive effects with upland intensification on Spirochaetota and Mortierellomycota. Upland agricultural intensification also exerted significant and consistent effects on microbial composition and diversity across microbial domains. Changes in microbial composition were partly manifested through modifications in water chemistry, such as dissolved oxygen, which acted as environmental regulators. In addition, upland intensification led to more complex but sparsely connected microbial networks, while invasive snail presence decreased network complexity and resulted in greater modularity, less edge density, and longer path length, indicative of lower molecular information exchange efficiency. Our research emphasizes the need for a comprehensive evaluation of microbial responses (i.e., composition, diversity, and co-occurrence patterns) to better understand multi-stressor impacts from human activities on wetland belowground microbial communities. By holistically characterizing microbial responses, our findings show how global change drivers may impact wetland microorganisms in subtropical biomes and infer their functional consequences. Our results have important implications for sustainable landscape management and conservation of wetlands that are experiencing escalating human-induced environmental changes.

Tributyrin oral administration significantly attenuates the loss of intestinal butyrate‐producing bacteria and the ensuing cognitive dysfunction associated with Alzheimer’s Disease pathogenesis in 3xTg‐AD mice

AbstractBackgroundAlzheimer’s Disease (AD) development is linked to the loss of overall gut microbial diversity. However, the specific alterations are only beginning to be examined. In this regard, decreases in intestinal butyrate‐producing bacteria have been indicated by pre‐clinical and clinical studies in AD. The current work, employing the 3xTg‐AD mouse model examined the causal association of loss of butyrate‐producing bacterial communities with cognitive dysfunction associated with AD pathogenesis.MethodCecal samples from tributyrin (TB) treated and untreated female 3xTg‐AD mice were used to perform metataxonomic analysis by sequencing the 16S rRNA gene (V4 region) on a large‐scale Illumina MiSeq platform. Inferred metagenomics analysis was performed using the PICRUSt2 pipeline. TB treatment (oral gavage, 2mg/kg, twice a week) was initiated at 6‐months of age until 17‐months. Spatial and short‐term memory functions were tested using the Y‐maze and Novel Object Recognition Test (NORT).ResultMetataxonomic analysis showed an age‐dependent, significant decline in alpha diversity represented by measures of OTUs, Chao‐1 and Shannon Index from 2‐ to 18‐months. Additionally, age‐dependent changes in gut microbial composition were demonstrated by a significant decrease in the Firmicutes‐to‐Bacteroidota (F/B) ratio. Further analysis of specific features of the gut microbiome demonstrated an age‐dependent decrease in total butyrate‐producing families within the Firmicutes phylum; particularly, a significant loss of critical butyrate producing family Ruminococcacea was identified. Predictive functional analysis using PICRUSt2 also showed a significant reduction in the abundance of specific bacterial genes involved in butyrate synthesis. Importantly, these age‐dependent markers of gut microbial dysbiosis coincided with diminished measures of spatial and short‐term memory. Notably, administration of TB, a butyrate pro‐drug, significantly attenuated the age‐dependent (i) decline in gut microbial diversity &amp; butyrate‐producing bacteria and (ii) loss of spatial and short‐term memory.ConclusionThe findings from this study identify that decline in total butyrate‐producing families is a key pathogenic feature of AD‐associated microbial dysbiosis and cognitive dysfunction. Importantly, these findings have the potential to inform the development of treatment strategies targeting gut microbial dysbiosis using TB, to prevent onset and development of cognitive decline in AD.

Gut Microbial Profile Differences in Autoimmune Diseases

The human gut microbiota has been widely studied due to the possibility of high-throughput sequencing. Humans are distinctly inhabited by normal flora and symbiotic microbial flora, with bacteria accounting for the vast bulk of the component microorganisms. These organisms can be found in a variety of locations throughout the body, including the oral cavity, vagina, skin and stomach. Microbe types and abundance vary in different organs of the same person, but they may also differ between persons. They are very important for human health and also affect the immune system by altering its metabolism and behavior. Conditions such as malnutrition, Crohn’s disease, inflammatory bowel disease and colon colitis, in addition to metabolic disorders including type II diabetes and obesity, have all been associated with the gut microbiota. Several studies in recent years have emphasized the relevance and involvement of commensal bacteria in the development of a variety of disorders, including autoimmune diseases. Autoimmune diseases, Such as Graves’ disease, systemic erythematosus lupus (SLE), and irritable bowel syndrome (IBS), are commonly known for their loss of self-tolerance, a hyperactive reaction against the body’s own tissue. Autoimmune diseases are triggered by the immune system targeting self-tissues, and their global frequency is estimated to be between 3 and 5%. This review reaffirms the links between autoimmune disorders and gut bacteria. The precise pathophysiology is unknown; however, environmental factors (such as lifestyle, diet, medications, and infections) and specific genetic conditions have been expected. The gut microbiota is important in autoimmunity because changes in microbial composition can trigger immunological tolerance loss.

Year-round activity of microbial communities in cold-climate peatlands treating mining-affected waters

Pristine peatlands are typically low in nitrogen, sulfur and metal compounds. Thus, input of high concentrations of those compounds as a result of anthropogenic activity pose a huge challenge to peatland ecosystems. At a mine site in Finnish Lapland, mining-affected waters are purified in two treatment peatlands (TPs) before they are released into downstream waters. The TPs experience long winters and are snow- and partly ice-covered from October to May. Contaminants in inflow waters include nitrogen compounds, sulfate, metals and metalloids. The TPs were intensively monitored for >10 years, and monitoring data was complemented with laboratory experiments. High levels of multiple contaminants, often in the mM range, were measured in TP inflow. Removal of some contaminants such as nitrogen compounds and sulfate was higher in summer months while removal of other contaminants such as arsenic and antimony was similar throughout the year. Potential process rates as assessed in laboratory incubations were generally higher at higher incubation temperatures and decreased with decreasing temperatures, but processes still occurred at 0 °C. The composition of the potentially active microbial community as assessed by 16S rRNA amplicon sequencing varied more strongly between the two TPs and the two layers, while seasonal variability was minor. Potentially active microorganisms included genera known for nitrification, denitrification, sulfate reduction, iron reduction as well as arsenate and antimonate reduction. The collective results indicate that (i) microbial communities in mining-affected peatlands were exposed to high concentrations of multiple contaminants, (ii) microbially mediated processes contributed to contaminant removal throughout the year, and (iii) differences in process rates and contaminant removal likely stem from overall lower activities rather than from changes in microbial community composition.

Altered intestinal microbiota enhances adenoid hypertrophy by disrupting the immune balance.

Adenoid hypertrophy (AH) is a common upper respiratory disorder in children. Disturbances of gut microbiota have been implicated in AH. However, the interplay of alteration of gut microbiome and enlarged adenoids remains elusive. 119 AH children and 100 healthy controls were recruited, and microbiome profiling of fecal samples in participants was performed using 16S rRNA gene sequencing. Fecal microbiome transplantation (FMT) was conducted to verify the effects of gut microbiota on immune response in mice. In AH individuals, only a slight decrease of diversity in bacterial community was found, while significant changes of microbial composition were observed between these two groups. Compared with HCs, decreased abundances of Akkermansia, Oscillospiraceae and Eubacterium coprostanoligenes genera and increased abundances of Bacteroides, Faecalibacterium, Ruminococcus gnavus genera were revealed in AH patients. The abundance of Bacteroides remained stable with age in AH children. Notably, a microbial marker panel of 8 OTUs were identified, which discriminated AH from HC individuals with an area under the curve (AUC) of 0.9851 in the discovery set, and verified in the geographically different validation set, achieving an AUC of 0.9782. Furthermore, transfer of mice with fecal microbiota from AH patients dramatically reduced the proportion of Treg subsets within peripheral blood and nasal-associated lymphoid tissue (NALT) and promoted the expansion of Th2 cells in NALT. These findings highlight the effect of the altered gut microbiota in the AH pathogenesis.

Intestinal Geographical Pattern of Gut Microbiome and Metabolites Identifies Novel Regulators of Graft-Versus-Host Disease

Introduction: The severity of T cell-mediated gastrointestinal graft-versus-host disease (GI-GVHD) correlates with a decrease in the gut microbiome diversity, loss of obligate anaerobic bacteria and alterations in levels of salutary metabolites like short chain fatty acids (SCFAs). However, it is unknown whether the intestinal anatomic geography of the microbiome and its metabolites impacts GI GVHD severity. Herein, we investigate the pattern of the gut microbiome and metabolites from four distinct anatomical sites of intestines after allogeneic stem cell transplant (allo-SCT) via shotgun metagenomics and untargeted mass-spectrometry. Methods: To determine the composition of the gut microbiome and gut metabolites of mice after allo-SCT, we utilized contemporaneous analyses of shotgun metagenomic sequencing and untargeted mass spectrometry on the gut contents of mice 7 or 21 days after major histocompatibility complex (MHC)-disparate BALB/c→C57BL/6 (B6) allogeneic SCT. We investigated the microbial community composition and gut metabolites from four distinct gut locations (terminal ileum, cecum, transverse colon, descending colon) and performed integrative analysis to assess for novel pathways that may regulate GVHD biology. For shotgun metagenomics analyses, reads were depth normalized with BBnorm v.38.96 and assembled per-sample with MEGAHIT v.1.2.9. Prodigal v.2.6.3 was used to find genes in each bin. KofamScan v.1.3.0 was used to assign KEGG ortholog IDs (KO) to translated genes predicted by Prodigal. Community composition profiles were produced with Kraken2 v.2.1.2 and Bracken v.2.6.1. Functional profiles for each sample were determined with the Kraken community composition profiles and Humann3 v.3.0.0, with a GTDB database built with Struo2. Results: Consistent with previous reports from direct stool analyses, our data demonstrated that after allo-SCT, gut microbial diversity is reduced, relative abundance of obligate anaerobes decreases, and relative abundance of facultative anaerobes increases at all the intestinal anatomic sites, but the difference was maximal in ileo-cecal contents. Furthermore, metabolomic analyses reveal a decrease in previously described metabolites such as, SCFAs, bile acids and indoles at these sites. The distinct patterns of change between control and allogeneic samples depended not only on the gut location probed but also correlated with timepoint after transplant (7 days or 21 days) highlighting the importance of probing different gut locations and timepoints. The largest driver of differences between sample groups was (1) gut location (2) time after transplant (3) transplant type. Integrative analyses demonstrated loss of microbial functional genes related to butyrate processing following allo-SCT complementing previous studies that demonstrated reduction in butyrate levels. Further bioinformatic analyses identified novel microbial functional genes and metabolites that may have biological implications. Analyses revealed that after allo-SCT, phenyllactic acid (PLA) levels increased in the transverse colon and distal colon (fig.1). PLA is an anti-microbial compound and has been shown to have immune modulatory properties. Administration of PLA in drinking water of mice after allo-SCT worsened GVHD severity and increased mortality indicating PLA may play a role in inducing dysbiosis and worsening GVHD severity. Conclusion: Contemporaneous analyses of shotgun metagenomic and untargeted mass spectrometry of gut contents after allo-SCT reveal changes in microbial composition and metabolites consistent with previous data from analyses from stool. However, our analysis demonstrates distinct patterns of key metabolites and microbes in between syngeneic and allogeneic depending on gut location and time after transplant. Furthermore, our analyses have identified novel functional genes and metabolites that are implicated in GVHD severity.

2960. A Gut Pathobiont Triggers Neuroinflammation and Neurocognitive Impairment via Breaching the Gut-Brain Axis in a Preclinical Model of Alzheimer’s Disease: From Microbial Pathogenesis to Neuropathogenesis

Abstract Background Klebsiella pneumoniae (Kpn) is notorious for causing nosocomial infections and is commonly found in elderly patients in hospitals with Alzheimer's disease (AD). This bacterium can cause bloodstream infection, which may worsen AD pathophysiology, but there are no studies demonstrating the mechanistic role of this pathogen in AD. Methods We infected APP/PS mice intestinally with Kpn with (Kpn+Ab) and without antibiotics (Kpn) for a week and then fecal and serum samples were collected 1 and 3 weeks afterwards. Neurocognitive function and motor coordination were tested followed by collection of intestinal and brain tissues at 5 weeks. Microbiome profiles were measured using 16S rRNA amplicon sequencing. Study design Results Kpn was found to have explosively increased in the gut of all mice that received antibiotics and negatively correlated with microbial diversity. Conversely, Kpn was barely detected in the mice that did not receive antibiotics. This underscores the role of antibiotic-induced gut dysbiosis in instigating a ‘pathobiome’ signature. Notably, after five weeks post-infection, Kpn was found to be more abundantly colonized in the small intestine than large colon. Importantly, in the Kpn+Ab group, Kpn was detected not only in the blood but also in the brain, indicating the translocation of Kpn from the intestine to the brain via circulation. In mice in which Kpn was found in the brain, a substantial amount of neuroinflammation caused by bacterial infection was observed. Subsequent neurocognitive and behavioral tests revealed that mice infected with Kpn, especially those in the Kpn+Ab group, had impaired memory function and motor coordination. Effects of Klebsiella pneumoniae colonization. A. Changes in microbial composition before and after K. pn colonization, B. Correlation between microbial diversity (Shannon entropy) and abundance of Kpn of Kpn+Ab group C. Assessment of motor coordination (incline screen and hanging wire test) and memory function (T-maze) test. D. Neuroinflammation after K.pn translocation from gut to brain, E. Abundance of K.pn in the three parts of small intestine, colon, blood, and brain. Conclusion These results corroborate the emerging notion of the implicating role of the gut dysbiosis and consequent gut-brain axis impairment in Alzheimer’s neuropathology. Our findings suggest that Alzheimer's patients who are hospitalized and treated with antibiotics are at a higher risk of contracting multi-drug resistant Kpn. Further, these data also hint that gut pathobiome may increase the host’s predisposition to AD by breaching the gut-brain axis thereby triggering neuroinflammation and impairing neurocognitive function. Our ongoing studies are anticipated to reveal underlying mechanisms and will be presented at the conference. Disclosures All Authors: No reported disclosures

Changes in Diversity and Composition of Rhizosphere Bacterial and Fungal Community between Resistant and Susceptible Pakchoi under Plasmodiophora brassicae

Plasmodiophora brassicae (P. brassicae) is a soil-born pathogen worldwide and can infect most cruciferous plants, which causes great yield decline and economic losses. It is not well known how microbial diversity and community composition change during P. brassicae infecting plant roots. Here, we employed a resistant and a susceptible pakchoi cultivar with and without inoculation with P. brassicae to analyze bacterial and fungal diversity using 16S rRNA V3-V4 and ITS_V1 regions, respectively. 16S rRNA V3-V4 and ITS_V1 regions were amplified and sequenced separately. Results revealed that both fungal and bacterial diversity increased, and composition was changed in the rhizosphere soil of the susceptible pakchoi compared with the resistant cultivar. In the four groups of R_mock, S_mock, R_10d, and S_10d, the most relatively abundant bacterium and fungus was Proteobacteria, accounting for 61.92%, 58.17%, 48.64%, and 50.00%, respectively, and Ascomycota, accounting for 75.11%, 63.69%, 72.10%, and 90.31%, respectively. A total of 9488 and 11,914 bacteria were observed uniquely in the rhizosphere soil of resistant and susceptible pakchoi, respectively, while only 80 and 103 fungi were observed uniquely in the correlated soil. LefSe analysis showed that 107 and 49 differentially abundant taxa were observed in bacteria and fungi. Overall, we concluded that different pakchoi cultivars affect microbial diversity and community composition, and microorganisms prefer to gather around the rhizosphere of susceptible pakchoi. These findings provide a new insight into plant–microorganism interactions.

Heat wave-induced microbial thermal trait adaptation and its reversal in the Subarctic.

Climate change predictions suggest that arctic and subarctic ecosystems will be particularly affected by rising temperatures and extreme weather events, including severe heat waves. Temperature is one of the most important environmental factors controlling and regulating microbial decomposition in soils; therefore, it is critical to understand its impact on soil microorganisms and their feedback to climate warming. We conducted a warming experiment in a subarctic birch forest in North Sweden to test the effects of summer heat waves on the thermal trait distributions that define the temperature dependences for microbial growth and respiration. We also determined the microbial temperature dependences 10 and 12 months after the heat wave simulation had ended to investigate the persistence of the thermal trait shifts. As a result of warming, the bacterial growth temperature dependence shifted to become warm-adapted, with a similar trend for fungal growth. For respiration, there was no shift in the temperature dependence. The shifts in thermal traits were not accompanied by changes in α- or β-diversity of the microbial community. Warming increased the fungal-to-bacterial growth ratio by 33% and decreased the microbial carbon use efficiency by 35%, and both these effects were caused by the reduction in moisture the warming treatments caused, while there was no evidence that substrate depletion had altered microbial processes. The warm-shifted bacterial thermal traits were partially restored within one winter but only fully recovered to match ambient conditions after 1 year. To conclude, a summer heat wave in the Subarctic resulted in (i) shifts in microbial thermal trait distributions; (ii) lower microbial process rates caused by decreased moisture, not substrate depletion; and (iii) no detectable link between the microbial thermal trait shifts and community composition changes.