Changes In Microbial Function Research Articles

Impact of wildfire ash on skin and gut microbiomes and survival of Rana dybowskii

Climate change and human activities escalate the frequency and intensity of wildfires, threatening amphibian habitats and survival; yet, research on these impacts remains limited. Wildfire ash alters water quality, introduces contaminants, and may disrupt microbial communities, impacting gut and skin microbiota; however, the effects on gut and skin microbiota remain unclear. Rana dybowskii were exposed to five concentrations (0 g L-1, 1.25 g L-1, 2.5 g L-1, 5 g L-1, and 10 g L-1) of aqueous extracts of wildfire ashes (AEAs) for 30 days to assess AEAs' metal content, survival, and microbiota diversity via Illumina sequencing. Our results showed that the major elements in ash were Ca > K > Mg > Al > Fe > Na > Mn, while in AEA they were K > Ca > Na > Mg > As > Al > Cu. A significant decrease in amphibian survival rates with increased AEA concentration was shown. The beta diversity analysis revealed distinct shifts in microbiota composition. Notably, bacterial genera associated with potential health risks showed increased abundance in skin microbiota, emphasising the potential for ash exposure to affect amphibian health. Functional prediction analyses revealed significant shifts in metabolic pathways related to health and disease, indicating that wildfire ash exposure may influence amphibian health through changes in microbial functions. This study highlights the urgent need for strategies to mitigate wildfire ash impacts on amphibians, as it significantly alters microbiota and affects their survival and health.

Study on the accelerated biodegradation of PAHs in subsurface soil via coupled low-temperature thermally treatment and electron acceptor stimulation based on metagenomic sequencing

In situ anoxic bioremediation is a sustainable technology to remediate PAHs contaminated soils. However, the limited degradation rate of PAHs under anoxic conditions has become the primary bottleneck hindering the application of this technology. In this study, coupled low-temperature thermally treatment (<50 °C) and EA biostimulation was used to enhance PAH removal. Anoxic biodegradation of PAHs in soil was explored in microcosms in the absence and presence of added EAs at 3 temperatures (15 °C, 30 °C, and 45 °C). The influence of temperature, EA, and their interaction on the removal of PAHs were identified. A PAH degradation model based on PLSR analysis identified the importance and the positive/negative role of parameters on PAH removal. Soil archaeal and bacterial communities showed similar succession patterns, the impact of temperature was greater than that of EA. Soil microbial community and function were more influenced by temperature than EAs. Close and frequent interactions were observed among soil bacteria, archaea, PAH-degrading genes and methanogenic genes. A total of 15 bacterial OTUs, 1 PAH-degrading gene and 2 methanogenic genes were identified as keystones in the network. Coupled low-temperature thermally treatment and EA stimulation resulted in higher PAH removal efficiencies than EA stimulation alone and low-temperature thermally treatment alone.

Altered rumen microbiome and correlations of the metabolome in heat-stressed dairy cows at different growth stages

ABSTRACT Heat stress is one of the major stressors affecting dairy cow production, which causes great losses in animal husbandry production and economic development. This study combined 16S rDNA sequencing, metagenomic sequencing, and metabolomic analysis to investigate the effects of heat stress on the rumen microbiome and metabolism of cows. To achieve this, 10 cows each of growing heifers, heifers, and lactating cows were selected for sample collection in April and August (a total of 60 cows). Ruminal fluid was collected, filtered through gauze, and immediately transferred to liquid nitrogen prior to metagenomic, 16S rDNA sequencing, and metabolomic analyses. Heat stress increased the abundance of pathogenic bacteria, such as Treponema_2 , Sphingobacterium , and Streptococcus , in cattle at all growth stages, with the structure and composition of rumen microbial communities being the most affected by heat stress in growing heifers and the least affected by heat stress in lactating cows. Heat stress led to a significant decrease in carbohydrate metabolic function in growing heifers and heifers, whereas microbial function was the most stable in lactating cows, suggesting that changes in microbial function are not only more conserved than microbial composition but are also affected by age. Heat stress led to significant enrichment of fatty acyl metabolites in growing heifers, heifers, and lactating cows, and the heat stress indicator species Bacillus , Lactococcus , Streptococcus , and Enterococcus were significantly associated with fatty acyl compounds in growing heifers and heifers. Therefore, heat stress alters the metabolic status of cows by modulating fatty acid biosynthesis, the PPAR signaling pathway, and arachidonic acid metabolism through the regulation of long-chain fatty acids and other biomarkers in cows at three growth stages. IMPORTANCE Heat stress is one of the main causes of economic losses in the dairy industry worldwide; however, the mechanisms associated with the metabolic and microbial changes in heat stress remain unclear. Here, we characterized both the changes in metabolites, rumen microbial communities, and their functional potential indices derived from rumen fluid and serum samples from cows at different growth stages and under different climates. This study highlights that the rumen microbe may be involved in the regulation of lipid metabolism by modulating the fatty acyl metabolites. Under heat stress, the changes in the metabolic status of growing heifers, heifers, and lactating cows were closely related to arachidonic acid metabolism, fatty acid biosynthesis, and energy metabolism. Moreover, this study provides new markers for further research to understand the effects of heat stress on the physiological metabolism of Holstein cows and the time-dependent changes associated with growth stages.

Diversity and composition of gut microbiota in healthy individuals and patients at different stages of hepatitis B virus-related liver disease

BackgroundHepatitis B virus (HBV) causes chronic hepatitis B (CHB), liver cirrhosis, and hepatocellular carcinoma. The evolution of human gut microbiota during the progression of HBV-related liver diseases remains unclear. Therefore, we prospectively enrolled patients with HBV-related liver diseases and healthy individuals. Through 16S ribosomal RNA amplicon sequencing, we characterized the gut microbiota of the participants and predicted the functions of microbial communities.ResultsWe analyzed the gut microbiota of 56 healthy controls and 106 patients with HBV-related liver disease [14 with resolved HBV infection, 58 with CHB, and 34 with advanced liver disease (15 with liver cirrhosis and 19 with hepatocellular carcinoma)]. Patients with HBV-related liver disease exhibited a higher degree of bacterial richness (all P < 0.05) than did healthy controls. Beta diversity analyses revealed a distinct clustering pattern between healthy controls and patients with HBV-related liver disease (all P < 0.05). The composition of bacteria (from the phylum level to the genus level) varied across the stages of liver disease. Linear discriminant analysis effect size revealed multiple taxa that differ significantly in abundance between healthy controls and patients with HBV-related liver disease; however, fewer differences were observed among patients with resolved HBV infection, those with CHB, and those with advanced liver disease. The ratio of Firmicutes to Bacteroidetes was increased in all three patient groups compared with the ratio in healthy controls (all P < 0.001). The analysis of the sequencing data by using PICRUSt2 revealed the changes in microbial functions with disease progression.ConclusionsThe diversity and composition of gut microbiota appear to vary significantly between healthy controls and patients at different stages of HBV-related liver disease. The understanding of gut microbiota may provide novel therapeutic options in these patients.

Metagenomic characterization of the maternal prenatal gastrointestinal microbiome by pregravid BMI.

The incidence of women entering into pregnancy with BMI indicating overweight or obesity is rising with concurrent increases in adverse complications such as gestational diabetes. Although several studies have examined the compositional changes to the microbiome across BMI classifications, there has been no investigation regarding changes in microbial function during pregnancy. A total of 105 gastrointestinal microbiome biospecimens were used in this analysis. Biospecimens were sequenced by using the Illumina NovaSeq 6000 shotgun metagenomics platform. Findingsindicatean enrichment in microbiota from the phylum Firmicutes across all pregravid BMI groups with a decrease in α diversity in groups with BMI indicating obesity or overweight compared with a group with BMI indicating normal weight (p=0.02). More specifically, women with BMI indicating obesity or overweight had enrichment in Bifidobacterium bifidum and B. adolescentis. Women with BMI > 25 kg/m2 had a higher abundance of microbiota that support biotin synthesis and regulate epithelial cells in the lower gastrointestinal tract. These epithelial cells are responsible for host adaptability to dietary lipid variation and caloric absorption. Our analysis suggests that there are differences in microbial composition and function between BMI groups. Future research should consider how these changes contribute to specific clinical outcomes during pregnancy.

Linking Microbial Functional Gene Abundance and Daqu Extracellular Enzyme Activity: Implications for Carbon Metabolism during Fermentation.

Daqu is the starter of Baijiu, it provides the microbes and enzymes necessary for fermentation. Studies have already established carbohydrate metabolism as the primary functional module in Daqu fermentation. The present study investigated the changes in microbial functions and the relationship between carbohydrate metabolism-related functional genes and extracellular enzyme activity during the Daqu fermentation. Amplicon sequencing identified 38 bacterial and 10 fungal phyla in Daqu samples, while shotgun metagenomic sequencing classified and annotated 40.66% of the individual features, of which 40.48% were prokaryotes. KEGG annotation showed that the pathways related to metabolites were less in the early fermentation stage, but higher in the middle and late stages. The functional genes related to pyruvate metabolism, glyoxylate and dicarboxylate metabolism, and propanoate metabolism were relatively high in the early and late stages of fermentation, while that for start and cross metabolism was relatively low. The study also found that amino sugar and nucleoside sugar metabolism were dominant in the middle stage of fermentation. Finally, the correlation network analysis showed that amylase activity positively correlated with many carbon metabolism-related pathways, while liquefaction activity negatively correlated with these pathways. In conclusion, the present study provides a theoretical basis for improving and stabilizing the quality of Daqu.

Microbial community succession in response to sludge composting efficiency and heavy metal detoxification during municipal sludge composting.

This study researched microbial community succession in response to sludge composting efficiency and heavy metal detoxification during municipal sludge co-composting with spent mushroom and spent bleaching. The change law of key physicochemical properties, the heavy metals contents and forms during composting were analyzed, and the passivation of heavy metals after composting was explored. High-throughput sequencing was used to analyze the microbial community structure of treat 2 during composting, and the correlation analysis of microbial community structure with heavy metal contents and forms were carried out. The results showed that the sludge of each treatment reached composting maturity after 26 days of composting. Organic matter content, electrical conductivity, pH and seed germination index of treat 2 were all in line with the standard limit of agricultural sludge. Because of the presence of compost bacteria addition, the passivating heavy metals performance of treat 2 satisfied the standard limit of agricultural sludge after composting, which was superior to that of treat 1 and treat 3. The diversity of microbial communities in treat 2 decreased during composting. Extensive bacteria such as Bacillus, Geobacter, Lactobacillus, and Pseudomonas, which possessed the abilities of heavy metal passivation and organic oxidizing, were dominant in treat 2 during the heating stage. However, as composting proceeded, Tuberibacillus with ability of organic oxidizing gradually became the most dominant species at the thermophilic and cooling stages. Changes in microbial function varied from changes of microbial community in treat 2, subsequently affected the performances of heavy metal passivation and organic oxidizing during composting.

Geochemistry and Multiomics Data Differentiate Streams in Pennsylvania Based on Unconventional Oil and Gas Activity.

ABSTRACTUnconventional oil and gas (UOG) extraction is increasing exponentially around the world, as new technological advances have provided cost-effective methods to extract hard-to-reach hydrocarbons. While UOG has increased the energy output of some countries, past research indicates potential impacts in nearby stream ecosystems as measured by geochemical and microbial markers. Here, we utilized a robust data set that combines 16S rRNA gene amplicon sequencing (DNA), metatranscriptomics (RNA), geochemistry, and trace element analyses to establish the impact of UOG activity in 21 sites in northern Pennsylvania. These data were also used to design predictive machine learning models to determine the UOG impact on streams. We identified multiple biomarkers of UOG activity and contributors of antimicrobial resistance within the order Burkholderiales. Furthermore, we identified expressed antimicrobial resistance genes, land coverage, geochemistry, and specific microbes as strong predictors of UOG status. Of the predictive models constructed (n = 30), 15 had accuracies higher than expected by chance and area under the curve values above 0.70. The supervised random forest models with the highest accuracy were constructed with 16S rRNA gene profiles, metatranscriptomics active microbial composition, metatranscriptomics active antimicrobial resistance genes, land coverage, and geochemistry (n = 23). The models identified the most important features within those data sets for classifying UOG status. These findings identified specific shifts in gene presence and expression, as well as geochemical measures, that can be used to build robust models to identify impacts of UOG development.IMPORTANCE The environmental implications of unconventional oil and gas extraction are only recently starting to be systematically recorded. Our research shows the utility of microbial communities paired with geochemical markers to build strong predictive random forest models of unconventional oil and gas activity and the identification of key biomarkers. Microbial communities, their transcribed genes, and key biomarkers can be used as sentinels of environmental changes. Slight changes in microbial function and composition can be detected before chemical markers of contamination. Potential contamination, specifically from biocides, is especially concerning due to its potential to promote antibiotic resistance in the environment. Additionally, as microbial communities facilitate the bulk of nutrient cycling in the environment, small changes may have long-term repercussions. Supervised random forest models can be used to identify changes in those communities, greatly enhance our understanding of what such impacts entail, and inform environmental management decisions.

Effects of Different Sources of Calcium in the Diet on Growth Performance, Blood Metabolic Parameters, and Intestinal Bacterial Community and Function of Weaned Piglets.

Despite a well-documented effect of calcium on the piglet's intestinal microbiota composition, it is less known about changes in microbial function or the effect of different sources of calcium. The experiment was designed to study the effects of dietary calcium from different sources on production, immune indexes, antioxidant capacity, serum biochemical indexes, and intestinal microflora of weaning piglets. A total of 1,000 piglets were randomly assigned to five groups (10 replicate pens per treatment with 20 pigs per pen) and fed diets supplemented with calcium carbonate, calcium citrate, multiple calcium, organic trace minerals, and different concentrations of acidifier. The results showed that the replacement of calcium carbonate with calcium citrate and multiple calcium had almost no significant difference in the growth performance of pigs compared with the control group, and only the diet of multiple calcium dramatically decreased the average daily feed intake (ADFI) compared to the calcium citrate diet on days 15–28 (p < 0.05). The five groups did not change the content of MDA, SOD, and GSH-Px (p > 0.10). A similar situation occurs in the immune function of the blood. There was no significant effect in immune indexes (IgA, IgG, and IgM) among different treatments after weaning at 6 weeks for piglets (p > 0.10). The 16S rRNA sequencing of ileal and cecal microbiota revealed that only the relative abundance of Actinobacteriota at the phyla level was significantly greater in the ileum of the A group compared to the other treatments (p < 0.05). There was a clear effect on seven bacteria in the top 30 genera of ileum and cecum for five groups (p < 0.05). The result of PICRUSt predicted that the intestinal microbe was mainly involved in carbohydrate and amino acid metabolism, membrane transport, and metabolism of cofactors and vitamins. Besides, adding calcium citrate to a weaned piglet diet is better than other choices from the third week to the fourth week. In conclusion, diets with different calcium sources changed ADFI and some intestinal microbial composition of weaned piglets but had little effect on intestinal microbial function.

Response of soil microbial community parameters to plastic film mulch: A meta-analysis

Plastic film mulch alters the soil environment and improves crop production. Although the response of aboveground parts of agroecosystems to plastic film mulch has been extensively studied, no studies have investigated the response of the soil microbiome to plastic film mulch and its effect on crop yield. Here, we performed a meta-analysis of 536 observations to elucidate the response of the soil microbial community to plastic film mulch. Plastic film mulch significantly increased soil microbial alpha-diversity (Shannon: +0.043, 95% CI: +0.022 to + 0.064; richness: +0.037, 95% CI: +0.007 to + 0.067), abundance (+0.104, 95% CI: +0.070 to + 0.139), and eco-functionality (+0.129, 95% CI: +0.087 to + 0.170). In neutral pH soil and field combined plastic film mulch with ridge–furrow tillage, plastic film mulch had a significant impact on microbial richness. Microbial abundance increased significantly when chemical fertilizer was used, but not when organic fertilizer was used. The effect of low-level nitrogen on N acquisition enzyme actives is greater than that of medium and high nitrogen input. Thick film mulch produced a larger positive response in microbial abundance, C acquisition, and oxidative enzyme activities than thin film mulch. Changes in microbial functionality were decoupled with diversity, while in tandem with its abundance and community structure. The increases in microbial C acquisition, N acquisition, and oxidative enzyme activities were significantly linked to yield. Our findings highlight the beneficial effects of plastic film mulch on the soil microbial community and have further implications for the development of soil health-friendly agricultural management.

The shifts in soil microbial community and association network induced by successive planting of Eucalyptus plantations

Successional planting of Eucalyptus is known to significantly affect soil quality. However, the accompanying changes in the bacterial and fungal community structure, co-occurrence network pattern, and microbial functions are unclear. This prevents a full assessment of the impact of successional planting patterns on soil ecosystem services. In this study, we investigated the effect of replacing Pinus massoniana plantations with multi-generational successional planting of Eucalyptus on soil bacterial and fungal communities. The results showed that it elicited significant declines in soil multifunctionality and the diversity and richness of the fungal community, together with a significant increase in soil bulk density. The third and fourth-generation plantations had notably reduced microbial network complexity, robustness, and association between microbial taxa. Successional planting also significantly changed the relative abundance of dominant microbial groups at the phylum and order levels, which subsequently caused dramatic changes in microbial functions. With successive planting generations, the soil bacterial community shifted from carbon-using to nitrogen-using bacteria, and the fungal community shifted from saprophytic and pathogenic to symbiotic fungi. From the above results, we concluded that multi-generation plantation of Eucalyptus has a significant negative impact on soil multifunctionality and microbial community, and after two generations of successive planting, it should be considered to change the plantation management pattern. This work provides a theoretical reference for the sustainable management of Eucalyptus plantations.

Decoupling of microbial community dynamics and functions in Arctic peat soil exposed to short term warming.

Temperature is an important factor governing microbe-mediated carbon feedback from permafrost soils. The link between taxonomic and functional microbial responses to temperature change remains elusive due to the lack of studies assessing both aspects of microbial ecology. Our previous study reported microbial metabolic and trophic shifts in response to short-term temperature increases in Arctic peat soil, and linked these shifts to higher CH4 and CO2 production rates (Proceedings of the National Academy of Sciences of the United States of America, 112, E2507-E2516). Here, we studied the taxonomic composition and functional potential of samples from the same experiment. We see that along a high-resolution temperature gradient (1-30°C), microbial communities change discretely, but not continuously or stochastically, in response to rising temperatures. The taxonomic variability may thus in part reflect the varied temperature responses of individual taxa and the competition between these taxa for resources. These taxonomic responses contrast the stable functional potential (metagenomic-based) across all temperatures or the previously observed metabolic or trophic shifts at key temperatures. Furthermore, with rising temperatures we observed a progressive decrease in species diversity (Shannon Index) and increased dispersion of greenhouse gas (GHG) production rates. We conclude that the taxonomic variation is decoupled from both the functional potential of the community and the previously observed temperature-dependent changes in microbial function. However, the reduced diversity at higher temperatures might help explain the higher variability in GHG production at higher temperatures.

Gut Microbiota Modulation and Fecal Transplantation: An Overview on Innovative Strategies for Hepatic Encephalopathy Treatment.

Simple SummaryTreatment of advanced liver disease and its complications continue to be a challenge due to the complexity of this illness. In recent years, the gut microbiome has been recognized to play a beneficial role in our health. Studies have shown that overgrowth of harmful organisms in the gut can contribute to worsened outcomes in liver disease. Fecal microbiota transplant (FMT) is an approved and effective treatment in other gastrointestinal conditions. FMT involves the administration of a solution of a fecal suspension from a healthy donor into the intestinal tract of a recipient. This has led researchers to attempt this treatment in liver disease. There have now been small clinical trials showing that FMT is safe and could be effective in improving outcomes in advanced liver disease. There remain several questions to be answered before FMT is implanted in clinical practice, including the best route to administer this treatment, how many doses are needed to achieve a therapeutic response, and how long we need to wait between treatments. In this review paper, we explore the role of the gut microbiome in the human body with emphasis on the gastrointestinal system, how it changes in liver disease, and how we can improve it with fecal microbiota transplant.Hepatic encephalopathy (HE) is a major complication of cirrhosis, which is associated with gut microbial composition and functional alterations. Current treatments largely focus on gut microbiota using lactulose, rifaximin and other agents. However, despite these treatments, patients with HE have a high rate of readmission, morbidity and cognitive impairment. Fecal microbiota transplant (FMT) involves introduction of a donor microbiota into a recipient and is currently mainly used for recurrent C. difficile infection (rCDI). The role of FMT in cirrhosis and HE is evolving. There have been two randomized clinical trials (RCT) and several case reports/series in cirrhosis. Both RCTs were safety-focused phase 1 trials. One involved pre-FMT antibiotics and FMT enema versus standard of care, while the other involved 15 FMT capsules versus placebo without pre-FMT antibiotics. There was evidence of safety in both trials and the FMT group demonstrated reduction in hospitalizations compared to the non-FMT group. Changes in microbial function centered around short-chain fatty acids, bile acids and brain function showed improvement in the FMT groups. Long-term follow-up demonstrated continued safety and reduction in the antibiotic-resistance gene carriage. However, larger trials of FMT in HE are needed that can refine the dose, duration and route of FMT administration.

Functional Gastrointestinal Disorders and the Microbiome—What Is the Best Strategy for Moving Microbiome-based Therapies for Functional Gastrointestinal Disorders into the Clinic?

There have been numerous human studies reporting associations between the intestinal microbiome and functional gastrointestinal disorders (FGIDs), and independently animal studies have explored microbiome-driven mechanisms underlying FGIDs. However, there is often a disconnect between human and animal studies, which hampers translation of microbiome findings to the clinic. Changes in the microbiota composition of patients with FGIDs are generally subtle, whereas changes in microbial function, reflected in the fecal metabolome, appear to be more precise indicators of disease subtype-specific mechanisms. Although we have made significant progress in characterizing the microbiome, to effectively translate microbiome science in a timely manner, we need concurrent and iterative longitudinal studies in humans and animals to determine the precise microbial functions that can be targeted to address specific pathophysiological processes in FGIDs. A systems approach integrating multiple data layers rather than evaluating individual data layers of symptoms, physiological changes, or -omics data in isolation will allow for validation of mechanistic insights from animal studies while also allowing new discovery. Patient stratification for clinical trials based on functional microbiome alterations and/or pathophysiological measurements may allow for more accurate determination of efficacy of individual microbiome-targeted interventions designed to correct an underlying abnormality. In this review, weoutline current approaches and knowledge, and identify gaps, to provide a potential roadmap for accelerating translation of microbiome science toward microbiome-targeted personalized treatments for FGIDs.

Long-term CO2 enrichment alters the diversity and function of the microbial community in soils with high organic carbon

The response of soil microorganisms to elevated atmospheric CO2 (eCO2) has the potential to alter the regulation of soil biogeochemical processes including carbon and nutrient cycling. A mechanistic understanding of this microbial response in agricultural systems is essential due to the potential impact on soil quality. This study used an eight-year free-air-CO2 enrichment (SoilFACE) experiment to assess the microbial response to eCO2 in three major agricultural soils (Chromosol, Vertosol, and Calcarosol) planted annually with grain crops. Elevated CO2 increased the number of operational taxonomic unit (OTU) by 14.3%, 13.3% and 4.1% and the Shannon diversity by 3.7%, 4.4%, and 2.6% in the top 5-cm soil layer of the Chromosol, Calcarosol and Vertosol, respectively. The relative abundance of the oligotroph Acidobacteriaceae Subgroup 1 in the top 5-cm soil of the Chromosol and Vertosol was significantly increased by eCO2. Elevated CO2 did not affect community diversity in the 5–10 cm soil layer. The functional attribute analysis of the bacterial communities showed that eCO2 increased pectin and benzene degradation, the pentose phosphate pathway and the production of phytase-6 in the top 5-cm soil of the Chromosol. These results suggest that eCO2 increases the presence of oligotrophs in the bacterial community and overall mineralization of soil organic carbon (SOC) in surface soils with high SOC. Changes in microbial function due to eCO2 likely impact the stability of SOC and, consequently, the quality of farming soils for sustainable crop production.

P: 11 Cognitive Improvement After Capsular Fecal Microbial Transplant in Hepatic Encephalopathy Is Associated With Changes in Microbial Function and Inflammation

BACKGROUND: Hepatic encephalopathy(HE) can recur despite standard of care therapies. Our trial of capsular fecal microbiota transplant (FMT) demonstrated improvement in dysbiosis and cognition in pts randomized to FMT versus placebo. Despite compositional improvement, interaction of inflammation, bacterial translocation, microbial function (bile acid, BA) with cognition needs to be evaluation. Gut microbiota can transform BAs by deconjugating, converting primary to secondary BAs &amp; tertiary(oxo, sulfated, urso and iso-BA) formation. Aim: Determine changes in fecal BA moieties as modulators of microbial function, inflammation and their linkage with cognition in FMT in cirrhosis and recurrent HE. METHODS: 20 cirrhotics with recurrent HE on lactulose/rifaximin were randomized 1:1 into 15 FMT capsules once vs identical placebo. FMT was from a single donor enriched in Lachnospiraceae/Ruminococcaceae, which are associated with secondary BA generation. We collected stool/blood &amp; analyzed cognition (EncephalApp; high = worse) at baseline and 30 days post-intervention (Figure 1a red arrows). Stool microbiota was analyzed using 16srRNA &amp; BAs using LC/MS. Fecal BA moieties analyzed were (a) total (b) primary (c) secondary (d) deconjugated (e) tertiary BAs. Secondary/primary BA ratios were calculated. Serum was also analyzed for lipopolysaccharide-binding protein (LBP) &amp; IL-6. Correlation networks between BAs, microbiota, LBP, IL-6 and cognition were created. Correlation network complexity was compared between post-FMT vs post-placebo states. RESULTS: All subjects completed the follow-up without any serious AEs related to FMT/placebo. EncephalApp total score (P &lt; 0.05) improved in FMT pts only Microbiota: there was a significant engraftment of donor microbiota with higher Ruminoccaceae &amp; Lachnospiraceae in stool/duodenum in FMT pts. Inflammation/translocation: A reduction in LBP &amp; IL-6 was seen only in FMT pts (Figure 1b,d). BAs: There was a significant increase in secondary/primary BA ratio (Figure 1c) in FMT pts. Deconjugation and tertiary BAs remained similar between groups. Correlation network showed higher complexity after FMT compared to post-placebo (Figure 1e). Beneficial bacteria (Ruminococcaeae and Verrucomicrobiaceae) became significantly positively correlated with each other (blue lines) and negatively with inflammation (IL6 redlines) and associated with better EncephalApp score post-FMT (Figure 1f) compared to placebo at study end. CONCLUSIONS: Capsular FMT is safe and improves cognition in pts with cirrhosis and HE compared to placebo. These improvements are associated with beneficial changes in microbial composition and function and differential correlations with bacterial translocation and inflammation.

Functional Microbiomics in Liver Transplantation: Identifying Novel Targets for Improving Allograft Outcomes.

Gut dysbiosis, defined as a maladaptive gut microbial imbalance, has been demonstrated in patients with end-stage liver disease, defined as a contributor to disease progression, and associated clinically with severity of disease and liver-related morbidity and mortality. Despite this well-recognized phenomena in patients with end-stage liver disease, the impact of gut dysbiosis and its rate of recovery following liver transplantation (LT) remains incompletely understood. The mechanisms by which alterations in the gut microbiota impact allograft metabolism and immunity, both directly and indirectly, are multifactorial and reflect the complexity of the gut-liver axis. Importantly, while research has largely focused on quantitative and qualitative changes in gut microbial composition, changes in microbial functionality (in the presence or absence of compositional changes) are of critical importance. Therefore, to translate functional microbiomics into clinical practice, one must understand not only the compositional but also the functional changes associated with gut dysbiosis and its resolution post-LT. In this review, we will summarize critical advances in functional microbiomics in LT recipients as they apply to immune-mediated allograft injury, posttransplant complications, and disease recurrence, while highlighting potential areas for microbial-based therapeutics in LT recipients.

Fungal Community Structural and Microbial Functional Pattern Changes After Soil Amendments by Oilseed Meals of Jatropha curcas and Camelina sativa: A Microcosm Study.

The meals after oil extraction from many oilseed crops have nutrition and biofumigation potential for land application. Oilseed meal (SM) from the dedicated bioenergy crop Jatropha curcas were implicated to contain compounds that have antibacterial properties on some soil pathogens. However, little is known about its effect on non-targeted soil microbial community, especially on fungi. SM from Camelina sativa contains moderate level of glucosinolates (GLS) and was under studied. To investigate soil fungal community responses to jatropha and camelina SMs, we conducted a lab based microcosm study, amending soil with 1% SMs of jatropha, camelina, flax, and biomass of wheat straw. Fungal community abundance and structure were analyzed based on the ITS region using qPCR and tag-pyrosequencing. Microbial functional changes were examined by community level physiological profile (CLPP) using Biolog assay. Both SMs from jatropha and camelina showed biofumigant properties and inhibited fungal proliferation. Jatropha SM significantly altered soil fungal community structures with lower fungal biodiversity and higher Chaetomium composition. Camelina SM amended soil promoted Fusarium proliferation. CLPP indicated sequential hierarchy for C metabolism in the oilseed-amended microcosms was generally complex C > phosphate-associated C > carboxylic acids > carbohydrates > amines > amino acids. No significant difference in CLPP was detected due to the type of SM treatment. Our data indicate that both SMs of jatropha and camelina have biofumigant properties and can differentially impact soil microbial communities, and the changes were relatively persistent over time. Microbial functional patterns on the other side were not impacted by SM type. Our study revealed biofumigant and nutritional influence of SMs from dedicated biofuel plants on soil microbial community. This information will help properly using jatropha and camelina SMs for pathogen control while minimizing their negative impacts on non-target microorganisms. However, further studies in the field are demanded to investigate their influences in real practice.

Effects of exotic plantation forests on soil edaphon and organic matter fractions

There is uncertainty and limited knowledge regarding soil microbial properties and organic matter fractions of natural secondary forest accompanying chemical environmental changes of replacement by pure alien plantation forests in a hilly area of southwest of Sichuan province China. The aim of this study was to evaluate the impact of natural secondary forest (NSF) to pure Cryptomeria fortunei forest (CFF) and Cunninghamia lanceolata forest (CLF) on soil organic fractions and microbial communities. The results showed that the soil total phospholipid fatty acids (PLFAs), total bacteria and fungi, microbial carbon pool, organic recalcitrant carbon (C) and (N) fractions, soil microbial quotient and labile and recalcitrant C use efficiencies in each pure plantation were significantly decreased, but their microbial N pool, labile C and N pools, soil carbon dioxide efflux, soil respiratory quotient and recalcitrant N use efficiency were increased. An RDA analysis revealed that soil total PLFAs, total bacteria and fungi and total Gram-positive and Gram-negative bacteria were significantly associated with exchangeable Al3+, exchangeable acid, Al3+, available P and Mg2+ and pH, which resulted into microbial functional changes of soil labile and recalcitrant substrate use efficiencies. Modified microbial C- and N-use efficiency due to forest conversion ultimately meets those of rapidly growing trees in plantation forests. Enlarged soil labile fractions and soil respiratory quotients in plantation forests would be a potential positive effect for C source in the future forest management. Altogether, pure plantation practices could provoke regulatory networks and functions of soil microbes and enzyme activities, consequently leading to differentiated utilization of soil organic matter fractions accompanying the change in environmental factors.

Transient influence of blood meal and natural environment on blacklegged tick bacterial communities

Blacklegged ticks (Ixodes scapularis) spend the majority of their life cycle off host, typically in woodland habitat, but require a blood meal at each of three life stages (larva, nymph, adult) to reach maturity and reproduce. Blood feeding usually lasts for several days each time and as blood is imbibed, a range of known pathogens from the host may also be acquired. Using next generation sequencing of 16S rRNA gene amplicons, we examined the influence of host blood meal on the internal bacterial community within nymphal blacklegged ticks across host-seeking, feeding, blood meal digestion, and after molting into the adult stage. Results demonstrate bacterial community structuring across host and ticks with 287 taxa found exclusively in ticks, suggesting the field environment plays a significant role in shaping the internal tick microbiome. A decrease in bacterial diversity was noted from unfed nymphs through feeding/digestion and after molting into adults, suggesting that bacterial species are lost during the corresponding physiological changes. The similarity in biochemical pathways across the different tick categories suggests that the loss of bacterial taxa does not mirror a large change in microbial function. Ticks likely lose bacterial taxa after feeding, but continual exposure to bacteria from the field environment counters this loss.