Changes In Microbial Composition Research Articles

Divergent responses in the gut microbiome and liver metabolome to ammonia stress in three freshwater turtles

Ammonia is a common pollutant in aquaculture system, and toxic to all aquatic animals. However, different aquatic animals exhibit diverse physiological responses to high-level ammonia exposure, potentially indicating their divergent resistance to ammonia stress. In this study, juveniles of three freshwater turtles (Mauremys reevesii, Pseudemys nelsoni and Trachemys scripta elegans) were exposed to different concentrations of ammonia (0, 0.3 and 3.0 mg/L) for 30 days, and their swimming, growth performance, gut microbiota, and hepatic metabolites were measured to evaluate the interspecific difference in physiological responses to ammonia stress. Despite no differences in swimming ability, growth rate, and gut microbial diversity, observable changes in microbial community composition and hepatic metabolite profiles were shown in ammonia-exposed turtles. A relatively higher abundance of potentially pathogenic bacteria was found in M. reevesii than in the other two species. Moreover, microbial compositions and metabolic responses differed significantly among the three species. M. reevesii was, out of the three tested species, the one in which exposure to ammonia had the greatest effect on changes in bacterial genera and hepatic metabolites. Conversely, only a few metabolites were significantly changed in T. scripta elegans. Integrating these findings, we speculated that native M. reevesii should be more vulnerable to ammonia stress compared to the invasive turtle species. Our results plausibly reflected divergent potential resistance to ammonia among these turtles, in view of differential physiological responses to ammonia exposure at environmentally relevant concentrations.

A less complex but more specialized microbial network resulted in faster fine-root decomposition in young stands of Robinia pseudoacacia

Microorganisms play an important role in litter decomposition. Bacteria and fungi colonize litter during the decomposition process; therefore, understanding the interactions of bacterial and fungal communities can yield insight into litter decomposition dynamics. Most studies have focused on leaf litter decomposition, but thus far, there has been little information on the dynamic changes in soil microbial composition at the different stages of fine-root decomposition. Therefore, we conducted a 210-day incubation experiment on the fine roots of Robinia pseudoacacia to explore how the temporal dynamics of soil enzyme activities and microbial communities are related to the decomposition of R. pseudoacacia at four different stand ages (15, 25, 35 and 45 years) during vegetation restoration. The results showed that the fine-root decomposition rate was higher for young stands of R. pseudoacacia. We found that the oxidase activity was significantly higher in the young stands (15 and 25 years) than in the old stands (35 and 45 years), while the hydrolase activity showed the opposite trend. The main reason for the higher decomposition rate in young stands of R. pseudoacacia was the high oxidase enzyme activities and less complex but more specialized microbial network of younger stands. The occurrence network was used to identify the keystone taxa by statistical analysis, and the key taxa changed from Acidobacteria to Proteobacteria during vegetation restoration. These findings demonstrate that vegetation restoration alters the soil microorganism community and network structure during fine-root decomposition of R. pseudoacacia. This finding is of great significance for understanding the role of microorganisms in regulating fine-root decomposition dynamics.

Red seaweed extracts reduce methane production by altering rumen fermentation and microbial composition in vitro.

A series of in vitro batch culture incubations were carried out to investigate changes in rumen fermentation characteristics, methane (CH4) production, and microbial composition in response to supplementation with five different red seaweed species (Amphiroa anceps, AANC; Asparagopsis taxiformis, ATAX; Chondracanthus tenellus, CTEN; Grateloupia elliptica, GELL; and Gracilaria parvispora, GPAR). Prior to the incubations, the total flavonoid and polyphenol content of the red seaweed extracts was quantified. The incubated substrate consisted of timothy hay and corn grain [60:40 dry matter (DM) basis]. Treatments were substrate mixtures without seaweed extract (CON) or substrate mixtures supplemented with 0.25 mg/mL of red seaweed extract. Samples were incubated for 6, 12, 24, 36, and 48 h. Each sample was incubated in triplicates in three separate runs. In vitro DM degradability, fermentation parameters (i.e., pH, volatile fatty acids, and ammonia nitrogen), total gas production, and CH4 production were analyzed for all time points. Microbial composition was analyzed using 16S rRNA amplicon sequencing after 24 h of incubation. The highest CH4 reduction (mL/g DM, mL/g digested DM, and % of total gas production) was observed in ATAX (51.3, 50.1, and 51.5%, respectively, compared to CON; P < 0.001) after 12 h of incubation. The other red seaweed extracts reduced the CH4 production (mL/g DM; P < 0.001) in the range of 4.6-35.0% compared to CON after 24 h of incubation. After 24 h of incubation, supplementation with red seaweed extracts tended to increase the molar proportion of propionate (P = 0.057) and decreased the acetate to propionate ratio (P = 0.033) compared to the CON. Abundances of the genus Methanobrevibacter and total methanogens were reduced (P = 0.050 and P = 0.016) by red seaweed extract supplementation. The linear discriminant analysis effect size (P < 0.05, LDA ≥ 2.0) showed that UG Succinivibrionaceae, Anaeroplasma, and UG Ruminococcaceae, which are associated with higher propionate production, starch degradation, and amylase activity were relatively more abundant in red seaweed extracts than in the CON. Our results suggest that supplementation with red seaweed extracts altered the microbiota, leading to the acceleration of propionate production and reduction in CH4 production.

Mediterranean Diet Intervention in Patients with Myeloproliferative Neoplasm

Reasoning that a Mediterranean diet intervention is a low-risk, low-cost approach to reduce inflammation, we set out to test whether MPN patients can adopt a Mediterranean style eating pattern. We completed two randomized clinical trials to address the feasibility of a Mediterranean diet intervention in MPN patients. The primary objective of the 1st study was to test whether MPN patients can adopt a Mediterranean diet eating pattern with registered dietician (RD) counseling. We enrolled 28 patients with MPN (14 PV, 6 ET, 8 MF) into a 15 week interventional study. After a two-week observation period, patients were randomized to either a Mediterranean diet (MED) or the United States Dietary Guidelines for Americans (USDA) diet groups. Participants received active intervention for 10 weeks, comprising of weekly educational curriculum and personalized RD visits at weeks 3, 5, and 7 geared toward their assigned diet. Participants were observed for an additional 3 weeks post intervention. Adoption of a Mediterranean style eating pattern was quantified using the 14-Item Mediterranean Diet Adherence Screener (MEDAS), with a score of ≥8 regarded as highly adherent to a Mediterranean eating pattern. Over 75% of the participants in the MED group maintained a MEDAS score of ≥8 over the entire active intervention period demonstrating that MPN patients can successfully adopt a Mediterranean diet eating pattern with RD counseling and written curriculum. Symptom burden was assessed using the MPN-Total Symptom Score (MPN-TSS) measured at baseline, weeks 3, 6, 9, 12, and 15. Approximately half of the Mediterranean diet cohort enjoyed a ≥ 50% reduction in MPN-TSS at weeks 9-15 compared to baseline, whereas the maximum percentage of participants in the USDA arm achieving ≥ 50% reduction in their MPN-TSS was 31% at 15 weeks. Exploratory biological correlates included CBC, CMP, lipid, hsCRP, cytokine panel, and fecal microbiome analysis at weeks 1, 6, 9, and 15. Blood counts, electrolytes, kidney and liver function remained stable throughout the intervention period for both groups. We found no significant changes in cytokines (TNFα, IL-6, IL-8, IL-10, IL-22) or hsCRP in either diet group. Shotgun sequencing of fecal samples found no significant changes in microbial diversity, composition, or function associated with a MED diet intervention over time. Instead, we found the MPN subtype played a greater role in determining microbiome diversity, composition, and function. Individuals with Essential Thrombocythemia and Polycythemia Vera were more similar to each other, while those with Myelofibrosis (MF) were more disparate. This difference in the MF microbiome composition was associated with an increase in TNFα. Notably, members of the Bacteroidaceae family were positively associated with high TNFα levels. In a second randomized trial we tested the feasibility of an online diet intervention, with zoom based dietician counseling, electronic curriculum, and online based questionnaires. We recruited 28 symptomatic MPN patients not already adherent to a MED diet and randomized them to either a MED arm or DASH diet. Participants received written curriculum and attended zoom one-on-one RD sessions at weeks 3, 4, 8, and 12. Participants completed an online MPN-TSS survey. Participants attended most dietician visits, with only a 3.5% and 7.5% no show rate in the MED and DASH diet groups respectively. Participants were also compliant with online based daily surveys, with an average completion rate of 93.2% in the MED group and 69.3% in the DASH group. At week 16, 43% of participants in the MED group had a ≥50% reduction in MPN-TSS compared with 29% of participants in the DASH group. Taken together, these two studies demonstrate that MPN patients can adopt a Mediterranean diet eating pattern if given written curriculum and RD counseling. Moreover, a remotely administered intervention is feasible in this patient population. Although patients in all diet groups had a ≥50% reduction in MPN-TSS, the percentage achieving the ≥50% benchmark was higher in the MED arm for both diet studies. These data suggest that a Mediterranean diet, which is rich in anti-inflammatory foods, may be particularly beneficial to manage symptom burden in MPN. We are now moving on to larger randomized studies to rigorously test the impact of a MED diet intervention on symptom burden in MPN patients.

Immunomodulatory Microbial Metabolites Identified in Allo-SCT Patients Protect from GvHD By Sting Dependent Modulation of Intestinal Tissue Homeostasis

Background: Graft-versus-host disease (GVHD) is a dreaded complication after allogeneic stem-cell transplantation (ASCT). Previously, we and others showed that activation of type I interferon (IFN-I) inducing pathways such as RIG-I/MAVS or cGAS/STING can promote the integrity of the intestinal barrier and limit GVHD. However, the signals that drive these protective IFN-I responses are poorly understood. Commensal microbiota can (i) have distant effects on immune responses through modulation of IFN-I signaling and (ii) predict mortality in ASCT patients. We hypothesized that microbiota-derived products such as microbial metabolites engage IFN-I signaling in immune and non-immune cells poising them for induction of protective responses. We established a prospective, multi-centric clinical study in patients newly diagnosed with acute leukemia and performed longitudinal stool sampling to track changes in microbial community composition and metabolites expression levels (Submitted as a separate abstract to ASH 2022 (Orberg & Meedt et al.)). We showed that patients with high metabolite expression are less likely to develop GVHD. In this study, we translated our clinical observations to mouse models of acute GVHD and human and mouse intestinal organoid models to uncover the molecular mechanisms of protective metabolites during ASCT. Methods: Stool samples from ASCT patients were obtained in Munich and Regensburg in accordance to IRB-approved study protocols. Patients were sampled at initial diagnosis (Dx), prior to conditioning and weekly after ASCT up to day 28. We analyzed samples by 16S rRNA sequencing and mass spectrometry. Next, we tested metabolites detected in patients in vitro in murine and human intestinal crypt-derived organoids and organoid/T cell coculture assays. To obtain a mechanistic understanding, we stimulated WT or IFN-I-signaling-impaired organoids or used small molecule inhibitors and analysed them regarding growth performance, cell composition and by scRNAseq. Finally, Metabolites were applied as treatment in preclinical intestinal damage models and GVHD mouse models. Outcomes were assessed by a novel organoid recovery assay in addition to established read-outs. Results: Here, we present expression profiles of metabolites including short-chain fatty acids, DAT, ICA and secondary bile acids. Following ASCT, and especially at the early time-points, metabolite expression declined drastically. We confirmed this trend in our multi-centric cohort of ASCT patients by comparing levels of DAT and ICA sampled at admission to the transplantation ward (Conditioning) versus at clinical diagnosis of GVHD: in patients with GVHD, metabolite levels were drastically reduced. Metabolite stimulation of mouse small intestinal organoids promoted organoid growth and required intact STING signaling. Additionally, organoids showed an increased stemness and resistance to T cell mediated damage. Both healthy donor and GvHD patient derived human colon organoids also responded to DAT and ICA, however the metabolite effect was lost when co-administered with the STING-inhibitor H151. Next, we prophylactically administered metabolites in a major mismatch mouse ASCT model. Metabolite-treated mice showed significantly better outcomes in barrier integrity and organoid based intestinal regeneration assays. Additionally, metabolite treatment was associated with an increased regulatory T cell infiltration. These effects were abrogated in STING-/- recipients, but not in IFNaR-/- recipients. Finally, metabolite treatment was protective in major mismatch GVHD mouse models. Conclusions: We identify that microbial-derived metabolites detected in patients can engage the STING pathway in humans and mice to confer resistance from immune damage. Thus, prophylactic administration of metabolite cocktails or bacterial consortia may reduce occurrence of GVHD in ASCT patients.

TCA and SSRI Antidepressants Exert Selection Pressure for Efflux-Dependent Antibiotic Resistance Mechanisms in Escherichia coli.

Microbial diversity is reduced in the gut microbiota of animals and humans treated with selective serotonin reuptake inhibitors (SSRIs) and tricyclic antidepressants (TCAs). The mechanisms driving the changes in microbial composition, while largely unknown, is critical to understand considering that the gut microbiota plays important roles in drug metabolism and brain function. Using Escherichia coli, we show that the SSRI fluoxetine and the TCA amitriptyline exert strong selection pressure for enhanced efflux activity of the AcrAB-TolC pump, a member of the resistance-nodulation-cell division (RND) superfamily of transporters. Sequencing spontaneous fluoxetine- and amitriptyline-resistant mutants revealed mutations in marR and lon, negative regulators of AcrAB-TolC expression. In line with the broad specificity of AcrAB-TolC pumps these mutants conferred resistance to several classes of antibiotics. We show that the converse also occurs, as spontaneous chloramphenicol-resistant mutants displayed cross-resistance to SSRIs and TCAs. Chemical-genomic screens identified deletions in marR and lon, confirming the results observed for the spontaneous resistant mutants. In addition, deletions in 35 genes with no known role in drug resistance were identified that conferred cross-resistance to antibiotics and several displayed enhanced efflux activities. These results indicate that combinations of specific antidepressants and antibiotics may have important effects when both are used simultaneously or successively as they can impose selection for common mechanisms of resistance. Our work suggests that selection for enhanced efflux activities is an important factor to consider in understanding the microbial diversity changes associated with antidepressant treatments. IMPORTANCE Antidepressants are prescribed broadly for psychiatric conditions to alter neuronal levels of synaptic neurotransmitters such as serotonin and norepinephrine. Two categories of antidepressants are selective serotonin reuptake inhibitors (SSRIs) and tricyclic antidepressants (TCAs); both are among the most prescribed drugs in the United States. While it is well-established that antidepressants inhibit reuptake of neurotransmitters there is evidence that they also impact microbial diversity in the gastrointestinal tract. However, the mechanisms and therefore biological and clinical effects remain obscure. We demonstrate antidepressants may influence microbial diversity through strong selection for mutant bacteria with increased AcrAB-TolC activity, an efflux pump that removes antibiotics from cells. Furthermore, we identify a new group of genes that contribute to cross-resistance between antidepressants and antibiotics, several act by regulating efflux activity, underscoring overlapping mechanisms. Overall, this work provides new insights into bacterial responses to antidepressants important for understanding antidepressant treatment effects.

Species shifts induce soil organic matter priming and changes in microbial communities

Invasion of plant species with functional traits that influences the rhizosphere can have significant effects on soil organic matter (SOM) dynamics if the invasive species stimulates soil microbial communities with, for example, an enhanced supply of labile carbon and oxygen. We evaluated these effects along a Phragmites invasion chronosequence spanning over 40 years. Using a δ13C and δ15N enriched substrate, we separated SOM-derived and substrate-derived carbon (C) and nitrogen (N) mineralization in surface (top 15 cm), shallow (30–45 cm), and deep (65–80 cm) soils collected from established, newly invaded, and native plant communities. We found all soils were susceptible to SOM priming, but priming profiles differed between vegetation communities, being highest at the surface in native assemblage soils, whereas highest at depth under invasive plants. Changes in functional microbial community composition at depth in Phragmites soils, evidenced by an increase in relative fungal laccase abundance, explained the SOM priming in these deep invaded soils. Our results show that invasive Phragmites maintains a microbial community at depth able to degrade SOM faster than that under native vegetation, evidencing that plant species shifts can fundamentally change soil biogeochemistry, altering element cycling and decreasing SOM residence time. Furthermore, our experimental design allowed to quantify real-time SOM-C and SOM-N gross mineralization, resulting in a new model relating C and N mineralization in these wetland soils and providing new insights on how SOM decomposition impacts N availability and cycling across wetland N pools.

Seasonal variations in microbial diversity and metabolite profiles of the gut of sea cucumber (Apostichopus japonicus)

The sea cucumber (Apostichopus japonicus) is the main economic species in China and has a significant role in aquaculture. Gut microbiome composition is closely related to external environments. In this study, we identified the effects of seasonal changes on the composition and main metabolites of symbiotic microorganisms in the intestine of A. japonicus. We used 16S rRNA sequencing to identify the composition of symbiotic microorganisms in different seasons. Intestinal metabolites were determined using liquid chromatography with tandem mass spectrometry, which linked symbiotic microorganisms to intestinal metabolites. Analyzing changes in intestinal microbial composition across different seasons. The results showed that seasonal changes of intestinal microorganisms were significant, A. japonicus were infected by Vibrio easily in summer, Stigmasterol and sitosterol could affect the growth of body wall of A. japonicus. It is vital importance for A. japonicus that the results benefit for the growth, immunity and aquaculture.

Exploring the Impacts of Full-Scale Distribution System Orthophosphate Corrosion Control Implementation on the Microbial Ecology of Hydrologically Connected Urban Streams.

Many cities across the nation are plagued by lead contamination in drinking water. As such, many drinking water utilities have undertaken lead service line (LSL) replacement to prevent further lead contamination. However, given the urgency of lead mitigation, and the socioeconomic challenges associated with LSL replacement, cities have used phosphate-based corrosion inhibitors (i.e., orthophosphate) alongside LSL replacement. While necessary to ensure public health protection from lead contamination, the addition of orthophosphate into an aging and leaking drinking water system may increase the concentration of phosphate leaching into urban streams characterized by century-old failing water infrastructure. Such increases in phosphate availability may cascade into nutrient and microbial community composition shifts. The purpose of this study was to determine how this occurs and to understand whether full-scale distribution system orthophosphate addition impacts the microbial ecology of urban streams. Through monthly collection of water samples from five urban streams before and after orthophosphate addition, significant changes in microbial community composition (16S rRNA amplicon sequencing) and in the relative abundance of typical freshwater taxa were observed. In addition, key microbial phosphorus and nitrogen metabolism genes (e.g., two component regulatory systems) were predicted to change via BugBase. No significant differences in the absolute abundances of total bacteria, Cyanobacteria, and "Candidatus Accumulibacter" were observed. Overall, the findings from this study provide further evidence that urban streams are compromised by unintentional hydrologic connections with drinking water infrastructure. Moreover, our results suggest that infiltration of phosphate-based corrosion inhibitors can impact urban streams and have important, as-yet-overlooked impacts on urban stream microbial communities. IMPORTANCE Elevated lead levels in drinking water supplies are a public health risk. As such, it is imperative for cities to urgently address lead contamination from aging drinking water supplies by way of lead service line replacements and corrosion control methods. However, when applying corrosion control methods, it is also important to consider the chemical and microbiological effects that can occur in natural settings, given that our water infrastructure is aging and more prone to leaks and breaks. Here, we examine the impacts on the microbial ecology of five urban stream systems before and after full-scale distribution system orthophosphate addition. Overall, the results suggest that infiltration of corrosion inhibitors may impact microbial communities; however, future work should be done to ascertain the true impact to protect both public and environmental health.

Uneven response of microbial communities to intense dust deposition across the coastal transition zone off Mauritania

The eastern North Atlantic region receives large Saharan dust deposition inputs, providing nutrients and trace metals to the surface waters. We assessed the effects of intense dust deposition on phytoplankton and bacteria cell abundances, metabolic activity, and community structure, along a surface productivity gradient in the Mauritanian-Senegalese upwelling system. Dust concentrations above 4 mg L-1 were added to triplicate microcosms in four bioassay experiments, each lasting three days, increasing nitrate, phosphate and, to a lesser extent, silicate seawater concentrations. Even though dust deposition enhanced both heterotrophic and photosynthetic activity, bacterial production responded faster and stronger than primary production, especially as oligotrophic conditions increased. Bacterial production rates in oligotrophic waters almost tripled one day after the enrichment. However, such favorable response could not be observed on the total organic carbon production until a lag phase of 2 days and whilst under moderate eutrophic conditions. Dust enrichment benefited the presence of certain planktonic groups over others according to their nutrient requirements. Indicator species analysis revealed that our dust-treated microcosms were consistently characterized by Raphid-pennate diatoms, as well as by Hyphomonas genus of Alphaproteobacteria and several species of Alteromonas Gammaproteobacteria. Yet, changes in microbial community structure and composition were primarily shaped by the starting conditions of each experiment. These findings indicate that increasing dust deposition events and the weakening of the Mauritanian-Senegalese upwelling system under climate change may result in a more heterotrophic system, particularly in oligotrophic waters, reducing its potential to function as an atmospheric carbon sink.

Effect of Resistant Dextrin on Intestinal Gas Homeostasis and Microbiota

Previous studies have shown that a resistant dextrin soluble fibre has prebiotic properties with related health benefits on blood glucose management and satiety. Our aim was to demonstrate the effects of continuous administration of resistant dextrin on intestinal gas production, digestive sensations, and gut microbiota metabolism and composition. Healthy subjects (n = 20) were given resistant dextrin (14 g/d NUTRIOSE®, Roquette Frères, Lestrem, France) for four weeks. Outcomes were measured before, at the beginning, end, and two weeks after administration: anal evacuations of gas during daytime; digestive perception, girth, and gas production in response to a standard meal; sensory and digestive responses to a comfort meal; volume of colonic biomass by magnetic resonance; taxonomy and metabolic functions of fecal microbiota by shotgun sequencing; metabolomics in urine. Dextrin administration produced an initial increase in intestinal gas production and gas-related sensations, followed by a subsequent decrease, which magnified after discontinuation. Dextrin enlarged the volume of colonic biomass, inducing changes in microbial metabolism and composition with an increase in short chain fatty acids-producing species and modulation of bile acids and biotin metabolism. These data indicate that consumption of a soluble fibre induces an adaptative response of gut microbiota towards fermentative pathways with lower gas production.

Intestinal microbial composition changes induced by Lactobacillus plantarum GBL 16, 17 fermented feed and intestinal immune homeostasis regulation in pigs

In this study, Rubus coreanus (R. coreanus) byproducts with high polyphenol content were fermented with R. coreanus-derived lactic acid bacteria (Lactobacillus plantarum GBL 16 and 17). Then the effect of R. coreanus-derived lactic acid bacteria fermented feed (RC-LAB fermented feed) with probiotics (Bacillus subtills, Aspergillus oryzae, Yeast) as a feed additive for pigs on the composition of intestinal microbes and the regulation of intestinal immune homeostasis was investigated. Seventy-two finishing Berkshire pigs were randomly allotted to four different treatment groups and 18 replicates. RC-LAB fermented feed with probiotics increased the genera Lactobacillus, Streptococcus, Mitsuokella, Prevotella, Bacteroides spp., Roseburia spp., and Faecalibacterium prausnitzii, which are beneficial bacteria of the digestive tract of pigs. Also, RC-LAB fermented feed with probiotics decreased the genera Clostridium, Terrisporobacter, Romboutsia, Kandleria, Megasphaera and Escherichia, which are harmful bacteria. In particular, the relative abundance of the genera Lactobacillus and Streptococcus increased by an average of 8.51% and 4.68% in the treatment groups and the classes Clostridia and genera Escherichia decreased by an average of 27.05% and 2.85% in the treatment groups. In mesenteric lymph nodes (MLN) and spleens, the mRNA expression of transcription factors and cytokines in Th1 and Treg cells increased and the mRNA expression of Th2 and Th17 transcription factors and cytokines decreased, indicating a regulatory effect on intestinal immune homeostasis. RC-LAB fermented feed regulates gut immune homeostasis by influencing the composition of beneficial and detrimental microorganisms in the gut and regulating the balance of Th1/Th2 and Th17/Treg cells.

Year-around survey and manipulation experiments reveal differential sensitivities of soil prokaryotic and fungal communities to saltwater intrusion in Florida Everglades wetlands

Global sea-level rise is transforming coastal ecosystems, especially freshwater wetlands, in part due to increased episodic or chronic saltwater exposure, leading to shifts in biogeochemistry, plant- and microbial communities, as well as ecological services. Yet, it is still difficult to predict how soil microbial communities respond to the saltwater exposure because of poorly understood microbial sensitivity within complex wetland soil microbial communities, as well as the high spatial and temporal heterogeneity of wetland soils and saltwater exposure. To address this, we first conducted a two-year survey of microbial community structure and bottom water chemistry in submerged surface soils from 14 wetland sites across the Florida Everglades. We identified ecosystem-specific microbial biomarker taxa primarily associated with variation in salinity. Bacterial, archaeal and fungal community composition differed between freshwater, mangrove, and marine seagrass meadow sites, irrespective of soil type or season. Especially, methanogens, putative denitrifying methanotrophs and sulfate reducers shifted in relative abundance and/or composition between wetland types. Methanogens and putative denitrifying methanotrophs declined in relative abundance from freshwater to marine wetlands, whereas sulfate reducers showed the opposite trend. A four-year experimental simulation of saltwater intrusion in a pristine freshwater site and a previously saltwater-impacted site corroborated the highest sensitivity and relative increase of sulfate reducers, as well as taxon-specific sensitivity of methanogens, in response to continuously pulsing of saltwater treatment. Collectively, these results suggest that besides increased salinity, saltwater-mediated increased sulfate availability leads to displacement of methanogens by sulfate reducers even at low or temporal salt exposure. These changes of microbial composition could affect organic matter degradation pathways in coastal freshwater wetlands exposed to sea-level rise, with potential consequences, such as loss of stored soil organic carbon.

Feed your microbes to deal with stress: a psychobiotic diet impacts microbial stability and perceived stress in a healthy adult population

The impact of diet on the microbiota composition and the role of diet in supporting optimal mental health have received much attention in the last decade. However, whether whole dietary approaches can exert psychobiotic effects is largely understudied. Thus, we investigated the influence of a psychobiotic diet (high in prebiotic and fermented foods) on the microbial profile and function as well as on mental health outcomes in a healthy human population. Forty-five adults were randomized into either a psychobiotic (n = 24) or control (n = 21) diet for 4 weeks. Fecal microbiota composition and function was characterized using shotgun sequencing. Stress, overall health and diet were assessed using validated questionnaires. Metabolic profiling of plasma, urine and fecal samples was performed. Intervention with a psychobiotic diet resulted in reductions of perceived stress (32% in diet vs. 17% in control group), but not between groups. Similarly, biological marker of stress were not affected. Additionally, higher adherence to the diet resulted in stronger decreases in perceived stress. While the dietary intervention elicited only subtle changes in microbial composition and function, significant changes in the level of 40 specific fecal lipids and urinary tryptophan metabolites were observed. Lastly, microbial volatility was linked to greater changes in perceived stress scores in those on the psychobiotic diet. These results highlight that dietary approaches can be used to reduce perceived stress in a human cohort. Using microbiota-targeted diets to positively modulate gut-brain communication holds possibilities for the reduction of stress and stress-associated disorders, but additional research is warranted to investigate underlying mechanisms, including the role of the microbiota.

The Analysis of Transcriptomes and Microorganisms Reveals Differences between the Intestinal Segments of Guinea Pigs

The intestine is a tubular organ with multiple functions such as digestion absorption and immunity, but the functions of each intestinal segments are different. Intestinal regionalization is necessary for normal physiological function, but it also means the research results obtained at specific sites may not be applicable to other intestinal segments. In order to comprehensively describe the functional changes in the intestine, different intestinal segments and their contents (duodenum, jejunum, ileum, cecum, colon, and rectum) of guinea pigs were collected for RNA seq and 16S rRNA seq, respectively. The results showed differential genes of each intestinal segment mainly involve mucosa, digestion, absorption, and immunity. The gene sets related to fat, bill salts, vitamins, aggregates, amino acids, and water absorption were highly expressed in the small intestine, and the gene sets related to metal ions, nucleotides, and SCFAs were highly expressed in the large intestine. In terms of immunity, the CD8+ T, Th1, eosinophils, pDCs, and natural killer (NK) T cells in the small intestine showed higher scores than those in the large intestine, while the pattern-recognition receptor signaling pathway-related genes are highly expressed in the large intestine. In terms of microbial composition, Proteobacteria and Actinobacteria are abundant in the small intestine, while Firmicutes and Spirochaete are abundant in large intestine. The correlation analysis showed a high correlation between intestinal microorganisms and gene modules related to digestion and absorption. In addition, cross-species analysis showed the SCFA metabolism gene expression trends in human and rodent intestine were different. In conclusion, we analyzed the changes in substance transport, immune and microbial composition between different intestinal segments of guinea pigs, and explored the relationship between intestinal transcriptome and microorganisms, our research will provides a reference for subsequent intestinal-related research.

Benthic exometabolites and their ecological significance on threatened Caribbean coral reefs

Benthic organisms are the architectural framework supporting coral reef ecosystems, but their community composition has recently shifted on many reefs. Little is known about the metabolites released from these benthic organisms and how compositional shifts may influence other reef life, including prolific microorganisms. To investigate the metabolite composition of benthic exudates and their ecological significance for reef microbial communities, we harvested exudates from six species of Caribbean benthic organisms including stony corals, octocorals, and an invasive encrusting alga, and subjected these exudates to untargeted and targeted metabolomics approaches using liquid chromatography-mass spectrometry. Incubations with reef seawater microorganisms were conducted to monitor changes in microbial abundances and community composition using 16 S rRNA gene sequencing in relation to exudate source and three specific metabolites. Exudates were enriched in amino acids, nucleosides, vitamins, and indole-based metabolites, showing that benthic organisms contribute labile organic matter to reefs. Furthermore, exudate compositions were species-specific, and riboflavin and pantothenic acid emerged as significant coral-produced metabolites, while caffeine emerged as a significant invasive algal-produced metabolite. Microbial abundances and individual microbial taxa responded differently to exudates from stony corals and octocorals, demonstrating that exudate mixtures released from different coral species select for specific bacteria. In contrast, microbial communities did not respond to individual additions of riboflavin, pantothenic acid, or caffeine. This work indicates that recent shifts in benthic organisms alter exudate composition and likely impact microbial communities on coral reefs.

Increasing adherence to the Mediterranean diet and lifestyle is associated with reduced fecal calprotectin and intra-individual changes in microbial composition of healthy subjects

ABSTRACT The Mediterranean diet (MED) is associated with the modification of gut microbial composition. In this pilot study, we investigate the feasibility of a microbiota-targeted MED-based lifestyle intervention in healthy subjects. MED intervention integrating dietary counseling, a supporting mobile application, and daily physical activity measurement using step trackers was prospectively applied for 4 weeks. Blood and fecal samples were collected at baseline, after the 4-week intervention, and at 6 and 12 months. Blood counts, inflammatory markers, microbial and eukaryotic composition were analyzed. Dietary adherence was assessed using daily questionnaires. All 20 healthy participants (females 65%, median age 37), completed the 4-week intervention. Adherence to MED increased from 15.6 ± 4.1 (baseline) to 23.2 ± 3.6 points (4 weeks), p < .01, reflected by increased dietary fiber and decreased saturated fat intake (both p < .05). MED intervention modestly reduced fecal calprotectin, white blood cell, neutrophil, and lymphocyte counts, within the normal ranges (P < .05). Levels of butyrate producers including Faecalibacterium and Lachnospira were positively correlated with adherence to MED and the number of daily steps. Bacterial composition was associated with plant-based food intake, while fungal composition with animal-based food as well as olive oil and sweets. Increasing adherence to MED correlated with increased absolute abundances of multiple beneficial gut symbionts. Therefore, increasing adherence to MED is associated with reduction of fecal calprotectin and beneficial microbial alterations in healthy subjects. Microbiota targeted lifestyle interventions may be used to modify the intestinal ecosystem with potential implications for microbiome-mediated diseases.

Acute liver injury progression is associated with dynamic enteric eubiosis alteration in mice

Liver health has long been linked to the homeostasis of gut microbiota. Although some studies have shown that alterations in the species and function of gut microbiota contribute to the initiation and development of acute liver injury (ALI), studies investigating the effects of ALI on gut microbial dynamic composition changes are still limited. To observe whether liver damage can alter the composition of gut microbiota dynamically, we established three chemical models (e.g., acetaminophen, carbon tetrachloride, lipopolysaccharide) of ALI. Using these models, multiple time points of liver injury and intestinal microbiome were analyzed through plasma biochemical analysis and 16S rRNA gene sequencing. We assessed α-diversity, Unifrac principal coordinates analysis (PCoA), and linear discriminant analysis effect size (LEfSe) in the injury and control groups. The composition of the gut microbiota underwent dramatic shifts with liver injury and recovery in each model. Additionally, specific microbial abundance was significantly correlated with the level of plasma alanine transaminase and aspartate transaminase. These data provide new evidence that liver dysfunction and restoration is dynamically linked with the changes in the intestinal microbiome.

Oral microbiota in oral cancer patients and healthy individuals: A scoping review

Background: Oral microbiota has been suggested to have a role in the etiopathogenesis of oral cancer; however, the oral microbiota diversity in patients with oral cancer compared to healthy individuals remains unclear. Purpose: This scoping review aimed to provide an overview of the current evidence regarding the oral microbiota composition colonized in oral cancer patients and its comparison with healthy individuals. Reviews: This study was conducted according to the preferred reporting items for systematic reviews and meta-analyses (PRISMA) guidelines. Eligible studies were searched in PubMed, Scopus, Web of Science, and ScienceDirect databases from January 2015 to March 2022. A total of 20 relevant studies were included according to the inclusion and exclusion criteria, including 14 cross-sectional studies and 6 cohort studies. All studies have identified various oral bacteria, but only one study has detected viruses and parasites diversity. A variety of oral microbiota found were 6 phyla of bacteria, 6 phyla of viruses, 7 phyla of fungi, and 7 phyla of parasitic. Seventeen studies proved that oral microbiota compositions were statistically significant differences compared to healthy controls, but not in 3 studies. Conclusion: The majority of studies showed various oral bacteria in oral cancer patients which were statistically significant difference compared to healthy controls. This study indicates the need for more research to evaluate viruses and parasites composition and diversity in oral cancer patients. Moreover, future research should focus to clarify whether the changes of oral microbial composition as a community may play a critical role in the etiopathogenesis of oral cancer.

Effects of Saccharomyces cerevisiae hydrolysate on growth performance, immunity function, and intestinal health in broilers

The current study was performed to explore the effects of dietary supplementation of Saccharomyces cerevisiae hydrolysate (SCH) on growth performance, immune function, and intestinal health in broiler chicken. A total of 300 Ross 308 male broilers (1-day-old) were randomly assigned to 2 dietary treatments including a basal diet (control group), and a basal diet supplemented with SCH feed additive (500 mg/kg in starter and grower phase, and 250 mg/kg in finisher phase). Each treatment had 6 replicates with 25 birds each. The results showed that the addition of SCH promoted growth during d 15 to 28 (P < 0.05). Although the addition of SCH had no significant effect on the intestinal relative indexes, it significantly increased the jejunum villus height (VH) and the ratio of villus height to crypt depth (VCR) of jejunum, and decreased the crypt depth (CD) of ileum (P < 0.05). Furthermore, SCH addition significantly downregulated the mRNA expression of immunomodulatory genes (TNF-α, IL-1β, and IL-6), and upregulated the tight junction genes (ZO-1 and Claudin-1) (P < 0.05). High throughput sequencing analysis of bacterial 16S rRNA revealed that dietary SCH supplementation altered cecum microbiota. Alpha diversity analysis showed that a higher bacterial richness in cecum of broilers fed with SCH. The composition of cecum microbiota regulated by SCH addition was characterized by an increased abundance of Firmicutes and a reduced abundance of Bacteroidetes. At the genus level, dietary SCH resulted in a decrease of Bacteroides and an increase of short-chain fatty acids (SCFA) -producing bacteria including Lactobacillus and Faecalibacterium. Taken together, dietary SCH supplementation can stimulate the growth of broilers by regulating the intestinal immunity and barrier function, and improving the intestinal morphology, which may be related to the enhancement of bacterial diversity and the changes of intestinal microbial composition.