Shifts In Microbial Composition Research Articles

Metagenomics analysis of mice gut microbiome to unravel the role of metal exposure and piperine.

The gut and intestinal microbiota consists of trillions of microorganisms inhabiting the human gastrointestinal tract. It plays a crucial role in human health leading to understanding the dynamic crosstalk of host-microbe interaction in the gut and has become necessary for the detection, prevention, or therapy of diseases. Gut microbiota deviations are linked with many diseases, suggesting that various pathways involved in immunity, energy, lipid, and glucose metabolism are affected. Further, it is also altered by external insults such as metal toxicity, antibiotics and pesticides. Heavy metals like arsenic, mercury, cadmium and chromium are some of the well-studied classes of environmental pollutants. Mouse models have become the model of choice for most studies in this emerging field, as they allow perturbations in the gut microbiota to be studied in a controlled experimental setup. Here, we investigate the composition and diversity of intestinal microbes utilizing cecal samples from different intervention groups: arsenic exposure (As(III)), arsenic and piperine co-administration (As +Pp), piperine per se and control group. We obtained DNA samples from these groups and performed PCR amplification and sequencing of the 16S V3-V4 region. The findings showed shift in microbial composition and abundance among different intervention groups, revealing taxa that may contribute to the microbial diversity.

Inflammatory Bowel Disease and Gut Microbiota Dysbiosis: Current understanding and Future Direction

Inflammatory Bowel Disease (IBD) represents a group of chronic, relapsing inflammatory disorders primarily affecting the gastrointestinal tract. The pathogenesis of IBD is multifaceted, involving genetic predisposition, environmental triggers, and dysregulation of the immune response. Recent research has illuminated the pivotal role of gut microbiota dysbiosis in the development and perpetuation of IBD. The human gut harbors a complex and dynamic ecosystem of microorganisms that profoundly influences host health and disease. Alterations in the composition, diversity, and function of the gut microbiota, termed dysbiosis, have been consistently linked to IBD. Shifts in microbial composition, reduction in microbial diversity, and imbalances in beneficial versus pathogenic microorganisms characterize the dysbiotic state associated with IBD.The intricate interplay between the host immune system and the gut microbiota is a key determinant in IBD pathogenesis. Dysbiosis triggers aberrant immune responses, leading to chronic mucosal inflammation and tissue damage. Furthermore, dysbiotic alterations disrupt essential microbial-derived metabolites and signaling molecules crucial for gut homeostasis, further exacerbating the disease. Advancements in high-throughput sequencing technologies and metagenomic analysis have enabled comprehensive characterization of microbial communities in IBD, uncovering microbial signatures and functional pathways associated with disease phenotypes and treatment responses. Therapeutic interventions targeting the gut microbiota, such as probiotics, prebiotics, fecal microbiota transplantation, and microbial-based therapies, have shown promise in preclinical and clinical studies for modulating dysbiosis and ameliorating IBD symptoms.
 Keywords: Inflammatory Bowel Disease, Dysbiosis, Fecal microbiota, Probiotics

Anodic biodegradation of phenol in a microbial desalination cell through microbial composition shift for energy recovery and water desalination

This study assessed the performance of a three-chamber microbial desalination cell (MDC) for simultaneous electricity generation, phenol biodegradation, and salt removal from water. The MDC operated with anaerobic sludge in the anode chamber at varying phenol concentrations in the range of 100–1000 mg L−1 and bio-cathode with sodium acetate as the catholyte. The highest power density (7.5 W m−3), desalination efficiency (66.9 %), and current efficiency (75.5 %) were obtained at optimal phenol concentration of 700 mg L−1. Non-electroactive bacteria dominated the anode microbial community through high-throughput sequencing analysis. The population of electroactive bacteria decreased, including Geobacter and Rhodopseudomonas from 9.8 % and 7.8 % to 0.9 % and 0.6 %, respectively, due to phenol toxicity, Cl− migration, and pH fluctuations. Meanwhile, other genera, such as Chryseobacterium (from 0.8 % to 4.5 %) and Clostridium (from 1.4 % to 2.2 %), were observed to thrive in the saline and acidic phenolic environment of the anode chamber.

Alterations in intestinal microbiota and enzyme activities under cold-humid stress: implications for diarrhea in cold-dampness trapped spleen syndrome.

Cold and humid environments alter the intestinal microbiota, and the role of the intestinal microbiota in the development of diarrhea associated with cold-dampness trapped spleen syndrome in Chinese medicine is unclear. The 30 mice were randomly divided into normal and model groups, with the model group being exposed to cold and humid environmental stresses for 7 days. Then, mouse intestinal contents were collected and analyzed their intestinal microbiota and digestive enzymes. Our findings revealed significant increases in sucrase and lactase activities, as well as microbial activity, in the model group (p < 0.05). β-diversity analysis highlighted distinct intestinal microbiota compositions between the two groups. Specifically, the experimental group showed a unique dominance of the genera and strains Clostridium sensu stricto 1 and Clostridium sp. ND2. LEfSe analysis identified Helicobacter, Roseburia, and Eubacterium plexicaudatum ASF492 as differentially abundant species in them model group. Network analysis demonstrated that rare bacterial species mostly governed the microbial interactions, exhibiting increased mutual promotion. On the other hand, abundant species like Lactobacillus johnsonii and Lactobacillus reuteri showed mutual inhibitory relationships. In summary, exposure to cold and humid conditions led to increased intestinal enzyme activities and a shift in microbial composition, favoring the growth of rare bacterial species. These changes suggest that rare bacteria in the intestinal microbiota play a critical role in the pathology of diarrhea associated with cold-dampness trapped spleen syndrome, revealing unique survival strategies among bacterial populations under stressful conditions.

Chronic supplementation of a multi-ingredient herbal supplement increases speed of cognitive task performance alongside changes in the urinary metabolism of dopamine and the gut microbiome in cognitively intact older adults experiencing subjective memory decline: a randomized, placebo controlled, parallel groups investigation.

The effects of herbs on brain function are often investigated in isolation, yet herbal preparations are often complex combinations of phytochemicals, designed to target widespread mechanisms. To assess the effects of chronic, 12 weeks, supplementation of a multi-ingredient herbal supplement (containing Bacopa monnieri, Gotu kola leaf, Turmeric whole powder, Reishi full spectrum, Rosemary, Cardamom, Holy Basil, Turmeric Wholistic™ extract, Green Tea & Seagreens) on cognitive function in older adults with subjective memory decline. Secondly, to investigate whether effects are underpinned by shifts in microbial composition and/or metabolism of the herbs. Male and female participants (N = 128) aged between 55-75 years completed lab-based cognitive assessments, and provided stool and urine samples, at baseline and then following 90 days of multi-ingredient herb, or placebo, supplementation. Deficits in memory were observed in response to 90 days of multi-ingredient herbal supplement supplementation but the positive effects were all focused on speed of cognitive task performance, with an additional improvement in the false alarm rate on the rapid visual information processing task. These improvements coincided with an increased presence of tyrosine in the urinary metabolome and this may implicate the role of dopamine in these processing and/or motor speed increases. Finally, multi-ingredient herbal supplementation significantly reduced levels of 3 bacterial species in the gut microbiome and one of these, Sutterella, coincides with lower levels of constipation reported in the multi-ingredient herbal supplement condition. A multi-ingredient herbal supplement increases speed of cognitive task performance and increased metabolism of tyrosine suggests that this is modulated by increased dopaminergic activity. Reduced levels of Sutterella in the gut is associated with improved bowel movements of participants. Interpretation of the negative effects on memory are, however, stymied by an unequal randomization of participants into treatment groups pre- and post-COVID 19.Clinical trial registration: identifier NCT05504668.

Isoxanthohumol improves obesity and glucose metabolism via inhibiting intestinal lipid absorption with a bloom of Akkermansia muciniphila in mice

ObjectivePolyphenols have health-promoting effects, such as improving insulin resistance. Isoxanthohumol (IX), a prenylated flavonoid found in beer hops, has been suggested to reduce obesity and insulin resistance; however, the mechanism remains unknown. MethodsHigh-fat diet-fed mice were administered IX. We analyzed glucose metabolism, gene expression profiles and histology of liver, epididymal adipose tissue and colon. Lipase activity, fecal lipid profiles and plasma metabolomic analysis were assessed. Fecal 16s rRNA sequencing was obtained and selected bacterial species were used for in vitro studies. Fecal microbiota transplantation and monocolonization were conducted to antibiotic-treated or germ-free (GF) mice. ResultsThe administration of IX lowered weight gain, decreased steatohepatitis and improved glucose metabolism. Mechanistically, IX inhibited pancreatic lipase activity and lipid absorption by decreasing the expression of the fatty acid transporter CD36 in the small intestine, which was confirmed by increased lipid excretion in feces. IX administration increased markers of intestinal barrier function, including thickening the mucin layer and increasing caludin-1, a tight-junction related protein in the colon. In contrast, the effects of IX were nullified by antibiotics. As revealed using 16S rRNA sequencing, the microbial community structure changed with a significant increase in the abundance of Akkermansia muciniphila in the IX-treated group. An anaerobic chamber study showed that IX selectively promoted the growth of A. muciniphila while exhibiting antimicrobial activity against some Bacteroides and Clostridium species. To further explore the direct effect of A. muciniphila on lipid and glucose metabolism, we monocolonized either A. muciniphila or Bacteroides thetaiotaomicron to GF mice. A. muciniphila monocolonization decreased CD36 expression in the jejunum and improved glucose metabolism, with decreased levels of multiple classes of fatty acids determined using plasma metabolomic analysis. ConclusionsOur study demonstrated that IX prevents obesity and enhances glucose metabolism by inhibiting dietary fat absorption. This mechanism is linked to suppressing pancreatic lipase activity and shifts in microbial composition, notably an increase in A. muciniphila. These highlight new treatment strategies for preventing metabolic syndrome by boosting the gut microbiota with food components.

Single-strain behavior predicts responses to environmental pH and osmolality in the gut microbiota.

Changes to gut environmental factors such as pH and osmolality due to disease or drugs correlate with major shifts in microbiome composition; however, we currently cannot predict which species can tolerate such changes or how the community will be affected. Here, we assessed the growth of 92 representative human gut bacterial strains spanning 28 families across multiple pH values and osmolalities in vitro. The ability to grow in extreme pH or osmolality conditions correlated with the availability of known stress response genes in many cases, but not all, indicating that novel pathways may participate in protecting against acid or osmotic stresses. Machine learning analysis uncovered genes or subsystems that are predictive of differential tolerance in either acid or osmotic stress. For osmotic stress, we corroborated the increased abundance of these genes in vivo during osmotic perturbation. The growth of specific taxa in limiting conditions in isolation in vitro correlated with survival in complex communities in vitro and in an in vivo mouse model of diet-induced intestinal acidification. Our data show that in vitro stress tolerance results are generalizable and that physical parameters may supersede interspecies interactions in determining the relative abundance of community members. This study provides insight into the ability of the microbiota to respond to common perturbations that may be encountered in the gut and provides a list of genes that correlate with increased ability to survive in these conditions.IMPORTANCETo achieve greater predictability in microbiota studies, it is crucial to consider physical environmental factors such as pH and particle concentration, as they play a pivotal role in influencing bacterial function and survival. For example, pH is significantly altered in various diseases, including cancers, inflammatory bowel disease, as well in the case of over-the-counter drug use. Additionally, conditions like malabsorption can affect particle concentration. In our study, we investigate how changes in environmental pH and osmolality can serve as predictive indicators of bacterial growth and abundance. Our research provides a comprehensive resource for anticipating shifts in microbial composition and gene abundance during complex perturbations. Moreover, our findings underscore the significance of the physical environment as a major driver of bacterial composition. Finally, this work emphasizes the necessity of incorporating physical measurements into animal and clinical studies to better understand the factors influencing shifts in microbiota abundance.

Limnospira indica PCC8005 and Lacticaseibacillus rhamnosus GG Mixed Dietary Combination Reduces Pelvic Irradiation-Induced Symptoms in Mice

Throughout their cancer treatments, around half of all patients will undergo irradiation that is accompanied by several side effects reducing their quality of life and leading to the interruption or extension of their treatment course. Pelvic irradiation leads to the triggering of mucositis and dysbiosis, further impairing the daily life of the patients. In this work, we address the ability of Limnospira indica strain PCC 8005 and Lacticaseibacillus rhamnosus GG ATCC 53103 in alleviating the above-mentioned side effects triggered by the local pelvic irradiation of 12 Gy in a mouse model. We found that the combinatorial administration of these food supplements was able to confer partial tight junction protection while the bacterial translocation towards the mesenteric lymph nodes was found to be identical between the saline sham-irradiated and supplemented irradiated group. Furthermore, the supplemented group did not present a significant shift in microbial composition following pelvic irradiation, indicating that the bacterial formulation was able to mitigate the dysbiosis induced by the latter treatment, as observed in the saline irradiated group. These very promising results will be further completed by investigating the mode of action and/or active molecules mediating the beneficial effects of both L. indica PCC 8005 and L. rhamnosus GG.

The Age of Absorptive Roots Impacts Root-Adjacent Microbial Composition in Grapevines

In grapevine, metabolic activity of absorptive roots changes rapidly as roots age but it is unclear whether nearby microbial assemblages shift as well. Here, we investigated whether first-order root age affects bacterial and fungal variation adjacent to the root surface, and whether root age should be integrated into future studies on root functional traits and associated microbes. We hypothesized that microbial diversity and composition would differ between young (≤11 days old) and old (11.5 to 40 days old) first-order roots due to expected differences in metabolism over the root lifespan (i.e., higher metabolism in young roots). Overall, we found that microbial composition was distinct between young and old absorptive roots, with stronger evidence at the phylum and amplicon sequence variant (ASV) taxonomic levels for fungi ( P = 0.003 and P = 0.038, respectively) than bacteria ( P = 0.082 and P = 0.129, respectively). Furthermore, we identified differentially abundant fungal and bacterial ASVs in young and old roots that related to expected differences in root function, including instances of microbes previously described as copiotrophs more abundant adjacent to young roots and microbes described as oligotrophs and saprotrophs more abundant adjacent to old roots. In contrast to the distinct shifts in microbial composition, there was little evidence of shifts in α diversity (i.e., observed ASVs and Shannon diversity) between young and old roots. Our study suggests that future work on the impacts of root functional traits on localized microbial composition may improve results interpretation and reduce some variation by accounting for root age at sampling.

Climate Warming Does Not Override Eutrophication, but Facilitates Nutrient Release from Sediment and Motivates Eutrophic Process.

The climate is changing. The average temperature in Wuhan, China, is forecast to increase by at least 4.5 °C over the next century. Shallow lakes are important components of the biosphere, but they are sensitive to climate change and nutrient pollution. We hypothesized that nutrient concentration is the key determinant of nutrient fluxes at the water-sediment interface, and that increased temperature increases nutrient movement to the water column because warming stimulates shifts in microbial composition and function. Here, twenty-four mesocosms, mimicking shallow lake ecosystems, were used to study the effects of warming by 4.5 °C above ambient temperature at two levels of nutrients relevant to current degrees of lake eutrophication levels. This study lasted for 7 months (April-October) under conditions of near-natural light. Intact sediments from two different trophic lakes (hypertrophic and mesotrophic) were used, separately. Environmental factors and bacterial community compositions of overlying water and sediment were measured at monthly intervals (including nutrient fluxes, chlorophyll a [chl a], water conductivity, pH, sediment characteristics, and sediment-water et al.). In low nutrient treatment, warming significantly increased chl a in the overlying waters and bottom water conductivity, it also drives a shift in microbial functional composition towards more conducive sediment carbon and nitrogen emissions. In addition, summer warming significantly accelerates the release of inorganic nutrients from the sediment, to which microorganisms make an important contribution. In high nutrient treatment, by contrast, the chl a was significantly decreased by warming, and the nutrient fluxes of sediment were significantly enhanced, warming had considerably smaller effects on benthic nutrient fluxes. Our results suggest that the process of eutrophication could be significantly accelerated in current projections of global warming, especially in shallow unstratified clear-water lakes dominated by macrophytes.

Fluorescence activated cell sorting and fermentation analysis to study rumen microbiome responses to administered live microbials and yeast cell wall derived prebiotics.

Rapid dietary changes, such as switching from high-forage to high-grain diets, can modify the rumen microbiome and initiate gastrointestinal distress, such as bloating. In such cases, feed additives, including prebiotics and live microbials, can be used to mitigate these negative consequences. Bio-Mos® is a carbohydrate-based prebiotic derived from yeast cells that is reported to increase livestock performance. Here, the responses of rumen bacterial cells to Bio-Mos® were quantified, sorted by flow cytometry using fluorescently-labeled yeast mannan, and taxonomically characterized using fluorescence in situ hybridization and 16S rRNA sequencing. Further, to evaluate the effects of bovine-adapted Bacteroides thetaiotaomicron administration as a live microbial with and without Bio-Mos® supplementation, we analyzed microbial fermentation products, changes to carbohydrate profiles, and shifts in microbial composition of an in vitro rumen community. Bio-Mos® was shown to be an effective prebiotic that significantly altered microbial diversity, composition, and fermentation; while addition of B. thetaiotaomicron had no effect on community composition and resulted in fewer significant changes to microbial fermentation. When combined with Bio-Mos®, there were notable, although not significant, changes to major bacterial taxa, along with increased significant changes in fermentation end products. These data suggest a synergistic effect is elicited by combining Bio-Mos® and B. thetaiotaomicron. This protocol provides a new in vitro methodology that could be extended to evaluate prebiotics and probiotics in more complex artificial rumen systems and live animals.

Skin microbiota signature distinguishes IBD patients and reflects skin adverse events during anti-TNF therapy.

Crohn's disease (CD) and ulcerative colitis (UC) are two forms of inflammatory bowel disease (IBD), where the role of gut but not skin dysbiosis is well recognized. Inhibitors of TNF have been successful in IBD treatment, but up to a quarter of patients suffer from unpredictable skin adverse events (SkAE). For this purpose, we analyzed temporal dynamics of skin microbiota and serum markers of inflammation and epithelial barrier integrity during anti-TNF therapy and SkAE manifestation in IBD patients. We observed that the skin microbiota signature of IBD patients differs markedly from healthy subjects. In particular, the skin microbiota of CD patients differs significantly from that of UC patients and healthy subjects, mainly in the retroauricular crease. In addition, we showed that anti-TNF-related SkAE are associated with specific shifts in skin microbiota profile and with a decrease in serum levels of L-FABP and I-FABP in IBD patients. For the first time, we showed that shifts in microbial composition in IBD patients are not limited to the gut and that skin microbiota and serum markers of the epithelium barrier may be suitable markers of SkAE during anti-TNF therapy.

Antagonistic interaction between two key endodontic pathogens Enterococcus faecalis and Fusobacterium nucleatum

ABSTRACT Background Endodontic infections are known to be caused by pathogenic bacteria. Numerous previous studies found that both Fusobacterium nucleatum and Enterococcus faecalis are associated with endodontic infections, with Fusobacterium nucleatum more abundant in primary infection while Enterococcus faecalis more abundant in secondary infection. Little is known about the potential interactions between different endodontic pathogens. Objective This study aims to investigate the potential interaction between F. nucleatum and E. faecalis via phenotypical and genetic approaches. Methods Physical and physiological interactions of F. nucleatum and E. faecalis under both planktonic and biofilm conditions were measured with co-aggregation and competition assays. The mechanisms behind these interactions were revealed with genetic screening and biochemical measurements. Results E. faecalis was found to physically bind to F. nucleatum under both in vitro planktonic and biofilm conditions, and this interaction requires F. nucleatum fap2, a galactose-inhibitable adhesin-encoding gene. Under our experimental conditions, E. faecalis exhibits a strong killing ability against F. nucleatum by generating an acidic micro-environment and producing hydrogen peroxide (H2O2). Finally, the binding and killing capacities of E. faecalis were found to be necessary to invade and dominate a pre-established in vitro F. nucleatum biofilm. Conclusions This study reveals multifaceted mechanisms underlying the physical binding and antagonistic interaction between F. nucleatum and E. faecalis, which could play a potential role in the shift of microbial composition in primary and secondary endodontic infections.

Progressive microbial adaptation of the bovine rumen and hindgut in response to a step-wise increase in dietary starch and the influence of phytogenic supplementation.

Microbial composition and activity in the gastrointestinal tract (GIT) of cattle has important implications for animal health and welfare, driving the focus of research toward ways to modify their function and abundance. However, our understanding of microbial adaption to nutritional changes remains limited. The aim of this study was to examine the progressive mechanisms of adaptation in the rumen and hindgut of cattle receiving increasing amounts of starch with or without dietary supplementation of a blended phytogenic feed additive (PFA; containing menthol, thymol and eugenol). We used 16S rRNA gene amplicon sequencing to assess the microbial composition and predicted metabolic pathways in ruminal solid and liquid digesta, and feces. Furthermore, we employed targeted liquid chromatography-mass spectrometry methods to evaluate rumen fluid metabolites. Results indicated a rapid microbial adaptation to diet change, starting on the second day of starch feeding for the particle associated rumen liquid (PARL) microbes. Solid rumen digesta- and feces-associated microbes started changing from the following day. The PARL niche was the most responsive to dietary changes, with the highest number of taxa and predicted pathways affected by the increase in starch intake, as well as by the phytogenic supplementation. Despite the differences in the microbial composition and metabolic potential of the different GIT niches, all showed similar changes toward carbohydrate metabolism. Metabolite measurement confirmed the high prevalence of glucose and volatile fatty acids (VFAs) in the rumen due to the increased substrate availability and metabolic activity of the microbiota. Families Prevotellaceae, Ruminococcaceae and Lachnospiraceae were found to be positively correlated with carbohydrate metabolism, with the latter two showing wide-ranging predicted metabolic capabilities. Phytogenic supplementation affected low abundant taxa and demonstrated the potential to prevent unwanted implications of feeding high-concentrate diet, such as reduction of microbial diversity. The inclusion of 50% concentrate in the diet caused a major shift in microbial composition and activity in the GIT of cattle. This study demonstrated the ability of microorganisms in various GIT niches to adjust differentially, yet rapidly, to changing dietary conditions, and revealed the potential beneficial effects of supplementation with a PFA during dietary adaptation.

5-α reductase inhibition by Epilobioum fleischeri extract modulates facial microbiota structure.

BackgroundFacial skin is a particularly complex environment made of different skin types such as sebaceous (forehead) and dry (cheeks). The skin microbiota composition on different facial sites has not yet been addressed.MethodsWe conducted a 4‐week‐long, single‐centre, randomized and placebo‐controlled clinical study involving 23 Caucasian females. We assessed both bacterial composition on five different facial areas and the microbiome modulatory effects resulting from the topical application of a plant extract (Epilobium fleischeri). Skin microbiome samples were collected before and after 4 weeks of product application. Microbiota profiling was performed via 16S rRNA gene sequencing, and relative abundance data were used to calculate differentials via a multinomial regression model.ResultsVia ‘reference frames’, we observed shifts in microbial composition after 4 weeks of twice‐daily product application and identify certain microbiota species, which were positively associated with the application of the product containing the Epilobium fleischeri extract. Staphylococcus hominis, Staphylococcus epidermidis, and Micrococcus yunnanensis appeared to be significantly enriched in the final microbiota composition of the active treatment group.ConclusionFacial skin was found to be colonized by an heterogenous microbiota, and the Epilobium fleischeri extract had a modulatory effect on commensal bacteria on the different facial sites.

Mitochondrial complex I dysfunction alters the balance of soluble and membrane-bound TNF during chronic experimental colitis

Inflammatory bowel disease (IBD) is a complex, chronic, relapsing and heterogeneous disease induced by environmental, genomic, microbial and immunological factors. MCJ is a mitochondrial protein that regulates the metabolic status of macrophages and their response to translocated bacteria. Previously, an acute murine model of DSS-induced colitis showed increased disease severity due to MCJ deficiency. Unexpectedly, we now show that MCJ-deficient mice have augmented tumor necrosis factor α converting enzyme (TACE) activity in the context of chronic inflammation. This adaptative change likely affects the balance between soluble and transmembrane TNF and supports the association of the soluble form and a milder phenotype. Interestingly, the general shifts in microbial composition previously observed during acute inflammation were absent in the chronic model of inflammation in MCJ-deficient mice. However, the lack of the mitochondrial protein resulted in increased alpha diversity and the reduction in critical microbial members associated with inflammation, such as Ruminococcus gnavus, which could be associated with TACE activity. These results provide evidence of the dynamic metabolic adaptation of the colon tissue to chronic inflammatory changes mediated by the control of mitochondrial function.

Relandscaping the Gut Microbiota with a Whole Food: Dose-Response Effects to Common Bean.

Underconsumption of dietary fiber and the milieu of chemicals with which it is associated is a health concern linked to the increasing global burden of chronic diseases. The benefits of fiber are partially attributed to modulation of the gut microbiota, whose composition and function depend on the amount and quality of microbiota-accessible substrates in the diet. However, not all types of fiber are equally accessible to the gut microbiota. Phaseolus vulgaris L., or common bean, is a food type rich in fiber as well as other prebiotics posing a great potential to positively impact diet-microbiota-host interactions. To elucidate the magnitude of bean’s effects on the gut microbiota, increasing doses of common bean were administered in macronutrient-matched diet formulations. The microbial communities in the ceca of female and male mice were evaluated via 16S rRNA gene sequencing. As the bean dose increased, the Bacillota:Bacteroidota ratio (formerly referred to as the Firmicutes:Bacteroidetes ratio) was reduced and α-diversity decreased, whereas the community composition was distinctly different between the diet groups according to β-diversity. These effects were more pronounced in female mice compared to male mice. Compositional analyses identified a dose-responsive bean-induced shift in microbial composition. With an increasing bean dose, Rikenellaceae, Bacteroides, and RF39, which are associated with health benefits, were enhanced. More taxa, however, were suppressed, among which were Allobaculum, Oscillospira, Dorea, and Ruminococcus, which are predominantly associated with chronic disease risk. Investigation of the origins of the dose dependent and biological sex differences in response to common bean consumption may provide insights into bean-gut microbiota-host interactions important to developing food-based precision approaches to chronic disease prevention and control.

Effect of high-fluoride dentifrice on root dentine and bacterial composition in a multispecies biofilm model

The present study evaluated the effect of high-fluoride dentifrice on dentine demineralization and bacterial composition in a multispecies biofilm model in vitro. A seven-organism bacterial consortium was grown on bovine dentine discs in a high-throughput active attachment model. The biofilms were submitted twice per day to the following dentifrices treatments: 5,000 ppm F, 1,100 ppm F, with placebo as a negative control. After 5 days of biofilm growth, dentine samples were assessed by transversal microradiography, the biofilm was collected for bacterial counts and the pH of the media was determined. Lower integrated mineral loss values were observed when 5,000 ppm F-treatment was used compared to the other treatments. Overall microbiological counts decreased with increasing F-concentration as well the pH of the media throughout the experiment. The 5,000 ppm F-treatment caused a shift in microbial composition and reduced dentine demineralization in the in-vitro experimental model.

A Pilot Study Exploring the Association of Entacapone, Gut Microbiota, and the Subsequent Side Effects in Patients With Parkinson's Disease.

Background and AimsEntacapone, one of the most common drugs distributed among patients with Parkinson’s disease, is a peripherally acting catechol-O-methyltransferase (COMT) inhibitor that is used in addition to levodopa to control symptoms. However, there have been negative effects reported against entacapone, namely, gastrointestinal (GI) problems and drowsiness. In this pilot study, we aim to examine the hypothesis that the discomfort induced by entacapone might be originated from the shift of microbial composition by adjusting the effect of levodopa.MethodsThe population in this pilot study consisted of 13 PD patients treated with levodopa only and 11 with both levodopa and entacapone. The 16S rRNA gene sequence data were processed, aligned, and categorized using the DADA2. Alpha diversity indices for Observed, Chao1, Shannon, and Simpson metrics were calculated with Phyloseq 1.32.0. Dissimilarities were calculated using unweighted unique fraction metrics (Unifrac), weighted Unifrac, and Canberra distance. Functional differences were calculated by PICRUSt2 based on the KEGG database.ResultsResults of 16S rRNA sequencing analysis showed that while entacapone did not influence the species richness, the composition of the microbial community shifted considerably. Relative abundances of bacteria related to constipation and other GI disorders also altered significantly. Functional enrichment analysis revealed changes in the metabolic activity of alanine, aspartate, and glutamate. These amino acids are related to common side effects of entacapone such as auditory hallucinations, fatigue, and nightmare.ConclusionOur findings provide testable hypothesis on the cause of unpleasant side effects of entacapone, which in the long run could possibly be reduced through gut microbiota manipulation.

An optimized approach for processing of frozen lung and lavage samples for microbiome studies.

The respiratory tract has a resident microbiome with low biomass and limited diversity. This results in difficulties with sample preparation for sequencing due to uneven bacteria-to-host DNA ratio, especially for small tissue samples such as mouse lungs. We compared effectiveness of current procedures used for DNA extraction in microbiome studies. Bronchoalveolar lavage fluid (BALF) and lung tissue samples were collected to test different forms of sample pre-treatment and extraction methods to increase bacterial DNA yield and optimize library preparation. DNA extraction using a pre-treatment method of mechanical lysis (lung tissue) and one-step centrifugation (BALF) increased DNA yield and bacterial content of samples. In contrast, a significant increase of environmental contamination was detected after phenol chloroform isoamyl alcohol (PCI) extraction and nested PCR. While PCI has been a standard procedure used in microbiome studies, our data suggests that it is not efficient for DNA extraction of frozen low biomass samples. Finally, a DNA Enrichment kit was tested and found to improve the 16S copy number of lung tissue with a minor shift in microbial composition. Overall, we present a standardized method to provide high yielding DNA and improve sequencing coverage of low microbial biomass frozen samples with minimal contamination.