Relative Abundance Of Specific Taxa Research Articles

Clinical relevance of lung microbiota composition in critically ill children with acute lower respiratory tract infections: insights from a retrospective analysis of metagenomic sequencing.

Acute lower respiratory tract infections (ALRIs) is a leading cause of child mortality worldwide. Metagenomic next-generation sequencing (mNGS) identifies ALRIs pathogens and explores the lung microbiota's role in disease severity and clinical outcomes. This study examines the association between lung microbiota and ALRIs outcomes in children, exploring its potential as a prognostic biomarker. We retrospectively analyzed mNGS data from the bronchoalveolar lavage fluid (BALF) of 83 pediatric ALRIs patients from 2019 to 2023. Microbial diversity and relative abundances of specific taxa were compared between survivor and non-survivor groups, as well as between varying severity levels. LEfSe was employed to identify key biomarkers related to survival and disease severity. Among the 83 patients, 68 survived and 15 died. Patients were also divided into a low severity group (n = 38) and a moderate-to-very-high severity group (n = 45) according to mPIRO score at admission. Significant differences in beta diversity were observed between the survival groups and across different severity levels. Prevotella, Haemophilus and Veillonella exhibited higher abundances in both the survivor and low severity groups, suggesting their potential as predictors of better outcomes. Conversely, Enterococcus and Acinetobacter baumannii were more prevalent in the non-survivor and moderate-to-very-high severity groups. Additionally, Streptococcus pneumoniae and Streptococcus mitis showed increased abundances in survivors. LEfSe further revealed that these microorganisms may predict outcomes and severity in ALRIs. Our findings underscore the complex relationship between lung microbiota and ALRIs, with specific microbial profiles associated with disease severity and clinical outcomes. This underscores the need for further research to explore and validate its prognostic predictive capacity. Not applicable.

Third generation sequencing analysis detects significant differences in duodenal microbiome composition between functional dyspepsia patients and control subjects.

Functional dyspepsia (FD) is a multifactorial disorder as its development may be based on several different pathophysiological mechanisms. Interaction of gut microbiome with the host has been proposed as a potential mechanism involved in the disease's pathogenesis. We aimed to characterize microbiome profiling on duodenal luminal content (DLC) of FD patients and compare it to that of controls (CG) and patients with irritable bowel syndrome (IBS). Outpatients fulfilling Rome IV criteria for FD, IBS, and control group (CG) underwent upper gastrointestinal endoscopy and 2 cc of duodenal aspirate (3rd - 4th part) was aspirated in sterile traps. Duodenal microbiome was assessed after DNA extraction and 16S gene-based sequencing on Oxford Nanopore MinION followed by EPI2ME analysis (ONT/Metrich-ore Ltd). Bioanalysis of the microbiome (alpha-, beta-diversity, comparisons of relative abundances for all taxonomic ranks) was implemented in Python. Multiple group means comparisons were performed with one-way Analysis of Variance (ANOVA) and Kruskal-Wallis test with Tuckey's and Dunn's post hoc tests respectively, in case of significance (P-value <0.05). 20 subjects with FD (8 females; age 49.9 ± 13.5 yrs.), 20 with IBS (14 females; age 57.6 ± 14.8 yrs.) and 10 CG (6 females; age 49.2 ± 13.8 yrs.) had their DLC analyzed. The α-diversity index of subjects with FD was significantly lower compared to controls (Shannon's index, p = 0.0218) and similar to that of patients with IBS. Principal Coordinate Analysis (PCoA) generated from species relative abundances (beta-diversity) showed no difference in the DLC profile of subjects with FD and IBS when compared to controls (p = 0.513). Compared to controls, the relative abundance (RA) of Chloroflexota phylum was lower in subjects with FD (p = 0.017) and IBS (p = 0.026), respectively. Additionally, the RA of the Rhodothermota and Thermotogota phyla was lower in FD (p = 0.017 and p = 0.018, respectively) but not in IBS patients (p = 0.15 and p = 0.06, respectively) compared to controls. Interestingly, the RA of specific taxa from Chloroflexota, Rhodothermota and Thermotogota phyla were consistently lower in subjects with FD when compared to CG but similar to IBS, during analysis of all the subsequent major ranks of taxonomy. At the class level, there were significant differences in Syntrophobacteria, Acidithiobacillia, Cytophagia and Flavobacteriia between the FD and CG groups (p < 0.05), but no such difference between FD and IBS was found. Finally, multiple significant differences at the order, family, genus and species level between the FD and CG groups were also detected. A positive relationship between the RA of Streptococcus and those from genus Granulicatella was observed both in FD (p = 0.014) and IBS (p = 0.014) patients. The microbiome profiling from duodenal luminal content of FD patients is significantly different to that of controls, including lower microflora diversity, different microflora structure/composition and specific taxa. Similar differences in the DLC between FD and IBS patients were not evident.

Relationship between jejunum ATPase activity and antioxidant function on the growth performance, feed conversion efficiency, and jejunum microbiota in Hu sheep (Ovis aries)

BackgroundATPase activity and the antioxidant function of intestinal tissue can reflect intestinal cell metabolic activity and oxidative damage, which might be related to intestinal function. However, the specific influence of intestinal ATPase activity and antioxidant function on growth performance, feed conversion efficiency, and the intestinal microbiota in sheep remains unclear.ResultsThis study analyzed the correlation between ATPase activity and antioxidant function in the jejunum of 92 Hu sheep and their growth performance and feed conversion efficiency. Additionally, individuals with the highest (H group) and lowest (L group) jejunum MDA content and Na+ K+-ATPase activity were further screened, and the effects of jejunum ATPase activity and MDA content on the morphology and microbial community of sheep intestines were analyzed. There was a significant correlation between jejunum ATPase and SOD activity and the initial weight of Hu sheep (P < 0.01). The H-MDA group exhibited significantly higher average daily gain (ADG) from 0 to 80 days old and higher body weight (BW) after 80 days. ATPase and SOD activities, and MDA levels correlated significantly and positively with heart weight. The jejunum crypt depth and circular muscle thickness in the H-ATP group were significantly higher than in the L-ATP group, and the villus length, crypt depth, and longitudinal muscle thickness in the H-MDA group were significantly higher than in the L-MDA group (P < 0.01). High ATPase activity and MDA content significantly reduced the jejunum microbial diversity, as indicated by the Chao1 index and observed species, and affected the relative abundance of specific taxa. Among species, the relative abundance of Olsenella umbonata was significantly higher in the H-MDA group than in the L-MDA group (P < 0.05), while Methanobrevibacter ruminantium abundance was significantly lower than in the L-MDA group (P < 0.05). In vitro culture experiments confirmed that MDA promoted the proliferation of Olsenella umbonata. Thus, ATPase and SOD activities in the jejunum tissues of Hu sheep are predominantly influenced by congenital factors, and lambs with higher birth weights exhibit lower Na+ K+-ATPase, Ca2+ Mg2+-ATPase, and SOD activities.ConclusionsThe ATPase activity and antioxidant performance of intestinal tissue are closely related to growth performance, heart development, and intestinal tissue morphology. High ATPase activity and MDA content reduced the microbial diversity of intestinal tissue and affect the relative abundance of specific taxa, representing a potential interaction between the host and its intestinal microbiota.

Soil quality reflects microbial resource availability and drives rhizosphere microbiome variation in Ghanaian cocoa farms

Cocoa (Theobroma cacao L.) is an important crop in Ghana and the source of livelihood for hundreds of thousands of smallholder farmers. Maintaining soil quality on these farms is critical to ensuring the long-term viability of cocoa farming and preventing deforestation to meet rising demand. However, increasing attention to soil health has revealed a significant knowledge gap related to the soil microbiome in cocoa production systems. Using a nested design of sixteen smallholder cocoa farms in agroforestry or monoculture, on different soil quality classes and in different agroecological zones, a study was conducted to identify 1) drivers of rhizosphere microbial diversity and community composition across scales and 2) the extent of microbial differentiation between soil quality classes. Soil quality had far greater impacts than agroecological zone or agroforestry vs. monoculture management on microbial diversity and community composition, accounting for 17 % of variation in prokaryotes and 10 % in fungi. Good-quality and poor-quality soils contrasted in soil and root parameters, creating variable microbial resources, which led to differences in microbial community composition and the relative abundance of specific taxa. Soil organic matter and root traits were key drivers of community composition in good-quality soils, while permanganate-oxidizable carbon was relatively more important in poor-quality soils. These results underscore the importance of considering rhizosphere microbial communities in assessments of soil quality and highlight taxa that may serve as biological indicators of soil health in cocoa agroforestry systems.

Limited effects of azithromycin on the oropharyngeal microbiome in children with CF and early pseudomonas infection

BackgroundTobramycin inhalation solution (TIS) and chronic azithromycin (AZ) have known clinical benefits for children with CF, likely due to antimicrobial and anti-inflammatory activity. The effects of chronic AZ in combination with TIS on the airway microbiome have not been extensively investigated. Oropharyngeal swab samples were collected in the OPTIMIZE multicenter, randomized, placebo-controlled trial examining the addition of AZ to TIS in 198 children with CF and early P. aeruginosa infection. Bacterial small subunit rRNA gene community profiles were determined. The effects of TIS and AZ were assessed on oropharyngeal microbial diversity and composition to uncover whether effects on the bacterial community may be a mechanism of action related to the observed changes in clinical outcomes.ResultsSubstantial changes in bacterial communities (total bacterial load, diversity and relative abundance of specific taxa) were observed by week 3 of TIS treatment for both the AZ and placebo groups. On average, these shifts were due to changes in non-traditional CF taxa that were not sustained at the later study visits (weeks 13 and 26). Bacterial community measures did not differ between the AZ and placebo groups.ConclusionsThis study provides further evidence that the mechanism for AZ’s effect on clinical outcomes is not due solely to action on airway microbial composition.

Otitis Media in Children with Down Syndrome Is Associated with Shifts in the Nasopharyngeal and Middle Ear Microbiotas.

Background: Otitis media (OM) is defined as middle ear (ME) inflammation that is usually due to infection. Globally, OM is a leading cause of hearing loss and is the most frequently diagnosed disease in young children. For OM, pediatric patients with Down syndrome (DS) demonstrate higher incidence rates, greater severity, and poorer outcomes. However, to date, no studies have investigated the bacterial profiles of children with DS and OM. Method: We aimed to determine if there are differences in composition of bacterial profiles or the relative abundance of individual taxa within the ME and nasopharyngeal (NP) microbiotas of pediatric OM patients with DS (n = 11) compared with those without DS (n = 84). We sequenced the 16S rRNA genes and analyzed the sequence data for diversity indices and relative abundance of individual taxa. Results: Individuals with DS demonstrated increased biodiversity in their ME and NP microbiotas. In children with OM, DS was associated with increased biodiversity and higher relative abundance of specific taxa in the ME. Conclusion: Our findings suggest that dysbioses in the NP of DS children contributes to their increased susceptibility to OM compared with controls. These findings suggest that DS influences regulation of the mucosal microbiota and contributes to OM pathology.

Algae drive convergent bacterial community assembly at low dilution frequency

Microbial community assembly is a complex dynamical process that determines community structure and function. The interdependence of inter-species interactions and nutrient availability presents a challenge for understanding community assembly. We sought to understand how external nutrient supply rate modulated interactions to affect the assembly process. A statistical decomposition of taxonomic structures of bacterial communities assembled with and without algae and at varying dilution frequencies allowed the separation of the effects of biotic (presence of algae) and abiotic (dilution frequency) factors on community assembly. For infrequent dilutions, the algae strongly impact community assembly, driving initially diverse bacterial consortia to converge to a common structure. Analyzing sequencing data revealed that this convergence is largely mediated by a decline in the relative abundance of specific taxa in the presence of algae. This study shows that complex phototroph-heterotroph communities can be powerful model systems for understanding assembly processes relevant to the global ecosystem functioning.

Comparison of the effects of probiotics, rifaximin, and lactulose in the treatment of minimal hepatic encephalopathy and gut microbiota.

Minimal hepatic encephalopathy (MHE) is an early stage in the pathogenesis of hepatic encephalopathy. Intestinal microbiota is involved in the pathogenesis of hepatic encephalopathy and has become an important therapeutic target. Since there is no unified treatment principle for MHE, this study was conducted to determine the safety and efficacy of different intestinal microecological modulators in the treatment of MHE, and to explore the potential mechanism through intestinal microbiota analysis. Patients with liver cirrhosis were screened for MHE using psychometric hepatic encephalopathy score test. Patients diagnosed with MHE were enrolled and received probiotics, rifaximin, or lactulose for 4 weeks. Adverse events were recorded. The psychometric hepatic encephalopathy score test was performed after treatment. Samples of blood and stool were collected at entry and 4 weeks. Blood samples were analyzed to assess blood ammonia, liver, kidney, and hemostatic functions. Stool microbiota were sequenced to confirm changes in microbial composition. Of 323 patients with liver cirrhosis, 74 patients were diagnosed with MHE. In all, 54 patients were enrolled and 52 who agree to follow-up were included in analysis. The recovery rates of MHE patients received probiotics, rifaximin, and lactulose were 58.8% (20/34), 45.5% (5/11), and 57.1% (4/7), respectively. Probiotics and rifaximin improved liver function in MHE patients to a certain extent. Taxonomic compositions of gut microbiota in MHE patients were distinct from healthy people before treatment; the differences were significantly reduced after treatment, and the gut microbiota gradually resembled the structure of healthy individuals. We found that the relative abundance of specific taxa associated with anti-inflammatory and good cognitive functions was increased in MHE patients after treatment. Accordingly, metabolic pathways in MHE patients were altered before and after treatment. Downregulated pathways after probiotics treatment included glycometabolism and degradation of aromatic compounds. After lactulose treatment, degradation pathways of arginine and ornithine showed a downward trend. Probiotics, rifaximin, and lactulose are safe and effective in the treatment of MHE, and improve the composition of gut microbiota to some extent.

Red mark syndrome: Is the aquaculture water microbiome a keystone for understanding the disease aetiology?

Aquaculture significantly contributes to the growing demand for food worldwide. However, diseases associated with intensive aquaculture conditions, especially the skin related syndromes, may have significant implications on fish health and industry. In farmed rainbow trout, red mark syndrome (RMS), which consists of multiple skin lesions, currently lacks recognized aetiological agents, and increased efforts are needed to elucidate the onset of these conditions. Most of the past studies were focused on analyzing skin lesions, but no study focused on water, a medium constantly interacting with fish. Indeed, water tanks are environmental niches colonized by microbial communities, which may be implicated in the onset of the disease. Here, we present the results of water and sediment microbiome analyses performed in an RMS-affected aquaculture facility, bringing new knowledge about the environmental microbiomes harbored under these conditions. On the whole, no significant differences in the bacterial community structure were reported in RMS-affected tanks compared to the RMS-free ones. However, we highlighted significant differences in microbiome composition when analyzing different samples source (i.e., water and sediments). Looking at the finer scale, we measured significant changes in the relative abundances of specific taxa in RMS-affected tanks, especially when analyzing water samples. Our results provide worthwhile insight into a mostly uncharacterized ecological scenario, aiding future studies on the aquaculture built environment for disease prevention and monitoring.

Amoxicillin and thiamphenicol treatments may influence the co-selection of resistance genes in the chicken gut microbiota

The aim of this study was to assess the dynamics of microbial communities and antimicrobial resistance genes (ARGs) in the chicken gut following amoxicillin and thiamphenicol treatments and potential co-selection of ARGs. To this purpose, the microbial community composition, using 16S rRNA NGS, and the abundance of ARGs conferring resistance to β-lactams and phenicols, using qPCRs, were determined. Results revealed that the administered antimicrobials did not significantly reduce the gut microbiota diversity, but changed its composition, with taxa (e.g. Gallibacterium and Megamonas) being enriched after treatment and replacing other bacteria (e.g. Streptococcus and Bifidobacterium). Positive correlations were found between ARGs (e.g. cmlA, blaCMY-2, and blaSHV) and the relative abundance of specific taxa (e.g. Lactobacillus and Subdoligranulum). The selective pressure exerted by both amoxicillin and thiamphenicol resulted in an increased abundance of ARGs conferring resistance to β-lactams (e.g. blaTEM-1, blaSHV, and blaCTX-M1-like) and phenicols (e.g. floR and cmlA). These findings, together with the co-occurrence of genes conferring resistance to the two antimicrobial classes (e.g. blaTEM-1 and cmlA), suggest a possible interaction among antimicrobials on resistance emergence, possibly due to the presence of mobile genetic elements (MGEs) carrying multiple resistance determinants.

Diversity and Taxonomy of Soil Bacterial Communities in Urban and Rural Mangrove Forests of the Panama Bay.

Mangrove ecosystems are threatened worldwide by a wide range of factors including climate change, coastal development, and pollution. The effects of these factors on soil bacterial communities of Neotropical mangroves and their temporal dynamics is largely undocumented. Here we compared the diversity and taxonomic composition of bacterial communities in the soil of two mangrove forest sites of the Panama Bay: Juan Diaz (JD), an urban mangrove forest in Panama City surrounded by urban development, with occurrence of five mangrove species, and polluted with solid waste and sewage; and Bayano (B), a rural mangrove forest without urban development, without solid waste pollution, and with the presence of two mangrove species. Massive amplicon sequencing of the V4 region of the 16S rRNA gene and community analyses were implemented. In total, 20,691 bacterial amplicon sequence variants were identified, and the bacterial community was more diverse in the rural mangrove forest based on Faith's phylogenetic diversity index. The three dominant phyla of bacteria found and shared between the two sites were Proteobacteria, Desulfobacterota, and Chloroflexi. The ammonia oxidizing archaea class Nitrosphaeria was found among the top 10 most abundant. Dominant genera of bacteria that occurred in the two mangrove sites were: BD2-11_terrestrial_group (Gemmatimonadota), EPR3968-O8a-Bc78 (Gammaproteobacteria), Salinimicrobium (Bacteroidetes), Sulfurovum (Campylobacteria), and Woeseia (Gammaproteobacteria) of which the first three and Methyloceanibacter had increased in relative abundance in the transition from rainy to dry to rainy season in the urban mangrove forest. Altogether, our study suggests that factors such as urban development, vegetation composition, pollution, and seasonal changes may cause shifts in bacterial diversity and relative abundance of specific taxa in mangrove soils. In particular, taxa with roles in biogeochemical cycles of carbon, nitrogen, sulfur, and phosphorus, and on rhizosphere taxa, could be important for mangrove plant resilience to environmental stress.

In Vitro Examination of the Effect of Honey in the Gastrointestinal Tract

ObjectivesHoney has shown beneficial antibacterial properties in wound healing, but little is known about the effects of honey consumption on human gut health. Herein, we investigate the effects of honey gastric digest on the growth of the common food-borne pathogen Enterotoxigenic E. coli (ETEC) and beneficial lactic acid bacteria within the gastric environment and a small intestine microbial community, respectively.Methods In Vitro Gastric Digestion: An in vitro digestion of both honey and a simple sugar control (42% fructose, 35% glucose, 23% water) was performed in a simulated gastric electrolyte solution containing pepsin and hydrochloric acid (HCl). Each solution was adjusted to a pH of 2.5, and placed in an incubating shaker at 37°C, 200rpm for 120 minutes. For ETEC survival experiments, 800,000 CFU/mL of ETEC in brain heart infusion (BHI) broth was added to each solution before pH adjustment. Samples were collected every 20 minutes, plated on BHI, and colonies counted the following morning. In Vitro Fermentation: Digested honey or control was added at 1% w/v to a small intestine microbial mock community, containing 100,000 cells each of 8 common small intestinal commensal bacteria, and fermented anaerobically for 40 hours at 37°C and an initial pH of 5.5. Samples were collected for 16S rRNA analysis; optical density and pH were measured to determine bacterial growth and estimate the relative production of acids in the culture media, respectively. 16S Analysis: For individual CFU, full length amplicons were analyzed by Sanger sequencing and NCBI BLAST. For fermentations, the V4 region was amplified and sequenced on Illumina MiSeq at UC Davis Tech Core. Sequences were analyzed in Qiime 2. Statistical analyses were performed via DESeq2 in R.ResultsOur preliminary data shows that under in vitro gastric digestion conditions, ETEC survival decreased more quickly in honey than a simple sugar control. Total CFU were similar between the two conditions at 120 minutes, but Sanger sequencing identified a majority of colonies plated from the honey condition as genus Bacillus. During in vitro fermentation, differences in the relative abundance of specific taxa between honey and control did not reach statistical significance.ConclusionsOur pilot experiments suggest honey may affect the survival of gastric pathogens within the stomach. Research is ongoing to confirm these results.Funding SourcesThe National Honey Board, USDA, and the Dean's Distinguished Graduate Fellowship, UC Davis.

Composition and short-term stability of gut microbiota in lean and spontaneously overweight healthy Labrador retriever dogs

BackgroundThe gut microbiota and its metabolic end-products act in close collaboration with the nutrient metabolism of the animal. A relationship between excess adiposity and alterations in gut microbiota composition has been identified in humans and rodents, but data are scarce for overweight dogs. This study compared composition and temporal variations of gut microbiota in healthy lean and spontaneously overweight dogs. The analysis was based on three individual fresh faeces samples from each dog during a 10-day period. Twenty-seven healthy and intact male Labrador retriever dogs were included, 12 of which were classified as lean (body condition score (BCS) 4–5 on a 9-point scale) and 15 as overweight (BCS 6–8). Gut microbiota was analysed by Illumina sequencing of the V3-V4 region of the 16S rRNA gene.ResultsLean and overweight groups of dogs were not separated by principal coordinate analysis (PCoA), analysis of similarity (one-way ANOSIM, P = 0.99) or species indicator analysis (IndVal) using operational taxonomic units (OTU) data. Gut microbial taxa at phylum, family or genus level did not differ between lean and overweight dogs in mixed-model repeated measures analyses. Short-term stability, evaluated by similarity index, did not differ between lean and overweight dogs over the 10-day period. Pooled Firmicutes/Bacteroidetes (F/B) ratio was 3.1 ± 3.7 in overweight dogs and 2.1 ± 1.2 in lean dogs (P = 0.83). Individual dogs, irrespective of body condition (lean or overweight), displayed variation in mean alpha diversity (Chao-1 index range 122–245, Shannon index range 2.6–3.6) and mean similarity index (range 44–85%).ConclusionsHealthy lean and spontaneously overweight Labrador retriever dogs had comparable gut microbiota composition and short-term stability over a 10-day sampling period. There were no alterations in microbial diversity or in relative abundance of specific taxa at phylum, family or genus level in overweight compared to lean dogs. Our findings suggest that there are few detectable differences in gut microbiota composition between healthy spontaneously overweight and lean dogs by the current method. Future application of metagenomic or metabolomic techniques could be used to investigate microbial genes or microbial end-products that may differ even when microbiota compositional analyses fail to detect a significant difference between lean and overweight dogs.

Effects of exercise intensity on gut microbiome composition and function in people with type 2 diabetes

ABSTRACT Exercise is positively associated with higher microbial diversity, but there is limited information on exercise intensity's effect on gut microbiome composition and function in clinical populations. This study examines whether different intensities of exercise exert differential effects on gut microbiome composition and function in low active people with type 2 diabetes. This is a sub-study of the Exercise for Type 2 Diabetes Study, a single centre, prospective, randomised controlled trial. Participants (n = 12) completed 8-weeks of combined aerobic and resistance moderate intensity continuous training (C-MICT) or combined aerobic and resistance high-intensity interval training (C-HIIT). Faecal samples were collected before and after intervention to measure gut microbiome composition and metabolic pathways (metagenome shotgun sequencing) and short-chain fatty acids. Post-exercise α-diversity was different between groups as was the relative abundance of specific taxa was (p < .05). Post-exercise relative abundance of Bifidobacterium, A. municiphila, and butyrate-producers Lachnospira eligens, Enterococcus spp., and Clostridium Cluster IV were higher at lower exercise intensity. Other butyrate-producers (from Eryspelothrichales and Oscillospirales), and methane producer Methanobrevibacter smithii were higher at higher exercise intensity. Pyruvate metabolism (ko00620),COG “Cell wall membrane envelope biogenesis” and “Unknown function” pathways were significantly different between groups and higher in C-MICT post-exercise. Differential abundance analysis on KO showed higher expression of Two-component system in C-HIIT. Transcription factors and “unknown metabolism” related pathways decreased in both groups. There were no significant between group changes in faecal short chain fatty acids. Exercise intensity had a distinct effect on gut microbiome abundance and metabolic function, without impacting short-chain fatty acid output. Highlights Evidence of exercise effect on gut microbiome outcomes is limited to healthy and athletic populations In low active people with type 2 diabetes, different exercise intensities increased specific health promoting and butyrate producers species, and showed differentially abundant gut microbiome metabolic pathways. Further investigation is warranted, and if this supports the present findings, then specific exercise intensities may be promoted to target specific species and optimise gut health.

Abstract 022: Association Of Nutritionally-Rich Plant-Centered Diets With Gut Microbial Diversity And Composition Columbia Heart Failure-Microbiome Study

Introduction: A plant-centered diet is related to lower risk of cardiovascular disease. However, its association with the gut microbiome has not been well studied in populations with heart failure (HF), and mechanisms linking diet to improved outcomes among HF patients are poorly understood. Hypothesis: Consuming a more nutritionally-rich plant-centered diet is associated with increased microbial alpha diversity and with favorable taxonomic composition and features as compared to consuming less plant-centered diets. Methods: We conducted a cross-sectional analysis of 152 patients with NYHA class I-IV HF with reduced ejection fraction. Diet was assessed using a food frequency questionnaire. Plant-centered diet quality was evaluated using A Priori Diet Quality Score (APDQS) and the APDQS was classified into quintiles; high scores were characterized by higher consumption of nutritionally-rich plant foods with lower consumption of high-fat meats and unhealthy plant foods. Stool samples were analyzed using 16S rRNA gene sequencing. Associations of the APDQS with alpha (Shannon Index and Inverse Simpson) and beta diversity (defined via Bray-Curtis dissimilarity index) were evaluated by linear regression and permutational multivariate analysis of variance (PERMANOVA), respectively. Negative-binomial regressions using DESeq2 were used to study the association between the APDQS and the relative abundance of specific taxa at the phylum and genus levels. Adjustments for multiple comparisons were performed using the false discovery rate. Results: Mean Shannon Index and Inverse Simpson values were 6.28±0.5 and 407.7±183.37, respectively. Among patients aged &lt;61y, after multivariable adjustment, the APDQS (per 12 units) was associated with higher Shannon Index (0.13±0.05; P for slope=0.007) and Inverse Simpson (46.87±15.5; P for slope=0.004); no associations were observed among those aged ≥ 61y (P for interaction &lt;0.05 for each). APDQS quintiles were not associated with beta-diversity (PERMANOVA, P=0.54). At the genus level, the highest quintile of the ADPQS (vs the lowest quintile) was associated with higher abundance of Enterobacter and lower abundance of Catenibacterium. Conclusions: Consuming nutritionally-rich plant-centered diets was significantly associated with higher gut microbiota diversity in younger HF patients, as well as significantly higher or lower abundance of certain bacterial taxa at the genus level.

A233 CHARACTERIZATION OF THE DUODENAL MICROBIOME IN PEDIATRIC CELIAC AND INFLAMMATORY BOWEL DISEASE PATIENTS

BackgroundBoth Celiac disease (CE) and inflammatory bowel disease (IBD) are lifelong gastrointestinal tract (GIT) disorders. CE is an autoimmune disorder triggered by gluten consumption and can result in small intestine villus atrophy, crypt hyperplasia and epithelial permeability, while IBD is characterized by chronic, reoccurring inflammation and ulcers in the GIT. There is increasing evidence linking GIT microbes to both CE and IBD pathogenesis. Studies have also shown that CE patients are at increased risk of developing IBD, suggesting a possible link between these diseases. The duodenum can be affected in both CE and IBD, but it is understudied as compared to other GIT regions.AimsWe thus aimed to characterize the duodenal microbiome of pediatric CE, IBD and control patients (n=76, 48 and 57 respectively) and hypothesized that the composition of microbes would vary between each diagnostic group.MethodsWe used mucosal luminal interface aspirates collected during upper endoscopy at the Children’s Hospital of Eastern Ontario. Metagenomic DNA was extracted from these samples and bacterial taxa was characterized by sequencing the V6 hypervariable region of the 16S rRNA gene.ResultsControl, CE, and IBD duodenal microbiotas showed no apparent differences in either α-diversity or β-diversity. However, we identified several significant differences between the relative abundances of specific taxa in these three patient groups. In particular, Atopobium parvulum was found to be enriched in Crohn’s disease samples when compared to non-IBD controls. There was also a trend for higher Bacteroides, Lactobacillus, Parabacteroides and Staphylococcus in CE patient MLI aspirates. These results are similar to what has been previously reported in CE patients. Finally, trends found in the duodenal MLI aspirates are more consistent with results previously found in the salivary microbiome in CD patients as opposed to studies of the large intestine.ConclusionsThis work provides unique insight into the microbial composition at the duodenum; a GIT region that has not been fully characterized in CE or IBD.Funding AgenciesCIHRGenome Canada

Tracking the impacts of nutrient inputs on estuary ecosystem function

Estuaries are one of the most impacted coastal environments globally, subjected to multiple stressors from urban, industry and coastal development. With increasing anthropogenic activity surrounding estuarine systems, sewage inputs have become a common concern. Stable isotope analysis provides a well-established tool to investigate the incorporation of nitrogen into marine organisms and identify major nutrient sources. Benthic macroinvertebrate communities are often used as bioindicators in ecological studies as they typically display predictable responses to anthropogenic pressures, however have a suite of limitations and costs associated with their use. 16S rDNA amplicon sequencing techniques allow for investigation of the microbial communities inhabiting complex environmental samples, with potential as a tool in the ecological assessment of pollution. These communities have not yet been adequately considered for ecological studies and biomonitoring, with a need to better understand interactions with environmental stressors and implications for ecosystem function. This study used a combination of stable isotope analysis to trace the uptake of anthropogenic nitrogen in biota, traditional assessment of benthic macroinvertebrate communities, and 16S rDNA genotyping of benthic microbial communities. Stable isotope analysis of seagrass and epiphytes identified multiple treated and untreated sewage inputs, ranges of 5.2–7.2‰ and 1.9–4.0‰ for δ15N respectively, as the dominant nitrogen source at specific locations. The benthic macroinvertebrate community reflected these inputs with shifts in dominant taxa and high abundances of polychaetes at some sites. Microbial communities provided a sensitive indication of impact with a breadth of information not available using traditional techniques. Composition and predicted function reflected sewage inputs, particularly within sediments, with the relative abundance of specific taxa and putative pathogens linked to these inputs. This research supports the growing body of evidence that benthic microbial communities respond rapidly to anthropogenic stressors and have potential as a monitoring tool in urban estuarine systems.

Investigation of the impact of commonly used medications on the oral microbiome of individuals living without major chronic conditions.

Commonly used medications produce changes in the gut microbiota, however, the impact of these medications on the composition of the oral microbiota is understudied. Saliva samples were obtained from 846 females and 368 males aged 35-69 years from a Canadian population cohort, the Atlantic Partnership for Tomorrow's Health (PATH). Samples were analyzed by 16S rRNA gene sequencing and differences in microbial community compositions between nonusers, single-, and multi-drug users as well as the 3 most commonly used medications (thyroid hormones, statins, and proton pump inhibitors (PPI)) were examined. Twenty-six percent of participants were taking 1 medication and 21% were reported taking 2 or more medications. Alpha diversity indices of Shannon diversity, Evenness, Richness, and Faith's phylogenetic diversity were similar among groups, likewise beta diversity as measured by Bray-Curtis dissimilarity (R2 = 0.0029, P = 0.053) and weighted UniFrac distances (R2 = 0.0028, P = 0.161) were non-significant although close to our alpha value threshold (P = 0.05). After controlling for covariates (sex, age, BMI), six genera (Saprospiraceae uncultured, Bacillus, Johnsonella, Actinobacillus, Stenotrophomonas, and Mycoplasma) were significantly different from non-medication users. Thyroid hormones, HMG-CoA reductase inhibitors (statins) and PPI were the most reported medications. Shannon diversity differed significantly among those taking no medication and those taking only thyroid hormones, however, there were no significant difference in other measures of alpha- or beta diversity with single thyroid hormone, statin, or PPI use. Compared to participants taking no medications, the relative abundance of eight genera differed significantly in participants taking thyroid hormones, six genera differed in participants taking statins, and no significant differences were observed with participants taking PPI. The results from this study show negligible effect of commonly used medications on microbial diversity and small differences in the relative abundance of specific taxa, suggesting a minimal influence of commonly used medication on the salivary microbiome of individuals living without major chronic conditions.

Microbial community alteration in tongue squamous cell carcinoma.

Tongue squamous cell carcinoma (TSCC) is the most common oral cavity malignancy. The role of the microbial community in TSCC development and progression is unclear. In the present study, 23 patients with TSCC were recruited. Tissue DNA was extracted from cancer and paracancerous normal tissues from all participants. Next-generation 16S rDNA amplicon sequencing and functional prediction were applied for taxonomic analysis. Alpha diversity measurements using the Shannon and Simpson diversity indexes indicated a significant increase in the microbiotic diversity of cancer samples (Shannon index: P = 0.001, Simpson index: P = 0.015); otherwise, no differences were found when using observed operational taxonomic units (OTUs) and Chao1 index (observed OTUs: P = 0.261, Chao1 index: P = 0.054). The dominant phyla of the microbiota included Bacteroidetes, Proteobacteria, Firmicutes, Actinobacteria, and Fusobacteria. Multivariate analysis of variance (Adonis) and nonparametric analysis of similarities (ANOSIM) based on unweighted unifrac distances demonstrated differences in the bacterial community structure between the two groups (P = 0.001 for Adonis, P = 0.001 for ANOSIM). Compared with the normal samples, Neisseria, Streptococcus, and Actinomyces levels decreased significantly in cancer samples. Co-occurrence network analysis implied that the bacterial community in cancer was more conserved than that in normal tissue. Matched-pair analysis of cancer and control samples revealed a significant alteration in the relative abundance of specific taxa. These findings will enrich our knowledge of the association between the oral microbial community and TSCC. Further experiments should investigate the potential carcinogenic mechanism of microbial community alterations in TSCC. KEY POINTS: • Microbial community role in tongue squamous cell carcinoma. • Significant alteration of microbiome found between cancer and normal tissues. • Microbial community alteration and potential carcinogenic mechanism.

Characterization of the gut microbiota among Veterans with unique military-related exposures and high prevalence of chronic health conditions: A United States-Veteran Microbiome Project (US-VMP) study

The gut microbiome is impacted by environmental exposures and has been implicated in many physical and mental health conditions, including anxiety disorders, affective disorders, and trauma- and stressor-related disorders such as posttraumatic stress disorder (PTSD). United States (US) military Veterans are a unique population in that their military-related exposures can have consequences for both physical and mental health, but the gut microbiome of this population has been understudied. In this publication, we describe exposures, health conditions, and medication use of Veterans in the US Veteran Microbiome Project (US-VMP) and examine the associations between these characteristics and the gut microbiota. This cohort included 331 US Veterans seeking healthcare with the Veterans Health Administration who were 83% male with an average (±SD) age of 47.6 ​± ​13.4 years. The cohort displayed a high prevalence of PTSD (49.8%) and history of traumatic brain injuries (76.1%), and high current use of prescription medications (74.9%) to treat various acute and chronic conditions. We observed significant associations between the gut microbiota composition and gastroenteritis, peripheral vascular disease (PVD), bipolar disorders, symptoms of severe depression based on the Beck Depression Inventory, stimulant and opioid use disorders, beta-blockers, serotonin and norepinephrine reuptake inhibitor antidepressants, diabetes medications, and proton pump inhibitors. Many of the Veteran characteristics examined were associated with altered relative abundances of specific taxa. We found that PVD and cardiovascular disease were associated with lower microbiota diversity in the gut (i.e., α-diversity), while supplemental vitamin use was associated with higher α-diversity. Our study contributes novel insights as to whether the unique exposures of Veterans in this cohort correlate with gut microbiota characteristics and, in line with previous findings with other population-level studies of the microbiome, confirms associations between numerous health conditions and medications with the gut microbiome.