Differences In Microbiota Diversity Research Articles

Association between Oral Microbiome and Gastroesophageal Reflux Severity.

Background/Objectives: Gastroesophageal reflux disease (GORD) is caused by gastric contents refluxing back into the oesophagus and oral cavity. It can lead to injuries to the mucosa in the form of erosion and ulcers. Our past research have shown acid reflux severity and disease progression is associated with alternations in the microbiota of the distal oesophagus. The aim of this study was to explore whether changes in the oral microbiota occurred in GORD patients and establish any associations with reflux severity. Methods: Fresh mouthwash samples were collected from 58 patients experiencing reflux symptoms referred for 24 h pH monitoring. The participants were categorised into three groups based on their DeMeester scores: Normal (<14.72), Mild (14.2-50), and Moderate/severe (>51). Microorganism identity and diversity were generated using hypervariable tag sequencing and analysing the V1-V3 region of the 16S rRNA gene. Results: No differences in microbiota diversity were found in oral microbiota between groups using the Chiao1 diversity index and Shannon diversity index. Microbiota in the Mild group showed reductions in Rothia dentocariosa and Lautropia, while Moryella and Clostridiales_1 were increased compared with the Normal group. In the Moderate/severe group, the abundance of Rothia aeria was reduced compared with the Normal group, while Schwartzia, Rs_045, Paludibacter, S. satelles, Treponema, and T. socranskii all had increased abundance. The abundance of Prevotella pallens was higher in the Mild group compared with Moderate/severe, while S. satelles and Paludibacter abundances were lower. Conclusions: Our study shows the oral microbiome show significant differences between acid reflux severity groups, as categorised by DeMeester score.

Impact of Microbiota and Metabolites on Intestinal Integrity and Inflammation in Severe Obesity.

Obesity is a multifactorial disease associated with low-grade inflammation. The gut is thought to be involved in obesity-related inflammation, as it is continuously exposed to antigens from food, microbiota and metabolites. However, the exact underlying mechanisms are still unknown. Therefore, we examined the relation between gut pathology, microbiota, its metabolites and cytokines in adults with severe obesity. Individuals eligible for bariatric surgery were included. Fecal and plasma samples were collected at surgery timepoint, to assess microbiota and metabolite composition. Jejunal biopsies were collected during surgery and stained for cytotoxic T cells, macrophages, mast cells and tight junction component zonula occludens-1. Based on these stainings, the cohort was divided into four groups: high versus low intestinal inflammation and high versus low intestinal integrity. We found no significant differences in microbiota diversity between groups, nor for individual bacterial species. No significant differences in metabolites were observed between the intestinal inflammatory groups. However, some metabolites and cytokines differed between the intestinal integrity groups. Higher plasma levels of interleukin-8 and tauro-chenodeoxycholic acid were found, whereas isovaleric acid and acetic acid were lower in the high intestinal integrity group. As the results were very subtle, we suggest that our cohort shows very early and minor intestinal pathology.

A virus induces alterations in root morphology while exerting minimal effects on the rhizosphere and endosphere microorganisms in rice.

The highly destructive southern rice black-streaked dwarf virus (SRBSDV) causes significant losses in rice production. To understand its impact on rice root, we studied fibrous root development and root microbiota variation (rhizosphere and endosphere) after SRBSDV infection. SRBSDV infection reduced the number and length of fibrous roots in rice. Interestingly, the rhizosphere had higher bacterial diversity and abundance at the initial (0 days) and 30-day postinfection stages, while 30-day-old roots showed increased diversity and abundance. However, there were no significant differences in microbiota diversity between infected and noninfected rice plants. The major rhizosphere microbiota included Proteobacteria, Bacteroidota, Acidobacteriota, and Planctomycetota, comprising about 80% of the community. The endosphere was dominated by Proteobacteria and Cyanobacteria, constituting over 90%, with Bacteroidota as the next most prominent group. Further, we identified differentially expressed genes related to plant-pathogen interactions, plant hormone signal, and ABC transporters, potentially affecting root morphology. Notably, specific bacteria (e.g. Inquilinus and Actinoplanes) showed correlations with these pathways. In conclusion, SRBSDV primarily influences root growth through host metabolism, rather than exerting direct effects on the root microbiota. These insights into the interactions among the pathogen, rice plant, and associated microbiota could have implications for managing SRBSDV's detrimental effects on rice production.

Comparison of iSeq and MiSeq as the two platforms for 16S rRNA sequencing in the study of the gut of rat microbiome

Amplicon-based next-generation sequencing (NGS) of the 16S ribosomal RNA (16S) regions is a culture-free method used to identify and analyze Procaryota occurring within a given sample. The prokaryotic 16S rRNA gene contains conserved regions and nine variable regions (V1-V9) frequently used for phylogenetic classification of genus or species in diverse microbial populations. This work compares the accuracy and efficacy of two platforms, iSeq and MiSeq from Illumina, used in sequencing 16S rRNA. The most important similarities and differences of 16S microbiome sequencing in 20 fecal rat samples were described. Genetic libraries were prepared according to 16S Metagenomic Sequencing Library Preparation (Illumina) for the V3 and V4 regions of the 16S. The species richness obtained using iSeq technology was lower compared to MiSeq. At the second taxonomy level (L2), the abundance of taxa was comparable for both platforms. At the L7, the taxa abundance was significantly different, and the number of taxa was higher for the MiSeq. The alpha diversity was lower for iSeq than for MiSeq, starting from the order to the species level. The beta diversity estimation revealed statistically significant differences in microbiota diversity starting from the class level to the species level in samples sequenced on two investigated platforms. This work disclosed that the iSeq platform could be used to evaluate the bacterial profile of the samples to characterize the overall profile. The MiSeq System seems to be better for a detailed analysis of the differences in the microbiota composition.Key points• iSeq platform allows to shorten the sequencing time three times compared to the MiSeq.• iSeq can only be used for an initial and quick microbiome assessment.• MiSeq is better for a detailed analysis of the differences in the microbiota composition.

Impact of host age on viral and bacterial communities in a waterbird population

Wildlife harbour pathogens that can harm human or livestock health and are the source of most emerging infectious diseases. It is rarely considered how changes in wildlife population age-structures or how age-stratified behaviours might alter the level of pathogen detection within a species, or risk of spillover to other species. Micro-organisms that occur in healthy animals can be an important model for understanding and predicting the dynamics of pathogens of greater health concern, which are hard to study in wild populations due to their relative rarity. We therefore used a metagenomic approach to jointly characterise viral and prokaryotic carriage in faeces collected from a healthy wild bird population (Cygnus olor; mute swan) that has been subject to long-term study. Using 223 samples from known individuals allowed us to compare differences in prokaryotic and eukaryotic viral carriage between adults and juveniles at an unprecedented level of detail. We discovered and characterised 77 novel virus species, of which 21% belong putatively to bird-infecting families, and described the core prokaryotic microbiome of C. olor. Whilst no difference in microbiota diversity was observed between juveniles and adult individuals, 50% (4/8) of bird-infecting virus families (picornaviruses, astroviruses, adenoviruses and bornaviruses) and 3.4% (9/267) of prokaryotic families (including Helicobacteraceae, Spirochaetaceae and Flavobacteriaceae families) were differentially abundant and/or prevalent between juveniles and adults. This indicates that perturbations that affect population age-structures of wildlife could alter circulation dynamics and spillover risk of microbes, potentially including pathogens.

Gut microbiota distinct between colorectal cancers with deficient and proficient mismatch repair: A study of 230 CRC patients.

Colorectal cancers (CRCs) with deficient DNA mismatch repair (dMMR) and proficient DNA mismatch repair (pMMR) exhibit heterogeneous tumor characteristics, distinct responses to immunotherapy, and different survival outcomes. However, it is unclear whether gut microbiota is distinct between CRCs with different MMR status. In this study, we used immunohistochemistry for four major MMR proteins to determine the MMR status in 230 CRC patients. The gut microbiota was profiled in cancerous and adjacent normal tissues by using bacterial 16S rRNA sequencing. The differences in microbiota diversity, composition and related metabolic pathways between patients with dMMR and pMMR CRCs were explored. Linear discriminant analysis effect size (LEfSe) analysis was further applied to validate the significant taxonomic differences at the genus level. In our study cohort, dMMR status was identified in 29 of 230 (12.61%) tumors. The richness (alpha-diversity) of gut microbiome in dMMR tumor tissue was higher compared with pMMR tumor tissues. The microbial community composition (beta-diversity) between the two groups was significantly different. The dMMR group was enriched considerably for some microbiota, including Fusobacteria, Firmicutes, Verrucomicrobia, and Actinobacteria at the phylum level and Fusobacterium, Akkermansia, Bifidobacterium, Faecalibacterium, Streptococcus, and Prevotella bacteria at the genus level. However, the pMMR group was dominated by Proteobacteria at the phylum level and Serratia, Cupriavidus and Sphingobium at the genus level. Moreover, a wide variety of microbiota associated functional pathways were observed with different MMR status. KEGG pathway analysis indicated a higher abundance of the biosynthesis and metabolic pathways of glycan and nucleotide, cell growth and death pathways, genetic replication and repair pathways in dMMR samples compared with the pMMR group. These findings demonstrate that CRC patients with different MMR status have distinct gut bacterial community richness, compositions and related metabolic pathways, suggesting basis that may explain the effectiveness of immunotherapy in dMMR tumors.

Effect of Climate on Bacterial and Archaeal Diversity of Moroccan Marine Microbiota.

The Moroccan coast is characterized by a diversity of climate, reflecting a great richness and diversity of fauna and flora. By this, marine microbiota plays a fundamental role in many biogeochemical processes, environmental modifications, and responses to temperature changes. To date, no exploration by high-throughput techniques has been carried out on the characterization of the Moroccan marine microbiota. The objective of this work is to study the diversity and metabolic functions of MMM from the Moroccan coast (Atlantic and Mediterranean) according to the water source (WS) and the type of climate (CT) using the approach high-throughput sequencing of the 16SrRNA gene. Four water samples of twelve sampling sites from the four major climates along the Moroccan coastline were collected, and prokaryotic DNA was extracted. V4 region of 16S rRNA gene was amplified, and the product PCR was sequenced by Illumina Miseq. The β-diversity and α-diversity indices were determined to assess the species richness and evenness. The obtained results were analyzed by Mothur and R software. A total of twenty-eight Bacterial phyla and twelve Archaea were identified from the samples. Proteobacteria, Bacteroidetes, and Cyanobacteria are the three key bacterial phyla, and the Archaeal phyla identified are: Euryarchaeota, Nanoarchaeaeota, Crenarchaeota, Hydrothermarchaeota, Asgardaeota, Diapherotrites, and Thaumarchaeota in the Moroccan coastline and the four climates studied. The whole phylum are involved in marine biogeochemical cycles, and through their functions they participate in the homeostasis of the ocean in the presence of pollutants or stressful biotic and abiotic factors. In conclusion, the obtained results reported sufficient deepness of sequencing to cover the majority of Archaeal and Bacterial genera in each site. We noticed a strong difference in microbiota diversity, abundance, and taxonomy inter- and intra-climates and water source without significant differences in function. To better explore this diversity, other omic approaches can be applied such as the metagenomic shotgun, and transcriptomic approaches allowing a better characterization of the Moroccan marine microbiota and to understand the mechanisms of its adaptation and its impacts in/on the ecosystem.

Aging gut microbiota of wild macaques are equally diverse, less stable, but progressively personalized

BackgroundPronounced heterogeneity of age trajectories has been identified as a hallmark of the gut microbiota in humans and has been explained by marked changes in lifestyle and health condition. Comparatively, age-related personalization of microbiota is understudied in natural systems limiting our comprehension of patterns observed in humans from ecological and evolutionary perspectives.ResultsHere, we tested age-related changes in the diversity, stability, and composition of the gut bacterial community using 16S rRNA gene sequencing with dense repeated sampling over three seasons in a cross-sectional age sample of adult female Assamese macaques (Macaca assamensis) living in their natural forest habitat. Gut bacterial composition exhibited a personal signature which became less stable as individuals aged. This lack of stability was not explained by differences in microbiota diversity but rather linked to an increase in the relative abundance of rare bacterial taxa. The lack of age-related changes in core taxa or convergence with age to a common state of the community hampered predicting gut bacterial composition of aged individuals. On the contrary, we found increasing personalization of the gut bacterial composition with age, indicating that composition in older individuals was increasingly divergent from the rest of the population. Reduced direct transmission of bacteria resulting from decreasing social activity may contribute to, but not be sufficient to explain, increasing personalization with age.ConclusionsTogether, our results challenge the assumption of a constant microbiota through adult life in a wild primate. Within the limits of this study, the fact that increasing personalization of the aging microbiota is not restricted to humans suggests the underlying process to be evolved instead of provoked only by modern lifestyle of and health care for the elderly.8UGmGK4ynviQrPL4KJ5rpeVideo abstract

Analysis of Gut Microbiota in Patients with Coronary Artery Disease and Hypertension.

Cardiovascular and cerebrovascular diseases are characterized by high rates of morbidity and mortality. Microbiota is closely associated with cardiovascular disease. We aimed to comprehensively analyze the microbiotas of 300 healthy controls, 300 patients with high blood pressure (HBP), and 300 patients with coronary heart disease (CHD). The results indicated no significant difference in microbiota diversity among the three groups (P > 0.05). However, differences in microbiota richness among the three groups were significant (P < 0.05). Bacteroidetes and Bacteroidia were the dominant bacteria in the CHD group, Enterobacteriales and Escherichia-shigella in the HBP group, and Acidaminococcaceae and Phascolarctobacterium in the healthy control group. The prediction results of the random forest model indicated that the population with CHD displayed prominent features with high sensitivity, indicating that microbiota detection might become a novel clinical indicator to predict and monitor the risk of cardiovascular events. The prediction of microbiota function suggested differences in oxygen supply and chronic inflammation between populations with HBP/CHD and healthy populations. Although there is no difference in gut microbiota diversity among the three groups, each group has its dominant microbiota in terms of richness.

The Effect of Intense Pulsed Light on the Skin Microbiota and Epidermal Barrier in Patients with Mild to Moderate Acne Vulgaris.

The skin microbiota partly determined by epidermal barrier plays an important role in acne vulgaris and intense pulsed light (IPL) has been verified as a safe and effective therapeutic option for this disease. Nevertheless, the exact role of the IPL treatment on the skin microbiota and epidermal barrier for patients with acne vulgaris remains unclear. This article was designed to solve this problem. Nineteen healthy controls and 20 patients with mild to moderate acne were enrolled in this study, who received IPL treatment for 12 weeks. The epidermal barrier and skin samples were collected at baseline and after treatment. The microbial diversity was analyzed based on a high-throughput sequencing approach, which targets the V3-V4 region of the bacteria 16S ribosomal RNA genes. After treatment of IPL, the Global Acne Grading System (GAGS) scores, sebum, sclererythrin, and red area of patients were significantly improved by IPL treatment (P < 0.05). Although there was no difference in microbiota diversity before and after IPL treatment, the Nonmetric Multidimension Scaling (NMDS) analysis showed that the samples of the acne patients before and after treatment could be divided into two different sets by skin microbiota (P = 0.011), which could be verified by heatmap analysis. Moreover, we found that the relative abundance of Staphylococcus epidermidis (S. epidermidis) significantly increased, but Cutibacterium acnes (C. acnes) decreased after IPL treatment. The sebum concentration was positively correlated with PH value (R = 0.525, P = 0.017), and the GAGS was positively associated with both sclererythrin (R = 0.477, P = 0.002) and red area (R = -0.503, P = 0.001). IPL could successfully improve the GAGS scores of acne vulgaris, as well as regulate the equilibrium between C. acnes and S. epidermidis, and inhibitthe sebum secretion. Lasers Surg. Med. © 2021 The Authors. Lasers in Surgery and Medicine published by Wiley Periodicals LLC.

Ocular surface microbiota in patients with aqueous tear-deficient dry eye

PurposeAn altered ocular surface microbiota may contribute to the pathophysiology of dry eye disease. The aim of the study was to explore potential differences in microbiota diversity and composition in aqueous tear-deficient dry eye (with and without ocular graft-versus-host disease) compared with controls. MethodsSwab samples from the inferior fornix of the conjunctiva were obtained from patients with aqueous tear-deficient dry eye with and without ocular graft-versus-host disease (n = 18, n = 21, respectively) and controls (n = 28). Isolated bacterial DNA from swabs were analyzed with 16S rRNA gene amplicon sequencing. ResultsDecreased microbiota diversity was observed in patients with aqueous tear-deficient dry eye (p ≤ 0.003) who also showed a difference in microbiota composition compared with controls (p = 0.001). Although several genera were less abundant in aqueous tear-deficient dry eye, a minimal core ocular surface microbiota comprising five genera was shared by >75% of the study participants: Enhydrobacter, Brevibacterium, Staphylococcus, Streptococcus and Cutibacterium. Pseudomonas was identified as a bacterial biomarker for controls and Bacilli for patients with aqueous tear-deficient dry eye. ConclusionsOcular surface microbiota in patients with aqueous tear-deficient dry eye was characterized by an aberrant microbiota composition in comparison to controls, with decreased diversity and reduced relative abundances of several genera. Additionally, a few genera were present in most of the study population, indicating that a minimal core ocular surface microbiota may exist.

Temporal variations in bacterial community diversity and composition throughout intensive care unit renovations

BackgroundInanimate surfaces within a hospital serve as a reservoir of microbial life that may colonize patients and ultimately result in healthcare associated infections (HAIs). Critically ill patients in intensive care units (ICUs) are particularly vulnerable to HAIs. Little is known about how the microbiome of the ICU is established or what factors influence its evolution over time. A unique opportunity to bridge the knowledge gap into how the ICU microbiome evolves emerged in our health system, where we were able to characterize microbial communities in an established hospital ICU prior to closing for renovations, during renovations, and then after re-opening.ResultsWe collected swab specimens from ICU bedrails, computer keyboards, and sinks longitudinally at each renovation stage, and analyzed the bacterial compositions on these surfaces by 16S rRNA gene sequencing. Specimens collected before ICU closure had the greatest alpha diversity, while specimens collected after the ICU had been closed for over 300 days had the least. We sampled the ICU during the 45 days after re-opening; however, within that time frame, the alpha diversity never reached pre-closure levels. There were clear and significant differences in microbiota compositions at each renovation stage, which was driven by environmental bacteria after closure and human-associated bacteria after re-opening and before closure.ConclusionsOverall, we identified significant differences in microbiota diversity and community composition at each renovation stage. These data help to decipher the evolution of the microbiome in the most critical part of the hospital and demonstrate the significant impacts that microbiota from patients and staff have on the evolution of ICU surfaces.BHPdWgKMfGXykoiGPVTgdiVideo

An in-vitro investigation into the prebiotic potential of xylan derived from the edible red seaweed Palmaria palmata

AbstractPrebiotics are considered beneficial to health owing to positive effects upon the gut microbiota (GM). These effects on the GM include stimulating the growth of beneficial species and increasing short chain fatty acid (SCFA) production (1). Accumulating evidence suggests that the putative health benefits associated with seaweed consumption may be, in part, owing to their effects on the GM(2). The red seaweed Palmaria palmata is a source of xylan, a β(1–3) and β(1–4) D-xylose polysaccharide. Given that xylo-oligosaccharides are a recently accepted prebiotic (3), the aim of this investigation was to assess the prebiotic potential of xylan from Palmaria palmata using an in-vitro fermentation gut model. Fibres were subjected to an in-vitro digestion and underwent in-vitro batch culture fermentation (MicroMatrix) over 24 hours. Fermentation vessels were inoculated using a pooled faecal slurry (5% v/v), prepared from six healthy volunteers. Xylan fibre (n = 4) was compared to Cellulose (negative control, n = 8) and Synergy 1 (positive control, n = 8). Changes to GM composition was determined using qPCR (total bacteria, Lactobacilli, and Bifidobacteria), and MiSeq 16S rRNA sequencing. Short chain fatty acid analysis was conducted using gas chromatography-mass spectrometry. The differential abundance of taxa between fermentation substrates was determined using linear discriminant analysis (LDA) effect size (LEfSe). A permutational multivariate analysis of variance (PerMANOVA) was used to determine statistical differences of beta diversity whilst treatment associated differences of short chain fatty acids were determined using an unpaired Mann-Whitney U Test. Xylan altered GM composition at Phylum, Family and Genus taxonomic levels, notably a significant reduction in the Firmicutes/Bacteroides ratio (p = 0.004). Both 16S sequencing data and qPCR analysis revealed a significant increase in Bifidobacteria relative to cellulose, where the effect was comparable to Synergy 1. No significant differences in microbiota diversity were noted for either Xylan or Synergy 1 in comparison to the cellulose control. Xylan was shown to significantly modulate GM activity through increased short chain fatty acid production with increased acetate, propionate and butyrate. The evidence gained from this study suggests that Xylan from Palmaria palmata is a fermentable fibre with potential prebiotic characteristics, and therefore warrants further investigation in humans.This research was funded under the National Development Plan, through the Food Institutional Research Measure, administered by the Department of Agriculture, Food and the Marine, Ireland (13/F/511) and a Northern Ireland Department of Education and Learning PhD scholarship to Paul Cherry.

Diversity and composition of the gut microbiota of Atlantic salmon (Salmo salar) farmed in Irish waters.

Information on the gut microbiota of salmon is essential for optimizing nutrition while maintaining host health and welfare. This study's objectives were to characterize the microbiota in the GI tract of Atlantic salmon (Salmo salar) farmed in waters off the west coast of Ireland and to investigate whether there is a difference in microbiota diversity between the proximal and distal regions of the intestine. The microbiota from the proximal and distal intestine (PI and DI, respectively) of Atlantic salmon was examined using MiSeq Illumina high-throughput sequencing of the 16S ribosomal RNA gene. The PI region had greater bacterial diversity than the DI region. Six phyla were present in the DI samples, dominated by Tenericutes and Firmicutes. These six phyla were also amongst the 12 phyla detected in the PI samples. The PI microbiota was dominated by Tenericutes, Firmicutes, Bacteroidetes and Proteobacteria. A core microbiota of 20 operational taxonomic units (OTUs) common to both regions was observed. It was concluded that Tenericutes were the dominant phylum in both PI and DI samples, and the PI region had greater Shannon and Simpson diversity of bacteria. However, further work is required to identify the functionality of the salmon microbiota. Our study determined the composition and diversity of the intestinal microbiota in adult salmon from a commercial fishery and provides data to improve our understanding of their contributions to the nutrition, health and welfare of Atlantic salmon farmed in Irish waters.

Fecal microbiota of different reproductive stages of the central population of the lesser-long nosed bat, Leptonycteris yerbabuenae.

In this study we analyzed the microbiota composition of fecal samples from the lesser-long nosed bat Leptonycteris yerbabuenae in different reproductive stages (juveniles and adult bats of both sexes as well as pregnant and lactating females). The V4 region of the 16s rRNA gene from 33 individuals was analyzed using alpha and beta diversity metrics. We found that microbiota diversity (expressed in Amplicon Sequence Variants) is higher in pregnant and lactating females. The microbiota of the juveniles and non-reproductive adults was dominated by Gammaproteobacteria and Firmicutes. Reproductive females had a much more diverse microbiota, with a significant increase in phyla such as Bacteroidetes and Alphaproteobacteria. There was no difference in fecal microbiota diversity between pregnant and lactating females and juveniles and non-reproductive adults. Results suggest that differences in microbiota diversity are related to reproduction. We infer that males maintain stable microbiota composition because they do not undergo the large physiological changes that females do during reproduction and maintain a more specialized diet throughout all life stages.

A Preliminary Study of Microbiota Diversity in Saliva and Bronchoalveolar Lavage Fluid from Patients with Primary Bronchogenic Carcinoma.

BackgroundThe present study aimed to evaluate the difference in microbiota diversity in the oral cavity and fluid bronchoalveolar lavage (BALF) of patients with lung cancer.Material/MethodsBuccal (saliva) and lower respiratory tract BALF samples were collected from 51 patients with primary bronchogenic carcinoma and 15 healthy controls, and bacterial genomic DNA was extracted. High-throughput 16S rDNA amplicon sequencing was performed, and microbial diversity, composition, and functions of microbiota were analyzed by bioinformatics methods.ResultsPatients with lung cancer have lower microbial diversity than healthy controls in both saliva and BALF samples. Significant segregation was observed between the different pathological types of lung cancer groups and the control group regardless of the sampling site. Treponema and Filifactor were identified as potential bacterial biomarkers in BALF samples, while Filifactor was ideal to distinguish healthy controls from lung cancer patients. Moreover, the predictive variation analysis of the KEGG (Kyoto Encyclopedia of Genes and Genomes) metabolic pathway showed that the metabolic differences in microbiota varied by sampling site.ConclusionsLung cancer patients carry a different and less diverse microorganism community than healthy controls. Certain bacterial taxa might be associated with lung cancer, but the exact species depends on the sampling site and the pathological type. This study provides basic data on the microbiota diversity in BALF and saliva samples from lung cancer patients. Further investigation with a larger sample size should help validate the enriched species in different pathological types of lung cancers.

Exploring the Link between Superimposed Preeclampsia and the Gut Microbiome

Preeclampsia, a hypertensive disorder of pregnancy, is a leading cause of maternal and fetal morbidity and mortality worldwide. Despite the rising prevalence and severity of this disease, the initiating factors responsible for the development of preeclampsia remain unknown. Recent evidence suggests an association of gut microbiome changes with certain forms of hypertension, but the effects of differences in the microbiome during preeclampsia are unknown. We hypothesized that gut dysbiosis contributes to the development of the preeclamptic phenotype in the Dahl salt‐sensitive rat (Dahl S) model of preeclampsia superimposed on hypertension and chronic kidney disease. Sprague Dawley (SD) rats were used for comparison as a model of healthy pregnancy, and comparisons were made to age matched virgin littermates in both strains. All rats were housed in the same room and maintained on a 0.3% NaCl diet (TD7034) for 5 months prior to study. Fecal samples were obtained on two separate days for baseline measures, and then half of the rats in each strain were mated (n=7–9/group). Samples were collected on days 6, 13, and 20 of pregnancy and then one week postpartum (Day ~29). Microbial DNA was isolated from fecal matter, and the V3‐V4 region of 16S ribosomal RNA was PCR amplified and processed through the Illumina 16S sequencing pipeline. A single library was generated (n=191) and run on Illumina MiSeq instrument. The sequencing reads were processed via QIIME application (Illumina Cloud BaseSpace) which provided an initial analysis of sequencing reads by quality filtering, operational taxonomic unit (OTU) picking, and taxonomic assignment. The web‐based Microbiome Analyst was used for statistical analysis to establish differences in microbiota diversity, composition, and tools for visualization. A preliminary analysis of the fecal microbiota between SD and Dahl S showed a distinct diversity (alpha and beta) in the microbiome between Dahl S and SD rats at baseline. The microbiome diversity stayed relatively constant over the course of pregnancy for SD (versus virgin control), whereas in Dahl S there was a significant difference at day 20 compared to virgin controls. Dahl S microbiome diversity at each time point in pregnancy (day 6, 13, and 20) trended higher than SD. Both pregnant Dahl S and SD (versus virgin) demonstrated a significant change at the Phylum level for several taxa. However, the ratio of Firmicutes:Bacteroidetes (F:B) ratio remained relatively constant across pregnancy for both Dahl S (average ratio 1.34) and SD (1.37), with the exception of day 20 in pregnant Dahl S which demonstrated a significant change in F:B ratio from 1.30 (virgin) to 0.78 (pregnant). Currently, we are working to perform a more systematic analysis, including potential changes in bacterial populations that produce beneficial short‐chain fatty acids (SCFA) that have been identified in other models of hypertension to place the differences in context of physiological changes. Future studies will determine if manipulation of the microbiota in the Dahl S strain will improve the preeclamptic phenotype and offspring outcomes.This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.

Changes of poultry faecal microbiota associated with Clostridium difficile colonisation

Bacterial, fungal and archaeal microbiota was analysed in 143 chicken faecal samples from a single poultry farm. After DHPLC (denaturing high performance liquid chromatography) 15 bacterial groups, 10 fungal groups and a single archaeal species were differentiated. Samples were grouped into two clusters with significantly different frequencies of C. difficile positive and negative samples in each cluster. Acidaminococcus intestini, described here for the first time as a part of poultry faecal microbiota, was significantly more likely present in C. difficile negative samples, while presence/absence of some other microorganisms (Enterococcus cecorum, Lactobacillus galinarum, Moniliella sp. and Trichosporon asahii) was close to significance. Two other groups not reported previously for poultry, Coprobacillus sp. and Turicibacter sp. did not differ significantly between C. difficile positive and negative samples. Differences in microbiota diversity depend on animal age, but not on the presence of C. difficile. With machine learning (WEKA J48) we have defined specific combinations of microbial groups predictive for C. difficile colonisation. Microbial groups associated with C. difficile colonisation in poultry are different than those reported for humans and include bacteria as well as fungi. Also with this approach A. intestini was found to be most strongly related to C. difficile negative samples.