Measures Of Microbial Diversity Research Articles

Associations of plant-based foods, red and processed meat, and dairy with gut microbiome in Finnish adults.

Population-based studies on the associations of plant-based foods, red meat or dairy with gut microbiome are scarce. We examined whether the consumption of plant-based foods (vegetables, potatoes, fruits, cereals), red and processed meat (RPM) or dairy (fermented milk, cheese, other dairy products) are related to gut microbiome in Finnish adults. We utilized data from the National FINRISK/FINDIET 2002 Study (n = 1273, aged 25-64 years, 55% women). Diet was assessed with 48-hour dietary recalls. Gut microbiome was analyzed using shallow shotgun sequencing. We applied multivariate analyses with linear models and permutational ANOVAs adjusted for relevant confounders. Fruit consumption was positively (beta = 0.03, SE = 0.01, P = 0.04), while a dairy subgroup including milk, cream and ice-creams was inversely associated (beta=-0.03, SE 0.01, P = 0.02) with intra-individual gut microbiome diversity (alpha-diversity). Plant-based foods (R2 = 0.001, P = 0.03) and dairy (R2 = 0.002, P = 0.01) but not RPM (R2 = 0.001, P = 0.38) contributed to the compositional differences in gut microbiome (beta-diversity). Plant-based foods were associated with several butyrate producers/cellulolytic species including Roseburia hominis. RPM associations included an inverse association with R. hominis. Dairy was positively associated with several lactic producing/probiotic species including Lactobacillus delbrueckii and potentially opportunistic pathogens including Citrobacter freundii. Dairy, fermented milk, vegetables, and cereals were associated with specific microbial functions. Our results suggest a potential association between plant-based foods and dairy or their subgroups with microbial diversity measures. Furthermore, our findings indicated that all the food groups were associated with distinct overall microbial community compositions. Plant-based food consumption particularly was associated with a larger number of putative beneficial species.

Gut Microbiome Response to the Reduction of Diet Induced Obesity by Vitamin B1 Supplementation

Dietary deficiencies in vitamins such as thiamine (Vitamin B1) produce a range of deleterious health effects and can occur even in developed countries. We’ve hypothesized that a physiological deficiency in thiamine can exacerbate conditions like obesity, diabetes, and fatty liver that are associated with consumption of high fat diets rich in soybean oil (SO) and that one or more of these conditions might be associated with changes in the composition of the gut microbiota. We first evaluated the short-term effect of thiamine deficiency on the gut microbial composition in fecal pellets from C57BL/6N male mice. Mice provided a thiamine regime of 1 mg/kg of low-fat diet for 4 weeks showed marked decreases in fecal community diversity and are characterized by “missing”’ microbes compared to animals provided a standard low-fat thiamine diet (5 mg/kg). Combined with a LC/MS metabolomic analysis these data confirmed changes in the microbiome are coincident with changes of physiological levels of thiamine in the mice. To test the effect of thiamine availability directly on obesity, a separate cohort of C57BL/6N male mice were fed either a low-fat chow (OSD) or an obesogenic soybean oil high fat diet (SO-HFD), with or without supplementation with a thiamine analog (640 mg/kg of diet). Over an 18-week period we found that animals on the SO-HFD with the added thiamine analog gained ~40% less weight compared to animals on the SO-HFD only. Longitudinal sampling of fecal pellets at week 0, 10, 16 and 18 demonstrate major shifts in the microbial composition and diversity over time for animals in all four diet groups. A nested PERMANOVA of Bray-Curtis dissimilarities confirmed the microbiome differences between the SO-HFD and OSD diet (adonis, p = 0.001) and with and without the thiamine analog supplementation (adonis, p = 0.009) at week 16. Measures of microbial diversity show significant increases in diversity for animals consuming the thiamine analog (Kruskall-Wallis, q < 0.05), consistent with the trend observed in the short-term diet trial. Taxonomic classifications for species (ASVs) that significantly increased in these animals are primarily in the Lachnospiraceae family from the Bacillota (Firmicutes) phylum. Together, these data identify major compositional and inferred functional changes to the microbiome in response to the SO-HFD diet as well as thiamine supplementation that may contribute to the observed differences in body weight gain. Funding: The Thiamine Advocacy Foundation. Acknowledgements: UCR Genomics Core. This is the full abstract presented at the American Physiology Summit 2024 meeting and is only available in HTML format. There are no additional versions or additional content available for this abstract. Physiology was not involved in the peer review process.

Oral microbial signatures associated with age and frailty in Canadian adults

This study aimed to assess the association between the oral microbiome, age, and frailty. Data and saliva samples were obtained from male and female participants aged 35–70 years (n = 1357). Saliva samples were analysed by 16S rRNA gene sequencing and differences in microbial diversity and community compositions were examined in relation to chronological age and the frailty index (FI). Most alpha diversity measures (Richness, Shannon Diversity, Faith’s Phylogenetic Diversity) showed an inverse association with frailty, whereas a positive association was observed with age and Shannon Diversity and Evenness. A further sex-stratified analysis revealed differences in measures of microbial diversity and composition. Multiple genera were detected as significantly differentially abundant with increasing frailty and age by at least two methods. With age, the relative abundance of Veillonella was reduced in both males and females, whereas increases in Corynebacterium appeared specific to males and Aggregatibacter, Fusobacterium, Neisseria, Stomatobaculum, and Porphyromonas specific to females. Beta diversity was significantly associated with multiple mental health components of the FI. This study shows age and frailty are differentially associated with measures of microbial diversity and composition, suggesting the oral microbiome may be a useful indicator of increased risk of frailty or a potential target for improving health in ageing adults.

Insights into the Adolescent Cystic Fibrosis Airway Microbiome Using Shotgun Metagenomics.

Cystic fibrosis (CF) is an inherited genetic disorder which manifests primarily in airway disease. Recent advances in molecular technologies have unearthed the diverse polymicrobial nature of the CF airway. Numerous studies have characterised the genus-level composition of this airway community using targeted 16S rDNA sequencing. Here, we employed whole-genome shotgun metagenomics to provide a more comprehensive understanding of the early CF airway microbiome. We collected 48 sputum samples from 11 adolescents and children with CF over a 12-month period and performed shotgun metagenomics on the Illumina NextSeq platform. We carried out functional and taxonomic analysis of the lung microbiome at the species and strain levels. Correlations between microbial diversity measures and independent demographic and clinical variables were performed. Shotgun metagenomics detected a greater diversity of bacteria than culture-based methods. A large proportion of the top 25 most-dominant species were anaerobes. Samples dominated by Staphylococcus aureus and Prevotella melaninogenica had significantly higher microbiome diversity, while no CF pathogen was associated with reduced microbial diversity. There was a diverse resistome present in all samples in this study, with 57.8% agreement between shotgun metagenomics and culture-based methods for detection of resistance. Pathogenic sequence types (STs) of S. aureus, Pseudomonas aeruginosa, Haemophilus influenzae and Stenotrophomonas maltophilia were observed to persist in young CF patients, while STs of S. aureus were both persistent and shared between patients. This study provides new insight into the temporal changes in strain level composition of the microbiome and the landscape of the resistome in young people with CF. Shotgun metagenomics could provide a very useful one-stop assay for detecting pathogens, emergence of resistance and conversion to persistent colonisation in early CF disease.

Mucosal Microbiome in Patients with Early Bowel Polyps: Inferences from Short-Read and Long-Read 16S rRNA Sequencing.

Numerous studies have correlated dysbiosis in stool microbiota with colorectal cancer (CRC); however, fewer studies have investigated the mucosal microbiome in pre-cancerous bowel polyps. The short-read sequencing of variable regions in the 16S rRNA gene has commonly been used to infer bacterial taxonomy, and this has led, in part, to inconsistent findings between studies. Here, we examined mucosal microbiota from patients who presented with one or more polyps, compared to patients with no polyps, at the time of colonoscopy. We evaluated the results obtained using both short-read and PacBio long-read 16S rRNA sequencing. Neither sequencing technology identified significant differences in microbial diversity measures between patients with or without bowel polyps. Differential abundance measures showed that amplicon sequence variants (ASVs) associated with Ruminococcus gnavus and Escherichia coli were elevated in mucosa from polyp patients, while ASVs associated with Parabacteroides merdae, Veillonella nakazawae, and Sutterella wadsworthensis were relatively decreased. Only R. gnavus was consistently identified using both sequencing technologies as being altered between patients with polyps compared to patients without polyps, suggesting differences in technologies and bioinformatics processing impact study findings. Several of the differentially abundant bacteria identified using either sequencing technology are associated with inflammatory bowel diseases despite these patients being excluded from the current study, which suggests that early bowel neoplasia may be associated with a local inflammatory niche.

Rotational Grazing Strategies Minimally Impact Soil Microbial Communities and Carbon Dynamics—A Texas Case Study

The goal of our study was to evaluate the long-term (>12 years) influence of stocking density and herd rotation frequency on plant and soil microbial community and carbon dynamics in three working ranches in Texas. One ranch utilized a high stocking density and high-frequency (HIGH) rotation where cattle were moved multiple times each day; the second ranch used a medium stocking density and rotation frequency (MED) where herds were moved every 2–3 weeks; and the third ranch used a low stocking density with continuous grazing (LOW). Neither plant nor microbial diversity measures differed between the ranches, but plant functional and microbial community compositions differentiated management strategies. The MED ranch was characterized by a plant community dominated by little bluestem (Schizachyrium scoparium) and had the greatest soil organic matter content (2.8%) and soil respiration rates compared to the LOW (SOM = 2.2%) and HIGH (SOM = 2.1%) ranches. The HIGH ranch had a relatively high abundance and diversity of forbs and introduced grasses, and the LOW ranch had an even mixture of tall, introduced, and cool-season grasses. All three ranches had relatively high levels of Gram-positive bacteria (>70%) with MED having a higher relative abundance of bacteria important for carbon cycling. Furthermore, network analyses suggest that soil microbial communities at all ranches were highly synergistic and exhibited well-defined ecological niches. Differences in soil properties between ranches tended to be minor and suggest that grazing strategies can differ without any substantial shifts in soil and microbial function.

INVESTIGATION OF BIOLOGICAL DETERMINANTS OF FRAILTY IN MALE AND FEMALE MICE

Abstract Frailty is quantified as the accumulation of health deficits over an organism’s lifetime and gives a measure of the overall health of an organism. Preliminary studies have found an association between frailty and some of the hallmarks of aging including inflammation and senescence. However, the molecular underpinnings of frailty, and whether the mechanisms of frailty are distinct from or overlap those of aging is unknown. Previously we developed clocks based on frailty assessments that accurately predict age and lifespan in older male mice. Here, we expand these clocks to predict age, lifespan and frailty itself in younger, and also female mice. Additionally, we incorporate molecular measures including blood cell composition, plasma metabolomics, PBMC DNA methylation and stool microbial diversity measures into the clocks. These clocks provide important tools for the field, and also provide an indication of the molecular underpinnings of frailty and sex differences in these.

The Bacterial Chaperone High-Temperature Protein G (HtpG) Decreases in Abundance with Induction Therapy in Children with Acute Lymphoblastic Leukemia

Introduction: Heat shock proteins (HSPs) are ancient and highly conserved genes that participate in protein quality control in eukaryotes and bacteria. These proteins are produced in large quantities when cells are exposed to stress that causes denaturation of essential proteins. HSPs help maintain cellular homeostasis, and act as molecular chaperones, assisting with protein folding and stability, multi-protein assembly, intracellular protein trafficking and degrading damaged proteins. The Hsp90 family of proteins includes 4 genes, with 1 (HtpG) being a bacterial form. Members of the Hsp90 family interact with a diverse set of client proteins, some involved in cell signalling and proliferation. Many of these client proteins are involved in growth, survival and adaptation of cancer cells. Eukaryotic Hsp90 plays an important role in tumorigenesis and there has been much research into the use of Hsp90 inhibitors to inhibit growth of cancer cells, but little has been done to examine what role the other paralogues have in stabilizing cancer cells. In addition, no work to date has looked at whether bacterial HtpG paralogues might interact with cancer cells. While it is anticipated that bacterial stress and the behaviour of HtpG would correlate to the host response to stress, this has not been examined. The first step is to examine bacterial HtpG gene levels before and during induction to determine if there are changes in HtpG gene abundance. Methods: Forty-eight stool samples were collected from 29 pediatric patients with Acute Lymphoblastic Leukemia (ALL) being treated at the IWK health centre, Nova Scotia, Canada after informed consent. DNA was extracted and whole shotgun metagenome sequencing (Illumina, Nextera XT) was performed. Low quality and contaminated sequences (human and PhiX174) were removed using the kneaddata pipeline (Trimmomatic and Bowtie2). Paired cleaned sequences were concatenated and HUMAnN3 was used to assign gene families to reads using the Uniref90 database. Genes assigned to HtpG or "Hsp90-like" gene families were included and summed from each sample and corrected for sequencing depth. Samples were grouped by phase of treatment (13 pre-treatment samples from 13 patients and 35 induction samples from 23 patients) for analysis. Comparisons between pre-treatment (PT) and induction (IN) samples were performed using Wilcoxon-Mann-Whitney U. Fisher's exact test was used to compare age group and sex between PT and IN samples. The study was approved by the IWK ethics board. Results: Neither sex nor age category differed between PT and IN (p=1). HtpG gene counts among the 48 stool samples from 29 patients ranged from 0 to 329 (mean 119). The mean counts of HtpG genes were significantly decreased in samples during induction therapy compared to pre-treatment (p=0.002). Shannon diversity, a measure of microbial diversity, did not differ between PT and IN samples (p=0.2793), nor did counts of bacteria (Chao-1 p=0.47). Discussion: Studies have found that Hsp90 is generally over expressed in cancer patients with elevated levels, suggesting poorer overall survival. They have been proposed as a potential biomarker of poor prognosis. We had anticipated increased stress and protein damage to occur in the gut environment as a result of chemotherapy, rather than as a result of the underlying cancer. The anticipated increase in HtpG during induction did not occur but rather declined with cancer remission. One possibility is that the decline in HtpG genes was a result of a loss of bacterial diversity due to treatment. However, we did not see significant differences in diversity between PT and IN. The increase in HtpG genes during PT and reduction during induction therapy seems to follow a similar pattern to Hsp90 expression in host cells, suggesting that bacterial HtpG might also serve as a marker of disease remission. It also highlights that a better understanding of bacterial HtpG, a protein known to be present in outer membrane vesicles, which are crucial for host communication and have been implicated in contributing to carcinogenic potential is warranted. Conclusion: This study suggests that the bacterial chaperone HtpG is possibly related to degree of inflammation caused by leukemic cells rather than leukemia treatment. A larger study is needed to verify the potential of HtpG as a marker of cancer remission or treatment toxicity or cancer immune response.

34954 Cutaneous microbial markers of squamous cell carcinoma risk in solid organ transplant recipients

Solid organ transplant recipients (SOTRs) are 100-times more prone to aggressive cutaneous squamous cell carcinoma (SCC) compared with the general population. Despite this increased mortality, our ability to prognosticate risk of cancer in SOTRs is still poor. Accumulating evidence suggests a detrimental influence of microbial dysbiosis on transplant outcomes and immunosuppressant metabolism. Additionally, altered skin microbiome, specifically excessive colonization of the skin by Staphylococcus aureus, has been found in cutaneous SCCs of immunocompetent individuals. We hypothesized that cutaneous dysbiosis is a potential modifier to the risk of SCC in SOTRs and that the microbiome of SOTRs with a history of SCC (>4 instances) is distinct from the microbiome of SOTRs without a history of SCC. To investigate this theory, we generated microbial genomic data from the skin samples of 2 matched cohorts: SOTRs with and without history of SCC. Analyses included testing for differences in microbial diversity measures and differentially relatively abundant microbiome species between cohorts. In the cutaneous microbiomes of SOTRs with SCC history, we identified a significantly reduced abundance of Roseomonas mucosa, which is a S aureus–suppressive species. This suggests a protective effect of R mucosa against the development of SCC through suppression of a bacterial species hypothesized to initiate inflammation-related signaling involved in SCC-genesis. Overall, these findings not only point to a potential role of cutaneous microbiomes as predictive biomarkers for the development of SCC in SOTRs but also suggest that the microbiome can be used for potential preventive and interventional strategies.

527 Characteristics of the gut microbiome in solid organ transplant recipients

Solid organ transplantation is the ultimate life-saving intervention in patients with end stage organ damage. However, despite revolutionary advances in transplant medicine, complications such as allograft rejection, malignancy, and disseminated infection continue be a major challenge. A growing body of evidence suggests a potential influence of microbial dysbiosis on transplant outcomes. We therefore aimed to investigate the gut microbiome of solid organ transplant recipients for comparison with healthy controls to identify possible dysbiosis. Microbial genomic data, both bacterial and fungal, was generated from fecal samples of 20 solid organ transplant recipients and 20 matched healthy controls. Analyses included testing for differences in microbial diversity measures and relatively abundant species between cohorts. The bacterial median Shannon diversity index, a measure for alpha diversity of the gut microbiome, was significantly higher in solid organ transplant samples with a median of 3.125 versus 2.449 for healthy controls (p<0.05). Additionally, principal coordinate analyses, based on Bray-Curtis distance, displayed significant differences in the bacterial and fungal microbiota composition between stool of transplant patients and healthy controls (PCo1 vs. PCo2, p<0.05). Furthermore, several alterations in abundance existed at different taxonomic levels, including a a 15-fold increased abundance of Clostridium perfringens (p<0.0001), a 3-fold increased abundance of Staph epidermidis (p<0.0001), and 2-fold increased abundance of Staph aureus (p<0.001) at the species level in transplant patients. Ultimately, we demonstrated that solid organ transplant recipients have gut microbiome dysbiosis, characterized by an increase in microbial diversity and several alterations in taxa abundance. This is in discordance with current trends in microbiome research that associate lower diversity with worse health outcomes; however, it supports the emerging role of the microbiome as a therapeutic target.

Bacterial Communities of the Uterus and Rumen During Heifer Development With Protein Supplementation

Bacterial communities play major roles in rumen and uterine function toward optimal animal performance and may be affected by changes occurring during heifer development such as nutritional supplementation for optimal growth and the attainment of puberty. The effect of different levels of protein supplementation on ruminal and uterine bacterial communities following weaning was examined through first breeding of heifers. Angus heifers (n = 39) were blocked by initial body weight (BW) and randomly assigned to one of three 163-day (d) crude protein (CP) supplementation diets including control (10% CP, n = 14), 20% CP (n = 11), or 40% CP (n = 14) treatment groups. Growth and development were monitored by body weight, with blood progesterone concentration determined every 14 d to determine pubertal status. Uterine flush and rumen fluid were collected on d 56, 112, and 163 relative to the start of supplementation. Bacterial DNA was extracted from fluid samples, the V1–V3 hypervariable region of the 16S rRNA gene was amplified, and amplicons were sequenced then processed in R 4.1. Statistical analyses were performed in SAS 9.4 with a GLIMMIX procedure utilizing fixed effects of protein, month, pubertal status, and interactions, with random effects including BW, interaction of BW and protein, and heifer within the interaction, and repeated measures of day. In the uterus, pubertal status and day of supplementation affected the observed amplicon sequence variants (ASVs) and led to clustering of samples in a principal coordinate analysis (PCoA; P &amp;lt; 0.05), but no effect of protein supplementation was observed. Ruminal samples clustered in PCoA (P = 0.001), and observed ASVs were impacted over time (P &amp;lt; 0.0001), but no effect of protein supplementation was detected. In contrast, protein supplementation, pubertal status, and day of supplementation affected the abundance of multiple phyla and genera in the uterus and rumen (P &amp;lt; 0.05). Temporal and pubertal status effects on the heifer’s uterine bacterial communities potentially indicate a maturing uterine microbiome. Protein supplementation did not impact microbial diversity measures but did affect the abundance of individual bacterial phyla and genera that may provide future opportunities to manipulate bacterial community composition and maximize productivity.

Association of Diet Quality Measured by Three A Priori-Defined Dietary Patterns With Gut Microbiota and Intestinal Permeability Among Obese Individuals

ObjectivesThe human gastrointestinal tract (GI) may play a critical role in the prevention of obesity and metabolic diseases. Considering the importance of a healthy diet for optimal health, this study examined associations of diet quality assessed by three a priori-defined dietary patterns (Healthy Eating Index 2010 [HEI-2010], Mediterranean Eating Pattern for Americans [MEPA], and Dietary Approaches to Stop Hypertension [DASH] with gut microbiota, short-chain fatty acids (SCFA) and intestinal permeability markers in adult obese participants. MethodsAnalyses utilized baseline data from 103 obese subjects (43.8 ± 11.3 years, body mass index ≥30 kg/m2, 72.8% females, 64.1% blacks) who participated in a probiotic/prebiotic supplement trial. Diet was assessed using a validated food frequency questionnaire. Associations of diet quality with outcome measures were assessed using partial correlation coefficient adjusting for relevant covariates. General linear models (GLM) were applied to compare covariate-adjusted means of outcomes for tertiles of respective dietary patterns scores. ResultsScores of HEI-2010 (r = 0.25, P = 0.02), MEPA (r = 0.24, P = 0.03) and DASH (r = 0.28, PP = 0.008) were positively associated with Blautia abundance. HEI-2010 score was positively associated butyrate and propionate to total SCFA ratio (r = 0.24, P = 0.048). Intestinal permeability marker, urinary 24-hr sucralose levels were inversely associated with HEI-2010 (r= –0.30, P = 0.009) and MEPA (r= –0.26, P = 0.02) score. The results were similar when GLM models were performed. No significant associations were observed between scores of dietary patterns and measures of microbial diversity. ConclusionsBlautia abundance and inversely associated with intestinal permeability markers such as urinary 24-h sucralose levels suggesting diet quality may have positive impact on the human GI community. Funding SourcesNo funding support.

The Gut Microbiome and Tacrolimus Dosing in the Peri-Heart Transplant Period

<h3>Purpose</h3> Recent evidence suggest that the gut microbiome may influence tacrolimus dosing requirements, potentially through direct metabolism. The impact of the gut microbiome on tacrolimus requirements among heart transplant (HT) recipients during medication initiation is unknown. We aimed to evaluate the effect of the gut microbiome on tacrolimus dosing requirements among HT recipients in the peri-HT period. <h3>Methods</h3> We conducted a prospective, observational cohort study of all single organ HT recipients at a single center from 2020-2021. Stool samples were collected within 2 weeks of HT and underwent shotgun metagenomic analysis. Measures of microbial diversity, composition, and metabolomics were correlated to the ratio of tacrolimus serum level (L) to the total 24-hour dose (D) at time of post-HT discharge. HT recipients were further divided into 2 groups: above-median L/D ratio (slow metabolizers) and below-median L/D ratio (fast metabolizers). <h3>Results</h3> Thirty-two patients were included in the study. Stool samples were collected a median of 8 days (IQR [5, 11]) post-HT. Median time to discharge was 18 days (IQR [12, 23]). Median L/D ratio was 0.86 (IQR [0.52, 1.13]) with 18 patients in the slow metabolizer group and 16 in the fast metabolizer group (median L/D 1.28 vs 0.61, p = 0.001). The fast metabolizer group was on a higher tacrolimus dose at discharge than the slow metabolizer group (19 vs 9 mg/day, p<0.001). Demographic factors and within sample microbial diversity, i.e. α-diversity, as measured by inverse Simpson index was similar between groups. The fast metabolizer group was found to have lower abundance of the phylum <i>Bacteroidetes</i> (19% vs 39%, p = 0.03) and higher abundance of <i>Firmicutes</i> (67% vs 47%, p = 0.04) (Fig. 1). Both groups had similar levels of the gut microbial metabolites, secondary bile acids and short chain fatty acids. <h3>Conclusion</h3> HT recipients have variable tacrolimus dosing requirements in the immediate post-HT period. Differences in the abundance of gut microbes in the peri-HT period may influence these needs.

26555 Characterizing the skin and fecal microbiome in solid organ transplant recipients

Solid organ transplant recipients (SOTRs) have a significantly increased risk of many malignancies, with squamous cell carcinomas accounting for the largest fraction of post-transplant skin cancers. Despite this knowledge of increased mortality, our ability to prognosticate which SOTRs have the highest risk of cancer is still poor. The microbiome (composed of both bacterial and fungal communities) plays a key role in the maintenance of immune homeostasis, as microbial dysbiosis has been implicated in the development of various skin disorders and malignancies. Immunosuppression posttransplantation affects the microbiome, and the dysregulation of immunosurveillance facilitates the development of cutaneous squamous cell carcinoma (cSCC). Thus, we hypothesize that the microbiome of SOTRs with a history of cSCC (>4 instances) is distinct from the microbiome of SOTRs without a history of cSCC. Studies suggest we may find a decreased prevalence of Malassezia species and a higher prevalence of S aureus-like operational taxonomic units (OTUs) on the skin of SOTRs with cSCC. We are generating microbial genomic data from skin and fecal samples of the two cohorts: SOTRs with or without a history of cSCC. Analyses include testing for the difference in microbial diversity measures and differentially abundant species between the samples. We are at the stage of recruiting and characterizing the microbial profiles of our preliminary patients. These pilot data may lead to prognostic markers of microbiome patterns that correlate with a higher incidence of cSCC.

Sampling cores and sequencing depths affected the measurement of microbial diversity in soil quadrats

Due to the massive quantity and broad phylogeny, an accurate measurement of microbial diversity is highly challenging in soil ecosystems. Initially, the deviation caused by sampling should be adequately considered. Here, we attempted to uncover the effect of different sampling strategies on α diversity measurement of soil prokaryotes. Four 1 m2 sampling quadrats in a typical grassland were thoroughly surveyed through deep 16S rRNA gene sequencing (over 11 million reads per quadrat) with numerous replicates (33 soil sampling cores with total 141 replicates per quadrat). We found the difference in diversity was relatively small when pooling soil cores before and after DNA extraction and sequencing, but they were both superior to a non-pooling strategy. Pooling a small number of soil cores (i.e., 5 or 9) combined with several technical replicates is sufficient to estimate diversities for soil prokaryotes, and there is great flexibility in pooling original samples or data at different experimental steps. Additionally, the distribution of local α diversity varies with sampling core number, sequencing depth, and abundance distribution of the community, especially for high orders of Hill diversity index (i.e., Shannon entropy and inverse Simpson index). For each grassland soil quadrat (1 m2), retaining 100,000 reads after taxonomic clustering might be a realistic option, as these number of reads can efficiently cover the majority of common species in this area. Our findings provide important guidance for soil sampling strategy, and the general results can serve as a basis for further studies.

2079-P: Racial Differences in Gut Microbiota, ß-Cell Function, Body Fat Distribution, and Their Relation with Incretins in Subjects with Normal Glucose Tolerance

Racial differences in the gut microbiota and its influence in development of diabetes have been previously reported. However, whether differences exist between Chinese and Africans, currently no study. We investigated whether differences in body fat may account for microbial communities to expound racial disparities in insulin secretion, sensitivity or resistance, and that GLP-1 may play a role. We measured fasting and stimulated GLP-1, insulin and glucose levels during a 3h OGTT in 27 Han-Chinese university students(HC) and 29 International students from East Africa(EA) healthy subjects with normal glucose tolerance. We also measured the whole body fat and the regions of interest of local body composition, and gut microbiota composition. HC group showed significantly higher triglyceride levels, total bile acids, glucose response at 30min, incremental glucose level at 30min, HOMA-IR at 30 min, body fat distribution and abundance of microbial phyla, but lower hip circumference and β-cell function than EA. Interestingly, HC had lower bacterial taxa and majority of measures of microbial diversity than EA. GLP-1 correlated with metabolic risk factors and microbial communities. The results suggest that body fats are associated with gut microbiota and that GPL-1 enhances their association, which in turn may result in Chinese developing T2DM. Disclosure P. Nizigiyimana: None. L. Liu: None. B. Xu: None. T. Liu: None. L. Gao: None. Z. Liu: None. C. Li: None. X. Luo: None. M. Lei: None.

Saliva microbiome in primary Sjögren's syndrome reveals distinct set of disease-associated microbes.

This study systematically aims to evaluate the salivary microbiome in patients with primary Sjögren's syndrome (pSS) using 16S rRNA sequencing approach. DNA isolation and 16S rRNA sequencing was performed on saliva of 37 pSS and 35 control (CC) samples on HiSeq 2500 platform. 16S rRNA sequence analysis was performed independently using two popular computational pipelines, QIIME and less operational taxonomic units scripts (LoTuS). There were no significant changes in the alpha diversity between saliva of patients and controls. However, four genera including Bifidobacterium, Lactobacillus, Dialister and Leptotrichia were found to be differential between the two sets, and common between both QIIME and LoTuS analysis pipelines (Fold change of 2 and p<.05). Bifidobacterium, Dialister and Lactobacillus were found to be enriched, while Leptotrichia was significantly depleted in pSS compared to the controls. Exploration of microbial diversity measures (Chao1, observed species and Shannon index) revealed a significant increase in the diversity in patients with renal tubular acidosis. An opposite trend was noted, with depletion of diversity in patients with steroids. Our analysis suggests that while no significant changes in the diversity of the salivary microbiome could be observed in Sjögren's syndrome compared to the controls, a set of four genera were significantly and consistently differential in the saliva of patients with pSS. Additionally, a difference in alpha diversity in patients with renal tubular acidosis and those on steroids was observed.

Microscale and molecular analyses of river biofilm communities treated with microgram levels of cerium oxide nanoparticles indicate limited but significant effects

Cerium oxide (CeO2) nanoparticles are used as in-fuel catalysts and in manufacturing processes, creating a potential for release to aquatic environments. Exposures at 1 and 10 μg/L CeO2-nanoparticles were made to assess effects during the development of river biofilm communities. Scanning transmission x-ray microscopy (STXM) indicated extensive sorption of nanoparticles to the community and co-localization with lipid moieties. Following 8 weeks of development, polycarbonate coupons were removed from the reactors and used for molecular analyses, denaturing gradient gel electrophoresis analysis (DGGE-16S rRNA) and 16S rRNA amplicon sequencing. Microscopic imaging of the biofilm communities (bacterial, photosynthetic biomass, exopolymer composition, thickness, protozoan numbers), as well as carbon substrate utilization fingerprinting was performed. There was a trend toward reduced photosynthetic biomass, but no significant effects of CeO2 exposure were found on photosynthetic and bacterial biomass or biofilm thickness. Sole carbon source utilization analyses indicated increased utilization of 10 carbon sources in the carbohydrate, carboxylic acid and amino acids categories related to CeO2 exposures; however, predominantly, no significant effects (p < 0.05) were detected. Measures of microbial diversity, lectin binding affinities of exopolymeric substances and results of DGGE analyses, indicated significant changes to community composition (p < 0.05) with CeO2 exposure. Increased binding of the lectin Canavalia ensiformis was observed, consistent with changes in bacterial-associated polymers. Whereas, no significant changes were observed in binding to residues associated with algal and cyanobacterial exopolymers. 16S rRNA amplicon sequencing of community DNA indicated changes in diversity and shifts in community composition; however, these did not trend with increasing CeO2 exposure. Counting of protozoans in the biofilm communities indicated no significant effects on this trophic level. Thus, based on biomass and functional measures, CeO2 nanoparticles did not appear to have significant effects; however, there was evidence of selection pressure resulting in significant changes in microbial community composition.

Defining microbial biomarkers for risk of preterm labor

Preterm birth remains the main contributor to early childhood mortality. The vaginal environment, including microbiota composition, might contribute to the risk of preterm delivery. Alterations in the vaginal microbial community structure might represent a risk factor for preterm birth. Here, we aimed to (a) investigate the association between preterm birth and the vaginal microbial community and (b) identify microbial biomarkers for risk of preterm birth. Microbial DNA was isolated from vaginal swabs in a cohort of 69 women enrolled at hospital admission for their delivery. Microbiota was analyzed by high-throughput 16S rRNA sequencing. While no differences in microbial diversity measures appeared associated with the spontaneous preterm and full-term outcomes, the microbial composition was distinct for these groups. Differential abundance analysis showed Lactobacillus species to be associated with full-term birth whereas an unknown Prevotella species was more abundant in the spontaneous preterm group. Although we studied a very miscegenated population from Brazil, our findings were similar to evidence pointed by other studies in different countries. The role of Lactobacillus species as a protector in the vaginal microbiome is demonstrated to be also a protector of spontaneous preterm outcome whereas the presence of pathogenic species, such as Prevotella spp., is endorsed as a factor of risk for spontaneous preterm delivery.

Effect of whole-grain consumption on changes in fecal microbiota: a review of human intervention trials.

Whole-grain (WG) consumption is known to have beneficial effects on human health. However, the influence of WGs on the microbiota is not well understood. To evaluate how WG intake modulates the gut microbiota composition, a literature review of human intervention studies was conducted. Whole grain, whether a mixed WG food or diet (n = 5) or specific WG intervention (WG wheat [n = 5], barley [n = 2], rye [n = 2] or rice, corn, or oats [n = 1 for each]), generally modified microbiota composition but did so inconsistently across measurements of microbial diversity and taxa. Interventions used both parallel and crossover designs and varied from single product substitutions to fully controlled diets with WG exposures of 3-12 weeks. The effect of amount of WG was difficult to capture due to variable reporting of WG. Methods used to measure microbiota varied in ability to resolve changes at different taxonomic levels, and comparisons of interventions using similar methods was lacking. Because many dietary components besides WGs alter gut microbiota, further research is needed, particularly in linking microbiota changes to health outcomes, and study design recommendations for future research on WGs and microbiota are warranted.