Inverse Simpson Index Research Articles

Gut microbiome as a response marker for pancreatic enzyme replacement therapy in a porcine model of exocrine pancreas insufficiency

BackgroundExocrine pancreatic insufficiency (EPI) is characterized by the loss of active pancreatic enzymes and a resulting severely reduced food digestion. EPI therapy requires orally applied pancreatic enzyme replacement. The gut microbiome is a known mediator of intestinal diseases and may influence the outcome of EPI and the effects of a pancreatic enzyme replacement therapy (PERT). Here, we analyzed the effects of EPI and PERT on the gut microbiome in the model of pancreatic duct ligated minipigs.ResultsThe microbial community composition in pig feces was analyzed by next generation sequencing of 16S rRNA amplicons. The data were evaluated for α- and β-diversity changes and changes at the different Operational Taxonomic Unit (OTU) levels by Shannon–Wiener and inverse Simpson index calculation as well as by Principal Coordinates Analysis based on Bray–Curtis dissimilarity. Microbial α-diversity was reduced after EPI induction and reverted to nearly healthy state after PERT. Analysis of microbial composition and β-diversity showed distinctive clusters of the three study groups and a change towards a composition comparable to healthy animals upon PERT. The relative abundance of possible pathobionts like Escherichia/Shigella, Acinetobacter or Stenotrophomonas was reduced by PERT.ConclusionThese data demonstrate that EPI-induced dysbiosis could be reverted by PERT to a nearly healthy state. Elevated α-diversity and the reduction of bacterial overgrowth after PERT promises benefits for EPI patients. Non-invasive microbiome studies may be useful for EPI therapy monitoring and as marker for response to PERT.

Distinct microbial assemblages associated with genetic selection for high- and low- muscle yield in rainbow trout

BackgroundFish gut microbial assemblages play a crucial role in the growth rate, metabolism, and immunity of the host. We hypothesized that the gut microbiota of rainbow trout was correlated with breeding program based genetic selection for muscle yield. To test this hypothesis, fecal samples from 19 fish representing an F2 high-muscle genetic line (ARS-FY-H) and 20 fish representing an F1 low-muscle yield genetic line (ARS-FY-L) were chosen for microbiota profiling using the 16S rRNA gene. Significant differences in microbial assemblages between these two genetic lines might represent the effect of host genetic selection in structuring the gut microbiota of the host.ResultsTukey’s transformed inverse Simpson indices indicated that high muscle yield genetic line (ARS-FY-H) samples have higher microbial diversity compared to those of the low muscle yield genetic line (ARS-FY-L) (LMM, χ2(1) =14.11, p < 0.05). The fecal samples showed statistically distinct structure in microbial assemblages between the genetic lines (F1,36 = 4.7, p < 0.05, R2 = 11.9%). Functional profiling of bacterial operational taxonomic units predicted characteristic functional capabilities of the microbial communities in the high (ARS-FY-H) and low (ARS-FY-L) muscle yield genetic line samples.ConclusionThe significant differences of the microbial assemblages between high (ARS-FY-H) and low (ARS-FY-L) muscle yield genetic lines indicate a possible effect of genetic selection on the microbial diversity of the host. The functional composition of taxa demonstrates a correlation between bacteria and improving the muscle accretion in the host, probably, by producing various metabolites and enzymes that might aid in digestion. Further research is required to elucidate the mechanisms involved in shaping the microbial community through host genetic selection.

Gut Bacterial Diversity Associates with Efficacy of Anti-CD19 CAR T-Cell Therapy in Patients with Large B-Cell Lymphoma

Gut Bacterial Diversity Associates with Efficacy of Anti-CD19 CAR T-Cell Therapy in Patients with Large B-Cell Lymphoma

Successful and Safe Treatment of Intestinal Graft-Versus-Host Disease (GvHD) with Pooled-Donor Full Ecosystem Microbiota Biotherapeutic: Results from a 29 Patient-Cohort of a Compassionate Use/Expanded Access Treatment Program

Introduction Intestinal graft-versus-host disease (GvHD), following allogeneic hematopoietic stem cell transplantation (allo-HSCT), has a high mortality rate and a reduced life-expectancy. In this context, failure to respond to steroid therapy is associated with limited further therapeutic options, thereby representing an unmet medical need. Aiming at restoring microbiome functions, fecal microbiota transfer (FMT) has proved to be a promising treatment modality in this challenging clinical setting, with recent studies reporting favorable results in steroid refractory-acute GVHD (SR-aGvHD) patients. Here we report on the use of a next-gen FMT product "MaaT013", a standardized, pooled-donor, high-richness microbiota biotherapeutic, used to treat 29 patients with intestinal aGvHD as part of a compassionate use/expanded access treatment program. Patients and methods Twenty-nine allo-HSCT recipients with steroid-dependent or SR intestinal GvHD (classical aGVHD n=22, late-onset aGVHD n=2; aGvHD with overlap syndrome n=5) were treated with MaaT013 biotherapeutic as part of a compassionate use/expanded access treatment program of the developer MaaT Pharma. These patients had previously received and failed 1 to 5 lines (median 3; 22/29 received ruxolitinib) of GvHD systemic treatments. Each patient received 1 to 3 doses (median: 3; total doses administered: 71) of MaaT013, a 150 mL bag, by enema (n=28) or nasogastric tube (n=1). GI-GvHD response was evaluated 7 days after each administration and 28 days after the first dose. Prepared under Good Manufacturing Practices, MaaT013 biotherapeutics are characterized by a highly consistent richness of 455 ±3% Operational Taxonomic Units and an Inverse Simpson index greater than 20. Batch release specifications are based on potency (viability), identity (diversity), and purity (microbiological safety testing and proportion of proinflammatory species), ensuring the desired consistency across batches. Results We observed a GI overall response rate of 59% (17/29) at day 28 after first dosing, including 9 complete response (CR), 6 very good partial response (VGPR), and 2 partial response (PR). Considering the best GI response achieved, 20/29 patients (69%) achieved at least a PR, with 9 CR, 8 VGPR and 3 PR. Among the 29 treated patients, 16 were still alive at last follow-up (median follow-up (FU): 131.5 days; range [28; 413]) and 6 months overall survival was 54%. Among the 9 patients achieving CR, all were still alive at last follow-up (median FU: 197 days; [49; 301]) and were able to taper or stop steroids and immunosuppressants. Among these 9 patients, three patients presented GI symptom recurrence between 2 and 3 months after dosing. In 2 patients, this recurrence occurred after heavy antibiotic treatment, one of them received an additional MaaT013 dose and achieved a second CR. Of note, among these 9 patients, mild chronic mucosal GvHD symptoms persisted in one patient, and molecular relapse of hematologic malignancy was observed in another. The safety of the MaaT013 microbiota biotherapeutic was satisfactory for all patients. One patient developed "possibly related" sepsis one day after the third dosing but no pathogen was identified in blood cultures, and the patient recovered after a course of antibiotics. Another patient developed C. difficile diarrhea 24 hours post-administration. This was not causally related to MaaT013, as C. difficile testing was negative in the MaaT013 lot. Nosocomial transmission was suspected as the cause as several patients with C. difficile infection were hospitalized in the same unit during this period. Conclusions We herein report for the first time the treatment of 29 patients with steroid-dependent or SR intestinal aGvHD using a full ecosystem, standardized, pooled-donor, high-richness biotherapeutic. The overall response rate was 59% with the off-the-shelf MaaT013 product, which was shown to be safe and effective in these heavily pre-treated and immunocompromised patients, warranting further exploration of the full ecosystem microbiota restoration approach. Disclosures Malard: Astellas: Honoraria; JAZZ pharmaceutical: Honoraria; Sanofi: Honoraria; Janssen: Honoraria; Keocyt: Honoraria; Theralos/Mallinckrodt: Honoraria; Biocodex: Honoraria. Plantamura:MaaT Pharma: Current Employment. Mohty:BMS: Consultancy, Honoraria, Research Funding, Speakers Bureau; Sanofi: Consultancy, Honoraria, Research Funding, Speakers Bureau; Novartis: Consultancy, Honoraria, Research Funding, Speakers Bureau; GSK: Consultancy, Honoraria, Research Funding, Speakers Bureau; Takeda: Consultancy, Honoraria, Research Funding, Speakers Bureau; Jazz Pharmaceuticals: Consultancy, Honoraria, Research Funding, Speakers Bureau; Amgen: Consultancy, Honoraria, Research Funding, Speakers Bureau; Janssen: Consultancy, Honoraria, Research Funding, Speakers Bureau; Stemline: Consultancy, Honoraria, Research Funding, Speakers Bureau; Celgene: Consultancy, Honoraria, Research Funding, Speakers Bureau.

Gut Microbiome During and after Pelvic Chemoradiation for Gynecologic Cancers

There is significant interest in the gut microbiome and its role in cancer response, with previous data showing that a more diverse and abundant gut microbiota can lead to improved response; however, the effect of radiation on gut diversity and composition complicates interpretations in the setting of radiation therapy. The purpose of this study was to prospectively describe the landscape of the gut microbiome during and after pelvic chemoradiation therapy (CRT) for patients with cervical, vaginal, or vulvar cancer. Anorectal swabs from 58 women with cervical, vaginal, or vulvar cancer from two institutions were prospectively analyzed at baseline, during CRT (weeks 1, 3, and 5), and at first follow up (week 12) using 16Sv4 rRNA gene sequencing. Observed OTUs, Shannon, Simpson, Inverse Simpson, and Fisher diversity indices were used to characterize Alpha (within sample) diversity. Changes over time were assessed using paired t-test to baseline, repeated measures ANOVA, and linear mixed modeling. Changes in specific bacteria were evaluated using linear discriminant analysis effect size (LEfSe) to identify bacterial genera that were differentially enriched in patients at baseline, week 5, and week 12. Gut microbiome diversity declined gradually over the course of treatment, reaching significance at week 5 (Shannon: 2.52 vs. 2.91; all P <0.01); however, the gut microbiome tends to return to baseline after treatment (week 12; 34.3% of patients). Patients with higher diversity at baseline have a steeper decrease in their gut microbiome diversity over time (Shannon: Slope = -0.81; all P <0.01). The relative abundance of the Clostridia class decreased over time (27.1% - 19.3%), while individual OTUs of Clostridia both increased and decreased over time (69.7%-38%). During CRT, patients’ gut microbiome diversity levels decreased but generally returned to baseline after treatment and varied by baseline diversity. Although patients’ gut microbiome diversity tends to return to baseline levels after treatment completion, the structure of their microbiomes may be affected for a longer period of time. These serial changes in the gut microbiome during CRT should be considered when designing studies to analyze the gut microbiome effects on treatment response and toxicity.

The Gut Microbiome of Adults with Allergic Rhinitis Is Characterised by Reduced Diversity and an Altered Abundance of Key Microbial Taxa Compared to Controls

Introduction: Unique gut microbial colonisation patterns are associated with the onset of allergic disease in infants; however, there is insufficient evidence to determine if aberrant microbial composition patterns persist in adult allergic rhinitis (AR) sufferers. Objective: To compare the gut microbiome composition between adult AR sufferers and controls. Methods: Gut microbial composition in stool samples was compared between 57 adult AR sufferers (39.06 ± 13.29 years) and 23 controls (CG; 36.55 ± 10.51 years) via next-generation sequencing of the V3–V4 hypervariable regions of the 16S rRNA gene. Taxonomic classification and identity assignment was performed using a reference-based approach with the NCBI database of 16S rRNA gene sequences. Results: Species richness determined via the Shannon index was significantly reduced in the AR cohort compared to the CG (4.35 ± 0.59 in AR vs. 4.65 ± 0.55 in CG, p = 0.037); trends for reductions in operational taxonomic unit (OTU) counts, inverse Simpson, and CHAO1 diversity indices were also noted. Bacteroidetes (p = 0.014) was significantly more abundant in the AR group than in the CG. In contrast, the Firmicutes phylum was significantly less abundant in the AR group than in the CG (p = 0.006). An increased abundance of Parabacteroides (p = 0.008) and a reduced abundance of Oxalobacter (p = 0.001) and Clostridiales (p = 0.005) were also observed in the AR cohort compared to the CG. Conclusion: Adult AR sufferers have a distinct gut microbiome profile, marked by a reduced microbial diversity and altered abundance of certain microbes compared to controls. The results of this study provide evidence that unique gut microbial patterns occur in AR sufferers in adulthood and warrant further examination in the form of mechanistic studies.

Biological observations in microbiota analysis are robust to the choice of 16S rRNA gene sequencing processing algorithm: case study on human milk microbiota

BackgroundIn recent years, the microbiome field has undergone a shift from clustering-based methods of operational taxonomic unit (OTU) designation based on sequence similarity to denoising algorithms that identify exact amplicon sequence variants (ASVs), and methods to identify contaminating bacterial DNA sequences from low biomass samples have been developed. Although these methods improve accuracy when analyzing mock communities, their impact on real samples and downstream analysis of biological associations is less clear.ResultsHere, we re-processed our recently published milk microbiota data using Qiime1 to identify OTUs, and Qiime2 to identify ASVs, with or without contaminant removal using decontam. Qiime2 resolved the mock community more accurately, primarily because Qiime1 failed to detect Lactobacillus. Qiime2 also considerably reduced the average number of ASVs detected in human milk samples (364 ± 145 OTUs vs. 170 ± 73 ASVs, p < 0.001). Compared to the richness, the estimated diversity measures had a similar range using both methods albeit statistically different (inverse Simpson index: 14.3 ± 8.5 vs. 15.6 ± 8.7, p = 0.031) and there was strong consistency and agreement for the relative abundances of the most abundant bacterial taxa, including Staphylococcaceae and Streptococcaceae. One notable exception was Oxalobacteriaceae, which was overrepresented using Qiime1 regardless of contaminant removal. Downstream statistical analyses were not impacted by the choice of algorithm in terms of the direction, strength, and significance of associations of host factors with bacterial diversity and overall community composition.ConclusionOverall, the biological observations and conclusions were robust to the choice of the sequencing processing methods and contaminant removal.

Andean bear diet near to and far from a road

Despite the existence of several regional studies on the diet of the Andean bear (Tremarctos ornatus), there is a lack of information about the effects of human disturbances on this species' foraging ecology. Our main goal was to compare Andean bear diet composition between a disturbed area (DA) close to a paved road versus an undisturbed area (UA) far away from it, within the Parque Nacional y Area Natural de Manejo Integrado Cotapata, Bolivia. We collected 120 feces samples between October and November 2014—60 samples from each area. We identified 13 species from the feces collected at UA, whereas we identified only 7 species from the feces at DA. Mean number of identified food items per fecal sample at UA was 2.90 (SD = 0.86) and significantly greater (t = –4.32, = 118 df, P < 0.001) than DA mean 1.95 (SD = 1.43). Levin's index points to a specialist diet for Andean bears at both areas, but niche breadth at the UA (0.083) was almost twice the value at DA (0.043). Almost half of the items were found at both the UA and the DA (Jaccard's index = 0.538). Simpson's Diversity index ([UA] = 0.310, [DA] = 0.167) shows that Andean bear diet at the UA was also more equitable, as well as less dominated by a single item (Inverse Simpson index N [DA] = 3.229, N [UA] = 5.997). These results suggest that the presence of a road may affect Andean bear foraging ecology.

Inconsistent diversity patterns of soil fungi and woody plants among habitat types in a karst broadleaf forest

The diversity patterns of macroorganisms (i.e., plants) among different habitats have been well documented, however, those of microorganisms (i.e., fungi) as well as the relationships between them are still unclear. Here, we tested whether and to what degree fungal diversity was related to habitat types and compared diversity patterns of woody plants and soil fungi. We carried out field investigations on soil fungi in different habitat types (i.e., valleys, foothills, hillsides, and hilltops) in a 25-ha karst broadleaf forest in Southwest China. The tree richness, Shannon index, and Simpson index significantly increased from valleys to hilltops. While the soil fungal N1 diversity (the exponential Shannon index) marginally increased toward valleys, fungal N0 (richness) and N2 (the inverse Simpson index) diversity exhibited significantly reduced and increased patterns, respectively, from valleys to hilltops. The major fungal functional groups (i.e., EcM, AM, saprotrophic, and pathogenic fungi) showed similar increasing richness patterns in valleys. Moreover, woody plant alpha diversity was an important indicator of fungal functional groups except for EcM and AM fungi. In addition, woody plants increased in species turnover rate (βSIM) from valleys to hilltops, while fungal species had a concave distribution. The patterns of nestedness (βSNE) for tree species decreased from valleys to hilltops, while the opposite was true for soil fungal species. Our findings indicated that the diversity patterns of woody plants and fungi were inconsistent among habitat types, and the relationships between fungal and woody plant communities depended on habitat types in the karst forest.

Perinatal risk factors for fecal antibiotic resistance gene patterns in pregnant women and their infants.

Perinatal factors can shape fecal microbiome patterns among pregnant women and their infants. However, there is scarce information about the effect of maternal demographics and perinatal exposures on antibiotic resistance genes (ARG) and mobile genetic element (MGE) patterns in pregnant women and infants. We examined fecal samples from pregnant women during their third trimester of pregnancy (n = 51) and 6-month-old infants (n = 40). Of the 91 participants, 72 represented 36 maternal-infant dyads, 15 were additional pregnant women, and 4 were additional infants. We assessed the effects of demographics, pre-pregnancy BMI, smoking and parity in the pregnancy resistome and the effects of demographics, delivery mode, feeding habits and prenatal antibiotic treatment on the infancy resistome. ARG and MGE richness and abundance were assessed using a SmartChip qPCR-array. Alpha diversity (Shannon and Inverse Simpson index) and beta diversity (Sorensen and Bray-Curtis index) were calculated. The Wilcoxon and the Kruskal non-parametric test were used for comparisons. There is a high variability in shared resistome patterns between pregnant women and their infants. An average of 29% of ARG and 24% of MGE were shared within dyads. Infants had significantly greater abundance and higher diversity of ARG and MGE compared to pregnant women. Pregnancy and infancy samples differed in ARG and MGE gene composition and structure. Composition of the fecal resistome was significantly associated with race in pregnant women, with non-white women having different patterns than white women, and, in infants, with extent of solid food consumption. Our data showed that the pregnancy and infancy resistome had different structure and composition patterns, with maternal race and infant solid food consumption as possible contributors to ARG. By characterizing resistome patterns, our results can inform the mechanism of antibiotic resistome development in pregnant women and their infants.

Airway microbial diversity is decreased in young children with cystic fibrosis compared to healthy controls but improved with CFTR modulation

BackgroundCulture-independent next generation sequencing has identified diverse microbial communities within the cystic fibrosis (CF) airway. The study objective was to test for differences in the upper airway microbiome of children with CF and healthy controls and age-related differences in children with CF. MethodsOropharyngeal swabs and clinical data were obtained from 25 children with CF and 50 healthy controls aged ≤6 years. Bacterial DNA was amplified and sequenced for the V4 region of 16S rRNA marker-gene. Alpha diversity was measured using operational taxonomic units (OTUs), Shannon diversity, and the inverse Simpson's index. Beta diversity was measured using Morisita-Horn and Bray-Curtis and Jaccard distances. General linear models were used for comparison of alpha diversity measures between groups to account for differences in demographics and exposures. Mixed effects general linear models were used for longitudinal comparisons 1) between children with CF of different ages and 2) between children with CF receiving CF transmembrane conductance regulator (CFTR) modulators, children with CF not receiving CFTR modulators, and healthy controls to adjust for repeated measures per subject. ResultsChildren with CF were more likely to have received antibiotics in the prior year than healthy controls (92% vs 24%, p < 0.001). Controlling age, race, ethnicity, length of breastfeeding, and having siblings, children with CF had a lower richness than healthy controls: OTUs 62.1 vs 83, p = 0.022; and trended toward lower diversity: Shannon 2.09 vs 2.35, p = 0.057; inverse Simpson 5.7 vs 6.92, p = 0.118. Staphylococcus, three Rothia OTUs, and two Streptococcus OTUs were more abundant in CF children versus healthy controls (all p < 0.05). Bray-Curtis and Jaccard distances, which reflect overall microbial community composition, were also significantly different (both p = 0.001). In longitudinally collected samples from children with CF, Morisita-Horn trended toward more similarity in those aged 0–2 years compared to those aged 3–6 years (p = 0.070). In children >2 years of age, there was a significant trend in increasing alpha diversity measures between children with CF not receiving CFTR modulators, children with CF receiving CFTR modulators, and healthy controls: OTUs 63.7 vs 74.7 vs 97.6, p < 0.001; Shannon 2.11 vs 2.34 vs 2.56, p < 0.001; inverse Simpson 5.78 vs 7.23 vs 7.96, p < 0.001. ConclusionsChildren with CF have lower bacterial diversity and different composition of organisms compared with healthy controls. This appears to start in early childhood, is possibly related to the use of antibiotics, and may be partially corrected with the use of CFTR modulators.

Meal Regularity Plays a Role in Shaping the Saliva Microbiota.

BackgroundDiet may influence health directly or indirectly via the human microbiota, emphasizing the need to unravel these complex relationships for future health benefits. Associations between eating habits and gut microbiota have been shown, but less is known about the association between eating habits and saliva microbiota.ObjectiveThe aim of this study was to investigate if eating habits and meal patterns are associated with the saliva microbiota.MethodsIn total, 842 adolescents, aged 11–14 years, from the Finnish Health in Teens (Fin-HIT) study cohort were included in this study. Eating habits and breakfast and dinner patterns were derived from a web-based questionnaire answered in school. Three major eating habit groups were identified: fruit and vegetable avoiders (FV avoiders), healthy and unhealthy. Microbiota profiles were produced from 16S rRNA gene (V3–V4) sequencing of DNA from the saliva samples. Statistical models were adjusted for gender, age, parental language, body mass index (BMI) categories, and sequencing depth.ResultsRegular breakfast eaters had a higher alpha diversity (Shannon index with mean (standard error of means) 2.27 (0.03) vs. 2.22 (0.03), p = 0.06, inverse Simpson’s index with 6.27 (0.17) vs. 5.80 (0.02), p = 0.01), and slight differences in bacterial composition (PERMANOVA: p = 0.001) compared with irregular breakfast eaters. A similar trend in alpha diversity was observed between regular and irregular dinner eaters (Shannon index with 2.27 (0.03) vs. 2.22 (0.03), p = 0.054, inverse Simpson’s index with 6.23 (0.17) vs. 6.04 (0.22), p = 0.28), while no difference was found in composition (PERMANOVA: p = 0.08). No differences were identified between eating habit groups and saliva microbiota diversity (Shannon index p = 0.77, inverse Simpson’s index p = 0.94) or composition (PERMANOVA: p = 0.13). FV avoiders, irregular breakfast eaters and irregular dinner eaters had high abundances of Prevotella.ConclusionRegularity of eating, especially breakfast eating, was associated with more diverse saliva microbiota and different composition compared with irregular eaters. However, the dissimilarities in composition were small between regular and irregular breakfast eaters. Our results suggest that Prevotella abundances in saliva were common in FV avoiders and meal skippers. However, the clinical implications of these findings need to be evaluated in future studies.

Abstract A23: Association of gut microbiome diversity with obesity and breast density in postmenopausal women

Abstract Purpose: The plausible roles of the gut microbiome (GM) in obesity as well as breast cancer have been discussed in recent reviews. The associations of GM with mammographic breast density (BD), a well-established strong breast cancer risk factor, also associated with body mass index (BMI), are poorly studied. We examined GM profiles in relation to BD and BMI in a sample of healthy postmenopausal women. Methods: Women were recruited in mammography clinics at Moffitt Cancer Center and via recruitment announcements at the University of Florida. Eligible women were postmenopausal, had a BMI ≤35 kg/m2, and had not taken oral/IV antibiotics within 30 days and/or more than two separate antibiotic regimens within the previous three months. All women provided a fecal sample and comprehensive information on breast cancer risk factors including body weight and height. Mammographic BD was available for 69 women recruited at Moffitt and was classified according to the American College of Radiology’s BI-RADS BD classification system. For this analysis, BD was dichotomized as low (BI-RADS I or II) or high (BI-RADS III and IV). DNA was isolated from fecal samples and the V1-V2 hypervariable regions of 16S rRNA amplified using barcoded primers for sequencing on the Illumina MiSeq platform. Chao1, Inverse Simpson, and Shannon indices were used to classify within sample diversity. The two-sample Wilcoxon test was used to examine associations of GM with BD and BMI. Associations were also examined according to the ratio of the two main phyla in the human GM (Firmicutes and Bacteroidetes; F/B ratio) that has been linked to obesity in previous studies. Results: Among 69 women with BD data, 39 had low BD and 30 had high BD. BMI was inversely associated with BD (mean BMI=23.8 in women with high BD and BMI=28.0 in women with low BD, p=1.07 × 10-5). The F/B ratio was not associated with BMI (median F/B ratio=0.90, 0.84, and 0.96 for normal weight, overweight, and obesity, respectively, p=0.57). Similar levels of diversity were found across weight groups according to the Shannon (4.05, 3.97, and 3.96, respectively, p=0.83); inverse Simpson (20.6, 20.1, and 19.3, respectively, p=0.97); and chao1 (433, 441, and 419, respectively, p=0.31) indices. F/B ratio and microbiota diversity were both suggestively greater in women with high vs. low BD (median F/B ratio=1.15 for high and 0.94 for low BD, p=0.35; Shannon index: 4.24 for high and 4.15 for low BD, p=0.14; inverse Simpson= 25.3 for high and 21.0 for low BD, p=0.15; chao1= 519 for high and 429 for low BD, p=0.17). Highest levels of alpha diversity were observed in women who had both high BD and low BMI. Taxonomic families that distinguished women with high vs. low BD included Ruminococcaceae, Mogibacteriaceae, Bacteroidaceae, Lachnospiraceae, Christensenellaceae, and Coriobacteriaceae. Conclusion: Results suggest that women with high and low BD may differ with respect to GM alpha diversity and GM composition. Citation Format: Lusine Yaghjyan, Xuefeng Wang, Maria Ukhanova, Yessica Martinez, Shannan Rich, Volker Mai, Kathleen Egan. Association of gut microbiome diversity with obesity and breast density in postmenopausal women [abstract]. In: Proceedings of the AACR Special Conference on the Microbiome, Viruses, and Cancer; 2020 Feb 21-24; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2020;80(8 Suppl):Abstract nr A23.

Fire and hydrologically mediated diversity change in subalpine forests through the Holocene

AbstractQuestionsWe consider whether: (a) fire frequency and hydrologic trends drive changes in subalpine forest community diversity and; (b) if there are cumulative effects on diversity when frequent fire and hydrologic drying occur synchronically?LocationWe use three high elevation sites from Wyoming, USA to investigate the response and resiliency of subalpine forests in the Rocky Mountains to centennial‐to‐millennial drought and fire disturbances in regards to shifts in pollen richness, evenness and diversity.Methods‘We examine ecological changes measured by pollen richness, evenness and diversity between subalpine communities under drying and wetting conditions to determine if there is an amplified effect when differing fire frequencies are considered. Using the inverse Simpson index of pollen diversity on pollen percentages as an estimate of biodiversity.ResultsPeriods of frequent fire display significantly higher diversity (p &lt; 0.05) than periods of infrequent or intermediate fire return intervals regardless of hydrologic trends at Little Windy Hill Pond. Further, sites in the northern and southern Rocky Mountains appear to operate under differing fire regimes with sites in the northern Rocky Mountains not recording periods of frequent fire (&gt;225 year mean fire return interval) through the Holocene.ConclusionsChanges in past pollen abundance and diversity have the ability to capture past landscape structure and ecosystem turnover prior to European settlement of the Americas. If fire regimes in subalpine forests of the Rocky Mountains continue trending towards higher frequencies there is the potential for these areas to experience an increase in vegetation diversity.

Microhabitats are associated with diversity-productivity relationships in freshwater bacterial communities.

Eukaryotic communities commonly display a positive relationship between biodiversity and ecosystem function (BEF) but the results have been mixed when assessed in bacterial communities. Habitat heterogeneity, a factor in eukaryotic BEFs, may explain these variable observations but it has not been thoroughly evaluated in bacterial communities. Here, we examined the impact of habitat on the relationship between diversity assessed based on the (phylogenetic) Hill diversity metrics and heterotrophic productivity. We sampled co-occurring free-living (more homogenous) and particle-associated (more heterogeneous) bacterial habitats in a freshwater, estuarine lake over three seasons: spring, summer and fall. There was a strong, positive, linear relationship between particle-associated bacterial richness and heterotrophic productivity that strengthened when considering dominant taxa. There were no observable BEF trends in free-living bacterial communities for any diversity metric. Biodiversity, richness and Inverse Simpson's index, were the best predictors of particle-associated production whereas pH was the best predictor of free-living production. Our findings show that heterotrophic productivity is positively correlated with the effective number of taxa and that BEF relationships are associated with microhabitats. These results add to the understanding of the highly distinct contributions to diversity and functioning contributed by bacteria in free-living and particle-associated habitats.

Multitrophic biodiversity patterns and environmental descriptors of sub‐Arctic lakes in northern Europe

Abstract Arctic and sub‐Arctic lakes in northern Europe are increasingly threatened by climate change, which can affect their biodiversity directly by shifting thermal and hydrological regimes, and indirectly by altering landscape processes and catchment vegetation. Most previous studies of northern lake biodiversity responses to environmental changes have focused on only a single organismal group. Investigations at whole‐lake scales that integrate different habitats and trophic levels are currently rare, but highly necessary for future lake monitoring and management. We analysed spatial biodiversity patterns of 74 sub‐Arctic lakes in Norway, Sweden, Finland, and the Faroe Islands with monitoring data for at least three biological focal ecosystem components (FECs)—benthic diatoms, macrophytes, phytoplankton, littoral benthic macroinvertebrates, zooplankton, and fish—that covered both pelagic and benthic habitats and multiple trophic levels. We calculated the richnessrelative (i.e. taxon richness of a FEC in the lake divided by the total richness of that FEC in all 74 lakes) and the biodiversity metrics (i.e. taxon richness, inverse Simpson index (diversity), and taxon evenness) of individual FECs using presence–absence and abundance data, respectively. We then investigated whether the FEC richnessrelative and biodiversity metrics were correlated with lake abiotic and geospatial variables. We hypothesised that (1) individual FECs would be more diverse in a warmer and wetter climate (e.g. at lower latitudes and/or elevations), and in hydrobasins with greater forest cover that could enhance the supply of terrestrial organic matter and nutrients that stimulated lake productivity; and (2) patterns in FEC responses would be coupled among trophic levels. Results from redundancy analyses showed that the richnessrelative of phytoplankton, macrophytes, and fish decreased, but those of the intermediate trophic levels (i.e. macroinvertebrates and zooplankton) increased with decreasing latitude and/or elevation. Fish richnessrelative and diversity increased with increasing temporal variation in climate (temperature and/or precipitation), ambient nutrient concentrations (e.g. total nitrogen) in lakes, and woody vegetation (e.g. taiga forest) cover in hydrobasins, whereas taxon richness of macroinvertebrates and zooplankton decreased with increasing temporal variation in climate. The similar patterns detected for richnessrelative of fish, macrophytes, and phytoplankton could be caused by similar responses to the environmental descriptors, and/or the beneficial effects of macrophytes as habitat structure. By creating habitat, macrophytes may increase fish diversity and production, which in turn may promote higher densities and probably more diverse assemblages of phytoplankton through trophic cascades. Lakes with greater fish richnessrelative tended to have greater average richnessrelative among FECs, suggesting that fish are a potential indicator for overall lake biodiversity. Overall, the biodiversity patterns observed along the environmental gradients were trophic‐level specific, indicating that an integrated food‐web perspective may lead to a more holistic understanding of ecosystem biodiversity in future monitoring and management of high‐latitude lakes. In future, monitoring should also focus on collecting more abundance data for fish and lower trophic levels in both benthic and pelagic habitats. This may require more concentrated sampling effort on fewer lakes at smaller spatial scales, while continuing to sample lakes distributed along environmental gradients.

Polymer-coated rock mineral fertilizer has potential to substitute soluble fertilizer for increasing growth, nutrient uptake, and yield of wheat

More than half of the fertilizer applied to farmers’ field is lost, causing significant economic losses. To overcome this, a polymer-coated rock mineral fertilizer was investigated using wheat (Triticum aestivum L. cv. Wyalkatchem). In addition, a multispecies microbial inoculant was added to seeds as a biostimulant to enhance fertilizer use efficiency. Thus, this glasshouse experiment investigated the effect of polymer-coated rock mineral fertilizer with or without a multispecies microbial inoculant on wheat growth in a sandy soil. We hypothesized that the polymer-coated rock mineral fertilizer combined with a microbial inoculant would be more effective than non-coated fertilizer at increasing growth, nutrient uptake, and yield of wheat in sandy soil. Both the polymer-coated and non-coated rock mineral fertilizer, either with or without microbial seed inoculation, increased shoot growth at tillering and maturity but root growth only increased at maturity. Grain yield did not differ between the fertilizer treatments except that they were lower for the non-coated rock mineral fertilizer when combined with microbial inoculation. In the absence of microbial inoculation, soil amended with polymer-coated fertilizer had lower residual soil P and K. The hypothesis that microbial inoculation would improve the growth, nutrient uptake, and yield of wheat was not supported in this experiment. Sequencing of 16S rRNA identified Proteobacteria and Actinobacteria as the key phyla in rhizosphere soil. Fertilizer treatments altered alpha diversity (OTU richness, Inverse Simpson and Fisher indices) but had no effect on evenness. This polymer-coated rock mineral fertilizer has potential to substitute for or complement more soluble fertilizers, but there was no benefit of inclusion of the multispecies microbial inoculant on plant growth or yield.

Evolution of gut microbial community through reproductive life in female rabbits and investigation of the link with offspring survival

The digestive microbiota plays a decisive role in shaping and preserving health throughout life. Rabbit younglings are born with a sterile digestive tract but then it gets progressively colonised by the microbiota of the nursing mother, by entering in contact with or ingesting the maternal droppings present in the nest. Here we posit that (i) offspring survival and (ii) lifespan of female rabbits are linked to how diverse their microbiota are. To test the hypothesis that maternal microbiota evolves in females having had different levels of offspring survival in their lifetime, we obtained 216 hard faecal samples from 75 female rabbits at ages 19.6, 31.6, 62.6 and 77.6 weeks. The annual mean offspring survival (MOS) at 64 days was calculated for each female then crossed against three alpha-diversity indexes (operational taxonomic units (OTUs), inverse Simpson index and Shannon index). Age was also analysed against these three parameters. The alpha-diversity indexes of the female faecal microbiota did not correlate with MOS, but they did decrease with age (e.g. from 712 OTUs at age 19.6 weeks to 444 OTUs at 77.6 weeks; P < 0.05). The age effect was also found in beta-diversity non-metric multidimensional scaling plots using the Bray–Curtis dissimilarity index and the unweighted UniFrac index but not for MOS. The ability of the microbiota composition from the faecal samples of young females (19.6 weeks old) to predict their lifespan was also evaluated. After subdividing the initial population into two classes (females that weaned a maximum of three litters and females living longer), we found no clear distinction between these two classes. To our knowledge, this is the first long-term study to characterise the gut microbiota of adult female rabbits through their reproductive life, thus laying foundations for using the gut microbiota data and its influence in studies on adult rabbits.

Pre-Transplant Fecal Microbial Diversity Independently Predicts Critical Illness after Hematopoietic Cell Transplantation

Background Fecal microbiota composition is associated with important outcomes after allo-HCT including survival, relapse, GVHD, and infections. We previously demonstrated in a multicenter observational study that HCT patients present with fecal microbiota configurations that have lower diversity and are distinct from those of healthy individuals, and that pre-HCT microbiota injury predicts poor overall survival. Here, we hypothesized that pre-HCT fecal microbiota features predict development of critical illness post-HCT. Methods We analyzed 828 adults who received a first allo-HCT from 2009 to 2017 at a single institution who had an evaluable fecal sample in our biobank collected within the 10 days prior to cell infusion. The patients were heterogeneous with respect to transplant indication, conditioning intensity, graft source (cord blood, peripheral blood, marrow) and graft manipulation (CD34-selection). The V4-V5 regions of 16S rRNA genes of DNA extracted from fecal samples were amplified and annotated taxonomically. The outcome of interest was time to ICU admission, which was assessed using survival-analysis methods. The reason for admission to the ICU was evaluated for each subject. Results Seventy-five (9%) patients were admitted to the intensive care unit (ICU) between the day of cell infusion and day +50; the peak incidence of ICU admission occurred on day +10. The most common indications for ICU admission were respiratory failure (65%) and infection (27%). Patients were stratified based on fecal microbiota diversity, as assessed by 16S sequencing of stool samples collected prior to transplantation, into high (inverse Simpson index ≥4) and low (&lt;4) diversity groups following a previously-published cutoff. Patients with low diversity pre-HCT had a strikingly higher risk of ICU admission than those with high diversity (HR 2.38 [95% CI 1.5-3.7], p &lt;0.001, see the Figure). This association remained significant in a multivariate Cox proportional hazard model that accounted for conditioning intensity, graft source, graft manipulation, and the HCT-CI comorbidity index (multivariate p = 0.003). HCT-CI score was also an independent predictor of ICU admission. The association between pre-HCT fecal diversity and ICU admission was also significant when the outcome definition was limited to ICU transfers for reason of respiratory failure or sepsis (to the exclusion of such indications as hemorrhage, anaphylaxis, or isolated dysfunctions of the cardiac, renal, or neurological systems). Conclusion Pre-transplant fecal microbial diversity is an independent predictor of intensive-care-requiring critical illness in the post-HCT period. These observations highlight the pre-HCT period as a window of opportunity to (a) assess microbiota injury in conjunction with comorbidity evaluation, (b) inform selection of antibiotic prophylaxis, gut-decontamination, GVHD-prophylaxis, or conditioning regimens, and (c) intervene with microbiota injury-remediation or prevention strategies. Figure Disclosures Brereton: Seres Therapeutics: Other: Salary Support. Clurman:Seres Therapeutics: Research Funding. Slingerland:Seres Therapeutics: Other: Salary supported by Seres funding. Shah:Janssen Pharmaceutica: Research Funding; Amgen: Research Funding. Scordo:McKinsey &amp; Company: Consultancy; Angiocrine Bioscience, Inc.: Consultancy. Politikos:Angiocrine Bioscience Inc: Research Funding. Gyurkocza:Actinium Pharmaceuticals: Research Funding. Barker:Angiocrine Bioscience Inc: Research Funding; Gamida Cell: Research Funding; Merck: Research Funding. Perales:Kyte/Gilead: Research Funding; Miltenyi: Research Funding; MolMed: Membership on an entity's Board of Directors or advisory committees; NexImmune: Membership on an entity's Board of Directors or advisory committees; Abbvie: Honoraria, Membership on an entity's Board of Directors or advisory committees; Bellicum: Honoraria, Membership on an entity's Board of Directors or advisory committees; Bristol-Meyers Squibb: Honoraria, Membership on an entity's Board of Directors or advisory committees; Incyte: Honoraria, Membership on an entity's Board of Directors or advisory committees, Research Funding; Nektar Therapeutics: Honoraria, Membership on an entity's Board of Directors or advisory committees; Novartis: Honoraria, Membership on an entity's Board of Directors or advisory committees; Omeros: Honoraria, Membership on an entity's Board of Directors or advisory committees; Takeda: Honoraria, Membership on an entity's Board of Directors or advisory committees; Merck: Consultancy, Honoraria; Medigene: Membership on an entity's Board of Directors or advisory committees; Servier: Membership on an entity's Board of Directors or advisory committees. Giralt:Amgen: Consultancy, Research Funding; Spectrum Pharmaceuticals: Consultancy; Actinium: Consultancy, Research Funding; Celgene: Consultancy, Research Funding; Kite: Consultancy; Johnson &amp; Johnson: Consultancy, Research Funding; Jazz Pharmaceuticals: Consultancy; Miltenyi: Research Funding; Takeda: Consultancy, Research Funding; Novartis: Consultancy. van den Brink:Merck &amp; Co, Inc.: Consultancy, Honoraria; Acute Leukemia Forum (ALF): Consultancy, Honoraria; Magenta and DKMS Medical Council: Membership on an entity's Board of Directors or advisory committees; Juno Therapeutics: Other: Licensing; Amgen: Consultancy, Honoraria; Therakos: Consultancy, Honoraria; Seres Therapeutics: Consultancy, Honoraria, Membership on an entity's Board of Directors or advisory committees, Research Funding; Flagship Ventures: Consultancy, Honoraria; Novartis: Consultancy, Honoraria; Evelo: Consultancy, Honoraria; Jazz Pharmaceuticals: Consultancy, Honoraria. Pamer:Bristol Myers Squibb: Honoraria; Celgene: Honoraria; Seres Therapeutics: Honoraria, Patents &amp; Royalties; MedImmune: Honoraria; Novartis: Honoraria; Ferring Pharmaceuticals: Honoraria. Peled:Seres Therapeutics: Research Funding.

Successful and Safe Treatment of Intestinal Graft-Versus-Host Disease (GvHD) with Pooled-Donor Full Ecosystem Microbiota Biotherapeutics

Introduction Intestinal Graft-versus-Host Disease (GvHD), following allogeneic Hematopoietic Stem Cell Transplantation (allo-HSCT), comes with a high mortality rate and a reduced life-expectancy. In this context, failure to respond to steroid therapy is associated with an absence of further therapeutic options, thereby representing an unmet medical need. A marked reduction in gut microbiota diversity leading to loss of functions was strongly associated with reduced overall survival in GvHD, while a high gut microbiota diversity appears to be protective. Aiming at restoring microbiome functions, Fecal Microbiota Transfer proved to be a promising treatment modality in this challenging clinical situation, with recent studies reporting favorable results in steroid refractory-acute GVHD (SR-aGvHD) patients. Here we report on the use of "MaaT013", a standardized, pooled-donor, high-richness microbiota biotherapeutic, used to treat 8 patients with intestinal-predominant aGvHD. Patients and methods Eight allo-HSCT recipients with steroid-dependent or steroid-refractory gastrointestinal GvHD (classical aGVHD n=3, late-onset aGVHD n=2; aGvHD with overlap syndrome n=3) were treated with the MaaT013 biotherapeutic as part of a compassionate use program. These patients had previously received and failed 1 to 5 lines (median 2.5) of GvHD systemic treatments. MaaT013 microbiota biotherapeutics were provided as a pharmaceutical preparation to hospitals by the developer, "MaaT Pharma". Each patient received 1 to 3 doses (median: 3; total doses administered: 21) of MaaT013, a 150 mL bag, by enema (n=7) or nasogastric tube (n=1). GvHD response was evaluated 7 days after each administration and 28 days after the first dose. Prepared under Good Manufacturing Practices, MaaT013 biotherapeutics are characterized by a highly consistent richness of 455 +/- 3% Operational Taxonomic Units (OTUs) and an Inverse Simpson index greater than 20. Batch release specifications are based on potency (viability), identity (diversity), and purity (microbiological safety testing following regulatory guidelines and proportion of proinflammatory species), ensuring the desired consistency between batches. Results We observed 6/8 positive responses at D28 after first dosing, including 3 Complete Responses (CR), one Very Good Partial Response (VGPR), and 2 Partial Responses (PR). Considering the best GI response achieved, all (8/8) patients experienced at least a PR, with 3 CRs, 2 VGPRs and 3 PRs. The 3 patients with CR were still alive at last follow-up (60 to 192 days after last dosing; median: 115 days) and were able to taper and stop steroids and immunosuppressants without relapse of GI symptoms. Of note, among these 3 patients, mild mouth chronic GvHD symptoms persisted in one patient, and relapse of hematologic malignancy was observed in another patient. Among the 8 treated patients, 5 were still alive at last follow-up (60 to 232 days after last dosing; median: 125 days). The safety of the MaaT013 microbiota biotherapeutic was satisfactory in all patients. One patient developed a possibly related sepsis one day after the third MaaT013 administration. In the latter case, no pathogen was identified in blood cultures, and the patient recovered after a course of antibiotics. Conclusions We herein report for the first time the treatment of 8 patients with steroid-dependent or steroid-refractory intestinal aGvHD using a full ecosystem, standardized, pooled-donor, high-richness biotherapeutic. Overall, 3/8 patients attained a complete response following treatment with the off-the-shelf MaaT013 product, shown to be safe and effective in these immunocompromised patients with severe conditions, warranting further exploration of the full ecosystem microbiota restoration approach. Disclosures Malard: Sanofi: Honoraria; JAZZ pharmaceutical: Honoraria; Astellas: Honoraria; Therakos/Mallinckrodt: Honoraria; Keocyte: Honoraria; Janssen: Honoraria. Plantamura:MaaT Pharma: Employment. Carter:MaaT Pharma: Employment. Chevallier:Jazz Pharmaceuticals: Honoraria; Incyte: Consultancy, Honoraria; Daiichi Sankyo: Honoraria. Blaise:Pierre Fabre medicaments: Honoraria; Molmed: Consultancy, Honoraria; Jazz Pharmaceuticals: Honoraria; Sanofi: Honoraria. Mohty:Jazz Pharmaceuticals: Honoraria, Research Funding.