Longitudinal associations between gut microbiome diversity and emotional well-being

OBJECTIVE

While a significant link between emotional well-being (EWB) and the gut microbiome has been reported recently, their temporal relationships remain elusive. This study aims to fill this gap by examining the longitudinal associations between EWB and the Shannon Index (SI), an indicator of gut microbiome diversity.

METHOD

The analysis focused on a dataset that collected participants' current EWB and fecal samples in both 2019 and 2022 (N = 57, 56.1% female, Mage = 52.47 years, SD = 12.65). Gut microbiome profiles were generated by sequencing the 16S rRNA gene, from which SI was subsequently calculated.

RESULTS

The cross-lagged panel analysis revealed significant positive cross-sectional associations between EWB and SI in both 2019 (β = .296, SE = 0.121, p = .014) and 2022 (β = .324, SE = 0.119, p = .006). However, no significant longitudinal associations were found between 2019 EWB and 2022 SI (β = .068, SE = 0.138, p = .623), nor between 2019 SI and 2022 EWB (β = -.016, SE = 0.13, p = .899).

CONCLUSIONS

Our findings indicate that emotional happiness may be associated with gut microbiome profiles at a particular time point, but they may not serve as predictive factors for each other over time. Future research is needed to establish causal relationships between them. (PsycInfo Database Record (c) 2024 APA, all rights reserved).

Gut microbial and clinical characteristics of individuals with autism spectrum disorder differ depending on the ecological structure of the gut microbiome

Understanding the relationship between the gut microbiome and autism spectrum disorder (ASD) is challenging due to the heterogeneous nature of ASD. Here, we analyzed the microbial and clinical characteristics of individuals with ASD using enterotypes. A total of 456 individuals participated in the study, including 249 participants with ASD, 106 typically developing siblings, and 101 controls. The alpha and beta diversities of the ASD, sibling, and control groups did not show significant differences. Analysis revealed a negative association between the Bifidobacterium longum group and the Childhood Autism Rating Scale, as well as a negative association between the Streptococcus salivarus group and the Social Responsiveness Scale (SRS) within the ASD group. When clustered based on microbial composition, participants with ASD exhibited two distinct enterotypes, E1 and E2. In the E2 group, the SRS score was significantly higher, and the Vineland Adaptive Behavior Scale score was significantly lower compared to the E1 group. Machine learning results indicated that the microbial species predicting SRS scores were distinct between the two enterotypes. Our study suggests that the microbial composition in individuals with ASD exhibits considerable variability, and the patterns of associations between the gut microbiome and clinical symptoms may vary depending on the enterotype.

Patient-Specific Deep Learning Model for Clinical Target Volume Delineation on Daily CBCT of Breast Cancer Patients based on Intentional Deep Overfit Learning (IDOL) Framework

PURPOSE/OBJECTIVE(S)

Increasingly complex target volumes and the use of modern irradiation techniques emphasize the importance of daily image guidance more than ever. Significant progress has been made in adjuvant breast cancer radiotherapy (RT) and the need for optimized image guidance is growing. Furthermore, the position of the breast during RT after breast-conserving surgery is highly variable than expected. In this context, cone beam computed tomography (CBCT) is a very effective tool enabling prompt and accurate adaptive radiation therapy (ART). In this study, we aim to develop a deep learning (DL)-based algorithm to segment clinical target volume (CTV) from daily CBCT scans. Also, we validate the optimization of further learning when applying the Intentional Deep Overfit Learning (IDOL) framework.

MATERIALS/METHODS

A total of 240 different CBCT scans obtained from 100 breast cancer patients were used for this study. CTV was defined as whole breast plus margin in all patients. The workflow consists of two training stages: (1) training a novel 'generalized' DL model (Swin_UNETR) to identify and delineate breast CTV on CBCT scans using 90 breast cancer patient cases (2) applying an 'intentional overfitting' to the 'generalized' DL model to generate a 'patient-specific' model using the remaining 10 breast cancer patients. In this study, for the intentionally overfitting stage, we additionally trained with CBCT scans from the patient's 1st fraction to the 14th fractions cases. The results of the proposed method were compared quantitatively with the expert's contours on 1st-15th fractions CBCT scans using Dice Similarity Coefficient (DSC).

RESULTS

The average DSC between the 'generalized' DL model-based breast CTV contours and reference contours for the patient's 15th fraction was 0.9672. When implementing the IDOL framework with the CBCT scan obtained during the patient's 1st treatment, the average DSC was improved to 0.9809. When additional CBCT scans taken during each of the 1st to 6th fractions were used for training, the average DSC could be most effectively raised to 0.9835. The p-value comparison between the 'generalized' DL model and the 1st fraction was found to be 3.62E-04, while the comparison with the 6th fractions resulted in a p-value of 8.36E-05. The average time required for IDOL training using one CBCT scan and six CBCT scans was 107 seconds and 127 seconds, respectively.

CONCLUSION

In this study, we developed a patient-specific DL-based training algorithm to segment CTV in CBCT scans for breast cancer patients. The performance improvement was relatively significant and was confirmed that using continual DL with additional CBCT scans, which are taken every day, can be more accurate and efficient than drawing breast CTV using a general model. Our novel patient-specific model can be effectively applied to various ARTs by not only reducing labor and time but also increasing accuracy.

UACG: Up-to-Date Archaeal Core Genes and Software for Phylogenomic Tree Reconstruction

In the post-genomic era, phylogenomics is a powerful and routinely-used tool to discover evolutionary relationships between microorganisms. Inferring phylogenomic trees by concatenating core gene sequences into a supermatrix is the standard method. The previously released up-to-date bacterial core gene (UBCG) tool provides a pipeline to infer phylogenomic trees using single-copy core genes for the Bacteria domain. In this study, we established up-to-date archaeal core gene (UACG), comprising 128 genes suitable for inferring archaeal phylogenomic trees. To test the gene set, we selected the Haloarcula genus and scrutinized its phylogeny. The phylogeny inferred using the UACG tool was consistent with the orthoANIu dendrogram, whereas the 16S rRNA gene phylogeny showed high intragenomic heterogeneity resulting in phylogenetic discrepancies. The software tool using the UACG set is available at https://www.ezbiocloud.net/tools/uacg .

Genomic and evolutionary study from SARS-CoV-2 virus isolates from Bangladesh during the early stage of pandemic strongly correlate with European origin and not with China

The goal of this study was to identify the genomic variants and determine molecular epidemiology of SARS-CoV-2 virus during the early pandemic stage in Bangladesh. Viral RNA was extracted, converted to cDNA, and amplified using Ion AmpliSeq™ SARS-CoV-2 Research Panel. 413 unique mutants from 151 viral isolates were identified. 80% of cases belongs to 8 mutants: 241C toT, 1163A toT, 3037C toT, 14408C toT, 23403A toG, 28881G toA, 28,882 G toA, and 28883G toC. Observed dominance of GR clade variants that have strong presence in Europe, suggesting European channel a possible entry route. Among 37 genomic mutants significantly associated with clinical symptoms, 3916CtoT (associated with sore-throat), 14408C to T (associated with cough-protection), 28881G to A, 28882G to A, and 28883G to C (associated with chest pain) were notable. These findings may inform future research platforms for disease management and epidemiological study.

Compositional Changes in the Gut Microbiota of Responders and Non-responders to Probiotic Treatment Among Patients With Diarrhea-predominant Irritable Bowel Syndrome: A Post Hoc Analysis of a Randomized Clinical Trial

Background/Aims

We aim to evaluate the differences in the microbiome of responders and non-responders, as well as predict the response to probiotic therapy, based on fecal microbiome data in patients with diarrhea-predominant irritable bowel syndrome (IBS-D).

Methods

A multi-strain probiotics that contains Lactobacillus acidophilus (KCTC 11906BP), Lactobacillus plantarum (KCTC11867BP), Lactobacillus rhamnosus (KCTC 11868BP), Bifidobacterium breve (KCTC 11858BP), Bifidobacterium lactis (KCTC 11903BP), Bifidobacterium longum (KCTC 11860BP), and Streptococcus thermophilus (KCTC 11870BP) were used. Patients were categorized into probiotic and placebo groups, and fecal samples were collected from all patients before and at the end of 8 weeks of treatment. The probiotic group was further divided into responders and non-responders. Responders were defined as patients who experienced adequate relief of overall irritable bowel syndrome symptoms after probiotic therapy. Fecal microbiota were investigated using Illumina MiSeq and analyzed using the EzBioCloud 16S database and microbiome pipeline (https://www.EZbiocloud.net).

Results

There was no significant difference in the alpha and beta diversity between the responder and non-responder groups. The abundances of the phylum Proteobacteria and genus Bacteroides significantly decreased after probiotic treatment. Bifidobacterium bifidum, Pediococcus acidilactici, and Enterococcus faecium showed a significantly higher abundance in the probiotic group after treatment compared to the placebo group. Enterococcus faecalis and Lactococcus lactis were identified as biomarkers of non-response to probiotics. The abundance of Fusicatenibacter saccharivorans significantly increased in the responders after treatment.

Conclusions

Probiotic treatment changes some composition of fecal bacteria in patients with IBS-D. E. faecalis and L. lactis may be prediction biomarkers for non-response to probiotics. Increased abundance of F. sccharivorans is correlated to symptom improvement by probiotics in patients with IBS-D.

UFCG: database of universal fungal core genes and pipeline for genome-wide phylogenetic analysis of fungi

In phylogenomics the evolutionary relationship of organisms is studied by their genomic information. A common approach to phylogenomics is to extract related genes from each organism, build a multiple sequence alignment and then reconstruct evolution relations through a phylogenetic tree. Often a set of highly conserved genes occurring in single-copy, called core genes, are used for this analysis, as they allow efficient automation within a taxonomic clade. Here we introduce the Universal Fungal Core Genes (UFCG) database and pipeline for genome-wide phylogenetic analysis of fungi. The UFCG database consists of 61 curated fungal marker genes, including a novel set of 41 computationally derived core genes and 20 canonical genes derived from literature, as well as marker gene sequences extracted from publicly available fungal genomes. Furthermore, we provide an easy-to-use, fully automated and open-source pipeline for marker gene extraction, training and phylogenetic tree reconstruction. The UFCG pipeline can identify marker genes from genomic, proteomic and transcriptomic data, while producing phylogenies consistent with those previously reported, and is publicly available together with the UFCG database at https://ufcg.steineggerlab.com.

Proposal of a health gut microbiome index based on a meta-analysis of Korean and global population datasets

The disruption of the human gut microbiota has been linked to host health conditions, including various diseases. However, no reliable index for measuring and predicting a healthy microbiome is currently available. Here, the sequencing data of 1,663 Koreans were obtained from three independent studies. Furthermore, we pooled 3,490 samples from public databases and analyzed a total of 5,153 fecal samples. First, we analyzed Korean gut microbiome covariates to determine the influence of lifestyle on variation in the gut microbiota. Next, patterns of microbiota variations across geographical locations and disease statuses were confirmed using a global cohort and di-sease data. Based on comprehensive comparative analysis, we were able to define three enterotypes among Korean cohorts, namely, Prevotella type, Bacteroides type, and outlier type. By a thorough categorization of dysbiosis and the evaluation of microbial characteristics using multiple datasets, we identified a wide spectrum of accuracy levels in classifying health and disease states. Using the observed microbiome patterns, we devised an index named the gut microbiome index (GMI) that could consistently predict health conditions from human gut microbiome data. Compared to ecological metrics, the microbial marker index, and machine learning approaches, GMI distinguished between healthy and non-healthy individuals with a higher accuracy across various datasets. Thus, this study proposes a potential index to measure health status of gut microbiome that is verified from multiethnic data of various diseases, and we expect this model to facilitate further clinical application of gut microbiota data in future.

Genome insights into the pharmaceutical and plant growth promoting features of the novel species Nocardia alni sp. nov

BACKGROUND

Recent studies highlighted the biosynthetic potential of nocardiae to produce diverse novel natural products comparable to that of Streptomyces, thereby making them an attractive source of new drug leads. Many of the 119 Nocardia validly named species were isolated from natural habitats but little is known about the diversity and the potential of the endophytic nocardiae of root nodule of actinorhizal plants.

RESULTS

The taxonomic status of an actinobacterium strain, designated ncl2T, was established in a genome-based polyphasic study. The strain was Gram-stain-positive, produced substrate and aerial hyphae that fragmented into coccoid and rod-like elements and showed chemotaxonomic properties that were also typical of the genus Nocardia. It formed a distinct branch in the Nocardia 16S rRNA gene tree and was most closely related to the type strains of Nocardia nova (98.6%), Nocardia jiangxiensis (98.4%), Nocardia miyuensis (97.8%) and Nocardia vaccinii (97.7%). A comparison of the draft genome sequence generated for the isolate with the whole genome sequences of its closest phylogenetic neighbours showed that it was most closely related to the N. jiangxiensis, N. miyuensis and N. vaccinii strains, a result underpinned by average nucleotide identity and digital DNA-DNA hybridization data. Corresponding taxogenomic data, including those from a pan-genome sequence analysis showed that strain ncl2T was most closely related to N. vaccinii DSM 43285T. A combination of genomic, genotypic and phenotypic data distinguished these strains from one another. Consequently, it is proposed that strain ncl2T (= DSM 110931T = CECT 30122T) represents a new species within the genus Nocardia, namely Nocardia alni sp. nov. The genomes of the N. alni and N. vaccinii strains contained 36 and 29 natural product-biosynthetic gene clusters, respectively, many of which were predicted to encode for a broad range of novel specialised products, notably antibiotics. Genome mining of the N. alni strain and the type strains of its closest phylogenetic neighbours revealed the presence of genes associated with direct and indirect mechanisms that promote plant growth. The core genomes of these strains mainly consisted of genes involved in amino acid transport and metabolism, energy production and conversion and transcription.

CONCLUSIONS

Our genome-based taxonomic study showed that isolate ncl2T formed a new centre of evolutionary variation within the genus Nocardia. This novel endophytic strain contained natural product biosynthetic gene clusters predicted to synthesize novel specialised products, notably antibiotics and genes associated with the expression of plant growth promoting compounds.

AMDB: a database of animal gut microbial communities with manually curated metadata

Variations in gut microbiota can be explained by animal host characteristics, including host phylogeny and diet. However, there are currently no databases that allow for easy exploration of the relationship between gut microbiota and diverse animal hosts. The Animal Microbiome Database (AMDB) is the first database to provide taxonomic profiles of the gut microbiota in various animal species. AMDB contains 2530 amplicon data from 34 projects with manually curated metadata. The total data represent 467 animal species and contain 10 478 bacterial taxa. This novel database provides information regarding gut microbiota structures and the distribution of gut bacteria in animals, with an easy-to-use interface. Interactive visualizations are also available, enabling effective investigation of the relationship between the gut microbiota and animal hosts. AMDB will contribute to a better understanding of the gut microbiota of animals. AMDB is publicly available without login requirements at http://leb.snu.ac.kr/amdb.

VicPred: A Vibrio cholerae Genotype Prediction Tool

Genomic information can be used to predict major pathogenic traits of pathogens without the need for laboratory experimentation. However, no Vibrio cholerae genome-based trait identification tools currently exist. The aim of this study was to develop a web-based prediction tool to identify Vibrio pathogenic traits using publicly available 796 whole-genome sequences of V. cholerae. Using this application, 68 structural O-antigen gene clusters belonging to 49 serogroups of V. cholerae were classified, and the composition of the genes within the O-antigen cluster of each serogroup was identified. The arrangement and location of the CTX prophage and related elements of the seventh cholera pandemic strains were also revealed. With the versatile tool, named VicPred, we analyzed the assemblage of various SXTs (sulfamethoxazole/trimethoprim resistance element) and major genomic islands (GIs) of V. cholerae, and the increasing trend in drug-resistance revealing high resistance of the V. cholerae strains to certain antibiotics. The pathogenic traits of newly sequenced V. cholerae strains could be analyzed based on these characteristics. The accumulation of further genome data will expedite the establishment of a more precise genome-based pathogenic traits analysis tool.

UBCG2: Up-to-date bacterial core genes and pipeline for phylogenomic analysis

Phylogenomic tree reconstruction has recently become a routine and critical task to elucidate the evolutionary relationships among bacterial species. The most widely used method utilizes the concatenated core genes, universally present in a single-copy throughout the bacterial domain. In our previous study, a bioinformatics pipeline termed Up-to-date Bacterial Core Genes (UBCG) was developed with a set of bacterial core genes selected from 1,429 species covering 28 phyla. In this study, we revised a new bacterial core gene set, named UBCG2, that was selected from the more extensive genome sequence set belonging to 3,508 species spanning 43 phyla. UBCG2 comprises 81 genes with nine Clusters of Orthologous Groups of proteins (COGs) functional categories. The new gene set and complete pipeline are available at http://leb.snu.ac.kr/ubcg2 .

The use of instant messaging in clinical data sharing: the EHRA SMS survey

Funding Acknowledgements

Type of funding sources: None.

Background

Nowadays, instant messaging (IM) provides fast and widespread communication. These platforms and apps enable the physicians to quickly share and send clinical data to their peers, to send information to their patients regarding their illnesses and to be reached for counselling and advise. Nevertheless, the use of IM has never been assessed in the cardiology community up until now.

Purpose

To assess the habits of cardiologists related to modern communication tools, their primary and secondary uses in clinical practice and the potential differences and preferences between different media in terms of ease of access, usefulness and trustworthiness.

Methods

An online survey was promoted by the EHRA e-Communication Committee and the EHRA Scientific Initiative Committee during the ESC Digital Health Week. All cardiologists were invited to participate via Twitter, LinkedIn, Facebook and other dedicated channels. The survey consisted of 22 questions and was made anonymous. The questions were made on an individual-basis and collected on SurveyMonkey.

Results

287 physicians from 33 countries responded to the survey. The mean age of the respondents was 43.4 ± 11.5 years, and 74.8% of them were male. 88.3% of all respondents routinely sends and 90.3% receives clinical data through IM. IM is used at least once a week (36.4%) or even once or more a day (40.4%) for sharing clinical data. WhatsApp is the most used IM app to share clinical data (79.4%). On a scale of 1 to 5, IM was second only to face-to-face contact (average 4.46) as the preferred method for sharing clinical data (average 3.69) and was considered better than phone calls (average 3.34) and e-mails (average 3.21). Twelve-lead ECGs (88.6%), medical history (61.4%) and echo loops (55.7%) are the data shared most often. Among potential pros of IM, the respondents listed being a fast way of communication (82.0%) and making it easy to contact colleagues (76.7%), while privacy issues regarding IM apps providers (62.7%) and other colleagues (45.6%) were commonly perceived as drawbacks. Only 57.4% of all respondents anonymize clinical data before sharing them through IM, and only 44.0% of the data received are reported to be anonymized. Of note, 29.3% of the respondents were not aware of the European General Data Protection Regulation (GDPR) on data protection at the time of the survey, and 29.8% do not know if their institution has a specific policy regarding the use of IM for professional use.

Conclusions

IM apps are used by cardiologists worldwide to share and discuss clinical data and are preferred to many other methods of data sharing, being second only to face-to-face contact. IM are often used and to share many different types of clinical data, being perceived as a fast and easy way of communication. Cardiologists should be sensitised to appropriate use of IM in accordance to GDPR and local policies in order to prevent legal and privacy issues.

Introducing EzAAI: a pipeline for high throughput calculations of prokaryotic average amino acid identity

The average amino acid identity (AAI) is an index of pairwise genomic relatedness, and multiple studies have proposed its application in prokaryotic taxonomy and related disciplines. AAI demonstrates better resolution in elucidating taxonomic structure beyond the species rank when compared with average nucleotide identity (ANI), which is a standard criterion in species delineation. However, an efficient and easy-to-use computational tool for AAI calculation in large-scale taxonomic studies is not yet available. Here, we introduce a bioinformatic pipeline, named EzAAI, which allows for rapid and accurate AAI calculation in prokaryote sequences. The EzAAI tool is based on the MMSeqs2 program and computes AAI values almost identical to those generated by the standard BLAST algorithm with significant improvements in the speed of these evaluations. Our pipeline also provides a function for hierarchical clustering to create dendrograms, which is an essential part of any taxonomic study. EzAAI is available for download as a standalone JAVA program at http://leb.snu.ac.kr/ezaai .

Taxonomic composition and variation in the gut microbiota of laboratory mice

The gut microbiota can affect host health, including humans. Mouse models have been used extensively to study the relationships between the host and the gut microbiota. With the development of cost-effective high-throughput DNA sequencing, several methods have been used to identify members of the gut microbiota of laboratory mice. In recent years, the amount of research and knowledge about the mouse gut microbiota has exploded, leading to significant breakthroughs in understanding of the taxonomic composition of and variation in this community. In addition, the rapidly increasing volume of data has allowed the development of public resources for exploring the mouse gut microbiota. In this review, we describe the concepts and pros and cons of basic methodologies that can be used to determine the gut bacterial profile in laboratory mice. We also present the key bacterial components of the mouse gut microbiota from the phylum to the species level and then compare them with those identified in other references. Additionally, we discuss variations in the mouse gut microbiota and their association with experiments using mice. Finally, we summarize the properties and functions of currently available public resources for exploring the mouse gut microbiota.

Characterization of Gut Microbiome in Korean Patients with Metabolic Associated Fatty Liver Disease

Metabolic associated fatty liver disease (MAFLD) is a new concept where the presence of both fatty liver and metabolic abnormality are necessary for diagnosis. Several studies have reported that altered gut microbiome is closely associated with metabolic diseases and non-alcoholic fatty liver disease. However, the studies on MAFLD population are scarce. This prospective study aimed to identify differences in gut microbiome between patients with MAFLD and healthy controls in Korean population. In this study, patients with MAFLD and age, sex-matched healthy controls were included, and their stool samples were collected. Taxonomic composition of gut microbiota was analyzed using 16S ribosomal ribonucleic acid pyrosequencing. Twenty-two MAFLD patients and 44 healthy controls were included. Taxonomic diversity was lower in patients with MAFLD in the aspect of alpha and beta diversity. The differences were also found at phylum, class, family, and genus levels between the two groups. Phylum Proteobacteria, family Enterobactereriaceae, genus Citrobacter abundance was significantly increased and genus Faecalibacterium was significantly decreased in patients with MAFLD. In addition, butyrate-producing bacteria were decreased and ethanol-producing bacteria were increased in patients with MAFLD. The composition of gut microbiome was different between MAFLD and healthy controls in Korean population. This could offer potential targets for therapeutic intervention in MAFLD.

Epidemiologic Linkage of COVID-19 Outbreaks at Two University-affiliated Hospitals in the Seoul Metropolitan Area in March 2020

BACKGROUND

Coronavirus disease 2019 (COVID-19) outbreaks emerged at two university-affiliated hospitals in Seoul (hospital A) and Uijeongbu City (hospital S) in the metropolitan Seoul area in March 2020. The aim of this study was to investigate epidemiological links between the outbreaks using whole genome sequencing (WGS) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2).

METHODS

Fifteen patients were enrolled in the study, including four non-outbreak (A1-A4) and three outbreak cases (A5-A7) in hospital A and eight cases (S1-S8) in hospital S. Patients' hospital stays, COVID-19 symptoms, and transfer history were reviewed. RNA samples were submitted for WGS and genome-wide single nucleotide variants and phylogenetic relationships were analyzed.

RESULTS

The index patient (A5) in hospital A was transferred from hospital S on 26 March. Patients A6 and A7 were the family caregiver and sister, respectively, of the patient who shared a room with A5 for 4 days. Prior to transfer, A5 was at the next bed to S8 in the emergency room on 25 March. Patient S6, a professional caregiver, took care of the patient in the room next to S8's room for 5 days until 22 March and then S5 for another 3 days. WGS revealed that SARS-CoV-2 in A2, A3, and A4 belong to clades V/B.2, S/A, and G/B.1, respectively, whereas that of A5-A7 and S1-S5 are of the V/B.2.1 clade and closely clustered. In particular, SARS-CoV-2 in patients A5 and S5 showed perfect identity.

CONCLUSION

WGS is a useful tool to understand epidemiology of SARS-CoV-2. It is the first study to elucidate the role of patient transfer and caregivers as links of nosocomial outbreaks of COVID-19 in multiple hospitals.

Emotional well-being and gut microbiome profiles by enterotype

With increasing attention being paid to improving emotional well-being, recent evidence points to gut microbiota as a key player in regulating mental and physical health via bidirectional communication between the brain and gut. Here, we examine the association between emotional well-being and gut microbiome profiles (i.e., gut microbiome composition, diversity, and the moderating role of the enterotypes) among healthy Korean adults (n = 83, mean age = 48.9, SD = 13.2). The research was performed using high-throughput 16S rRNA gene sequencing to obtain gut microbiome profiles, as well as a self-report survey that included the Positive Affect Negative Affect Schedule (PANAS). The cluster-based analysis identified two enterotypes dominated by the genera Bacteroides (n = 49) and Prevotella (n = 34). Generalized linear regression analysis reveals significant associations between positive emotion and gut microbiome diversity (Shannon Index) among participants in the Prevotella dominant group, whereas no such relationship emerged among participants in the Bacteroides group. Moreover, a novel genus from the family Lachnospiraceae is associated with emotional well-being scores, both positive and negative. Together, the current findings highlight the enterotype-specific links between the gut microbiota community and emotion in healthy adults and suggest the possible roles of the gut microbiome in promoting mental health.

Metagenomic Association Analysis of Gut Symbiont Limosilactobacillus reuteri Without Host-Specific Genome Isolation

Limosilactobacillus reuteri is a model symbiont that colonizes the guts of vertebrates in studies on host adaptation of the gut symbiont. Previous studies have investigated host-specific phylogenetic and functional properties by isolating the genomic sequence. This dependency on genome isolation is a significant bottleneck. Here, we propose a method to study the association between L. reuteri and its hosts directly from metagenomic reads without strain isolation using pan-genomes. We characterized the host-specificity of L. reuteri in metagenomic samples, not only in previously studied organisms (mice and pigs) but also in dogs. For each sample, two types of profiles were generated: (1) genome-based strain type abundance profiles and (2) gene composition profiles. Our profiles showed host-association of L. reuteri in both phylogenetic and functional aspects without depending on host-specific genome isolation. We observed not only the presence of host-specific lineages, but also the dominant lineages associated with the different hosts. Furthermore, we showed that metagenome-assembled genomes provide detailed insights into the host-specificity of L. reuteri. We inferred evolutionary trajectories of host-associative L. reuteri strains in the metagenomic samples by placing the metagenome-assembled genomes into a phylogenetic tree and identified novel host-specific genes that were unannotated in existing pan-genome databases. Our pan-genomic approach reduces the need for time-consuming and expensive host-specific genome isolation, while producing consistent results with previous host-association findings in mice and pigs. Additionally, we predicted associations that have not yet been studied in dogs.

Comparative analysis of the tonsillar microbiota in IgA nephropathy and other glomerular diseases

Immunoglobulin A nephropathy (IgAN) involves repeated events of gross haematuria with concurrent upper airway infections. The mucosal immune system, especially the tonsil, is considered the initial site of inflammation, although the role of the tonsillar microbiota has not been established in IgAN. In this study, we compared the tonsillar microbiota of patients with IgAN (n = 21) and other glomerular diseases (n = 36) as well as, healthy controls (n = 23) from three medical centres in Korea. The microbiota was analysed from tonsil swabs using the Illumina MiSeq system based on 16S rRNA gene. Tonsillar bacterial diversity was higher in IgAN than in other glomerular diseases, although it did not differ from that of healthy controls. Principal coordinates analysis revealed differences between the tonsillar microbiota of IgAN and both healthy and disease controls. The proportions of Rahnella, Ruminococcus_g2, and Clostridium_g21 were significantly higher in patients with IgAN than in healthy controls (corrected p < 0.05). The relative abundances of several taxa were correlated with the estimated glomerular filtration rate, blood urea nitrogen, haemoglobin, and serum albumin levels. Based on our findings, tonsillar microbiota may be associated with clinical features and possible immunologic pathogenesis of IgAN.

Connecting particle interactions to agglomerate morphology and rheology of boehmite nanocrystal suspensions

HYPOTHESIS

The rheology of complex suspensions, such as nuclear waste slurries at the Hanford and Savannah River sites, imposes significant challenges on industrial-scale processing. Investigating the rheology and connecting it to the agglomerate morphology and underlying particle interactions in slurries will provide important fundamental knowledge, as well as prescriptive data for practical applications. Here, we use suspensions of nano-scale aluminum oxyhydroxide minerals in the form of boehmite as an analog of the radioactive waste slurry to investigate the correlation between particle interactions, agglomerate morphology, and slurry rheology.

EXPERIMENTS

A combination of Couette rheometry and small-angle scattering techniques (independently and simultaneously) were used to understand how agglomerate structure of slurry changes under flow and how these structural changes manifest themselves in the bulk rheology of the suspensions.

FINDINGS

Our experiments show that the boehmite slurries are thixotropic, with the rheology and structure of the suspensions changing with increasing exposure to flow. In the slurries, particle agglomerates begin as loose, system-spanning clusters, but exposure to moderate shear rates causes the agglomerates to irreversibly consolidate into denser clusters of finite size. The structural changes directly influence the rheological properties of the slurries such as viscosity and viscoelasticity. Our study shows that solution pH affects the amount of structural rearrangement and the kinetics of the rearrangement process, with an increase in pH leading to faster and more dramatic changes in bulk rheology, which can be understood via correlations between particle interactions and the strength of particle network. Nearly identical structural changes were also observed in Poiseuille flow geometries, implying that the observed changes are relevant in pipe flow as well.

Genome-based reclassification of Paenibacillus jamilae Aguilera et al. 2001 as a later heterotypic synonym of Paenibacillus polymyxa (Prazmowski 1880) Ash et al. 1994

Paenibacillus is one of the genera that has high species diversity and Paenibacillus polymyxa, the type species of the genus, is mainly isolated from plant-associated environments. Among the plant-associated species, Paenibacillus jamilae B.3^T (=CECT 5266^T=DSM 13815^T=KACC 10925^T=KCTC 13919^T) was proposed to be a novel species according to 16S rRNA gene similarity and DNA-DNA relatedness with related species, including Paenibacillus polymyxa. Nevertheless, in the description of Paenibacillus jamilae the used strain of Paenibacillus polymyxa was not the type strain of this species. In this work we found that the type strains of both species showed 16S rRNA gene similarity of 99.6 %. Therefore, in this study, we sequenced the genome of Paenibacillus jamilae KACC 10925^T and compared it with those of the type strain of Paenibacillus polymyxa ATCC 842^T and other phylogenetically related species. Genome relatedness value calculated by DNA-DNA hybridization between type strains of Paenibacillus polymyxa and Paenibacillus jamilae was 73.5 %, which is higher than the threshold value (70 %). For more objective and repeatable results of genome relatedness, we analysed an average nucleotide identity (ANI) between two strains. Our results showed that ANI value between the type strains of Paenibacillus jamilae and Paenibacillus polymyxa is 98.5 %, a phylogenetic distance also higher than the threshold values (95~96 %). These values were proposed by Yoon et al. (2017). In addition, their phylogenetic distance based on 92 bacterial core genes is highly close compared to other species. These mean that Paenibacillus jamilae and Paenibacillus polymyxa should be reclassified as a single species. Based on the results from genomic level comparison as well as reexamination results of physiological and chemotaxonomic features, we propose reclassification of Paenibacillus jamilae as a later heterotypic synonym of Paenibacillus polymyxa.

Changes in the Intestinal Microbiota of Patients with Inflammatory Bowel Disease with Clinical Remission during an 8-Week Infliximab Infusion Cycle

This study investigated changes in the intestinal microbiota during 8-week infliximab maintenance therapy in inflammatory bowel disease (IBD) patients in clinical remission. Microbial compositional differences were analyzed according to the trough level of infliximab (TLI) and mucosal healing (MH) status. 16S rRNA gene-based microbiome profiling was performed on 10 and 74 fecal samples from 10 healthy volunteers and 40 adult IBD patients, respectively. Fecal sampling occurred at 1–2 weeks (1W) and 7–8 weeks (7W) after infliximab infusion. TLI was measured by ELISA at 8 weeks, immediately before the subsequent infusion; MH was evaluated by endoscopy within 3 months. There were no significant changes in microbial composition, species richness, or diversity indices between 1W and 7W. However, 7W samples from the patients with TLI ≥ 5 μg/mL showed an increased species richness compared with patients with TLI < 5 μg/mL, and patients with MH showed increased diversity compared with non-MH patients. Beta-diversity analysis showed clustering between samples in the MH and non-MH groups. LEfSe analysis identified differential composition of Faecalibacterium prausnitzii group according to TLI and MH. In conclusion, these results suggest the potential of fecal microbiota as a response indicator.

In situ liquid SEM imaging analysis revealing particle dispersity in aqueous solutions

A quantitative description on dispersity of boehmite (γ-AlOOH) particles, a key component for waste slurry at Hanford sites, can provide useful knowledge for understanding various physicochemical nature of the waste. In situ liquid scanning electron microscopy (SEM) was used to evaluate the dispersity of particles in aqueous conditions using a microfluidic sample holder, System for Analysis at Liquid Vacuum Interface (SALVI). Secondary electron (SE) images and image analyses were performed to determine particle centroid locations and the distance to the nearest neighbour particle centroid, providing reliable rescaled interparticle distances as a function of ionic strength in acidic and basic conditions. Our finding of the particle dispersity is consistent with physical insights from corresponding particle interactions under physicochemical conditions, demonstrating delicate changes in dispersity of boehmite particles based on novel in situ liquid SEM imaging and analysis. LAY DESCRIPTION: In situ liquid scanning electron microscopy (SEM) was used to determine the interparticle distance of boehmite (γ-AlOOH) particles, a key component for waste slurry at Hanford sites. This type of quantitative measurement is important to understand various physicochemical nature of the radiological waste containing boehmite. In situ liquid SEM was enabled by a unique vacuum compatible microfluidic cell, System for Analysis at Liquid Vacuum Interface (SALVI). We collected secondary electron (SE) images and performed image analyses to determine particle centroid locations and the distance to the nearest neighbour particle centroid to arrive at the interparticle distances in acidic and basic conditions. Our results show that delicate changes occur among boehmite particles under different pH conditions using novel in situ SEM imaging.

Roles of notch signaling pathway and endothelial-mesenchymal transition in vascular endothelial dysfunction and atherosclerosis

OBJECTIVE

To investigate the role of the Notch signaling pathway on the endothelial-mesenchymal transition (EndMT) during vascular endothelial dysfunction and atherosclerosis.

MATERIALS AND METHODS

Human coronary artery endothelial cells (HCAEC) were treated with the exogenous Notch homolog 1 (Notch1) factor to activate the Notch1 pathway, and cells were then observed under the microscope for morphologic changes. Changes in the expression of related proteins were detected by Western blot. In vivo experiments were performed using 18 Sprague Dawley® (SD) rats, and GSI factor was used to specifically inhibit Notch pathway activation. Rats were used and randomly divided into three groups: normal diet (ND) group, high-fat diet (HFD) group, and high-fat diet + GSI (HFD+GSI) group, 6 rats in each group. Hematoxylin and eosin (H&E) staining was used to examine the cardiac aortic morphology of the rats in each treatment group. Real-time polymerase chain reaction (RT-PCR) and Western blot were used to detect the expression of Notch1, Hes1, VE-cadherin and α-SMA in the aortic tissues of rats in each group at mRNA and protein levels, respectively.

RESULTS

After HCAECs were treated with Notch1, endothelial protein levels of VE-cadherin were significantly decreased and levels of the interstitial protein α-SMA were significantly increased. In the animal model, the rats fed with high-fat diet for two months presented obvious atherosclerosis spots in their aorta, but those fed with the same diet and treated with GSI inhibitor of Notch pathway showed significantly fewer atherosclerosis signs. Compared with ND group, mRNA and protein expression levels of Notch1, Hes1 and α-SMA were significantly increased, and the expression levels of endothelial marker VE-cadherin were significantly decreased in aortas of rats in HFD group. Compared with the rats in HFD group, the rats in HFD+GSI group showed significantly reduced expression levels of Notch1, Hes1 and α-SMA.

CONCLUSIONS

The activation of Notch signaling pathway can induce the EndMT progression and promote the development of atherosclerotic lesions.

Application of the Whole Genome-Based Bacterial Identification System, TrueBac ID, Using Clinical Isolates That Were Not Identified With Three Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry (MALDI-TOF MS) Systems

BACKGROUND

Next-generation sequencing is increasingly used for taxonomic identification of pathogenic bacterial isolates. We evaluated the performance of a newly introduced whole genome-based bacterial identification system, TrueBac ID (ChunLab Inc., Seoul, Korea), using clinical isolates that were not identified by three matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) systems and 16S rRNA gene sequencing.

METHODS

Thirty-six bacterial isolates were selected from a university-affiliated hospital and a commercial clinical laboratory. Species was identified by three MALDI-TOF MS systems: Bruker Biotyper MS (Bruker Daltonics, Billerica, MA, USA), VITEK MS (bioMérieux, Marcy l'Étoile, France), and ASTA MicroIDSys (ASTA Inc., Suwon, Korea). Whole genome sequencing was conducted using the Illumina MiSeq system (Illumina, San Diego, CA, USA), and genome-based identification was performed using the TrueBac ID cloud system (www.truebacid.com).

RESULTS

TrueBac ID assigned 94% (34/36) of the isolates to known (N=25) or novel (N=4) species, genomospecies (N=3), or species group (N=2). The remaining two were identified at the genus level.

CONCLUSIONS

TrueBac ID successfully identified the majority of isolates that MALDI-TOF MS failed to identify. Genome-based identification can be a useful tool in clinical laboratories, with its superior accuracy and database-driven operations.

Comparative Genomic and Phylogenomic Analyses Clarify Relationships Within and Between Bacillus cereus and Bacillus thuringiensis: Proposal for the Recognition of Two Bacillus thuringiensis Genomovars

The present study was designed to clarify the taxonomic status of two species classified as Bacillus cereus sensu lato, namely B. cereus sensu stricto and Bacillus thuringiensis. To this end, nearly 900 whole genome sequences of strains assigned to these taxa were the subject of comparative genomic and phylogenomic analyses. A phylogenomic tree based on core gene sequences showed that the type strains of B. cereus and B. thuringiensis formed a well-supported monophyletic clade that was clearly separated from corresponding clades composed of the remaining validly published species classified as B. cereus sensu lato. However, since average nucleotide identity and digital DNA-DNA hybridization similarities between the two types of Bacillus were slightly higher than the thresholds used to distinguish between closely related species we conclude that B. cereus and B. thuringiensis should continue to be recognized as validly published species. The B. thuringiensis strains were assigned to two genomically distinct groups, we propose that these taxa be recognized as genomovars, that is, as B. thuringiensis gv. thuringiensis and B. thuringiensis gv. cytolyticus. The extensive comparative genomic data clearly show that the distribution of pesticidal genes is irregular as strains identified as B. thuringiensis were assigned to several polyphyletic groups/subclades within the B. cereus-B. thuringiensis clade. Consequently, we recommend that genomic or equivalent molecular systematic features should be used to identify B. thuringiensis strains as the presence of pesticidal genes cannot be used as a diagnostic marker for this species. Comparative taxonomic studies are needed to find phenotypic properties that can be used to distinguish between the B. thuringiensis genomovars and between them and B. cereus.

Comparative Genomic Analysis of the 2016 Vibrio cholerae Outbreak in South Korea

In August 2016, South Korea experienced a cholera outbreak that caused acute watery diarrhea in three patients. This outbreak was the first time in 15 years that an outbreak was not linked to an overseas source. To identify the cause and to study the epidemiological implications of this outbreak, we sequenced the whole genome of Vibrio cholerae isolates; three from each patient and one from a seawater sample. Herein we present comparative genomic data which reveals that the genome sequences of these four isolates are very similar. Interestingly, these isolates form a monophyletic clade with V. cholerae strains that caused an outbreak in the Philippines in 2011. The V. cholerae strains responsible for the Korean and Philippines outbreaks have almost identical genomes in which two unique genomic islands are shared, and they both lack SXT elements. Furthermore, we confirm that seawater is the likely source of this outbreak, which suggests the necessity for future routine surveillance of South Korea's seashore.

Comparison of the Gut Microbiota of Centenarians in Longevity Villages of South Korea with Those of Other Age Groups

Several studies have attempted to identify factors associated with longevity and maintenance of health in centenarians. In this study, we analyzed and compared the gut microbiota of centenarians in longevity villages with the elderly and adults in the same region and urbanized towns. Fecal samples were collected from centenarians, elderly, and young adults in longevity villages, and the gut microbiota sequences of elderly and young adults in urbanized towns of Korea were obtained from public databases. The relative abundance of Firmicutes was found to be considerably higher in subjects from longevity villages than those from urbanized towns, whereas Bacteroidetes was lower. Age-related rearrangement of gut microbiota was observed in centenarians, such as reduced proportions of Faecalibacterium and Prevotella, and increased proportion of Escherichia, along with higher abundances of Akkermansia, Clostridium, Collinsella, and uncultured Christensenellaceae. Gut microbiota of centenarians in rehabilitation hospital were also different to those residing at home. These differences could be due to differences in diet patterns and living environments. In addition, phosphatidylinositol signaling system, glycosphingolipid biosynthesis, and various types of N-glycan biosynthesis were predicted to be higher in the gut microbiota of centenarians (corrected p < 0.05). These three metabolic pathways of gut microbiota can be associated with the immune status and healthy gut environment of centenarians. Although further studies are necessary to validate the function of microbiota between groups, this study provides valuable information on centenarians' gut microbiota.

Large-Scale Genomics Reveals the Genetic Characteristics of Seven Species and Importance of Phylogenetic Distance for Estimating Pan-Genome Size

For more than a decade, pan-genome analysis has been applied as an effective method for explaining the genetic contents variation of prokaryotic species. However, genomic characteristics and detailed structures of gene pools have not been fully clarified, because most studies have used a small number of genomes. Here, we constructed pan-genomes of seven species in order to elucidate variations in the genetic contents of >27,000 genomes belonging to Streptococcus pneumoniae, Staphylococcus aureus subsp. aureus, Salmonella enterica subsp. enterica, Escherichia coli and Shigella spp., Mycobacterium tuberculosis complex, Pseudomonas aeruginosa, and Acinetobacter baumannii. This work showed the pan-genomes of all seven species has open property. Additionally, systematic evaluation of the characteristics of their pan-genome revealed that phylogenetic distance provided valuable information for estimating the parameters for pan-genome size among several models including Heaps' law. Our results provide a better understanding of the species and a solution to minimize sampling biases associated with genome-sequencing preferences for pathogenic strains.

Abstract P4-10-11: Pregnancy-associated breast cancer in a contemporary cohort of newly diagnosed women

Introduction: Pregnancy-associated breast cancer (PABC) refers to breast cancer (BC) diagnosed during pregnancy, lactation, or in the postpartum period. There is evidence that PABC is associated with a poorer prognosis, and that the development of the disease is influenced by the unique hormonal milieu of pregnancy. The purpose of this study was to investigate the clinicopathologic characteristics associated with PABC in a contemporary cohort of women with newly diagnosed BC.

Methods: Our institutional Breast Cancer Database was queried for women diagnosed with breast cancer between 2010-17 who had at least one full term pregnancy (FTP). Variables of interest included patient demographics and clinical and tumor characteristics. PABC was defined as breast cancer diagnosed within 24 months of delivery. Statistical analyses included Pearson's chi-square and logistic regression.

Results: Out of a total of 1934 women, 42 (2.2%) had PABC. Median follow up in the total cohort was 4.5 years. After adjusting for age at diagnosis, PABC was associated with older age at first FTP, ethnic minority status, BRCA mutation carriers, presentation with a palpable mass, higher histologic grade, and ER-negative and triple negative receptor status. Variables that were not significantly different between PABC and non-PABC cases included tumor histology, multifocality, presence of lymphovascular invasion, and family history of breast cancer.

Table:Selected Characteristics of Women with PABCVariableNon-PABC (n=1892)PABC (n=42)P-value*Age at first full term pregnancy  &lt;0.001&lt;35 years1610 (85%)28 (66.7%) ≥35 years277 (15%)14 (33.3%) Race  0.001White1397 (73.8%)23 (54.8%) Black181 (9.6%)8 (19%) Asian175 (9.2%)10 (23.8%) Hispanic131 (6.9%)1 (2.4%) Other8 (0.4%)0 (0%) BRCA 1,2 Positive56 (3%)9 (21.4%)&lt;0.001Method of Presentation  0.002Breast Exam579 (30.6%)30 (71.4%) Mammography1137 (60.1%)10 (23.8%) Ultrasound87 (1.6%)2 (4.8%) MRI67 (3.5%)0 (0%) Other22 (1.2%)0 (0%) Invasive Grade  0.014Low213 (15%)0 (0%) Intermediate763 (53.8%)12 (37.5%) High442 (31.2%)20 (62.5%) Estrogen Receptor  0.034Positive1572 (83.9%)29 (69%) Negative301 (16.1%)13 (31%) Triple Negative135 (7.1%)7 (16.7%)0.041*P-values are age-adjusted.

Conclusions: The association of PABC with ethnic minority status in our cohort is interesting and may be reflected in the increased proportion of triple negative breast cancers in the PABC group. In our contemporary cohort, PABC was associated with older age at first FTP. As more women delay childbearing, risk for PABC may increase. Our findings suggest that women who become pregnant at older ages should be followed carefully during pregnancy and in the postpartum period, especially if they are BRCA mutation carriers. The optimal approach for monitoring older women during pregnancy and the postpartum period is unclear. Clinical breast exam may play an important role, especially for those women known to be at increased risk for breast cancer.

Citation Format: Gooch JC, Chun J, Jubas T, Guth A, Schnabel F. Pregnancy-associated breast cancer in a contemporary cohort of newly diagnosed women [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr P4-10-11.

Abstract P4-10-07: Breastfeeding experience among breast cancer patients in the modern era

Introduction: In recent years, the uptake of breastfeeding has become more common as it is regarded as healthy and beneficial for both mother and infant. The process of parturition and lactation plays a role in the normal differentiation and development of breast tissue, and multiparity has been associated with a decreased risk for breast cancer. The current study sought to describe the breastfeeding experience of a modern cohort of women with newly diagnosed BC, and to examine the clinicopathologic characteristics of their disease.

Methods: A retrospective review of our institutional Breast Cancer Database from 2009-2017 was performed to identify women with at least one full term pregnancy (FTP). Clinicopathologic and demographic information was recorded, including breastfeeding experience and cumulative duration of nursing. Women were grouped by self-reported breastfeeding experience and duration of breastfeeding for analysis. Pearson's chi-square tests were performed.

Results: Of 1919 patients, 1053 (54.9%) reporting breastfeeding. Breastfeeding increased from a low of 30.4% among women with first FTP (FFTP) in the 1950's to 84.6% with FFTP in the 2010's. There were no significant differences between those who did and did not breast feed with regards to race, family history, BRCA status, pathologic stage, grade, tumor histology, lymphovascular invasion (LVI), multifocality, tumor size or receptor status. When stratified by duration of breastfeeding, the most striking finding was that women who breastfed for &gt;12 months were more likely to have tumors associated with LVI (p = 0.028).

Table– Breastfeeding Experience Among Parous Women with Breast CancerVariableNo Breastfeeding (n=866)Breastfeeding (n=1053)p-valueRace  0.432White648 (74.8%)767 (72.8%) Black73 (8.5%)112 (10.6%) Asian78 (9%)102 (9.7%) Hispanic64 (7.4%)67 (6.4%) Other3 (0.3%)5 (0.5%) Family history272 (31.4%)311 (29.6%)0.397BRCA 1,2 positive23 (2.7%)42 (4.0%)0.108Final Pathology Stage  0.2240190 (21.9%)222 (21.1%) I426 (49.2%)507 (48.1%) II197 (22.8%)229 (21.7%) III40 (4.6%)63 (6.0%) IV1 (0.1%)3 (0.3%) No residual (neoadjuvant)12 (1.4%)29 (34.1%) Invasive Grade  0.127Low92 (14.1%)120 (15.3%) Intermediate371 (56.7%)398 (50.6%) High191 (29.2%)268 (34.1%) Histology  0.130DCIS189 (21.8%)223 (21.2%) IDC531 (61.3%)688 (65.3%) ILC113 (13.1%)99 (9.4%) Other33 (3.8%)43 (4.1%) LVI127 (14.7%)174 (16.5%) Multifocality147 (17%)183 (17.4%) Median tumor size (cm; range)1.4 (0-9.5)1.3 (0-12.5)0.489Estrogen Receptor  0.206Positive726 (84.7%)861 (82.6%) Negative131 (15.3%)182 (17.4%) Progesterone Receptor  0.275Positive621 (72.5%)732 (70.2%) Negative236 (27.5%)311 (29.8%) HER2/neu Receptor  0.068Positive78 (12%)121 (15.4%) Negative571 (88%)667 (84.6%) 

Conclusions: Breastfeeding experience was not generally associated with significant differences in tumor or patient characteristics. However, breastfeeding for longer than 12 months was associated with LVI. It is possible that changes in the breast tissue that occur during the process of pregnancy and prolonged lactation may influence future tumor development. These findings are hypothesis generating and suggest that the relationship of prolonged breastfeeding and breast cancer development should be investigated further.

Citation Format: Gooch JC, Chun J, Jubas T, Guth A, Schnabel F. Breastfeeding experience among breast cancer patients in the modern era [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr P4-10-07.

Abstract P5-02-01: The relationship of breast density in mammography and magnetic resonance imaging (MRI) in women with triple negative breast cancer (TNBC)

Introduction:

TNBC represent 10%–20% of invasive breast cancers. Previous studies showed that TNBC usually present with benign features on mammography, ultrasound and MRI. However, there is a dearth of information on the relationship of mammographic breast density (MBD), background parenchymal enhancement (BPE) and fibroglandular tissue (FGT) on MRI with TNBC. The purpose of this study was to evaluate the relationship between BD, BPE, and FGT in women with TNBC compared to non-TNBC in a contemporary cohort of women with breast cancer.

Methods:

The Institutional Breast Cancer Database was queried for women who had invasive breast cancer and underwent mammography and MRI between (2010-2017). Variables of interest included clinical, pathologic, and imaging characteristics. Statistical analyses included Pearson's Chi Square and logistic regression.

Results:

Of 2224 women, 210 (9%) had TNBC. The median age was 59 years (22-95) and median follow up was 4 years. When we looked at the clinical characteristics of women with TNBC compared to non-TNBC, race, BRCA1,2 status, method of presentation, palpability, histology, grade, and Ki67 were statistically different (Table 1). When we looked at the correlation of MBD, FGT, and BPE for women with TNBC, MBD was correlated with FGT (r=0.64) but weakly correlated with BPE (r=0.22). We found a significant association of low BPE and TNBC compared to the non-TNBCs (p=0.021) (Table 1). In a short period of time, only 8 women with TNBC had a recurrence with no significant association with MBD, BPE, or FGT (Table 1).

Table 1.Imaging Characteristics among TNBC compared to non-TNBCVariableTNBC (N=210)%Non-TNBC (N=2014)%P-valueRace    0.001White13665153376 Black35171749 Hispanic1261156 Asian23111739 Other42191 BRCA1/2    &lt;0.001Positive3025425 Negative897579195 Method of Presentation    &lt;0.001Breast exam1125475738 Mammography7737105753 Ultrasound731106 MRI126553 Palpable    &lt;0.001Yes1185783342 No9144115258 Histology    &lt;0.001DCIS with Microinvasion21382 IDC19693159079 ILC5226913 Invasive Other731176 Invasive Grade    &lt;0.001Grade 11131016 Grade 22714111858 Grade 31688650126 ER    &lt;0.001Positive00189194 Negative2101001226 PR    &lt;0.001Positive00160080 Negative21010041221 Ki67    &lt;0.001Median (range)60 (0-99) 10 (0-99)  Mammographic Density    0.165Less dense82417846 More dense11959103454 MRI BPE    0.021Low BPE707655564 High BPE222431236 MRI FGT    0.370Less dense475440449 More dense404642151 

Conclusions:

In our study population, MBD and FGT did not differ between patients with TNBC compared to non-TNBC. Interestingly, we found a higher proportion of women with lower BPE in the TNBC compared to the non-TNBC group. BPE refers to the amount of enhancing fibroglandular tissue and has been demonstrated to reflect variations in estrogen-mediated vascular permeability. Lower BPE in TNBC may reflect the fact that these tumors are not hormonally sensitive. This may also have implications for radiogenomics, which aims to correlate imaging characteristics with gene expression and genome-related characteristics in tumor biology. Further studies are warranted in looking at these imaging biomarkers and TNBC.

Citation Format: Chun J, Schnabel F, Gooch J, Lee J, Jubas T, Goodgal J, Guth A, Moy L. The relationship of breast density in mammography and magnetic resonance imaging (MRI) in women with triple negative breast cancer (TNBC) [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr P5-02-01.

Effects of Ionic Strength, Salt, and pH on Aggregation of Boehmite Nanocrystals: Tumbler Small-Angle Neutron and X-ray Scattering and Imaging Analysis

The US government currently spends significant resources managing the legacies of the Cold War, including 300 million liters of highly radioactive wastes stored in hundreds of tanks at the Hanford (WA) and Savannah River (SC) sites. The materials in these tanks consist of highly radioactive slurries and sludges at very high pH and salt concentrations. The solid particles primarily consist of aluminum hydroxides and oxyhydroxides (gibbsite and boehmite), although many other materials are present. These form complex aggregates that dramatically affect the rheology of the solutions and, therefore, efforts to recover and treat these wastes. In this paper, we have used a combination of transmission and cryo-transmission electron microscopy, dynamic light scattering, and X-ray and neutron small and ultrasmall-angle scattering to study the aggregation of synthetic nanoboehmite particles at pH 9 (approximately the point of zero charge) and 12, and sodium nitrate and calcium nitrate concentrations up to 1 m. Although the initial particles form individual rhombohedral platelets, once placed in solution they quickly form well-bonded stacks, primary aggregates, up to ∼1500 Å long. These are more prevalent at pH = 12. Addition of calcium nitrate or sodium nitrate has a similar effect as lowering pH, but approximately 100 times less calcium than sodium is needed to observe this effect. These aggregates have fractal dimension between 2.5 and 2.6 that are relatively unaffected by salt concentration for calcium nitrate at high pH. Larger aggregates (>∼4000 Å) are also formed, but their size distributions are discrete rather than continuous. The fractal dimensions of these aggregates are strongly pH-dependent, but only become dependent on solute at high concentrations.

Genomic Insight Into the Predominance of Candidate Phylum Atribacteria JS1 Lineage in Marine Sediments

Candidate phylum Atribacteria JS1 lineage is one of the predominant bacterial groups in anoxic subseafloor sediments, especially in organic-rich or gas hydrate-containing sediments. However, due to the lack of axenic culture representatives, metabolic potential and biogeochemical roles of this phylum have remained elusive. Here, we examined the microbial communities of marine sediments of the Ross Sea, Antarctica, and found candidate phylum Atribacteria JS1 lineage was the most abundant candidate phylum accounting for 9.8-40.8% of the bacterial communities with a single dominant operational taxonomic unit (OTU). To elucidate the metabolic potential and ecological function of this species, we applied a single-cell genomic approach and obtained 18 single-cell amplified genomes presumably from a single species that was consistent with the dominant OTU throughout the sediments. The composite genome constructed by co-assembly showed the highest genome completeness among available Atribacteria JS1 genomes. Metabolic reconstruction suggested fermentative potential using various substrates and syntrophic acetate oxidation coupled with hydrogen or formate scavenging methanogens. This metabolic potential supports the predominance of Atribacteria JS1 in anoxic environments expanding our knowledge of the ecological function of this uncultivated group.

Genomic characterization of Nocardia seriolae strains isolated from diseased fish

Members of the genus Nocardia are widespread in diverse environments; a wide range of Nocardia species are known to cause nocardiosis in several animals, including cat, dog, fish, and humans. Of the pathogenic Nocardia species, N. seriolae is known to cause disease in cultured fish, resulting in major economic loss. We isolated two N. seriolae strains, CK‐14008 and EM15050, from diseased fish and sequenced their genomes using the PacBio sequencing platform. To identify their genomic features, we compared their genomes with those of other Nocardia species. Phylogenetic analysis showed that N. seriolae shares a common ancestor with a putative human pathogenic Nocardia species. Moreover, N. seriolae strains were phylogenetically divided into four clusters according to host fish families. Through genome comparison, we observed that the putative pathogenic Nocardia strains had additional genes for iron acquisition. Dozens of antibiotic resistance genes were detected in the genomes of N. seriolae strains; most of the antibiotics were involved in the inhibition of the biosynthesis of proteins or cell walls. Our results demonstrated the virulence features and antibiotic resistance of fish pathogenic N. seriolae strains at the genomic level. These results may be useful to develop strategies for the prevention of fish nocardiosis.