bluuebunny/crossref_metadata_2025_split huggingface dataset:
P914 An adult zebrafish model for adherent-invasive Escherichia coli indicates protection from infection by treatment with probiotic E. coli Nissle
Authors: Nag D , Raychaudhuri S , Withey J 
Published: January 2023

Abstract

Background
Adherent-invasive Escherichia coli (AIEC) is an opportunistic pathogen associated with major inflammatory bowel disease (IBD), Crohn’s disease (CD) and ulcerative colitis (UC). AIEC is a human commensal but during unfavorable gastric conditions it exhibits pathogenic properties and induces inflammation in the gut, sometimes progressing to inflammation-induced colon cancer. The exact mechanisms for AIEC pathogenesis are still being discovered. As a human opportunistic pathogen, AIEC has few animal models. In recent years, zebrafish have emerged as a useful model for studies of various human pathogens. Here, a zebrafish model to study AIEC infection was developed.

Methods
Colonization of AIEC from overnight culture was determined with different infectious doses (103, 104, 105 and 106 CFU/ml of infection water) in zebrafish, incubating fish with AIEC in water for 6 h and then in fresh water for 18 h at 28o C. The invasive property of AIEC in zebrafish gut was determine by gentamycin protection assay. Persistent colonization of AIEC in zebrafish gut was also assessed for 10 days. Induction of pro-inflammatory markers such as IL-1β, TNFα, IFNγ and S100A-10b (akin to human calprotectin) in zebrafish intestinal cells in response to AIEC infection was determined by qRT PCR and ELISA. A probiotic strain, E. coli Nissle 1917 (EcN) was used as a therapeutic and prophylactic against AIEC infection. Propionic acid was used to augment the AIEC infection and the efficacy of ECN was tested against the hyper-infectious condition of AIEC in zebrafish.

Results
Bath inoculation with AIEC resulted in colonization, invasion and tissue disruption in the zebrafish intestine. The AIEC infection induced neutrophil recruitment and showed significant pro-inflammatory responses in zebrafish gut. S100A-10b protein of zebrafish, equivalent of a human IBD marker, calprotectin, was significantly increased in the zebrafish gut during AIEC infection. The probiotic E. coli Nissle 1917 (EcN) reduced AIEC colonization, tissue damage and pro-inflammatory responses in zebrafish in both prophylactic and therapeutic ways. Furthermore, EcN diminished the propionic acid-augmented hyper infection of AIEC in the zebrafish model.

Conclusion
In this study a new zebrafish model was developed to study the infection and inflammation induced by AIEC. Probiotic strain, EcN was used successfully against AIEC to reduce the inflammation in AIEC-zebrafish model.
P917 Intestinal complement interacts with commensal microbiota and provides pattern recognition in Inflammatory Bowel Disease
Authors: Reider S , Posch W , Koch R , Orth-Höller D , Würzner R , Wilflingseder D , Tilg H , Moschen A 
Published: January 2023

Abstract

Background
The complement system is a central humoral part of innate immunity and provides essential pattern recognition capabilities as well as effector functions such as opsonisation and target cell lysis. Its prominent role in infection and immunity is undisputed but its involvement in the pathogenesis of inflammatory bowel diseases remains less clear. Published data point to a role of complement within the intestinal lumen supporting clearance of pathogens1.

Methods
Expression of complement proteins within the intestinal epithelium was quantified by real-time qPCR on lesional and non-lesional biopsy samples from patients with IBD and healthy controls. The concentration of complement proteins was measured in fecal supernatants using ELISA. Flow cytometry of fecal bacterial single cell suspensions was used to assess complement (C3) and antibody (IgA) opsonisation status. Finally, cytometrically distinct populations were isolated by fluorescence-assisted cell sorting (FACS) and microbial community composition was investigated using 16S rDNA sequencing. Prediction of functional profiles from amplicon data was performed using Tax4Fun2.

Results
Complement expression in intestinal tissue was increased during active inflammation but certain targets were significantly less expressed in lesional mucosal sites (e.g. C6, C7). Free complement proteins in fecal supernatants were mostly undetectable by ELISA. In contrast, complement opsonisation was verified on fecal bacteria using flow cytometry. The degree of complement deposited on bacterial surfaces was significantly correlated with fecal calprotectin (p &lt; 0.01). The percentage of complement-opsonized bacteria ranged from 0 to 5.3 % and did not correlate with intestinal inflammation while percentages of IgA opsonisation were generally higher (0.4 - 90.1%) and increased with fecal calprotectin (p &lt; 0.01).
FACS followed by 16S amplicon sequencing detected differences in bacterial taxa abundance between complement-opsonized, IgA-opsonized and non-opsonized fractions. Functional in-silico profiling revealed associations of complement-opsonization with bacterial virulence factors.

Conclusion
Luminal and mucosal complement expression and activity is evident in patients with IBD. Complement opsonisation profiles are distinct from IgA opsonisation and show features of specificity regarding recognition of microbial features.
References:
1 K.P. Aßhauer, B. Wemheuer, R. Daniel, P. Meinicke (2015) Tax4Fun: predicting functional profiles from metagenomic 16S rRNA dataBioinformatics (2015) 31 (17): 2882-2884.
2 Sorbara, M. T., et al. (2018). Complement C3 Drives Autophagy-Dependent Restriction of Cyto-invasive Bacteria. Cell Host Microbe 23(5): 644-652 e645.
P918 Clostridium butyricum inhibits epithelial-mesenchymal transition of intestinal carcinogenesis through downregulating METTL3
Authors: Zhang K , Dong Y , Li M , Zhang W , Ding Y , Wang X , Chen D , Liu T , Wang B , Zhong W , Cao H 
Published: January 2023

Abstract

Background
Colorectal cancer (CRC) is related to gut microbiota dysbiosis, especially butyrate-producing bacteria reduction. Our previous study suggested administration of Clostridium butyricum (C. butyricum), a butyrate-producing bacterium, exerts a crucial effect against CRC. Methyltransferase-like 3 (METTL3) contributes to tumorigenic epigenetic regulation. We aimed to investigate the effects of C. butyricum on METTL3 in the prevention of CRC.

Methods
TCGA and CancerSEA databases were used to investigate METTL3 co-expressed genes, and the GO and KEGG enrichment analysis was conducted on METTL3. Tissue specimens of human normal colonic tissue, adenoma and carcinoma were obtained and examined the expression of METTL3, EMT-associated markers, and VM formation. We overexpressed METTL3 in CRC cells to assess cell migration and tube formation. Meanwhile, the effects of C. butyricum on METTL3, epithelial-mesenchymal transition (EMT), and vasculogenic mimicry (VM) formation in CRC cells were evaluated. Furthermore, a murine xenograft model was established to provide further evidence of the inhibition of C. butyricum on tumor growth.

Results
Database analysis suggested that METTL3 showed a positive correlation with proliferation, EMT, DNA repair, metastasis, and invasion. The expression of METTL3 gradually increased from human normal colon tissue, adenoma to carcinoma, and was positively correlated with VM formation and EMT. METTL3 overexpression promoted the proliferation, migration, and invasion of CRC cells and induced VM formation. C. butyricum could downregulate METTL3 expression in CRC cells and decrease the expression of vimentin and vascular endothelial growth factor receptor 2 to reduce EMT and VM formation. Moreover, C. butyricum alleviated the pro-oncogenic effect of METTL3 overexpressing plasmid in CRC cells. Accordingly, C. butyricum downregulated the expression of METTL3 in tumors and prevented EMT in nude mice.

Conclusion
C. butyricum could inhibit EMT and VM of intestinal carcinogenesis through downregulating METTL3. These findings broaden our understanding of probiotics supplement in the prevention and treatment of CRC.
P919 Gut microbial signature and phenotype-specific Indicators in fecal microbiota of Korean patients with Inflammatory Bowel Disease
Authors: Lee C K , Oh S J , Kim H J , Kim B H , Kim B K , Park Y K , Yang B G 
Published: January 2023

Abstract

Background
The incidence and prevalence of inflammatory bowel disease (IBD) in Asian countries have been increasing rapidly over the last few decades. This study was aimed to reveal gut metagenomic characteristics and identify a robust fecal microbial marker in Korean patients with IBD through a large-scale comparative study.

Methods
Gut metagenomic study using 640 fecal samples collected from patients with 523 IBD (223 Crohn’s disease [CD], 300 ulcerative colitis [UC]) and 117 healthy controls was conducted by 16S rRNA sequencing. Unsupervised cluster analysis based on the predicted functional genes was conducted. Microbiome Multivariable Association with Linear Models was used to determine relationship between metagenomic data and clinical metadata after adjusting for multiple covariates.

Results
Patients with IBD, particularly CD, had a significantly lower alpha diversity than the controls (p &lt;0.05). An increase in stool consistency was positively associated with community diversity in controls and UC (p = 5.3e-11, Kruskal-Wallis test), but not in patients with CD. Differential abundance analysis revealed an expansion of the phylum Proteobacteria and its constituent taxa in CD, and Ruminococcaceae and Bacteroidaceae families in UC, LDA score [log10] &gt;2.0, p &lt;0.05. Patients with CD had a strong association with Escherichia-Shigella in their fecal microbiome compared to the controls in a multivariable model (FDR &lt;0.01). Microbial functional prediction revealed the strong upregulation of bacterial invasion of epithelial cells and Shigellosis pathways in CD (FDR &lt;0.01, absolute coefficient &gt;2.0). Strong enhancement of the siderophores biosynthesis pathways, the aerobactin and enterobactin biosynthesis pathways (FDR &lt;0.01, absolute coefficient of 2.947 and 1.971, respectively), with abundant contribution from the genus Escherichia-Shigella, is in line with the results obtained from taxonomic profiles. Clustering analysis identified two distinct function-based clusters showing a contrast in the diseae behavior of IBD. Cluster II enriched in patients with stricturing/penetrating Crohn's and extensive UC displayed a significant increase of the genus Escherichia-Shigella (Fig. 1a) and a simultaneous depletion of the genus Faecalibacterium (Fig. 1b), all FDR &lt;10-50.

Conclusion
The present study adds to the growing evidence that the pathogenesis of CD is underpinned by the genus Escherichia-Shigella. Escherichia-Shigella may be a universal pathobiont in IBD, irrespective of ethnic and life-style backgrounds. Abundance shifting of Escherichia-Shigella and Faecalibacterium in fecal microbiomes is strongly linked with advanced behavior of IBD, which will have significant implications for future research on the diagnosis and treatment of the disease.
P922 Gut microbiome and mycobiome in inflammatory bowel disease patients with Clostridium difficile infection
Authors: Yu S , Ge X , Tan B , Tian B , Shi Y , Dai Y , Hu S , Li Y , Qian J 
Published: January 2023

Abstract

Background
Clostridium difficile infection (CDI) is common in patients with inflammatory bowel disease (IBD) and has been reported as a risk factor for poor outcome. However, gut microbiome and mycobiome of IBD patients with CDI have been barely investigated. This study aimed to assess the gut microbiome and mycobiome in IBD patients with CDI.

Methods
We collected fecal samples from patients with IBD and concomitant CDI (IBD-CDI group, n=38), patients with IBD and no CDI (IBD-only group, n=91), and healthy subjects (HC, n=40). Patients characteristics including demographic data, disease severity, and medication history were collected. 16S rRNA sequencing, metagenomic sequencing, and untargeted metabolomic analysis were carried out in the samples.

Results
We found that the bacterial alpha diversity of the IBD-CDI group was lower than the IBD-only group and HC. And the bacterial and fungal beta diversity variations between IBD patients and HC were significant, regardless of CDI status. But the IBD-CDI group did not significantly cluster separately from the IBD-only group. Several bacterial taxa, including Ruminococcus gnavus, Clostridium innocuum, and Veillonella were overrepresented in the IBD-CDI group compared with IBD-only group and HC. Furthermore, IBD patients with CDI were distinguished from the IBD-only group and HC by several fungal taxa, including underrepresentation of Candida albicans, and overrepresentation of Saccharomyces cerevisiae, Eremothecium sinecaudum, Torulaspora delbrueckii, Grosmannia clavigera, and Eremothecium gossypii. The fungal-bacterial transkingdom network was altered in the IBD patients with CDI with a decreased network density. Notably, the relative abundance of Grosmannia clavigera was markedly higher in severe ulcerative colitis patients (defined by Truelove and Witts criteria and Mayo score). Besides, prior antibiotic exposure was associated with decreased biodiversity and increased dysbiosis. Functional differences in IBD patients with CDI include enrichment of branched-chain fatty acid biosynthesis, succinate fermentation to butanoate, peptidoglycan biosynthesis, and tetrahydrofolate biosynthesis. The metabolomic data indicated that the differential metabolites were predominantly involved in amino sugar and nucleotide sugar metabolism, fatty acid metabolism, porphyrin and chlorophyll metabolism, and neomycin, kanamycin and gentamicin biosynthesis.

Conclusion
IBD patients with CDI had pronounced microbial dysbiosis. Gut micro-ecological changes and interkingdom crosstalk in IBD patients with CDI might provide insight into the pathological process and potential strategies for diagnosis and treatment in this subset of patients.
P926 Blautia Obeum Aggravates Colitis in a Murine Model
Authors: Lee C , Koh S J , Hong H T , Park H , Im J P , Kim J S 
Published: January 2023

Abstract

Background
Blautia is a genus of anaerobic bacteria known as having probiotic properties in several studies. The aim of this study was to investigate the role of Blautia obeum in inflammatory bowel disease which has not yet been elucidated.

Methods
To assess the role of B. obeum, 7 weeks-old C57BL/6 mice were treated with 3% dextran sulfate sodium (DSS) for 5 days with or without oral administration of B. obeum simultaneously in the first experiment. Comparing with negative (only phosphate buffered saline) and positive (without intake of microbiome) controls, prior daily administration of B. obeum (day 0 to 7) and subsequent administration of DSS (day 7 to 15) were done in the second experiment. Body weight was evaluated daily in those acute colitis models. Macroscopic analysis and histological evaluation for inflammatory activity were evaluated after sacrifice. Moreover, inflammatory cytokines such as interleukin (IL), tumor necrosis factor alpha (TNF-α), and interferon gamma (IFN-γ) in the colonic lamina propria mononuclear cells were measured by quantitative real-time polymerase chain reaction. Fecal samples were collected from all subjects during experiments, and the influences on gut microbiota were analyzed by 16S rRNA gene-pyrosequencing.

Results
B. obeum aggravated colitis assessed by body weight loss. Histologic severity was higher in mice treated with B. obeum than in controls. IL-17, IFN-γ, and TNF-α were increased in mice treated with B. obeum, compared with controls. A significantly lower richness (P&lt;0.05) and difference in community composition (P=0.009) of metagenomic species was seen in mice treated by B. obeum, compared with controls. To confirm the direct role of B. obeum in a murine colitis, we treated antibiotics for 7 days before the administration of B. obeum. In this experiment. B. obeum aggravated colitis assessed by body weight reduction and colon shortening as well as histologic severity.

Conclusion
B. obeum aggravates colitis in mice. B. obeum can be an organism that is associated with the pathogenesis in inflammatory bowel disease.
P928 Identification of mucosal microbiome-host gene interactions in ulcerative colitis patients
Authors: Namjoo K , Beom Jae Pro L , Dr. f , Jeong-An G , Seung Han K , Moon Kyung J , Jong-Jae P 
Published: January 2023

Abstract

Background
With the development of NGS analysis, many studies have been performed on the role of gut microbiota in the pathogenesis of inflammatory bowel disease and the possibility of gut bacteria as a diagnosis and treatment modality for IBD. However, the role of gut microbiota in clinical applications such as markers for diagnosis, prognosis prediction and the therapeutic agents is still unclear, and further studies on host-microbe interactions are still needed. In this study, we tried to detect mucosal bacterial species which can discriminate between ulcerative colitis and normal control and the correlations between the microbiome and gene expression through integrated analysis of metagenomic sequencing and RNA-sequencing in the colonic mucosa of UC patients and normal controls.

Methods
Colonic tissues obtained from UC patients (n = 7) and normal control (n = 13) were subjected to 16S rRNA sequencing of the microbiome and next-generation sequencing (NGS) RNA-seq. The differentially expressed genes (DEGs) and DEGs-based enrichment terms were obtained. Gene set enrichment analysis (GSEA) and PathfindR were also used to reveal significant differences of meaningful gene sets. The datasets were analyzed individually and integrated including sociomedical factors for combined analysis using bioinformatics approaches. Correlation analyses were performed between microbiome and gene expression and network analysis were presented.

Results
From DEG results, 28 and 18 genes were higher expressed in the UC and normal groups, respectively. GSEA provided total 1,857 gene sets enriched in the UC group. We identified that patients with UC show decreased species such as Bacteroides coprocola, Bacteroides phlebeius, Parabacteroides merdae and increased abundance of other species, such as Eubacterium._eligens, Clostridium_clostridioforme, Faecalibacterium_prausnitzii. An integrative analysis identified immunomodulatory genes including HLA-G, PSMA4 for which gene expression is negatively correlated with Bacteroides species.

Conclusion
In addition to identifying mucosal microbiome and host-genes expression patterns in the UC patients, we showed the potential role of host-microbe interactions in the development of UC. These findings provided the integrated analysis of microbe- host gene can be served as a biomarker for diagnosis and treatment target in patients with UC.
N02 Our life is a roller-coaster! A qualitative phenomenological study exploring the impact of IBD on family members
Authors: Thapwong P , Norton C , Rowland E , Czuber-dochan W 
Published: January 2023

Abstract

Background
IBD significantly impacts individuals’ and their family members’ physical, psychosocial and emotional wellbeing. These then reduce quality of life. Whilst there are studies exploring the impact of IBD on children and their families, little is known about the impact of IBD on family members of adults with IBD. This study explored the impact of IBD on family members of adults diagnosed with IBD, what coping strategies they use and what support they need to manage the psychosocial and emotional burdens associated with supporting patients in managing their IBD.

Methods
An interpretive phenomenological study conducted, using an individual in-depth, semi-structured online interviews via MS Team, Zoom, or telephone. The interviews were audio recorded and transcribed verbatim. An inductive and deductive reflexive thematic analysis followed the Braun and Clark technique.

Results
Forty-three participants, including 17 people with IBD and 26 family members (parents, children, siblings, partners), were purposively selected. Three main themes and accompanying subthemes were created: (1) “Life is a roller coaster” (2) “There have been a lot of bridges to cross along the way” and (3) “My life would be better if...” Participants revealed that the impact of IBD on family members has better and worse aspects in terms of emotional wellbeing, relationship, pressure around roles and responsibilities, day-to-day burden, and siblings’ suffering. Positive coping strategies such as creating meaningful social networks, learning through living with the condition, and open communication were used by some. However, many used negative coping strategies such as avoidance, denial, and “battling on” without asking for help. To mitigate the negative impact of IBD, many family members expressed the need for support. This included proactive and effective communication from healthcare professionals, referral to meaningful sources of information and support, and support groups.

Conclusion
IBD impacts the emotional and psychosocial wellbeing of family members in both positive and negative ways. Some family members were able to use positive coping strategies, however many developed negative coping which affected their daily life. Interventions that support families to communicate better about the impacts of the condition on their wellbeing and/or provide psychosocial support will help family members of people with IBD better cope with disease and have a more fulfilling life. Health professionals need to understand the impact of IBD on family members and support them to cope with the psychosocial and emotional demands of the condition as well as the physical implications.