4,707 results on '"mucosal microbiome"'
Search Results
2. Prediction of anastomotic insufficiency based on the mucosal microbiome prior to colorectal surgery: a proof-of-principle study
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Lehr, Konrad, Lange, Undine Gabriele, Hipler, Noam Mathias, Vilchez-Vargas, Ramiro, Hoffmeister, Albrecht, Feisthammel, Jürgen, Buchloh, Dorina, Schanze, Denny, Zenker, Martin, Gockel, Ines, Link, Alexander, and Jansen-Winkeln, Boris
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- 2024
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3. Alterations of the duodenal mucosal microbiome in patients with metabolic dysfunction-associated steatotic liver disease
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Ren, Mengting, Pan, Hanghai, Zhou, Xinxin, Yu, Mosang, and Ji, Feng
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- 2024
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4. Prediction of anastomotic insufficiency based on the mucosal microbiome prior to colorectal surgery: a proof-of-principle study
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Konrad Lehr, Undine Gabriele Lange, Noam Mathias Hipler, Ramiro Vilchez-Vargas, Albrecht Hoffmeister, Jürgen Feisthammel, Dorina Buchloh, Denny Schanze, Martin Zenker, Ines Gockel, Alexander Link, and Boris Jansen-Winkeln
- Subjects
Medicine ,Science - Abstract
Abstract Anastomotic leakage (AL) is a potentially life-threatening complication following colorectal cancer (CRC) resection. In this study, we aimed to unravel longitudinal changes in microbial structure before, during, and after surgery and to determine if microbial alterations may be predictive for risk assessment between sufficient anastomotic healing (AS) and AL prior surgery. We analysed the microbiota of 134 colon mucosal biopsies with 16S rRNA V1-V2 gene sequencing. Samples were collected from three location sites before, during, and after surgery, and patients received antibiotics after the initial collection and during surgery. The microbial structure showed dynamic surgery-related changes at different time points. Overall bacterial diversity and the abundance of some genera such as Faecalibacterium or Alistipes decreased over time, while the genera Enterococcus and Escherichia_Shigella increased. The distribution of taxa between AS and AL revealed significant differences in the abundance of genera such as Prevotella, Faecalibacterium and Phocaeicola. In addition to Phocaeicola, Ruminococcus2 and Blautia showed significant differences in abundance between preoperative sample types. ROC analysis of the predictive value of these genera for AL revealed an AUC of 0.802 (p = 0.0013). In summary, microbial composition was associated with postoperative outcomes, and the abundance of certain genera may be predictive of postoperative complications.
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- 2024
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5. The Effect of Nutrient Deprivation on Early Life Small Intestinal Mucosal Microbiome and Host Proteome
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Bar-Yoseph, Haggai, Krekhno, Zakhar, Cirstea, Mihai, Holani, Ravi, Moon, Kyung-Mee, Foster, Leonard J, Wieck, Minna, Piper, Hannah G, and Finlay, B Brett
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- 2024
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6. The Characteristics and Role of Mucosal Microbiome After Treatment of Clostridioides Difficile Infection
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Purna C. Kashyap, MBBS, Principal Investigator
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- 2023
7. Alterations of the duodenal mucosal microbiome in patients with metabolic dysfunction-associated steatotic liver disease
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Mengting Ren, Hanghai Pan, Xinxin Zhou, Mosang Yu, and Feng Ji
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Gut microbiota ,Metabolic dysfunction-associated steatotic liver disease ,Small intestine ,Mucosa-associated microbiota ,Medicine ,Science - Abstract
Abstract Metabolic dysfunction-associated steatotic liver disease (MASLD), formerly known as nonalcoholic fatty liver disease (NAFLD), is associated with altered gut microbiota; however, there has been a focus on fecal samples, which are not representative of the entire digestive tract. Mucosal biopsies of the descending duodenum were collected. Five regions of the 16S rRNA gene were amplified and sequenced. Other assessments conducted on the study subjects included body mass index, transient elastography, liver enzymes, and lipid profile. Fifty-one subjects (36 with MASLD and 15 controls) were evaluated. There was no significant difference between the two groups regarding alpha- or beta-diversity of the duodenal mucosal microbiota. Linear discriminant analysis effect size (LEfSe) analysis showed that the genera Serratia and Aggregatibacter were more abundant in the duodenal mucosa of patients with MASLD, whereas the duodenal mucosal microbiota of the healthy controls was enriched with the genus Petrobacter. PICRUSt2 analysis revealed that genes associated with amino acid degradation and carboxylate degradation were significantly enriched in the duodenal mucosal microbiota of patients with MASLD. Our findings reveal the duodenal mucosal microbiota in patients with MASLD, which could contribute to future studies investigating the causal relationship between duodenal microbiota and MASLD.
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- 2024
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8. The Southern Bluefin Tuna Mucosal Microbiome Is Influenced by Husbandry Method, Net Pen Location, and Anti-parasite Treatment
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Minich, Jeremiah J, Power, Cecilia, Melanson, Michaela, Knight, Rob, Webber, Claire, Rough, Kirsten, Bott, Nathan J, Nowak, Barbara, and Allen, Eric E
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Microbiology ,Biological Sciences ,Life Below Water ,aquaculture ,mucosal microbiome ,tuna ,phylosymbiosis ,parasite ,praziquantel ,Southern Bluefin Tuna ,microbiome ,Environmental Science and Management ,Soil Sciences ,Medical microbiology - Abstract
Aquaculture is the fastest growing primary industry worldwide. Marine finfish culture in open ocean net pens, or pontoons, is one of the largest growth areas and is currently the only way to rear high value fish such as bluefin tuna. Ranching involves catching wild juveniles, stocking in floating net pens and fattening for 4 to 8 months. Tuna experience several parasite-induced disease challenges in culture that can be mitigated by application of praziquantel (PZQ) as a therapeutic. In this study, we characterized the microbiome of ranched southern Bluefin Tuna, Thunnus maccoyii, across four anatomic sites (gill, skin, digesta, and anterior kidney) and evaluated environmental and pathological factors that influence microbiome composition, including the impact of PZQ treatment on microbiome stability. Southern bluefin tuna gill, skin, and digesta microbiome communities are unique and potentially influenced by husbandry practices, location of pontoon growout pens, and treatment with the antiparasitic PZQ. There was no significant relationship between the fish mucosal microbiome and incidence or abundance of adult blood fluke in the heart or fluke egg density in the gill. An enhanced understanding of microbiome diversity and function in high-value farmed fish species such as bluefin tuna is needed to optimize fish health and improve aquaculture yield. Comparison of the bluefin tuna microbiome to other fish species, including Seriola lalandi (yellowtail kingfish), a common farmed species from Australia, and Scomber japonicus (Pacific mackerel), a wild caught Scombrid relative of tuna, showed the two Scombrids had more similar microbial communities compared to other families. The finding that mucosal microbial communities are more similar in phylogenetically related fish species exposes an opportunity to develop mackerel as a model for tuna microbiome and parasite research.
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- 2020
9. The Role of Mucosal Microbiome in Recurrence of Clostridioides Difficile Infection
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Purna C. Kashyap, MBBS, Principal Investigator
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- 2023
10. The Role of Mucosal Microbiome in the Development, Clearance and Recurrence of Clostridioides Difficile Infection
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Purna C. Kashyap, MBBS, Principal Investigator
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- 2022
11. Integrated analysis of rectal mucosal microbiome and transcriptome reveals a distinct microenvironment among young MSM.
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Ackerley CG, Smith SA, Murray PM, Amancha PK, Van Doren VE, Tharp GK, Arthur RA, Amara RR, Hu YJ, and Kelley CF
- Abstract
Cross-talk between the microbiome and gut mucosa-resident immune cells plays a pivotal role in modulating immune responses to pathogens, including responses to HIV infection. However, how these interactions may differ between young MSM (YMSM) disproportionately impacted by HIV, as compared to older adult MSM (AMSM), is not well understood. A broad analysis of associations between the microbiome and rectal transcriptome revealed 10 microbial families/genera correlated with immunologic gene pathways. Specifically, the rectal transcriptome of YMSM is characterized by upregulation of T cell activation/differentiation pathways and signaling from multiple cytokine families, compared to AMSM. The microbiome of YMSM is enriched with pathogenic genera including Peptostreptococcus, shown to be positively correlated with type I interferon pathways important for antiviral immunity. These findings demonstrate that YMSM have a unique immune phenotype and rectal microenvironment and support further evaluation of biological factors that influence rectal HIV transmission.
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- 2024
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12. The mucosal microbiome and IgA nephropathy: a new target for treatment?
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Selvaskandan H and Barratt J
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- 2024
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13. Sex Differences in Colonic Mucosal Microbiome of Irritable Bowel Syndrome Patients Compared to Healthy Controls.
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Mahurkar-Joshi S, Shera S, Labus J, Dong TS, Jacobs JP, and Chang L
- Abstract
Background: Irritable bowel syndrome (IBS) is a female-predominant disorder of brain-gut interactions. Our previous study on colonic mucosal microbiota demonstrated significant differences between IBS bowel habit subtypes and showed that gut microbiota is associated with abdominal pain in IBS patients. However, there is no consensus on sex-related differences in mucosal microbiota in IBS compared to healthy controls (HC). We aimed to identify sex-related differences in the mucosal microbes associated with IBS., Methods: Sigmoid mucosal biopsies were obtained from 97 Rome+ IBS patients and 54 healthy controls (HC). Mucosal microbiome was characterized using 16S rRNA sequencing and analyzed and general linear models were used to test group differences between IBS diagnosis and sex. Sex-specific relationships between mucosal microbiome and IBS symptoms were assessed using sparse partial least squares (sPLS) regression., Results: Beta diversity was significantly different between men and women overall (p=.03) but not within IBS or HC. IBS women showed lower abundance of Catenibacterium and Ruminoclstridium_9 and increased abundance of Bacteroides, Escherichia/Shigella, Lachnoclostridium and Ruminococcaceae compared to men with IBS (p<0.05). However, healthy women had a lower abundance of six distinct genera compared to healthy men. In women, higher IBS symptoms were associated with an increased abundance of bacteria including prevotella_9, and paraprevotella, however, in men, IBS symptoms were associated with increased abundances of genera such as Dialister. Interestingly, increased abundance of Desulfovibrio was associated with higher symptoms in women but lower symptoms in men., Conclusion: There are distinct sex-related differences in the mucosal microbiome between IBS and healthy participants supporting the importance of studying sex-specific mechanisms in IBS pathophysiology.
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- 2024
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14. Mucosal microbiome of surgically treated terminal ileal Crohn’s disease
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Florian N. Loch, Carsten Kamphues, Peter Menzel, Rolf Schwarzer, Katharina Beyer, and Christian Schineis
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Crohn’s disease ,microbiome ,surgery ,ileocecal resection ,mucosa ,Microbiology ,QR1-502 - Abstract
Crohn’s disease (CD) is associated with changes in the microbiome. The role of these changes and their precise association with disease course and activity remain ambiguous. In this prospective single-center study, the mucosal microbiome of surgical CD and non-CD patients was compared at the time of surgery. Microbial analyses were individually performed for ileal and colonic tissue samples obtained during surgery using 16S-rRNA-gene amplicon sequencing. Three groups out of the 46 included patients were formed: 1) a study group of CD of patients who received ileocecal resection due to CD involvement (CD study, n=10); 2) a control group of non-CD of patients who received intestinal resection due to indications other than CD (non-CD control, n=27); and 3) a second control group of CD who underwent resection of the intestine not affected by CD (CD non-affected control, n=9). Species richness and Shannon diversity were not different between all formed groups and regions analyzed (p>0.05). Several significant taxonomic differences were seen at the phylum-, order-, and genus-levels between the formed groups, such as a decrease of Firmicutes (phylum-level) and an increase of Bacteroides and Escherichia/Shigella/Pseudescherichia (genus-level) in CD study – colon vs. the non-CD control – colon (p ≤ 0.05). The CD non-affected control presented the largest amount of differentially abundant taxa in comparison to the other groups. These results underline that CD is accompanied by changes in affected and non-affected intestinal regions compared to non-CD controls. This study contributes the mucosal microbiome of a well-defined subset of surgical CD patients without confounding aspects of the fecal microbiome or regional microbial differences to the existing literature.
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- 2024
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15. The comparison of changes in fecal and mucosal microbiome in metabolic endotoxemia induced by a high-fat diet
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Sagkan-Ozturk, Aliye and Arpaci, Abdullah
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- 2022
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16. Impacts of the Marine Hatchery Built Environment, Water and Feed on Mucosal Microbiome Colonization Across Ontogeny in Yellowtail Kingfish, Seriola lalandi
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Minich, Jeremiah J, Nowak, Barbara, Elizur, Abigail, Knight, Rob, Fielder, Stewart, and Allen, Eric E
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Microbiology ,Biological Sciences ,Human Genome ,Genetics ,Life Below Water ,microbiome ,built environment ,yellowtail kingfish ,Seriola lalandi ,aquaculture ,fisheries ,ontogeny ,mariculture ,Oceanography ,Ecology ,Geology - Abstract
The fish gut microbiome is impacted by a number of biological and environmental factors including fish feed formulations. Unlike mammals, vertical microbiome transmission is largely absent in fish and thus little is known about how the gut microbiome is initially colonized during hatchery rearing nor the stability throughout growout stages. Here we investigate how various microbial-rich surfaces from the built environment "BE" and feed influence the development of the mucosal microbiome (gill, skin, and digesta) of an economically important marine fish, yellowtail kingfish, Seriola lalandi, over time. For the first experiment, we sampled gill and skin microbiomes from 36 fish reared in three tank conditions, and demonstrate that the gill is more influenced by the surrounding environment than the skin. In a second experiment, fish mucous (gill, skin, and digesta), the BE (tank side, water, inlet pipe, airstones, and air diffusers) and feed were sampled from indoor reared fish at three ages (43, 137, and 430 dph; n = 12 per age). At 430 dph, 20 additional fish were sampled from an outdoor ocean net pen. A total of 304 samples were processed for 16S rRNA gene sequencing. Gill and skin alpha diversity increased while gut diversity decreased with age. Diversity was much lower in fish from the ocean net pen compared to indoor fish. The gill and skin are most influenced by the BE early in development, with aeration equipment having more impact in later ages, while the gut "allochthonous" microbiome becomes increasingly differentiated from the environment over time. Feed had a relatively low impact on driving microbial communities. Our findings suggest that S. lalandi mucosal microbiomes are differentially influenced by the BE with a high turnover and rapid succession occurring in the gill and skin while the gut microbiome is more stable. We demonstrate how individual components of a hatchery system, especially aeration equipment, may contribute directly to microbiome development in a marine fish. In addition, results demonstrate how early life (larval) exposure to biofouling in the rearing environment may influence fish microbiome development which is important for animal health and aquaculture production.
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- 2021
17. 55 Diagnostic utility of the whole blood transcriptome and mucosal microbiome alterations in patients with primary immunodeficiency
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Cocks, Ben, primary, Gail, Emma, additional, Green, Simon, additional, Bryant, Vanessa, additional, Slade, Charlotte, additional, Tang, Mimi, additional, Cole, Theresa, additional, and Douglass, Jo, additional
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- 2024
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18. Temporal, Environmental, and Biological Drivers of the Mucosal Microbiome in a Wild Marine Fish, Scomber japonicus.
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Minich, Jeremiah J, Petrus, Semar, Michael, Julius D, Michael, Todd P, Knight, Rob, and Allen, Eric E
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Cecum ,Mucous Membrane ,Gills ,Skin ,Animals ,Perciformes ,Environment ,Temperature ,Oceans and Seas ,Genetic Variation ,Microbiota ,Gastrointestinal Microbiome ,Scomber japonicus ,fish microbiome ,mackerel ,marine microbiology ,microbial biogeography ,microbial ecology ,veterinary microbiology ,Genetics ,Human Genome - Abstract
Changing ocean conditions driven by anthropogenic activities may have a negative impact on fisheries by increasing stress and disease. To understand how environment and host biology drives mucosal microbiomes in a marine fish, we surveyed five body sites (gill, skin, digesta, gastrointestinal tract [GI], and pyloric ceca) from 229 Pacific chub mackerel, Scomber japonicus, collected across 38 time points spanning 1 year from the Scripps Institution of Oceanography Pier (La Jolla, CA). Mucosal sites had unique microbial communities significantly different from the surrounding seawater and sediment communities with over 10 times more total diversity than seawater. The external surfaces of skin and gill were more similar to seawater, while digesta was more similar to sediment. Alpha and beta diversity of the skin and gill was explained by environmental and biological factors, specifically, sea surface temperature, chlorophyll a, and fish age, consistent with an exposure gradient relationship. We verified that seasonal microbial changes were not confounded by regional migration of chub mackerel subpopulations by nanopore sequencing a 14,769-bp region of the 16,568-bp mitochondria across all temporal fish specimens. A cosmopolitan pathogen, Photobacterium damselae, was prevalent across multiple body sites all year but highest in the skin, GI, and digesta between June and September, when the ocean is warmest. The longitudinal fish microbiome study evaluates the extent to which the environment and host biology drives mucosal microbial ecology and establishes a baseline for long-term surveys linking environment stressors to mucosal health of wild marine fish.IMPORTANCE Pacific chub mackerel, Scomber japonicus, are one of the largest and most economically important fisheries in the world. The fish is harvested for both human consumption and fish meal. Changing ocean conditions driven by anthropogenic stressors like climate change may negatively impact fisheries. One mechanism for this is through disease. As waters warm and chemistry changes, the microbial communities associated with fish may change. In this study, we performed a holistic analysis of all mucosal sites on the fish over a 1-year time series to explore seasonal variation and to understand the environmental drivers of the microbiome. Understanding seasonality in the fish microbiome is also applicable to aquaculture production for producers to better understand and predict when disease outbreaks may occur based on changing environmental conditions in the ocean.
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- 2020
19. Mucosal microbiome dysbiosis associated with duodenum bulb inflammation
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Fan, Hui-Ning, Zhu, Pei, Zhang, Jing, and Zhu, Jin-Shui
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- 2021
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20. Mucosal Microbiome Disruption in Acute Laryngeal Injury Following Intubation.
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Davis RJ, Shilts MH, Strickland BA, Rajagopala SV, Das SR, Wootten CT, and Gelbard A
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- Humans, Cross-Sectional Studies, Intubation, Intratracheal adverse effects, Laryngeal Diseases etiology, Laryngostenosis etiology, Microbiota
- Abstract
The objective of this study was to characterize mucosal microbial shifts in patients with acute laryngeal injury (ALgI) after intubation. This cross-sectional study included 20 patients with ALgI who underwent early endoscopic intervention with tissue culture, 20 patients with idiopathic subglottic stenosis (iSGS) who underwent tissue culture during the routine endoscopic intervention, and 3 control patients who underwent mucosal swab culture. 70% of the ALgI patients had a positive culture compared to 5% of the iSGS patients and none of the controls. The most identified microbes isolated from ALgI patients included Staphylococcus species in 30% and Streptococcus species in 25%. The high rate of pathologic bacterial infiltration into postintubation laryngeal wounds supports efforts to reduce bacterial colonization of endotracheal tubes and highlights the role of culture-directed antibiotic therapy as a part of early intervention to improve outcomes for patients with ALgI., (© 2023 American Academy of Otolaryngology-Head and Neck Surgery Foundation.)
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- 2024
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21. Heterogeneity of the Tissue-specific Mucosal Microbiome of Normal Grass Carp (Ctenopharyngodon idella)
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Zhao, Na, Guo, Jiamin, Zhang, Bo, Liu, Kai, Liu, Yuting, Shen, Yubang, and Li, Jiale
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- 2022
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22. Multi-omic profiling reveals associations between the gut mucosal microbiome, the metabolome, and host DNA methylation associated gene expression in patients with colorectal cancer
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Qing Wang, Jianzhong Ye, Daiqiong Fang, Longxian Lv, Wenrui Wu, Ding Shi, Yating Li, Liya Yang, Xiaoyuan Bian, Jingjing Wu, Xianwan Jiang, Kaicen Wang, Qiangqiang Wang, Mark P. Hodson, Loïc M. Thibaut, Joshua W. K. Ho, Eleni Giannoulatou, and Lanjuan Li
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Colorectal cancer ,Mucosal microbiome ,Metabolome ,Transcriptome ,DNA methylation ,Butyrate ,Microbiology ,QR1-502 - Abstract
Abstract Background The human gut microbiome plays a critical role in the carcinogenesis of colorectal cancer (CRC). However, a comprehensive analysis of the interaction between the host and microbiome is still lacking. Results We found correlations between the change in abundance of microbial taxa, butyrate-related colonic metabolites, and methylation-associated host gene expression in colonic tumour mucosa tissues compared with the adjacent normal mucosa tissues. The increase of genus Fusobacterium abundance was correlated with a decrease in the level of 4-hydroxybutyric acid (4-HB) and expression of immune-related peptidase inhibitor 16 (PI16), Fc Receptor Like A (FCRLA) and Lymphocyte Specific Protein 1 (LSP1). The decrease in the abundance of another potentially 4-HB-associated genus, Prevotella 2, was also found to be correlated with the down-regulated expression of metallothionein 1 M (MT1M). Additionally, the increase of glutamic acid-related family Halomonadaceae was correlated with the decreased expression of reelin (RELN). The decreased abundance of genus Paeniclostridium and genus Enterococcus were correlated with increased lactic acid level, and were also linked to the expression change of Phospholipase C Beta 1 (PLCB1) and Immunoglobulin Superfamily Member 9 (IGSF9) respectively. Interestingly, 4-HB, glutamic acid and lactic acid are all butyrate precursors, which may modify gene expression by epigenetic regulation such as DNA methylation. Conclusions Our study identified associations between previously reported CRC-related microbial taxa, butyrate-related metabolites and DNA methylation-associated gene expression in tumour and normal colonic mucosa tissues from CRC patients, which uncovered a possible mechanism of the role of microbiome in the carcinogenesis of CRC. In addition, these findings offer insight into potential new biomarkers, therapeutic and/or prevention strategies for CRC.
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- 2020
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23. Interactive Effect of Combined Intermittent and Sustained Hypoxia and High-Fat Diet on the Colonic Mucosal Microbiome and Host Gene Expression in Mice
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Mashaqi S, Laubitz D, Morales EJD, De Armond R, Alameddin H, Ghishan FK, Kiela PR, and Parthasarathy S
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hypoxia ,microbiome ,obesity ,diet ,gene expression ,sleep apnea ,Psychiatry ,RC435-571 ,Neurophysiology and neuropsychology ,QP351-495 - Abstract
Saif Mashaqi,1,2 Daniel Laubitz,3 Efreim Joseph D Morales,3 Richard De Armond,1,2 Hanan Alameddin,4 Fayez K Ghishan,3 Pawel R Kiela,3,5 Sairam Parthasarathy1,2 1Department of Pulmonary, Allergy, Critical Care, and Sleep, University of Arizona College of Medicine, Tucson, AZ, USA; 2University of Arizona Health Sciences Center for Sleep & Circadian Sciences, University of Arizona College of Medicine, Tucson, AZ, USA; 3Department of Pediatrics, Steele Children’s Research Center, University of Arizona College of Medicine, Tucson, AZ, USA; 4The University of Arizona College of Pharmacy, Tucson, AZ, USA; 5Department of Immunobiology, University of Arizona College of Medicine, Tucson, AZ, USACorrespondence: Saif Mashaqi, Department of Pulmonary, Allergy, Critical Care, and Sleep Medicine, The University of Arizona, College of Medicine Tucson, 1625 N Campbell Ave, Tucson, AZ, 85719, USA, Tel +1 520-626-8309, Fax +1 520-626-1876, Email saifmashaqi@email.arizona.eduPurpose: Gut dysbiosis can cause cardiometabolic disease. Gut dysbiosis can be independently caused by high-fat diet (HFD) and intermittent hypoxia (IH; characterizing obstructive sleep apnea), but the interactive effect of combined intermittent and sustained hypoxia (IH+SH) (characterizing obesity hypoventilation syndrome) and HFD on gut dysbiosis is unclear. We aimed to investigate the interactive effect of a combination of IH and SH and HFD on proximal colonic microbiota and colonic gene expression pattern.Methods: Male mice (n=16) were randomly received four different combinations of diet (normal versus HFD) and oxygen conditions (normoxia versus IH+SH) for 4 weeks. Bacterial DNA and mucosal epithelial cell RNA from proximal colon were collected for analysis of adherent microbiome and host’s gene expression analysis.Results: HFD during IH+SH (22.6 ± 5.73; SD) led to greater Firmicutes: Bacteroidetes ratio than HFD during normoxia (5.89 ± 1.19; p=0.029). HFD significantly decreased microbial diversity as compared to normal diet, but the addition of IH+SH to HFD mildly reversed such effects. When compared to HFD during normoxia, HFD with combination of IH+SH resulted in changes to host mucosal gene expression for apical junctional complexes and adhesion molecules. Specifically, when compared to HFD during normoxia, HFD during IH+SH led to upregulation of Claudin 2 and Syk (tight junction dysfunction and increased mucosal permeability), while the barrier promoting claudin 4 was downregulated.Conclusion: HFD during combined IH and SH causes greater gut dysbiosis and potentially adverse changes in colonic epithelial transcriptome than HFD during normoxia. The latter changes are suggestive of impaired gut barrier function.Keywords: hypoxia, microbiome, obesity, diet, gene expression, sleep apnea
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- 2022
24. Sex Differences in Colonic Mucosal Microbiome of Irritable Bowel Syndrome Patients Compared to Healthy Controls
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Microbiota (Symbiotic organisms) -- Comparative analysis ,Irritable bowel syndrome -- Comparative analysis ,Health - Abstract
2024 AUG 23 (NewsRx) -- By a News Reporter-Staff News Editor at Health & Medicine Week -- According to news reporting based on a preprint abstract, our journalists obtained the [...]
- Published
- 2024
25. Mild changes in the mucosal microbiome during terminal ileum inflammation
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Fan, Hui-Ning, Zhu, Pei, Lu, Yun-Min, Guo, Jing-Hui, Zhang, Jing, Qu, Guo-Qiang, and Zhu, Jin-Shui
- Published
- 2020
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26. Identification of mucosal microbiome-host gene interactions in ulcerative colitis patients
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Kim, Namjoo, primary, Gim, Jeong-An, additional, Lee, Beom Jae, additional, Choi, Byung il, additional, Yoon, Hee Sook, additional, Kim, Won Shik, additional, Kim, Seung Han, additional, Joo, Moon Kyung, additional, and Park, Jong-Jae, additional
- Published
- 2024
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27. Mucosal microbiome is predictive of pediatric Crohn’s disease across geographic regions in North America [version 2; peer review: 2 approved]
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Rajesh Shah, Kristi Hoffman, Lee Denson, Subramaniam Kugathasan, and Richard Kellermayer
- Subjects
Research Article ,Articles ,Crohn’s disease ,microbiome ,inflammatory bowel disease ,machine learning - Abstract
Background: Patients with Crohn’s disease (CD) have an altered intestinal microbiome, which may facilitate novel diagnostic testing. However, accuracy of microbiome classification models across geographic regions may be limited. Therefore, we sought to examine geographic variation in the microbiome of patients with CD from North America and test the performance of a machine learning classification model across geographic regions. Methods: The RISK cohort included 447 pediatric patients with CD and 221 non-inflammatory bowel disease controls from across North America. Terminal ileum, rectal and fecal samples were obtained prior to treatment for microbiome analysis. We divided study sites into 3 geographic regions to examine regional microbiome differences. We trained and tested the performance of a machine learning classification model across these regions. Results: No differences were seen in the mucosal microbiome of patients with CD across regions or in either the fecal or mucosal microbiomes of controls. Machine learning classification algorithms for patients with CD performed well across regions (area under the receiver operating characteristic curve [AUROC] range of 0.85-0.91) with the best results from terminal ileum. Conclusions: This study demonstrated the feasibility of microbiome based diagnostic testing in pediatric patients with CD within North America, independently from regional influences.
- Published
- 2023
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28. Multi-omic profiling reveals associations between the gut mucosal microbiome, the metabolome, and host DNA methylation associated gene expression in patients with colorectal cancer
- Author
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Wang, Qing, Ye, Jianzhong, Fang, Daiqiong, Lv, Longxian, Wu, Wenrui, Shi, Ding, Li, Yating, Yang, Liya, Bian, Xiaoyuan, Wu, Jingjing, Jiang, Xianwan, Wang, Kaicen, Wang, Qiangqiang, Hodson, Mark P., Thibaut, Loïc M., Ho, Joshua W. K., Giannoulatou, Eleni, and Li, Lanjuan
- Published
- 2020
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29. Epithelial Dual Oxidase 2 Shapes the Mucosal Microbiome and Contributes to Inflammatory Susceptibility
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Juan Camilo Castrillón-Betancur, Víctor Alonso López-Agudelo, Nina Sommer, Sven Cleeves, Joana Pimenta Bernardes, Saskia Weber-Stiehl, Philip Rosenstiel, and Felix Sommer
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inflammation ,DUOX2 ,ROS ,microbiome ,Therapeutics. Pharmacology ,RM1-950 - Abstract
Reactive oxygen species (ROS) are highly reactive molecules formed from diatomic oxygen. They act as cellular signals, exert antibiotic activity towards invading microorganisms, but can also damage host cells. Dual oxidase 2 (DUOX2) is the main ROS-producing enzyme in the intestine, regulated by cues of the commensal microbiota and functions in pathogen defense. DUOX2 plays multiple roles in different organs and cell types, complicating the functional analysis using systemic deletion models. Here, we interrogate the precise role of epithelial DUOX2 for intestinal homeostasis and host-microbiome interactions. Conditional Duox2∆IEC mice lacking DUOX2, specifically in intestinal epithelial cells, were generated, and their intestinal mucosal immune phenotype and microbiome were analyzed. Inflammatory susceptibility was evaluated by challenging Duox2∆IEC mice in the dextran sodium sulfate (DSS) colitis model. DUOX2-microbiome interactions in humans were investigated by paired analyses of mucosal DUOX2 expression and fecal microbiome data in patients with intestinal inflammation. Under unchallenged conditions, we did not observe any obvious phenotype of Duox2∆IEC mice, although intestinal epithelial ROS production was drastically decreased, and the mucosal microbiome composition was altered. When challenged with DSS, Duox2∆IEC mice were protected from colitis, possibly by inhibiting ROS-mediated damage and fostering epithelial regenerative responses. Finally, in patients with intestinal inflammation, DUOX2 expression was increased in inflamed tissue, and high DUOX2 levels were linked to a dysbiotic microbiome. Our findings demonstrate that bidirectional DUOX2-microbiome interactions contribute to mucosal homeostasis, and their dysregulation may drive disease development, thus highlighting this axis as a therapeutic target to treat intestinal inflammation.
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- 2023
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30. Field study examining the mucosal microbiome in equine glandular gastric disease.
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Linda J Paul, Aaron C Ericsson, Frank M Andrews, Zachary McAdams, Michael L Keowen, Michael P St Blanc, and Heidi E Banse
- Subjects
Medicine ,Science - Abstract
Equine glandular gastric disease (EGGD) is a common disease among athletic horses that can negatively impact health and performance. The pathophysiology of this EGGD remains poorly understood. Previous studies using controlled populations of horses identified differences in the gastric glandular mucosal microbiome associated with disease. The objective of this study was to compare the gastric microbiome in horses with EGGD and those without across multiple barns and differing management practices. We hypothesized that alterations in the microbiome of the gastric glandular mucosa are associated with EGGD. A secondary objective was to perform a risk factor analysis for EGGD using the diet and management data collected. Microbial populations of biopsies from normal pyloric mucosa of horses without EGGD (control biopsies), normal pyloric mucosa of horses with EGGD (normal biopsies) and areas of glandular mucosal disruption in horses with EGGD (lesion biopsies) were compared. Lesion biopsies had a different microbial community structure than control biopsies. Control biopsies had a higher read count for the phylum Actinomycetota compared to lesion biopsies. Control biopsies also had an enrichment of the genera Staphylococcus and Lawsonella and the species Streptococcus salivarius. Lesion biopsies had an enrichment of the genera Lactobacillus and Actinobacillus and the species Lactobacillus equigenerosi. These results demonstrate differences in the gastric glandular microbiome between sites of disrupted mucosa in horses with EGGD compared to pyloric mucosa of horses without EGGD. Risk factor analysis indicated that exercise duration per week was a risk factor for EGGD.
- Published
- 2023
- Full Text
- View/download PDF
31. Mucosal microbiome is predictive of pediatric Crohn’s disease across geographic regions in North America [version 2; peer review: 2 approved]
- Author
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Richard Kellermayer, Subramaniam Kugathasan, Rajesh Shah, Lee Denson, and Kristi Hoffman
- Subjects
Crohn’s disease ,microbiome ,inflammatory bowel disease ,machine learning ,eng ,Medicine ,Science - Abstract
Background: Patients with Crohn’s disease (CD) have an altered intestinal microbiome, which may facilitate novel diagnostic testing. However, accuracy of microbiome classification models across geographic regions may be limited. Therefore, we sought to examine geographic variation in the microbiome of patients with CD from North America and test the performance of a machine learning classification model across geographic regions. Methods: The RISK cohort included 447 pediatric patients with CD and 221 non-inflammatory bowel disease controls from across North America. Terminal ileum, rectal and fecal samples were obtained prior to treatment for microbiome analysis. We divided study sites into 3 geographic regions to examine regional microbiome differences. We trained and tested the performance of a machine learning classification model across these regions. Results: No differences were seen in the mucosal microbiome of patients with CD across regions or in either the fecal or mucosal microbiomes of controls. Machine learning classification algorithms for patients with CD performed well across regions (area under the receiver operating characteristic curve [AUROC] range of 0.85-0.91) with the best results from terminal ileum. Conclusions: This study demonstrated the feasibility of microbiome based diagnostic testing in pediatric patients with CD within North America, independently from regional influences.
- Published
- 2023
- Full Text
- View/download PDF
32. Mucosal microbiome of surgically treated terminal ileal Crohn's disease.
- Author
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Loch FN, Kamphues C, Menzel P, Schwarzer R, Beyer K, and Schineis C
- Subjects
- Humans, Prospective Studies, Intestinal Mucosa, Crohn Disease surgery, Gastrointestinal Microbiome, Microbiota
- Abstract
Crohn's disease (CD) is associated with changes in the microbiome. The role of these changes and their precise association with disease course and activity remain ambiguous. In this prospective single-center study, the mucosal microbiome of surgical CD and non-CD patients was compared at the time of surgery. Microbial analyses were individually performed for ileal and colonic tissue samples obtained during surgery using 16S-rRNA-gene amplicon sequencing. Three groups out of the 46 included patients were formed: 1) a study group of CD of patients who received ileocecal resection due to CD involvement (CD study, n=10); 2) a control group of non-CD of patients who received intestinal resection due to indications other than CD (non-CD control, n=27); and 3) a second control group of CD who underwent resection of the intestine not affected by CD (CD non-affected control, n=9). Species richness and Shannon diversity were not different between all formed groups and regions analyzed (p>0.05). Several significant taxonomic differences were seen at the phylum-, order-, and genus-levels between the formed groups, such as a decrease of Firmicutes (phylum-level) and an increase of Bacteroides and Escherichia/Shigella/Pseudescherichia (genus-level) in CD study - colon vs. the non-CD control - colon (p ≤ 0.05). The CD non-affected control presented the largest amount of differentially abundant taxa in comparison to the other groups. These results underline that CD is accompanied by changes in affected and non-affected intestinal regions compared to non-CD controls. This study contributes the mucosal microbiome of a well-defined subset of surgical CD patients without confounding aspects of the fecal microbiome or regional microbial differences to the existing literature., Competing Interests: Authors PM and RS were employed by the company Labor Berlin – Charité Vivantes GmbH. The remaining authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2024 Loch, Kamphues, Menzel, Schwarzer, Beyer and Schineis.)
- Published
- 2024
- Full Text
- View/download PDF
33. Field study examining the mucosal microbiome in equine glandular gastric disease.
- Author
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Paul LJ, Ericsson AC, Andrews FM, McAdams Z, Keowen ML, St Blanc MP, and Banse HE
- Subjects
- Horses, Animals, Gastric Mucosa pathology, Risk Factors, Stomach Diseases pathology, Horse Diseases pathology, Microbiota, Stomach Ulcer pathology
- Abstract
Equine glandular gastric disease (EGGD) is a common disease among athletic horses that can negatively impact health and performance. The pathophysiology of this EGGD remains poorly understood. Previous studies using controlled populations of horses identified differences in the gastric glandular mucosal microbiome associated with disease. The objective of this study was to compare the gastric microbiome in horses with EGGD and those without across multiple barns and differing management practices. We hypothesized that alterations in the microbiome of the gastric glandular mucosa are associated with EGGD. A secondary objective was to perform a risk factor analysis for EGGD using the diet and management data collected. Microbial populations of biopsies from normal pyloric mucosa of horses without EGGD (control biopsies), normal pyloric mucosa of horses with EGGD (normal biopsies) and areas of glandular mucosal disruption in horses with EGGD (lesion biopsies) were compared. Lesion biopsies had a different microbial community structure than control biopsies. Control biopsies had a higher read count for the phylum Actinomycetota compared to lesion biopsies. Control biopsies also had an enrichment of the genera Staphylococcus and Lawsonella and the species Streptococcus salivarius. Lesion biopsies had an enrichment of the genera Lactobacillus and Actinobacillus and the species Lactobacillus equigenerosi. These results demonstrate differences in the gastric glandular microbiome between sites of disrupted mucosa in horses with EGGD compared to pyloric mucosa of horses without EGGD. Risk factor analysis indicated that exercise duration per week was a risk factor for EGGD., Competing Interests: I have read the journal’s policy and the authors of this manuscript have the following competing interests: HEB has previously received (greater than five years ago) other grant funding and performed consultancy work for Boehringer Ingelheim Animal Health. The other authors (LJP, FMA, ACE, ZM, MLK, MPS) have declared that no competing interests exist., (Copyright: © 2023 Paul et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)
- Published
- 2023
- Full Text
- View/download PDF
34. Intestinal and Mucosal Microbiome Response to Oral Challenge of Enterotoxigenic Escherichia coli in Weaned Pigs
- Author
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Shan-Shan Peng, Yingjie Li, Qiuhong Chen, Qi Hu, Ying He, Lianqiang Che, and Ping-Ping Jiang
- Subjects
infant diarrhoea ,enterotoxigenic Escherichia coli ,proteomics ,mucosal microbiome ,regularised canonical correlation analysis ,bile acid ,Medicine - Abstract
Enterotoxigenic Escherichia coli (ETEC) is closely associated with diarrhoea in children in resource-limited countries. This study aims to investigate the change of the mucosal microbiome and protein expression in the ileum induced by E. coli K88 (ETEC) using pigs as a model. Seven weaned male pigs were orally given ETEC (1 × 109 CFU, n = 7), and the other seven received saline (CON, n = 7). Ileal tissues were obtained 48 hours after the ETEC challenge for both proteomic and mucosal microbiome analyses. Nine proteins were found with altered abundance between the two groups, including a decrease in FABP1 and FABP6, involved in bile acid circulation. The TLR-9 mediated pathway was also affected showing increased transcription of genes SIGIRR and MyD88. Correlations between the ileal proteins and mucosal bacterial taxa found included a positive correlation between Lactobacilllus and PPP3CA (r = 0.9, p < 0.001) and a negative correlation between Prevotella with CTNND1 (r = −0.7, p < 0.01). In conclusion, ETEC infection caused inflammation and impaired the circulation of bile acids and the mucosal microbiome may affect the expression of intestinal proteins. Further studies are needed to explain the exact roles of these affected processes in the pathogenesis of ETEC-triggered diarrhoea.
- Published
- 2022
- Full Text
- View/download PDF
35. The Southern Bluefin Tuna Mucosal Microbiome Is Influenced by Husbandry Method, Net Pen Location, and Anti-parasite Treatment
- Author
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Jeremiah J. Minich, Cecilia Power, Michaela Melanson, Rob Knight, Claire Webber, Kirsten Rough, Nathan J. Bott, Barbara Nowak, and Eric E. Allen
- Subjects
aquaculture ,mucosal microbiome ,tuna ,phylosymbiosis ,parasite ,praziquantel ,Microbiology ,QR1-502 - Abstract
Aquaculture is the fastest growing primary industry worldwide. Marine finfish culture in open ocean net pens, or pontoons, is one of the largest growth areas and is currently the only way to rear high value fish such as bluefin tuna. Ranching involves catching wild juveniles, stocking in floating net pens and fattening for 4 to 8 months. Tuna experience several parasite-induced disease challenges in culture that can be mitigated by application of praziquantel (PZQ) as a therapeutic. In this study, we characterized the microbiome of ranched southern Bluefin Tuna, Thunnus maccoyii, across four anatomic sites (gill, skin, digesta, and anterior kidney) and evaluated environmental and pathological factors that influence microbiome composition, including the impact of PZQ treatment on microbiome stability. Southern bluefin tuna gill, skin, and digesta microbiome communities are unique and potentially influenced by husbandry practices, location of pontoon growout pens, and treatment with the antiparasitic PZQ. There was no significant relationship between the fish mucosal microbiome and incidence or abundance of adult blood fluke in the heart or fluke egg density in the gill. An enhanced understanding of microbiome diversity and function in high-value farmed fish species such as bluefin tuna is needed to optimize fish health and improve aquaculture yield. Comparison of the bluefin tuna microbiome to other fish species, including Seriola lalandi (yellowtail kingfish), a common farmed species from Australia, and Scomber japonicus (Pacific mackerel), a wild caught Scombrid relative of tuna, showed the two Scombrids had more similar microbial communities compared to other families. The finding that mucosal microbial communities are more similar in phylogenetically related fish species exposes an opportunity to develop mackerel as a model for tuna microbiome and parasite research.
- Published
- 2020
- Full Text
- View/download PDF
36. Research from Zhejiang University School of Medicine Has Provided New Data on Liver Diseases and Conditions (Alterations of the duodenal mucosal microbiome in patients with metabolic dysfunction-associated steatotic liver disease)
- Subjects
Medical research -- Reports ,Medicine, Experimental -- Reports ,Microbiota (Symbiotic organisms) -- Reports ,Liver diseases -- Reports ,Health - Abstract
2024 MAY 10 (NewsRx) -- By a News Reporter-Staff News Editor at Health & Medicine Week -- Investigators publish new report on liver diseases and conditions. According to news reporting [...]
- Published
- 2024
37. P1226 Determination of oral and gut mucosal microbiome profiles of patients with treatment-naïve ulcerative colitis
- Author
-
Karakan, T, primary, Özmeriç Kurtuluş, N, additional, Ünsal, B, additional, Çağrı İşler, S, additional, Akça, G, additional, Soysal, F, additional, Cindoruk, M, additional, Elgün Ulkar, S, additional, Açık, L, additional, Ergin, M, additional, Abbasov, Z, additional, Özkul Koçak, C, additional, Ekmen, N, additional, Yalınay, A M, additional, Özkan, S, additional, Karataş, A, additional, and Paes Batista Da Silva, A, additional
- Published
- 2024
- Full Text
- View/download PDF
38. PP443 Microbial dysbiosis in extrahepatic cholangiocarcinoma patients: A comparison of gut and mucosal microbiome with healthy controls
- Author
-
Kang, Sora, primary, Kang, Jihee, additional, Park, Gun-Seok, additional, Ko, Seung-Hyun, additional, Park, Jung-Hyun, additional, Jang, Yunseon, additional, Song, Ik-Chan, additional, Ryu, Hyewon, additional, and Kim, Seok-Hwan, additional
- Published
- 2023
- Full Text
- View/download PDF
39. Mucosal Microbiome Disruption in Acute Laryngeal Injury Following Intubation
- Author
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Davis, Ruth J., primary, Shilts, Meghan H., additional, Strickland, Britton A., additional, Rajagopala, Seesandra V., additional, Das, Suman R., additional, Wootten, Christopher T., additional, and Gelbard, Alexander, additional
- Published
- 2023
- Full Text
- View/download PDF
40. Mucosal microbiome is predictive of pediatric Crohn’s disease across geographic regions in North America [version 1; peer review: 1 approved, 1 approved with reservations]
- Author
-
Rajesh Shah, Kristi Hoffman, Lee Denson, Subramaniam Kugathasan, and Richard Kellermayer
- Subjects
Research Article ,Articles ,Crohn’s disease ,microbiome ,inflammatory bowel disease ,machine learning - Abstract
Background: Patients with Crohn’s disease (CD) have an altered intestinal microbiome, which may facilitate novel diagnostic testing. However, accuracy of microbiome classification models across geographic regions may be limited. Therefore, we sought to examine geographic variation in the microbiome of patients with CD from North America and test the performance of a machine learning classification model across geographic regions. Methods: The RISK cohort included 447 pediatric patients with CD and 221 non-inflammatory bowel disease controls from across North America. Terminal ileum, rectal and fecal samples were obtained prior to treatment for microbiome analysis. We divided study sites into 3 geographic regions to examine regional microbiome differences. We trained and tested the performance of a machine learning classification model across these regions. Results: No differences were seen in the mucosal microbiome of patients with CD across regions or in either the fecal or mucosal microbiomes of controls. Machine learning classification algorithms for patients with CD performed well across regions (area under the receiver operating characteristic curve [AUROC] range of 0.85-0.91) with the best results from terminal ileum. Conclusions: This study demonstrated the feasibility of microbiome based diagnostic testing in pediatric patients with CD within North America, independently from regional influences.
- Published
- 2022
- Full Text
- View/download PDF
41. Epithelial Dual Oxidase 2 Shapes the Mucosal Microbiome and Contributes to Inflammatory Susceptibility.
- Author
-
Castrillón-Betancur JC, López-Agudelo VA, Sommer N, Cleeves S, Bernardes JP, Weber-Stiehl S, Rosenstiel P, and Sommer F
- Abstract
Reactive oxygen species (ROS) are highly reactive molecules formed from diatomic oxygen. They act as cellular signals, exert antibiotic activity towards invading microorganisms, but can also damage host cells. Dual oxidase 2 (DUOX2) is the main ROS-producing enzyme in the intestine, regulated by cues of the commensal microbiota and functions in pathogen defense. DUOX2 plays multiple roles in different organs and cell types, complicating the functional analysis using systemic deletion models. Here, we interrogate the precise role of epithelial DUOX2 for intestinal homeostasis and host-microbiome interactions. Conditional Duox2 mice lacking DUOX2, specifically in intestinal epithelial cells, were generated, and their intestinal mucosal immune phenotype and microbiome were analyzed. Inflammatory susceptibility was evaluated by challenging
∆IEC mice in the dextran sodium sulfate (DSS) colitis model. DUOX2-microbiome interactions in humans were investigated by paired analyses of mucosal DUOX2 expression and fecal microbiome data in patients with intestinal inflammation. Under unchallenged conditions, we did not observe any obvious phenotype of Duox2 mice, although intestinal epithelial ROS production was drastically decreased, and the mucosal microbiome composition was altered. When challenged with DSS,∆IEC mice were protected from colitis, possibly by inhibiting ROS-mediated damage and fostering epithelial regenerative responses. Finally, in patients with intestinal inflammation, DUOX2 expression was increased in inflamed tissue, and high DUOX2 levels were linked to a dysbiotic microbiome. Our findings demonstrate that bidirectional DUOX2-microbiome interactions contribute to mucosal homeostasis, and their dysregulation may drive disease development, thus highlighting this axis as a therapeutic target to treat intestinal inflammation.Duox2∆IEC mice, although intestinal epithelial ROS production was drastically decreased, and the mucosal microbiome composition was altered. When challenged with DSS, Duox2∆IEC mice were protected from colitis, possibly by inhibiting ROS-mediated damage and fostering epithelial regenerative responses. Finally, in patients with intestinal inflammation, DUOX2 expression was increased in inflamed tissue, and high DUOX2 levels were linked to a dysbiotic microbiome. Our findings demonstrate that bidirectional DUOX2-microbiome interactions contribute to mucosal homeostasis, and their dysregulation may drive disease development, thus highlighting this axis as a therapeutic target to treat intestinal inflammation.- Published
- 2023
- Full Text
- View/download PDF
42. Mucosal Microbiome in Patients with Early Bowel Polyps: Inferences from Short-Read and Long-Read 16S rRNA Sequencing.
- Author
-
Welham Z, Li J, Engel AF, and Molloy MP
- Abstract
Numerous studies have correlated dysbiosis in stool microbiota with colorectal cancer (CRC); however, fewer studies have investigated the mucosal microbiome in pre-cancerous bowel polyps. The short-read sequencing of variable regions in the 16S rRNA gene has commonly been used to infer bacterial taxonomy, and this has led, in part, to inconsistent findings between studies. Here, we examined mucosal microbiota from patients who presented with one or more polyps, compared to patients with no polyps, at the time of colonoscopy. We evaluated the results obtained using both short-read and PacBio long-read 16S rRNA sequencing. Neither sequencing technology identified significant differences in microbial diversity measures between patients with or without bowel polyps. Differential abundance measures showed that amplicon sequence variants (ASVs) associated with Ruminococcus gnavus and Escherichia coli were elevated in mucosa from polyp patients, while ASVs associated with Parabacteroides merdae , Veillonella nakazawae , and Sutterella wadsworthensis were relatively decreased. Only R. gnavus was consistently identified using both sequencing technologies as being altered between patients with polyps compared to patients without polyps, suggesting differences in technologies and bioinformatics processing impact study findings. Several of the differentially abundant bacteria identified using either sequencing technology are associated with inflammatory bowel diseases despite these patients being excluded from the current study, which suggests that early bowel neoplasia may be associated with a local inflammatory niche.
- Published
- 2023
- Full Text
- View/download PDF
43. Interactive Effect of Combined Intermittent and Sustained Hypoxia and High-Fat Diet on the Colonic Mucosal Microbiome and Host Gene Expression in Mice
- Author
-
Mashaqi,Saif, Laubitz,Daniel, Morales,Efreim Joseph, De Armond,Richard, Alameddin,Hanan, Ghishan,Fayez K, Kiela,Pawel R, Parthasarathy,Sairam, Mashaqi,Saif, Laubitz,Daniel, Morales,Efreim Joseph, De Armond,Richard, Alameddin,Hanan, Ghishan,Fayez K, Kiela,Pawel R, and Parthasarathy,Sairam
- Abstract
Saif Mashaqi,1,2 Daniel Laubitz,3 Efreim Joseph D Morales,3 Richard De Armond,1,2 Hanan Alameddin,4 Fayez K Ghishan,3 Pawel R Kiela,3,5 Sairam Parthasarathy1,2 1Department of Pulmonary, Allergy, Critical Care, and Sleep, University of Arizona College of Medicine, Tucson, AZ, USA; 2University of Arizona Health Sciences Center for Sleep & Circadian Sciences, University of Arizona College of Medicine, Tucson, AZ, USA; 3Department of Pediatrics, Steele Childrenâs Research Center, University of Arizona College of Medicine, Tucson, AZ, USA; 4The University of Arizona College of Pharmacy, Tucson, AZ, USA; 5Department of Immunobiology, University of Arizona College of Medicine, Tucson, AZ, USACorrespondence: Saif Mashaqi, Department of Pulmonary, Allergy, Critical Care, and Sleep Medicine, The University of Arizona, College of Medicine Tucson, 1625 N Campbell Ave, Tucson, AZ, 85719, USA, Tel +1 520-626-8309, Fax +1 520-626-1876, Email saifmashaqi@email.arizona.eduPurpose: Gut dysbiosis can cause cardiometabolic disease. Gut dysbiosis can be independently caused by high-fat diet (HFD) and intermittent hypoxia (IH; characterizing obstructive sleep apnea), but the interactive effect of combined intermittent and sustained hypoxia (IH+SH) (characterizing obesity hypoventilation syndrome) and HFD on gut dysbiosis is unclear. We aimed to investigate the interactive effect of a combination of IH and SH and HFD on proximal colonic microbiota and colonic gene expression pattern.Methods: Male mice (n=16) were randomly received four different combinations of diet (normal versus HFD) and oxygen conditions (normoxia versus IH+SH) for 4 weeks. Bacterial DNA and mucosal epithelial cell RNA from proximal colon were collected for analysis of adherent microbiome and hostâs gene expression analysis.Results: HFD during IH+SH (22.6 ± 5.73; SD) led to greater Firmicutes: Bacteroidetes ratio than HFD during normoxia (5.89 ± 1.19; p=0.029). HFD significantly decreased microbial diversity
- Published
- 2022
44. SAMBA: A Bayesian network application to predict changes in the composition and function of mucosal microbiome in farmed fish
- Author
-
Ministerio de Economía y Competitividad (España), Ministerio de Ciencia, Innovación y Universidades (España), Agencia Estatal de Investigación (España), European Commission, Soriano, Beatriz, Hafez, Ahmed, Naya-Català, Fernando, Toxqui-Rodríguez, S., Piazzon de Haro, María Carla, Arnau, Vicente, Sitjà-Bobadilla, Ariadna, Llorens, Carlos, Pérez-Sánchez, Jaume, Ministerio de Economía y Competitividad (España), Ministerio de Ciencia, Innovación y Universidades (España), Agencia Estatal de Investigación (España), European Commission, Soriano, Beatriz, Hafez, Ahmed, Naya-Català, Fernando, Toxqui-Rodríguez, S., Piazzon de Haro, María Carla, Arnau, Vicente, Sitjà-Bobadilla, Ariadna, Llorens, Carlos, and Pérez-Sánchez, Jaume
- Abstract
SAMBA (Scanning Aquaculture Microbiome via Bayesian Approach) is a Guide User Interface application developed in R and powered by a Bayesian network model that indexes the frequencies of the bacterial taxa in a given biological system, correlating microbial architectures with a number of biotic and abiotic factors (e.g. sex, age, season, diet composition, genetic background, etc.). The application identifies conditional dependencies and interrelations among the distinct variables indexed in the network, allowing to predict how the taxa abundance of the pan-microbiome will vary depending on experimental variables. The application permits to predict and assign a metagenome to each inferred microbiome in order to determine its functional profile. SAMBA also permits to interrogate the Bayesian Network model to identify which experimental conditions are optimal for obtaining a given panmicrobiome and associated metagenome. At this stage, a locally run application of SAMBA was used to interrogate the pan-microbiome of farmed gilthead sea bream (a highly valued farmed fish in all the Mediterranean region) with different nutritional and genetic backgrounds across the production cycle. The application can also be used to model the host, metagenome and environment interrelations in a wide range of organisms, including humans. Interfaces of SAMBA were wrapped by Shiny, a framework to build interactive web applications by R. The application uses distinct R dependencies such as 1) bnlearn, for learning the structure of Bayesian Networks and estimate their parameters based on its structure using data from 16s amplicon experiments, 2) visNetwork and bnviewer for network visualization, and 3) PICRUSt2 to infer metagenomic functions from the microbiome population determined by 16s data given specific environmental conditions. SAMBA will be implemented to be accessible as a web server at www.nutrigroup-iats.org
- Published
- 2022
45. Signatures of Mucosal Microbiome in Oral Squamous Cell Carcinoma Identified Using a Random Forest Model
- Author
-
Zhou J, Wang L, Yuan R, Yu X, Chen Z, Yang F, Sun G, and Dong Q
- Subjects
oral squamous cell carcinoma ,microbiome ,random forest machine learning ,predicted functions ,Neoplasms. Tumors. Oncology. Including cancer and carcinogens ,RC254-282 - Abstract
Jianhua Zhou,1,* Lili Wang,2,* Rongtao Yuan,1 Xinjuan Yu,2 Zhenggang Chen,1 Fang Yang,1 Guirong Sun,3 Quanjiang Dong2 1Department of Stomatology, Qingdao Municipal Hospital, Qingdao University, Qingdao 266071, Shandong, People’s Republic of China; 2Central Laboratories and Department of Gastroenterology, Qingdao Municipal Hospital, Qingdao University, Qingdao 266071, Shandong, People’s Republic of China; 3Clinical Laboratory, The Affiliated Hospital, Qingdao University, Qingdao 266011, Shandong, People’s Republic of China*These authors contributed equally to this workCorrespondence: Quanjiang DongCentral Laboratories and Department of Gastroenterology, Qingdao Municipal Hospital, Qingdao University, Qingdao 266071, Shandong, People’s Republic of ChinaTel +86-532-88905289Fax +86-532-85968434Email jiangacer@126.comGuirong SunClinical Laboratory, The Affiliated Hospital, Qingdao University, Qingdao 266011, Shandong, People’s Republic of ChinaEmail sungr@qduhospital.cnObjective: The aim of this study was to explore the signatures of oral microbiome associated with OSCC using a random forest (RF) model.Patients and Methods: A total of 24 patients with OSCC were enrolled in the study. The oral microbiome was assessed in cancerous lesions and matched paracancerous tissues from each patient using 16S rRNA gene sequencing. Signatures of mucosal microbiome in OSCC were identified using a RF model.Results: Significant differences were found between OSCC lesions and matched paracancerous tissues with respect to the microbial profile and composition. Linear discriminant analysis effect size analyses (LEfSe) identified 15 bacteria genera associated with cancerous lesions. Fusobacterium, Treponema, Streptococcus, Peptostreptococcus, Carnobacterium, Tannerella, Parvimonas and Filifactor were enriched. A classifier based on RF model identified a microbial signature comprising 12 bacteria, which was capable of distinguishing cancerous lesions and paracancerous tissues (AUC = 0.82). The network of the oral microbiome in cancerous lesions appeared to be simplified and fragmented. Functional analyses of oral microbiome showed altered functions in amino acid metabolism and increased capacity of glucose utilization in OSCC.Conclusion: The identified microbial signatures may potentially be used as a biomarker for predicting OSCC or for clinical assessment of oral cancer risk.Keywords: oral squamous cell carcinoma, microbiome, random forest machine learning, predicted functions
- Published
- 2020
46. Gut Mucosal Microbiome Signatures of Colorectal Cancer Differ According to BMI Status
- Author
-
Sophie Shaw, Susan Berry, John Thomson, Graeme I. Murray, Emad El-Omar, and Georgina L. Hold
- Subjects
colorectal cancer ,gut microbiota ,high throughput sequencing ,increased body mass index ,colonic mucosa ,Medicine (General) ,R5-920 - Abstract
BackgroundCarrying excess body weight is a strong risk factor for colorectal cancer (CRC) development with ~11% of CRC cases in Europe linked to being overweight. The mechanisms through which excess body weight influences CRC development are not well understood but studies suggest the involvement of the presence of chronic low-grade inflammation and changes in the gut microbiota are involved.AimTo compare the mucosal associated microbiota of patients with CRC to understand whether carrying excess body weight was associated with a unique CRC microbial signature.MethodsMicrobiota signatures from colonic mucosal biopsies of CRC lesions and adjacent normal mucosal samples from 20 patients with overt CRC were compared with 11 healthy controls to see if having a BMI of >25 kg/m2 influenced colonic microbial composition.ResultsColonic mucosa samples from patients with CRC confirmed previously reported over-abundance of Fusobacteria associated with CRC but also an increase in Fusobacteria and Prevotella were associated with a BMI of >25 kg/m2. Correlation analysis of bacterial taxa indicated co-exclusive relationships were more common in CRC patients with a BMI >25 kg/m2 with an increase in transphylum relationships also seen in this patient group.ConclusionsThe findings suggest that gut microbiota composition in patients with CRC is influenced by BMI status. Further understanding/defining these differences will provide valuable information in terms of developing novel pre-onset screening and providing post-manifestation therapeutic intervention.
- Published
- 2022
- Full Text
- View/download PDF
47. Mo1210 THE MUCOSAL MICROBIOME DIFFERS ALONG THE NON-INFLAMED INTESTINAL TRACT OF CROHN'S DISEASE PATIENTS.
- Author
-
Ryu, Erica P., Koltun, Walter, Yochum, Gregory, and Davenport, Emily R.
- Published
- 2024
- Full Text
- View/download PDF
48. 119 INDIVIDUALS WITH IBD-ASSOCIATED ARTHRITIS HAVE INCREASED ABUNDANCE OF CORYNEBACTERIUM IN INTESTINAL MUCOSAL MICROBIOME.
- Author
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Alizadeh, Madeline A., Wong, Uni, Siaton, Bernadette C., Patil, Seema, George, Lauren, Raufman, Jean-Pierre, Scott, William H., Rosenvinge, Erik C. von, Ravel, Jacques, and Cross, Raymond K.
- Published
- 2024
- Full Text
- View/download PDF
49. Association Between Confocal Laser Endomicroscopic (CLE) Features and Colorectal Mucosal Microbiome
- Author
-
Yanqing Li, Vice president of Qilu Hospital
- Published
- 2015
50. Mucosal Microbiome in Human Gastric Intestinal Metaplasia and Duodenal Tissue.
- Author
-
Yanqing Li, Mucosal Microbiome in human gastric Intestinal Metaplasia and duodenal tissue.
- Published
- 2015
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