subject:( Mycobiome)

University of Manitoba

1. Moossavi, Shirin. Human milk microbiota and mycobiota in the CHILD cohort study.

Degree: Medical Microbiology and Infectious Diseases, 2020, University of Manitoba

URL: http://hdl.handle.net/1993/34683

► Introduction: Previous studies have confirmed the existence of a highly diverse bacterial community in human milk and suggested that its composition might be affected by… (more)

▼ Introduction: Previous studies have confirmed the existence of a highly diverse bacterial community in human milk and suggested that its composition might be affected by mode of delivery and maternal health. However, these findings have not yet been reproduced in large-scale studies. Additionally, the compositions of milk microbiota such as milk fungi are less frequently studied. Methods: Milk microbiota (bacteria) and mycobiota (fungi) were profiled in 393 and 271 mother-infant dyads from the CHILD Cohort Study using amplicon sequencing. Additionally, the milk microbiota was examined in a pilot study using culture-enriched molecular profiling. Finally, the impact of the bioinformatics processing on the results of downstream statistical analysis was compared. Results: Using multiple analytic techniques including causal modelling, evidence is provided that mode of breastfeeding (directly at the breast vs. pumped and bottle-fed) has a significant association with the composition of milk bacteria potentially highlighting the importance of exogenously-derived bacteria as sources of milk bacteria. The composition of other major milk components were associated with the overall composition of the milk microbiota while controlling for relevant confounding factors. Defining fungal presence at minimum threshold of 1000 reads per sample, the majority of milk samples did not contain detectable fungi and that presence of fungi was associated with residential characteristics and milk microbiota composition. Fungi diversity was associated with mode of delivery, maternal atopy, and home environment. We were able to isolate major milk bacteria using culture-enriched methods. Short-term freezing considerably impacted the composition of milk bacteria while we were not able to grow any bacterial isolates from the long-term frozen samples. Finally, milk microbiota richness was strongly impacted by the choice of the bioinformatics approach. However, there was an acceptable agreement and consistency in the relative abundances of the dominant milk bacteria and milk diversity. Importantly, the main conclusions remained robust to the choice of data processing. Conclusion: This is among the largest studies of human milk microbiota and mycobiota performed to date. Moreover, this is among the first studies of milk microbiota culture-enriched molecular profiling. Together, these results considerably expand upon existing knowledge about milk microbiota and mycobiota. Advisors/Committee Members: Bay, Denice (Medical Microbiology and Infectious Diseases), Wylie, John (Medical Microbiology and Infectious Diseases).

Subjects/Keywords: Microbiome; Mycobiome; Breastfeeding

Record Details Similar Records Cite « Share

❌

APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Moossavi, S. (2020). Human milk microbiota and mycobiota in the CHILD cohort study. (Thesis). University of Manitoba. Retrieved from http://hdl.handle.net/1993/34683

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Moossavi, Shirin. “Human milk microbiota and mycobiota in the CHILD cohort study.” 2020. Thesis, University of Manitoba. Accessed January 21, 2021. http://hdl.handle.net/1993/34683.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Moossavi, Shirin. “Human milk microbiota and mycobiota in the CHILD cohort study.” 2020. Web. 21 Jan 2021.

Vancouver:

Moossavi S. Human milk microbiota and mycobiota in the CHILD cohort study. [Internet] [Thesis]. University of Manitoba; 2020. [cited 2021 Jan 21]. Available from: http://hdl.handle.net/1993/34683.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Moossavi S. Human milk microbiota and mycobiota in the CHILD cohort study. [Thesis]. University of Manitoba; 2020. Available from: http://hdl.handle.net/1993/34683

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

University of Connecticut

2. Cardenas, Anibal. Oral Colonization of Malassezia species.

Degree: Master of Dental Science, Dental Science, 2018, University of Connecticut

URL: https://opencommons.uconn.edu/gs_theses/1249

Subjects/Keywords: Fungi; Malassezia; Mycobiome

Record Details Similar Records Cite « Share

❌

APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Cardenas, A. (2018). Oral Colonization of Malassezia species. (Masters Thesis). University of Connecticut. Retrieved from https://opencommons.uconn.edu/gs_theses/1249

Chicago Manual of Style (16^th Edition):

Cardenas, Anibal. “Oral Colonization of Malassezia species.” 2018. Masters Thesis, University of Connecticut. Accessed January 21, 2021. https://opencommons.uconn.edu/gs_theses/1249.

MLA Handbook (7^th Edition):

Cardenas, Anibal. “Oral Colonization of Malassezia species.” 2018. Web. 21 Jan 2021.

Vancouver:

Cardenas A. Oral Colonization of Malassezia species. [Internet] [Masters thesis]. University of Connecticut; 2018. [cited 2021 Jan 21]. Available from: https://opencommons.uconn.edu/gs_theses/1249.

Council of Science Editors:

Cardenas A. Oral Colonization of Malassezia species. [Masters Thesis]. University of Connecticut; 2018. Available from: https://opencommons.uconn.edu/gs_theses/1249

University of California – San Francisco

3. Mar, Jordan Samuel. Investigating the Clinical Utility of the Gastrointestinal Microbiome in Ulcerative Colitis.

Degree: Biomedical Sciences, 2016, University of California – San Francisco

URL: http://www.escholarship.org/uc/item/56z385v7

► Despite centuries of research, the etiology of Ulcerative Colitis (UC; a chronic form of colonic inflammation) remains a mystery. As such, diagnosis is difficult, relying… (more)

▼ Despite centuries of research, the etiology of Ulcerative Colitis (UC; a chronic form of colonic inflammation) remains a mystery. As such, diagnosis is difficult, relying on clinical manifestations and resulting in an incredibly heterogeneous patient population. Furthermore, no cure (save colectomy) is available for UC, leading to a lifetime of therapies (many having variable efficacy; a consequence of UC patient heterogeneity). As UC prevalence rises, substantial need for enhanced therapies exists.The gastrointestinal microbiome represents a promising avenue for improved treatment practices for UC. Being a diverse microbial community with substantial metabolic activity, opportunity exists for commensal microbes to influence host health, specifically the immune system. Indeed, several common colonizers of the mammalian gut regulate specific aspects of host immunity relevant to UC (such as Th17 and regulatory T-cell abundance, lymphocyte recruitment, and epithelial barrier function) through production of immunomodulatory metabolites. While UC was originally described as non-infectious diarrhea, studies demonstrating the potential efficacy of microbe-based treatments (i.e., probiotics) and the impact of microbes on animal models of UC suggest the microbiome contributes in a non-classical form of pathogenesis. Building on this, independent researchers found the gastrointestinal microbiome of UC patients to be less diverse and more compositionally variable compared to healthy people. Though these findings implicate the gastrointestinal microbiome in UC, questions remain regarding the therapeutic potential of gut microbes to improve patient outcomes.This thesis addresses the clinical utility of the gastrointestinal microbiome in improving UC treatment. The therapeutic potential of microbiome manipulation was demonstrated using a murine model of UC and indicated gastrointestinal niches upstream of the colon harbor microbial activity associated with both disease induction and remission, suggesting patients might benefit from remodeling of microbial communities throughout the intestines. Additionally, a human study was conducted to demonstrate the utility of the microbiome with respect to improved stratification of UC patients. This work indicated discrete microbial states exist within the UC population, associate with symptom severity, and, via unique metabolic programming, differentially regulate T-cell activity. Together, this work highlights the microbiome as a resource for the development of both novel therapies and personalized treatment regimens for UC.

Subjects/Keywords: Microbiology; Immunology; Microbiome; Microbiota; Mycobiome; Patient Stratification; Probiotics; Ulcerative Colitis

Record Details Similar Records Cite « Share

❌

APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Mar, J. S. (2016). Investigating the Clinical Utility of the Gastrointestinal Microbiome in Ulcerative Colitis. (Thesis). University of California – San Francisco. Retrieved from http://www.escholarship.org/uc/item/56z385v7

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Mar, Jordan Samuel. “Investigating the Clinical Utility of the Gastrointestinal Microbiome in Ulcerative Colitis.” 2016. Thesis, University of California – San Francisco. Accessed January 21, 2021. http://www.escholarship.org/uc/item/56z385v7.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Mar, Jordan Samuel. “Investigating the Clinical Utility of the Gastrointestinal Microbiome in Ulcerative Colitis.” 2016. Web. 21 Jan 2021.

Vancouver:

Mar JS. Investigating the Clinical Utility of the Gastrointestinal Microbiome in Ulcerative Colitis. [Internet] [Thesis]. University of California – San Francisco; 2016. [cited 2021 Jan 21]. Available from: http://www.escholarship.org/uc/item/56z385v7.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Mar JS. Investigating the Clinical Utility of the Gastrointestinal Microbiome in Ulcerative Colitis. [Thesis]. University of California – San Francisco; 2016. Available from: http://www.escholarship.org/uc/item/56z385v7

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

University of Toronto

4. Kim, Sang Hu. Molecular Analysis of Phenotypic Diversity in Human Fungal Pathogens.

Degree: PhD, 2018, University of Toronto

URL: http://hdl.handle.net/1807/92028

► Fungal pathogens are a leading cause of human mortality, in part due to their ability to thwart therapeutic regimens by rapidly evolving resistance to antifungal… (more)

▼ Fungal pathogens are a leading cause of human mortality, in part due to their ability to thwart therapeutic regimens by rapidly evolving resistance to antifungal drugs, and their ability to readily adapt to the hostile conditions experienced in a mammalian host. Candida species can colonize various niches in the human body making them common commensals of the mucosal microbiota, where the maintenance of a stable host-fungus relationship is presumably critical for avoiding disease. However, the importance of fungi is only beginning to be appreciated in context of the human microbiome. My doctoral research focuses on two aspects of how Candida species influence human health and disease. First, I characterized fungal communities of 28 cystic fibrosis patients by coupling high-throughput ITS1 sequencing with phenotypic analyses of fungal isolates from sputum samples. Fungal communities were not determined by clinical characteristics, but considerable phenotypic variation in traits such as antifungal resistance and morphogenesis was identified within Candida species. Notably, filamentation in the absence of inducing cues was observed in 28 Candida isolates from six patients, with most isolates harboring mutations in a transcriptional repressor of filamentation, NRG1. These mutants were resistant to the filament inhibitory effects of Pseudomonas aeruginosa, implicating interkingdom interactions as the driver of adaptation. Second, I characterized the role of the molecular chaperone Hsp90 in drug resistance and morphogenesis in an emerging fungal pathogen, Candida auris. I showed that fluconazole resistance of C. auris was independent of HSP90 expression, but in part mediated by the ABC transporter CDR1. Further, I showed that C. auris is capable of filamentous growth in response to Hsp90 depletion or inhibition. Transcriptomic analysis upon HSP90 depletion showed that filamentous growth is associated with upregulation of putative cell wall associated genes. Overall, my research provides key insights into mechanisms governing phenotypic diversity in human fungal pathogens. Advisors/Committee Members: Cowen, Leah E, Molecular and Medical Genetics.

Subjects/Keywords: Cystic fibrosis; Drug resistance; Fungal microbiome; Fungal pathogen; Mycobiome; 0410

Record Details Similar Records Cite « Share

❌

APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Kim, S. H. (2018). Molecular Analysis of Phenotypic Diversity in Human Fungal Pathogens. (Doctoral Dissertation). University of Toronto. Retrieved from http://hdl.handle.net/1807/92028

Chicago Manual of Style (16^th Edition):

Kim, Sang Hu. “Molecular Analysis of Phenotypic Diversity in Human Fungal Pathogens.” 2018. Doctoral Dissertation, University of Toronto. Accessed January 21, 2021. http://hdl.handle.net/1807/92028.

MLA Handbook (7^th Edition):

Kim, Sang Hu. “Molecular Analysis of Phenotypic Diversity in Human Fungal Pathogens.” 2018. Web. 21 Jan 2021.

Vancouver:

Kim SH. Molecular Analysis of Phenotypic Diversity in Human Fungal Pathogens. [Internet] [Doctoral dissertation]. University of Toronto; 2018. [cited 2021 Jan 21]. Available from: http://hdl.handle.net/1807/92028.

Council of Science Editors:

Kim SH. Molecular Analysis of Phenotypic Diversity in Human Fungal Pathogens. [Doctoral Dissertation]. University of Toronto; 2018. Available from: http://hdl.handle.net/1807/92028

Kansas State University

5. Pedrozo, Rodrigo. Characterization of soybean seedborne Fusarium spp. in the state of Kansas, USA.

Degree: PhD, Department of Plant Pathology, 2017, Kansas State University

URL: http://hdl.handle.net/2097/35737

► Fusarium spp. are among the most important pathogen groups on soybeans. However, information regarding this genus on soybean seeds in the state of Kansas remains… (more)

▼ Fusarium spp. are among the most important pathogen groups on soybeans. However, information regarding this genus on soybean seeds in the state of Kansas remains underexplored. Therefore, the goal of this study was to characterize the identity, frequency, and pathogenicity of soybean seedborne Fusarium spp. in the state of Kansas. For the identification and frequency of seedborne Fusarium spp., culture-dependent (i.e. semi-selective medium) and -independent (i.e. DNA metabarcoding) approaches were used. Also, information regarding the pathogenicity of the most common seedborne Fusarium spp. from soybeans was assessed to better understand their role as soybean pathogens. Overall, eleven Fusarium spp. were identified in this study. Semi-selective media showed that approximately 33% of soybean seed samples were infected with Fusarium spp. Moreover, Fusarium spp. were isolated from seed sampled from 80% of the locations in Kansas. Furthermore, a low incidence of Fusarium spp. was observed within infected seed samples and averaged 2%. Nine Fusarium spp. were found in soybean seeds using the culture-dependent approach. Fusarium semitectum was the most frequent, followed by F. proliferatum and F. verticillioides. Fusarium acuminatum, F. equiseti, F. fujikuroi, F. graminearum, F. oxysporum, and F. thapsinum were found in lower frequencies among naturally infected seeds. DNA metabarcoding experiments showed that Fusarium spp. are more frequent in soybean seeds than previously known. All asymptomatic soybean seeds analyzed, using Illumina MiSeq platform, showed the presence of the genus Fusarium including two pathogenic species, F. proliferatum and F. thapsinum. Fusarium acuminatum, F. merismoides, F. solani, F. semitectum, and Fusarium sp. were also identified using the culture-independent approach. Preliminary results also showed that F. proliferatum and F. thapsinum were observed in all three major soybean seed tissues: seed coat, cotyledons, and the embryo axis. Depending on the soybean genotype, inoculum potential and aggressiveness, F. proliferatum, F. graminearum, F. fujikuroi, F. oxysporum, F. semitectum, F. thapsinum, and F. verticillioides were pathogenic to soybean and negatively affect soybean seed quality, at different levels, in controlled conditions. Moreover, F. equiseti and F. acuminatum did not cause significant damage to soybean seeds and seedlings. Understanding seedborne Fusarium spp. and their influence on soybean seed and seedling diseases is critical for the development of effective disease control strategies, especially regarding early detection of pathogenic strains in seeds (i.e., seed health testing), ensuring the crop productivity, quality, and safety. Advisors/Committee Members: Christopher R. Little.

Subjects/Keywords: Soybean; Seed quality; Seedborne pathogens; Seed mycobiome; Fusarium spp.

Record Details Similar Records Cite « Share

❌

APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Pedrozo, R. (2017). Characterization of soybean seedborne Fusarium spp. in the state of Kansas, USA. (Doctoral Dissertation). Kansas State University. Retrieved from http://hdl.handle.net/2097/35737

Chicago Manual of Style (16^th Edition):

Pedrozo, Rodrigo. “Characterization of soybean seedborne Fusarium spp. in the state of Kansas, USA.” 2017. Doctoral Dissertation, Kansas State University. Accessed January 21, 2021. http://hdl.handle.net/2097/35737.

MLA Handbook (7^th Edition):

Pedrozo, Rodrigo. “Characterization of soybean seedborne Fusarium spp. in the state of Kansas, USA.” 2017. Web. 21 Jan 2021.

Vancouver:

Pedrozo R. Characterization of soybean seedborne Fusarium spp. in the state of Kansas, USA. [Internet] [Doctoral dissertation]. Kansas State University; 2017. [cited 2021 Jan 21]. Available from: http://hdl.handle.net/2097/35737.

Council of Science Editors:

Pedrozo R. Characterization of soybean seedborne Fusarium spp. in the state of Kansas, USA. [Doctoral Dissertation]. Kansas State University; 2017. Available from: http://hdl.handle.net/2097/35737

6. Nguyen, Do Ngoc Linh. Mise au point de l’analyse par séquençage à haut-débit du microbiote fongique et bactérien respiratoire chez les patients atteints de mucoviscidose : Optimization of high-throughput sequencing approach to study lung mycobiota and bacteriota of cystic fibrosis patients.

Degree: Docteur es, Microbiologie, 2016, Université Lille II – Droit et Santé

URL: http://www.theses.fr/2016LIL2S011

► L’infection broncho-pulmonaire représente le problème majeur des malades atteints de la mucoviscidose. Plusieurs bactéries sont connues depuis des dizaines années comme les principaux agents responsables… (more)

▼ L’infection broncho-pulmonaire représente le problème majeur des malades atteints de la mucoviscidose. Plusieurs bactéries sont connues depuis des dizaines années comme les principaux agents responsables de ces infections (par exemple Pseudomonas aeruginosa, Staphylococcus aureus, Burkholderia cepacia, Achromobacter xylosoxidans…). Récemment, certains genres fongiques notamment les champignons filamenteux (comme Aspergillus, Scedosporium…) ont été identifiés comme des pathogènes émergeants ou ré-émergeants pouvant être responsables d’infection invasive. Ainsi, la détection des microorganismes impliqués dans ces colonisations et/ou infections respiratoires demeure importante sur le plan physiopathologique et clinique.Si la culture microbiologique reste la méthode la plus utilisée à ce jour pour le diagnostic des infections microbiennes, elle ne permet pas d’identifier les microbes non-cultivables ou difficiles à cultiver. Depuis quelques années, grâce au développement de la technique moléculaire de séquençage à haut-débit (next generation sequencing ou NGS), plusieurs études ont montré que l’écologie microbienne du poumon des patients atteints de la mucoviscidose est très complexe et correspond à une flore poly-microbienne, appelée le microbiote pulmonaire, comprenant non seulement des bactéries mais également des micromycètes (levures et/ou champignons filamenteux) et des virus et phages. Une dysbiose (modification en abondance et diversité) de cette flore pourrait influencer la fonction respiratoire et l’état clinique du patient.Alors que le microbiome bactérien et son rôle en pathogenèse sont largement étudiés, peu d’études ont porté sur la composante fongique (mycobiote/mycobiome) du microbiote pulmonaire. Notre travail de thèse s’inscrit dans les différents projets développés au sein de l’axe de recherche « Microbiote pro- et eucaryote pulmonaire » coordonné par le Pr Laurence Delhaes dans l’équipe Biologie et Diversité des Pathogènes Eucaryotes Emergeants (BDPEE) dirigée par le Dr Eric Viscogliosi. Il se focalise sur l’analyse NGS du microbiote pro- et eucaryotique respiratoire chez les patients atteints de la mucoviscidose et notamment la comparaison de différentes approches méthodologiques en vue d’une optimisation et standardisation de la méthode.Dans un premier temps, nous présenterons une synthèse des connaissances actuelles d’une part des phénomènes de colonisations/infections fongiques chez les patients atteints de mucoviscidose et d’autre part dans le domaine du microbiote pulmonaire et surtout du mycobiote pulmonaire autour duquel notre équipe se focalise.2Dans un deuxième temps, nous avons travaillé à mieux adapter l’approche NGS aux études du microbiote pulmonaire dans la mucoviscidose. En effet, le séquençage à haut-débit est une technique puissante mais pour laquelle des biais peuvent être introduits à de nombreuses étapes méthodologiques. Un des biais les plus importants est que l’approche NGS ne permet pas de différencier les microorganismes vivants, des cellules mortes ou endommagées, ni de l’ADN… Advisors/Committee Members: Delhaes, Laurence (thesis director).

Subjects/Keywords: Microbiote; Microflore; Mucoviscidose; Séquençage à haut-débit; Mycobiome; Microbiome

Record Details Similar Records Cite « Share

❌

APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Nguyen, D. N. L. (2016). Mise au point de l’analyse par séquençage à haut-débit du microbiote fongique et bactérien respiratoire chez les patients atteints de mucoviscidose : Optimization of high-throughput sequencing approach to study lung mycobiota and bacteriota of cystic fibrosis patients. (Doctoral Dissertation). Université Lille II – Droit et Santé. Retrieved from http://www.theses.fr/2016LIL2S011

Chicago Manual of Style (16^th Edition):

Nguyen, Do Ngoc Linh. “Mise au point de l’analyse par séquençage à haut-débit du microbiote fongique et bactérien respiratoire chez les patients atteints de mucoviscidose : Optimization of high-throughput sequencing approach to study lung mycobiota and bacteriota of cystic fibrosis patients.” 2016. Doctoral Dissertation, Université Lille II – Droit et Santé. Accessed January 21, 2021. http://www.theses.fr/2016LIL2S011.

MLA Handbook (7^th Edition):

Nguyen, Do Ngoc Linh. “Mise au point de l’analyse par séquençage à haut-débit du microbiote fongique et bactérien respiratoire chez les patients atteints de mucoviscidose : Optimization of high-throughput sequencing approach to study lung mycobiota and bacteriota of cystic fibrosis patients.” 2016. Web. 21 Jan 2021.

Vancouver:

Nguyen DNL. Mise au point de l’analyse par séquençage à haut-débit du microbiote fongique et bactérien respiratoire chez les patients atteints de mucoviscidose : Optimization of high-throughput sequencing approach to study lung mycobiota and bacteriota of cystic fibrosis patients. [Internet] [Doctoral dissertation]. Université Lille II – Droit et Santé 2016. [cited 2021 Jan 21]. Available from: http://www.theses.fr/2016LIL2S011.

Council of Science Editors:

Nguyen DNL. Mise au point de l’analyse par séquençage à haut-débit du microbiote fongique et bactérien respiratoire chez les patients atteints de mucoviscidose : Optimization of high-throughput sequencing approach to study lung mycobiota and bacteriota of cystic fibrosis patients. [Doctoral Dissertation]. Université Lille II – Droit et Santé 2016. Available from: http://www.theses.fr/2016LIL2S011

7. Clausen Lind, Andrea. Exploring the mycobiota for the treatment of gut-related diseases .

Degree: Chalmers tekniska högskola / Institutionen för biologi och bioteknik, 2020, Chalmers University of Technology

URL: http://hdl.handle.net/20.500.12380/300767

► Our gut harbors trillions of microorganisms that form a bridge between our diet and whole-body metabolism. This collection of microorganisms, referred to as the gut… (more)

Subjects/Keywords: Yeast Probiotics; Live biotherapeutics; Phenylketonuria; Mycobiome; Metagenomic analysis; Inflammatory Bowel Disease

Record Details Similar Records Cite « Share

❌

APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Clausen Lind, A. (2020). Exploring the mycobiota for the treatment of gut-related diseases . (Thesis). Chalmers University of Technology. Retrieved from http://hdl.handle.net/20.500.12380/300767

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Clausen Lind, Andrea. “Exploring the mycobiota for the treatment of gut-related diseases .” 2020. Thesis, Chalmers University of Technology. Accessed January 21, 2021. http://hdl.handle.net/20.500.12380/300767.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Clausen Lind, Andrea. “Exploring the mycobiota for the treatment of gut-related diseases .” 2020. Web. 21 Jan 2021.

Vancouver:

Clausen Lind A. Exploring the mycobiota for the treatment of gut-related diseases . [Internet] [Thesis]. Chalmers University of Technology; 2020. [cited 2021 Jan 21]. Available from: http://hdl.handle.net/20.500.12380/300767.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Clausen Lind A. Exploring the mycobiota for the treatment of gut-related diseases . [Thesis]. Chalmers University of Technology; 2020. Available from: http://hdl.handle.net/20.500.12380/300767

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Oklahoma State University

8. Robinson, Kelsy. Chicken intestinal mycobiome: Biogeography, succession, and response to in-feed antibiotics.

Degree: Animal Science, 2019, Oklahoma State University

URL: http://hdl.handle.net/11244/324874

► In-feed antibiotics increase animal performance primarily through modulation of the intestinal microbiota. However, the exact mechanism of action is not understood. Furthermore, a majority of… (more)

▼ In-feed antibiotics increase animal performance primarily through modulation of the intestinal microbiota. However, the exact mechanism of action is not understood. Furthermore, a majority of research on intestinal microbiota has focused solely on the intestinal bacterial population with very little being known about smaller populations such as fungi. Deep sequencing of the internal transcribed spacer 2 (ITS2) region of fungal rRNA genes was utilized in two studies to characterize the biogeography of the chicken intestinal fungal community, the mycobiome, along the gastrointestinal tract of broiler chickens on days 28 and 42 and its possible shift in response to bacitracin methylene disalicylate (BMD), a commonly used in-feed antibiotic. Intestinal luminal contents were also collected from the duodenum, jejunum, ileum, and cecum at seven different time points throughout an entire production cycle to determine the succession of the mycobiome. The phyla Ascomycota and Basidiomycota were found to be predominant regardless of age or GI location. Genera commonly associated with feed ingredients or soil such as Microascus, Gibberella, Trichosporon, and Aspergillus were the most abundant. However, their abundance varied greatly between studies indicating a strong environmental influence. A clear succession of the cecal mycobiome was observed, in which specific fungal consortia moved down the intestinal tract as birds aged indicating that this population is transient in nature. Dietary supplementation of BMD at a subtherapeutic level of 55 mg/kg resulted in a decrease in the cecal fungal diversity. To further elucidate effect of antibiotics on cecal bacterial populations, broiler chicks were supplemented with or without one of five commonly used antibiotics for 14 days followed by deep sequencing of the V3-V4 region of the bacterial 16S rRNA gene. Although each antibiotic modulated the gut microbiota differently, the closer the antibacterial spectrum, the more similarly the microbiota is regulated with treatments classified as ionophores having the greatest effect. Importantly, all antibiotics had a strong tendency to enrich butyrate- and lactic acid-producing bacteria, while reducing bile salt hydrolase-producing bacteria, suggesting in-feed antibiotics improve animal growth performance through enhanced metabolism and utilization of dietary carbohydrates and lipids and improved energy harvest. Advisors/Committee Members: Zhang, Guolong (advisor), Conway, Tyrell (committee member), Burnap, Rob (committee member), Ritchey, Jerry (committee member).

Subjects/Keywords: antibiotic alternatives; antimicrobial growth promoters; broiler; chicken; fungi; mycobiome

Record Details Similar Records Cite « Share

❌

APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Robinson, K. (2019). Chicken intestinal mycobiome: Biogeography, succession, and response to in-feed antibiotics. (Thesis). Oklahoma State University. Retrieved from http://hdl.handle.net/11244/324874

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Robinson, Kelsy. “Chicken intestinal mycobiome: Biogeography, succession, and response to in-feed antibiotics.” 2019. Thesis, Oklahoma State University. Accessed January 21, 2021. http://hdl.handle.net/11244/324874.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Robinson, Kelsy. “Chicken intestinal mycobiome: Biogeography, succession, and response to in-feed antibiotics.” 2019. Web. 21 Jan 2021.

Vancouver:

Robinson K. Chicken intestinal mycobiome: Biogeography, succession, and response to in-feed antibiotics. [Internet] [Thesis]. Oklahoma State University; 2019. [cited 2021 Jan 21]. Available from: http://hdl.handle.net/11244/324874.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Robinson K. Chicken intestinal mycobiome: Biogeography, succession, and response to in-feed antibiotics. [Thesis]. Oklahoma State University; 2019. Available from: http://hdl.handle.net/11244/324874

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Swedish University of Agricultural Sciences

9. Agostinelli, Marta. Fungal assemblages in forest trees.

Degree: 2018, Swedish University of Agricultural Sciences

URL: https://pub.epsilon.slu.se/15772/

► Forest trees host a plethora of microorganisms (bacteria, viruses, fungi) whose roles and diversity are still poorly understood despite the increased scientific interest for the… (more)

▼ Forest trees host a plethora of microorganisms (bacteria, viruses, fungi) whose roles and diversity are still poorly understood despite the increased scientific interest for the past decades. The thesis focuses on the diversity of endophytic and epiphytic fungi in the aerial tissues of broadleaved trees. It tests a basic hypothesis that the diversity and frequency of endophytic and epiphytic fungi vary depending on the vitality and disease susceptibility of the host. Additionally the thesis explores if the chemical variation in trees may relate to differences in fungal community. Particularly, the aim was to describe how the fungal communities of three broadleaved species relate to the general vitality or specific pathogen resistance of the trees, and if herbivory or fertilization influence the fungi through altered levels of potentially antimicrobial metabolites, condensed tannins. Culture-based and culture-independent (NGS) techniques were used to capture the fungal community in the twigs of pedunculate oak (Quercus robur L), in the leaves of aspen (Populus tremula L), and in the leaves and twigs of European ash (Fraxinus excelsior L). The secondary metabolites were studied with HPLC, LC-MS, and GC-MS analyses. The results showed that the fungal assemblages are influenced by a complex network of factors related to the status of the host (internal factors: health, chemotype) and its environment (season, site, nitrogen, herbivory). Trees with different vitality or different phenotypic response to pathogen hosted quantitatively and qualitatively diverse fungal communities. Tissue type and seasonal variation were confirmed to be highly selective factors in shaping fungal communities of forest trees. The endophytic communities associated with xylem seemed to be shaped by the tree vitality more readily than the fungi associated with leaf or bark. Condensed tannins, nitrogen fertilization, and herbivory did not explain the structure of fungal communities in aspen leaves. Leaf phenolic metabolites reflected well the general vitality phenotype of the trees, but the relationship between fungi and phenolics may not be straightforward. The technological advances and the use of different methods to survey fungal communities may help disclosing the unknown fungal biodiversity hosted by forest trees. Further studies on fungal communities are needed to reveal the ecological relevance that fungal assemblages have in the regulation of major ecological cycles. Understanding the mechanisms regulating the establishment of fungal communities may contribute to the possibility of using fungal assemblages in forest practices to help forest coping with sudden changes and be able to provide different ecosystem services.

Subjects/Keywords: endophyte; epiphyte; broadleaves mycobiome; fungal diversity; chemotype; fungal assemblages; phenolics; forest trees

Record Details Similar Records Cite « Share

❌

APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Agostinelli, M. (2018). Fungal assemblages in forest trees. (Doctoral Dissertation). Swedish University of Agricultural Sciences. Retrieved from https://pub.epsilon.slu.se/15772/

Chicago Manual of Style (16^th Edition):

Agostinelli, Marta. “Fungal assemblages in forest trees.” 2018. Doctoral Dissertation, Swedish University of Agricultural Sciences. Accessed January 21, 2021. https://pub.epsilon.slu.se/15772/.

MLA Handbook (7^th Edition):

Agostinelli, Marta. “Fungal assemblages in forest trees.” 2018. Web. 21 Jan 2021.

Vancouver:

Agostinelli M. Fungal assemblages in forest trees. [Internet] [Doctoral dissertation]. Swedish University of Agricultural Sciences; 2018. [cited 2021 Jan 21]. Available from: https://pub.epsilon.slu.se/15772/.

Council of Science Editors:

Agostinelli M. Fungal assemblages in forest trees. [Doctoral Dissertation]. Swedish University of Agricultural Sciences; 2018. Available from: https://pub.epsilon.slu.se/15772/

10. Hoarau, Gautier. Caractérisation du mycobiome intestinal et fécal chez les patients atteints de maladie de Crohn, et leurs parents sains du premier degré : Characterization of the faecal mycobiome in familial Crohn's disease.

Degree: Docteur es, Parasitologie et mycologie, 2016, Université Lille II – Droit et Santé

URL: http://www.theses.fr/2016LIL2S033

►

Introduction : La maladie de Crohn (MC), maladie inflammatoire chronique intestinale, est une maladie multifactorielle, d’origine inconnue. La dysbiose bactérienne a été largement évoquée dans… (more)

▼

Introduction : La maladie de Crohn (MC), maladie inflammatoire chronique intestinale, est une maladie multifactorielle, d’origine inconnue. La dysbiose bactérienne a été largement évoquée dans la pathogénèse de la MC. Notre objectif était de caractériser la flore fongique, conjointement à la flore bactérienne au cours de formes familiales de MC.Méthodes: Nous avons utilisé une plateforme de séquençage à haut débit pour caractériser la flore fongique et bactérienne fécale, échantillonnée dans 9 familles multiplexes atteints de MC (20 patients, et 28 sujets sains apparentés), et 4 familles contrôles (21 individus sains non apparentés). Une analyse bioinformatique a été réalisée pour analyser l’abondance, la biodiversité, et les interactions microbiennes.Résultats : Le microbiote fécal des membres issus des familles multiplexes était statistiquement différent de celui des membres issus des familles contrôles. L’analyse en composantes principales a montré qu’au sein des familles multiplexes, les membres malades et sains partageaient un répertoire fongique commun. Les patients MC avaient en revanche un microbiote enrichi en Candida tropicalis, Escherichia coli et en Serratia marcescens, et appauvri en bactéries dites bénéfiques (Faecalibacterium prausnitzii). De plus les taux d’ASCA (Anticorps anti- S. cerevisiae), marqueur sérologique de MC étaient corrélées à la présence de C. tropicalis (P = .01). Enfin nous avons mis en évidence une synergie entre C. tropicalis, E. coli, et S. marcescens, suggérant une interaction microbienne in vivo participant à l’initiation de l’inflammation intestinale. Ces données ont été validées par la suite avec un modèle de biofilm.Conclusion : Dans ces formes familiales de MC, les interactions microbiennes entre bactéries et champignons sont déterminantes dans l’initiation de la réponse inflammatoire.

Introduction: Crohn's disease (CD) results from a complex interplay between host genetic factors and endogenous microbial communities.Methods: In the current study, we used Ion Torrent sequencing to characterize the gut bacterial microbiota (bacteriome) and fungal community (mycobiome) in patients with CD and their non-diseased first degree relatives (NCDR) in 9 familial clusters living in Northern France/Belgium, and in healthy individuals from 4 families living in the same area (non-CD unrelated, NCDU). Principal components analysis, diversity, and abundance analyses were conducted and CD-associated inter- and intra-kingdom microbial correlations determined. Significant microbial interactions were identified and validated using single- and mixed-species biofilms.Results: CD and NCDR groups clustered together in the mycobiome, but not in bacteriome. Microbiota of familial (CD, NCDR) samples were distinct from that of non-familial (NCDU) samples. Abundance of Serratia marcescens (SM), Escherichia coli (EC) was elevated in CD patients, while that of beneficial bacteria was decreased. Abundance of the fungus Candida tropicalis (CT) was significantly higher in CD compared to NCDR (P = .003),…

Advisors/Committee Members: Sendid, Boualem (thesis director), Beghin, Laurent (thesis director).

Subjects/Keywords: Maladie de Crohn; Microbiotes; Candida albicans; Biofilms; Mycobiotes; Crohn's disease; Microbiota; Mycobiome

Record Details Similar Records Cite « Share

❌

APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Hoarau, G. (2016). Caractérisation du mycobiome intestinal et fécal chez les patients atteints de maladie de Crohn, et leurs parents sains du premier degré : Characterization of the faecal mycobiome in familial Crohn's disease. (Doctoral Dissertation). Université Lille II – Droit et Santé. Retrieved from http://www.theses.fr/2016LIL2S033

Chicago Manual of Style (16^th Edition):

Hoarau, Gautier. “Caractérisation du mycobiome intestinal et fécal chez les patients atteints de maladie de Crohn, et leurs parents sains du premier degré : Characterization of the faecal mycobiome in familial Crohn's disease.” 2016. Doctoral Dissertation, Université Lille II – Droit et Santé. Accessed January 21, 2021. http://www.theses.fr/2016LIL2S033.

MLA Handbook (7^th Edition):

Hoarau, Gautier. “Caractérisation du mycobiome intestinal et fécal chez les patients atteints de maladie de Crohn, et leurs parents sains du premier degré : Characterization of the faecal mycobiome in familial Crohn's disease.” 2016. Web. 21 Jan 2021.

Vancouver:

Hoarau G. Caractérisation du mycobiome intestinal et fécal chez les patients atteints de maladie de Crohn, et leurs parents sains du premier degré : Characterization of the faecal mycobiome in familial Crohn's disease. [Internet] [Doctoral dissertation]. Université Lille II – Droit et Santé 2016. [cited 2021 Jan 21]. Available from: http://www.theses.fr/2016LIL2S033.

Council of Science Editors:

Hoarau G. Caractérisation du mycobiome intestinal et fécal chez les patients atteints de maladie de Crohn, et leurs parents sains du premier degré : Characterization of the faecal mycobiome in familial Crohn's disease. [Doctoral Dissertation]. Université Lille II – Droit et Santé 2016. Available from: http://www.theses.fr/2016LIL2S033

11. ELMAGHRAWY, KHALID MUFTAH. Analysis of the oral bacteriome and mycobiome in children with inflammatory bowel disease compared to healthy children by 16S and ITS2 profiling.

Degree: School of Dental Sciences. Discipline of Dental Science, 2019, Trinity College Dublin

URL: http://hdl.handle.net/2262/88800

► Abstract Aims: This study aimed to analyse the oral mucosal microbiota (bacteria and fungi) in paediatric IBD patients. The mucosa was selected rather than the… (more)

▼ Abstract Aims: This study aimed to analyse the oral mucosal microbiota (bacteria and fungi) in paediatric IBD patients. The mucosa was selected rather than the saliva as this is the region where tissue and immune cells directly interact with the microbiome Methods: The oral microbiome and mycobiome were examined in a cohort of children diagnosed with Crohn s disease (n=38, CD), and ulcerative colitis (n=21, UC). Children were treatment na?ve at the time of sampling. A cohort of 36 children who were attending DDUH were grouped as a healthy control (HC) group. DNA was extracted from tongue and buccal swabs and the V1-V2 region of the 16S gene and ITS2 barcode of fungal DNA were amplified and sequenced using the Illumina MiSeq. Sequences were analysed with the Mothur and DADA2 pipelines. Additionally, IBD children following therapy were also analysed. Results: The tongue and buccal microbiota of CD children exhibted reduced biodiversity and lower species richness compared to healthy children. Our finding shows a reduction in the levels of several major oral bacterial genera, including Veillonella, and H. parinfluenza, and increased levels of oral Enterobacteriaceae and Actinobacteria in patients with severe IBD. Previous studies have implicated these taxa in the pathogenesis of IBD. In our follow up studies, remission from IBD symptoms was associated with loss of Enterobacteriaceae from the oral microbiome. We observed an increase in C. albicans and S. cerevisiae in the oral mycobiota in IBD. Interestingly, C. krusei and C. dubliniensis were also observed in the oral cavity in IBD. Overall, the mycobiome changes observed were more related to IBD disease activity compared to microbiome changes. Shifting of the oral microbial community was noted in follow up samples from patients after therapy, returning some taxa (Veillonella, Enterobacteriaceae) to levels close to the normal oral community. Conclusion: Children with IBD have an altered microbiota that may contribute to their oral health problems and may be linked to the pathogenesis of IBD. These data could potentially important to understand the aetiology of IBD and could be used in practical applications in diagnosis and monitoring disease progression. Advisors/Committee Members: Moran, Gary.

Subjects/Keywords: Oral microbiome and mycobiome; gut microbiomta; Crohn s disease; ulcerative colitis; dysbiosis; 16S and ITS2 profiling

10 more images…

Record Details Similar Records Cite « Share

❌

APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

ELMAGHRAWY, K. M. (2019). Analysis of the oral bacteriome and mycobiome in children with inflammatory bowel disease compared to healthy children by 16S and ITS2 profiling. (Thesis). Trinity College Dublin. Retrieved from http://hdl.handle.net/2262/88800

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

ELMAGHRAWY, KHALID MUFTAH. “Analysis of the oral bacteriome and mycobiome in children with inflammatory bowel disease compared to healthy children by 16S and ITS2 profiling.” 2019. Thesis, Trinity College Dublin. Accessed January 21, 2021. http://hdl.handle.net/2262/88800.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

ELMAGHRAWY, KHALID MUFTAH. “Analysis of the oral bacteriome and mycobiome in children with inflammatory bowel disease compared to healthy children by 16S and ITS2 profiling.” 2019. Web. 21 Jan 2021.

Vancouver:

ELMAGHRAWY KM. Analysis of the oral bacteriome and mycobiome in children with inflammatory bowel disease compared to healthy children by 16S and ITS2 profiling. [Internet] [Thesis]. Trinity College Dublin; 2019. [cited 2021 Jan 21]. Available from: http://hdl.handle.net/2262/88800.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

ELMAGHRAWY KM. Analysis of the oral bacteriome and mycobiome in children with inflammatory bowel disease compared to healthy children by 16S and ITS2 profiling. [Thesis]. Trinity College Dublin; 2019. Available from: http://hdl.handle.net/2262/88800

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

		in
And / Or
		in
And / Or
		in
And / Or
		in

Open Access Theses and Dissertations