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Subject = Virome;
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Displaying Results 1 - 9 of 9 on page 1 of 1
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Choice of assembly software has a critical impact on virome characterisation
(2019)
Sutton, Thomas D S; Clooney, Adam G; Ryan, Feargal J; Ross, R Paul; Hill, Colin
Choice of assembly software has a critical impact on virome characterisation
(2019)
Sutton, Thomas D S; Clooney, Adam G; Ryan, Feargal J; Ross, R Paul; Hill, Colin
Abstract:
Background The viral component of microbial communities plays a vital role in driving bacterial diversity, facilitating nutrient turnover and shaping community composition. Despite their importance, the vast majority of viral sequences are poorly annotated and share little or no homology to reference databases. As a result, investigation of the viral metagenome (virome) relies heavily on de novo assembly of short sequencing reads to recover compositional and functional information. Metagenomic assembly is particularly challenging for virome data, often resulting in fragmented assemblies and poor recovery of viral community members. Despite the essential role of assembly in virome analysis and difficulties posed by these data, current assembly comparisons have been limited to subsections of virome studies or bacterial datasets. Design This study presents the most comprehensive virome assembly comparison to ...
http://hdl.handle.net/11019/1663
Marked
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Choice of assembly software has a critical impact on virome characterisation
(2019)
Sutton, Thomas D. S.; Clooney, Adam G.; Ryan, Feargal J.; Ross, R. Paul; Hill, Colin
Choice of assembly software has a critical impact on virome characterisation
(2019)
Sutton, Thomas D. S.; Clooney, Adam G.; Ryan, Feargal J.; Ross, R. Paul; Hill, Colin
Abstract:
Background: The viral component of microbial communities plays a vital role in driving bacterial diversity, facilitating nutrient turnover and shaping community composition. Despite their importance, the vast majority of viral sequences are poorly annotated and share little or no homology to reference databases. As a result, investigation of the viral metagenome (virome) relies heavily on de novo assembly of short sequencing reads to recover compositional and functional information. Metagenomic assembly is particularly challenging for virome data, often resulting in fragmented assemblies and poor recovery of viral community members. Despite the essential role of assembly in virome analysis and difficulties posed by these data, current assembly comparisons have been limited to subsections of virome studies or bacterial datasets. Design: This study presents the most comprehensive virome assembly comparison to date, featuring 16 metagenomic assembly approaches which have featured in hu...
http://hdl.handle.net/10468/9221
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Comparative compositional analysis of the gut microbiome in animal models of addiction and stress
(2018)
Peterson, Veronica L.
Comparative compositional analysis of the gut microbiome in animal models of addiction and stress
(2018)
Peterson, Veronica L.
Abstract:
Intro: The microbiome-gut-brain axis (MGBA) has been shown to be instrumental to brain and behaviour, including psychological disorders affecting stress, depression, and anxiety. Many of the aforementioned disorders are comorbid with substance abuse disorders, and on a larger scale with addiction. In this body of work, we seek to characterize addiction-related phenotypes in the microbiome and correlate with measures of addiction-related behaviours, along with changes in the virome following chronic social stress. Aims: We first examined if vapor administration of ethanol is capable of altering the microbiome and to assess if substances of abuse, such as ethanol, can alter the microbiome outside of oral/gastrointestinal administration. To characterize addictive phenotypes behavioural measures of impulsivity, reward learning, and dopaminergic response to novelty were used. Methods: All studies were carried out in rodents. Following behavioural testing, gut microbiota samples were anal...
http://hdl.handle.net/10468/7941
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Gut bacteriophage: Current understanding and challenges
(2019)
Sutton, Thomas D. S.; Hill, Colin
Gut bacteriophage: Current understanding and challenges
(2019)
Sutton, Thomas D. S.; Hill, Colin
Abstract:
The gut microbiome is widely accepted to have a significant impact on human health yet, despite years of research on this complex ecosystem, the contributions of different forces driving microbial population structure remain to be fully elucidated. The viral component of the human gut microbiome is dominated by bacteriophage, which are known to play crucial roles in shaping microbial composition, driving bacterial diversity, and facilitating horizontal gene transfer. Bacteriophage are also one of the most poorly understood components of the human gut microbiome, with the vast majority of viral sequences sharing little to no homology to reference databases. If we are to understand the dynamics of bacteriophage populations, their interaction with the human microbiome and ultimately their influence on human health, we will depend heavily on sequence based approaches and in silico tools. This is complicated by the fact that, as with any research field in its infancy, methods of analyses...
http://hdl.handle.net/10468/9381
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Profiling bacteriophages of the human gut and exploring their application in food and medicine
(2020)
Lewis, Rhea
Profiling bacteriophages of the human gut and exploring their application in food and medicine
(2020)
Lewis, Rhea
Abstract:
Bacteriophages (phages) are viruses which infect bacteria and are ubiquitous in nature. Phage research has undergone periods of interest and indifference, but are now common tools with some suggesting that they will become important as antimicrobial agents in food and in medicine. The first chapter of this thesis is in two parts. Chapter 1a reviews the discovery, basic biology, and applications of phages. They have varied uses such as in models for predator and prey dynamics studies, as a last resort in the fight against antibiotic resistant infections, in the treatment of illness and disease by faecal transplant, in food safety, in phage display and the expression of antibodies and peptides, and in metagenomics studies to understand human health and disease. In the chapters that follow four of these applications were investigated. Chapter 1b addresses the barriers that should be taken into account in order to use phages successfully in food and feed. These issues can also arise whe...
http://hdl.handle.net/10468/10466
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Reproducible protocols for metagenomic analysis of human faecal phageomes
(2018)
Shkoporov, Andrey N; Ryan, Feargal J; Draper, Lorraine A.; Forde, Amanda; Stockdale, St...
Reproducible protocols for metagenomic analysis of human faecal phageomes
(2018)
Shkoporov, Andrey N; Ryan, Feargal J; Draper, Lorraine A.; Forde, Amanda; Stockdale, Stephen R.; Daly, Karen M.; McDonnell, Siobhan A.; Nolan, James A.; Sutton, Thomas D S; Dalmasso, Marion; McCann, Angela; Ross, R Paul; Hill, Colin
Abstract:
All sequence data used in the analyses were deposited in the Sequence read Archive (SRA) (http://www.ncbi.nlm.nih.gov/sra) under BioProject PRJNA407341. Sample IDs, meta data and corresponding accession numbers are summarised in Additional file 2: Table S2. All raw count tables, 16S taxonomic assignments, BLAST top hits for viral contigs and R code used for the analysis are available at (https://figshare.com/s/71163558b4f78e3e7ed6).
Background Recent studies have demonstrated that the human gut is populated by complex, highly individual and stable communities of viruses, the majority of which are bacteriophages. While disease-specific alterations in the gut phageome have been observed in IBD, AIDS and acute malnutrition, the human gut phageome remains poorly characterised. One important obstacle in metagenomic studies of the human gut phageome is a high level of discrepancy between results obtained by different research groups. This is often due to the use of dif...
http://hdl.handle.net/11019/1542
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The first microbial colonizers of the human gut: composition, activities, and health implications of the infant gut microbiota
(2017)
Milani, Christian; Duranti, Sabrina; Bottacini, Francesca; Casey, Eoghan; Turroni, Fran...
The first microbial colonizers of the human gut: composition, activities, and health implications of the infant gut microbiota
(2017)
Milani, Christian; Duranti, Sabrina; Bottacini, Francesca; Casey, Eoghan; Turroni, Francesca; Mahony, Jennifer; Belzer, Clara; Delgado Palacio, Susana; Arboleya, Silvia; Mancabelli, Leonardo; Lugli, Gabriele A.; Miguel Rodriguez, Juan; Bode, Lars; de Vos, Willem M.; Gueimonde, Miguel; Margolles, Abelardo; van Sinderen, Douwe; Ventura, Marco
Abstract:
The human gut microbiota is engaged in multiple interactions affecting host health during the host's entire life span. Microbes colonize the neonatal gut immediately following birth. The establishment and interactive development of this early gut microbiota are believed to be (at least partially) driven and modulated by specific compounds present in human milk. It has been shown that certain genomes of infant gut commensals, in particular those of bifidobacterial species, are genetically adapted to utilize specific glycans of this human secretory fluid, thus representing a very intriguing example of host-microbe coevolution, where both partners are believed to benefit. In recent years, various metagenomic studies have tried to dissect the composition and functionality of the infant gut microbiome and to explore the distribution across the different ecological niches of the infant gut biogeography of the corresponding microbial consortia, including those corresponding to bacteri...
http://hdl.handle.net/10468/6878
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Tracing mother-infant transmission of bacteriophages by means of a novel analytical tool for shotgun metagenomic datasets: METAnnotatorX
(2018)
Milani, Christian; Caballero-Fonseca, F.; Lugli, Gabriele Andrea; Moore, Rebecca; Kaczo...
Tracing mother-infant transmission of bacteriophages by means of a novel analytical tool for shotgun metagenomic datasets: METAnnotatorX
(2018)
Milani, Christian; Caballero-Fonseca, F.; Lugli, Gabriele Andrea; Moore, Rebecca; Kaczorowska, Joanna; Feehily, Conor; Mangifesta, Marta; Mancabelli, Leonardo; Duranti, Sabrina; Turroni, Francesca; Bottacini, Francesca; Mahony, Jennifer; Cotter, Paul D.; McAuliffe, Fionnuala M.; van Sinderen, Douwe; Ventura, Marco
Abstract:
Background: Despite the relevance of viral populations, our knowledge of (bacterio) phage populations, i.e., the phageome, suffers from the absence of a “gold standard” protocol for viral DNA extraction with associated in silico sequence processing analyses. To overcome this apparent hiatus, we present here a comprehensive performance evaluation of various protocols and propose an optimized pipeline that covers DNA extraction, sequencing, and bioinformatic analysis of phageome data. Results: Five widely used protocols for viral DNA extraction from fecal samples were tested for their performance in removal of non-viral DNA. Moreover, we developed a novel bioinformatic platform, METAnnotatorX, for metagenomic dataset analysis. This in silico tool facilitates a range of read- and assembly-based analyses, including taxonomic profiling using an iterative multi-database pipeline, classification of contigs at genus and species level, as well as functional characterizations of reads and ass...
http://hdl.handle.net/10468/9205
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Viromes of one year old infants reveal the impact of birth mode on microbiome diversity
(2018)
McCann, Angela; Ryan, Feargal J.; Stockdale, Stephen R.; Dalmasso, Marion; Blake, Tony;...
Viromes of one year old infants reveal the impact of birth mode on microbiome diversity
(2018)
McCann, Angela; Ryan, Feargal J.; Stockdale, Stephen R.; Dalmasso, Marion; Blake, Tony; Ryan, C. Anthony; Stanton, Catherine; Mills, Susan; Ross, R. Paul; Hill, Colin
Abstract:
Establishing a diverse gut microbiota after birth is being increasingly recognised as important for preventing illnesses later in life. It is well established that bacterial diversity rapidly increases post-partum; however, few studies have examined the infant gut virome/phageorne during this developmental period. We performed a metagenornic analysis of 20 infant faecal viromes at one year of age to determine whether spontaneous vaginal delivery (SVD) or caesarean section (CS) influenced viral composition. We find that birth mode results in distinctly different viral communities, with SVD infants having greater viral and bacteriophage diversity. We demonstrate that CrAssp age is acquired early in life, both in this cohort and two others, althoughno difference in birth mode is detected. A previous study has shown that bacterial OTU's (operational taxonomic units) identified in the same infants could not discriminate between birth mode at 12 months of age. Therefore, our results ...
http://hdl.handle.net/10468/6871
Displaying Results 1 - 9 of 9 on page 1 of 1
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Institution
Teagasc (2)
University College Cork (7)
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Doctoral thesis (2)
Journal article (4)
Review (1)
Other (2)
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Peer-reviewed (7)
Non-peer-reviewed (2)
Year
2020 (1)
2019 (3)
2018 (4)
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