Quince Christopher

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Quince
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Christopher
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  • Article
    DESMAN : a new tool for de novo extraction of strains from metagenomes
    (BioMed Central, 2017-09-21) Quince, Christopher ; Delmont, Tom O. ; Raguideau, Sébastien ; Alneberg, Johannes ; Darling, Aaron ; Collins, Gavin ; Eren, A. Murat
    We introduce DESMAN for De novo Extraction of Strains from Metagenomes. Large multi-sample metagenomes are being generated but strain variation results in fragmentary co-assemblies. Current algorithms can bin contigs into metagenome-assembled genomes but are unable to resolve strain-level variation. DESMAN identifies variants in core genes and uses co-occurrence across samples to link variants into haplotypes and abundance profiles. These are then searched for against non-core genes to determine the accessory genome of each strain. We validated DESMAN on a complex 50-species 210-genome 96-sample synthetic mock data set and then applied it to the Tara Oceans microbiome.
  • Article
    Anvi’o : an advanced analysis and visualization platform for ‘omics data
    (PeerJ, 2015-10-08) Eren, A. Murat ; Esen, Ozcan C. ; Quince, Christopher ; Vineis, Joseph H. ; Morrison, Hilary G. ; Sogin, Mitchell L. ; Delmont, Tom O.
    Advances in high-throughput sequencing and ‘omics technologies are revolutionizing studies of naturally occurring microbial communities. Comprehensive investigations of microbial lifestyles require the ability to interactively organize and visualize genetic information and to incorporate subtle differences that enable greater resolution of complex data. Here we introduce anvi’o, an advanced analysis and visualization platform that offers automated and human-guided characterization of microbial genomes in metagenomic assemblies, with interactive interfaces that can link ‘omics data from multiple sources into a single, intuitive display. Its extensible visualization approach distills multiple dimensions of information about each contig, offering a dynamic and unified work environment for data exploration, manipulation, and reporting. Using anvi’o, we re-analyzed publicly available datasets and explored temporal genomic changes within naturally occurring microbial populations through de novo characterization of single nucleotide variations, and linked cultivar and single-cell genomes with metagenomic and metatranscriptomic data. Anvi’o is an open-source platform that empowers researchers without extensive bioinformatics skills to perform and communicate in-depth analyses on large ‘omics datasets.
  • Article
    Extensive modulation of the fecal metagenome in children With Crohn’s disease during exclusive enteral nutrition
    (Nature Publishing Group, 2015-11-03) Quince, Christopher ; Ijaz, Umer Zeeshan ; Loman, Nick ; Eren, A. Murat ; Saulnier, Delphine ; Russell, Julie ; Haig, Sarah J. ; Calus, Szymon T. ; Quick, Joshua ; Barclay, Andrew H. ; Bertz, Martin ; Blaut, Michael ; Hansen, Richard ; McGrogan, Paraic ; Russell, Richard K. ; Edwards, Christine A. ; Gerasimidis, Konstantinos
    Exploring associations between the gut microbiota and colonic inflammation and assessing sequential changes during exclusive enteral nutrition (EEN) may offer clues into the microbial origins of Crohn’s disease (CD). Fecal samples (n=117) were collected from 23 CD and 21 healthy children. From CD children fecal samples were collected before, during EEN, and when patients returned to their habitual diets. Microbiota composition and functional capacity were characterized using sequencing of the 16S rRNA gene and shotgun metagenomics. Microbial diversity was lower in CD than controls before EEN (P=0.006); differences were observed in 36 genera, 141 operational taxonomic units (OTUs), and 44 oligotypes. During EEN, the microbial diversity of CD children further decreased, and the community structure became even more dissimilar than that of controls. Every 10 days on EEN, 0.6 genus diversity equivalents were lost; 34 genera decreased and one increased during EEN. Fecal calprotectin correlated with 35 OTUs, 14 of which accounted for 78% of its variation. OTUs that correlated positively or negatively with calprotectin decreased during EEN. The microbiota of CD patients had a broader functional capacity than healthy controls, but diversity decreased with EEN. Genes involved in membrane transport, sulfur reduction, and nutrient biosynthesis differed between patients and controls. The abundance of genes involved in biotin (P=0.005) and thiamine biosynthesis decreased (P=0.017), whereas those involved in spermidine/putrescine biosynthesis (P=0.031), or the shikimate pathway (P=0.058), increased during EEN. Disease improvement following treatment with EEN is associated with extensive modulation of the gut microbiome.
  • Article
    Metabolic independence drives gut microbial colonization and resilience in health and disease
    (BioMed Central, 2023-04-17) Watson, Andrea R. ; Füssel, Jessika ; Veseli, Iva ; DeLongchamp, Johanna Zaal ; Silva, Marisela ; Trigodet, Florian ; Lolans, Karen ; Shaiber, Alon ; Fogarty, Emily ; Runde, Joseph M. ; Quince, Christopher ; Yu, Michael K. ; Söylev, Arda ; Morrison, Hilary G. ; Lee, Sonny T. M. ; Kao, Dina ; Rubin, David T. ; Jabri, Bana ; Louie, Thomas ; Eren, A. Murat
    Changes in microbial community composition as a function of human health and disease states have sparked remarkable interest in the human gut microbiome. However, establishing reproducible insights into the determinants of microbial succession in disease has been a formidable challenge.Here we use fecal microbiota transplantation (FMT) as an in natura experimental model to investigate the association between metabolic independence and resilience in stressed gut environments. Our genome-resolved metagenomics survey suggests that FMT serves as an environmental filter that favors populations with higher metabolic independence, the genomes of which encode complete metabolic modules to synthesize critical metabolites, including amino acids, nucleotides, and vitamins. Interestingly, we observe higher completion of the same biosynthetic pathways in microbes enriched in IBD patients.These observations suggest a general mechanism that underlies changes in diversity in perturbed gut environments and reveal taxon-independent markers of "dysbiosis" that may explain why widespread yet typically low-abundance members of healthy gut microbiomes can dominate under inflammatory conditions without any causal association with disease.