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The dynamics of the human infant gut microbiome in development and in progression toward type 1 diabetes.

Cell host & microbe

Kostic AD, Gevers D, Siljander H, Vatanen T, Hyötyläinen T, Hämäläinen AM, Peet A, Tillmann V, Pöhö P, Mattila I, Lähdesmäki H, Franzosa EA, Vaarala O, de Goffau M, Harmsen H, Ilonen J, Virtanen SM, Clish CB, Orešič M, Huttenhower C, Knip M, Xavier RJ.
PMID: 25662751
Cell Host Microbe. 2015 Feb 11;17(2):260-73. doi: 10.1016/j.chom.2015.01.001. Epub 2015 Feb 05.

Colonization of the fetal and infant gut microbiome results in dynamic changes in diversity, which can impact disease susceptibility. To examine the relationship between human gut microbiome dynamics throughout infancy and type 1 diabetes (T1D), we examined a cohort...

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Kostic AD, Gevers D, Siljander H, et al. The dynamics of the human infant gut microbiome in development and in progression toward type 1 diabetes. Cell Host Microbe. 2015;17(2):260-73doi: 10.1016/j.chom.2015.01.001.
Kostic, A. D., Gevers, D., Siljander, H., Vatanen, T., Hyötyläinen, T., Hämäläinen, A. M., Peet, A., Tillmann, V., Pöhö, P., Mattila, I., Lähdesmäki, H., Franzosa, E. A., Vaarala, O., de Goffau, M., Harmsen, H., Ilonen, J., Virtanen, S. M., Clish, C. B., Orešič, M., Huttenhower, C., Knip, M., & Xavier, R. J. (2015). The dynamics of the human infant gut microbiome in development and in progression toward type 1 diabetes. Cell host & microbe, 17(2), 260-73. https://doi.org/10.1016/j.chom.2015.01.001
Kostic, Aleksandar D, et al. "The dynamics of the human infant gut microbiome in development and in progression toward type 1 diabetes." Cell host & microbe vol. 17,2 (2015): 260-73. doi: https://doi.org/10.1016/j.chom.2015.01.001
Kostic AD, Gevers D, Siljander H, Vatanen T, Hyötyläinen T, Hämäläinen AM, Peet A, Tillmann V, Pöhö P, Mattila I, Lähdesmäki H, Franzosa EA, Vaarala O, de Goffau M, Harmsen H, Ilonen J, Virtanen SM, Clish CB, Orešič M, Huttenhower C, Knip M, Xavier RJ. The dynamics of the human infant gut microbiome in development and in progression toward type 1 diabetes. Cell Host Microbe. 2015 Feb 11;17(2):260-73. doi: 10.1016/j.chom.2015.01.001. Epub 2015 Feb 05. PMID: 25662751; PMCID: PMC4689191.
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bioBakery: a meta'omic analysis environment.

Bioinformatics (Oxford, England)

McIver LJ, Abu-Ali G, Franzosa EA, Schwager R, Morgan XC, Waldron L, Segata N, Huttenhower C.
PMID: 29194469
Bioinformatics. 2018 Apr 01;34(7):1235-1237. doi: 10.1093/bioinformatics/btx754.

SUMMARY: bioBakery is a meta'omic analysis environment and collection of individual software tools with the capacity to process raw shotgun sequencing data into actionable microbial community feature profiles, summary reports, and publication-ready figures. It includes a collection of pre-configured...

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McIver LJ, Abu-Ali G, Franzosa EA, et al. bioBakery: a meta'omic analysis environment. Bioinformatics. 2018;34(7):1235-1237doi: 10.1093/bioinformatics/btx754.
McIver, L. J., Abu-Ali, G., Franzosa, E. A., Schwager, R., Morgan, X. C., Waldron, L., Segata, N., & Huttenhower, C. (2018). bioBakery: a meta'omic analysis environment. Bioinformatics (Oxford, England), 34(7), 1235-1237. https://doi.org/10.1093/bioinformatics/btx754
McIver, Lauren J, et al. "bioBakery: a meta'omic analysis environment." Bioinformatics (Oxford, England) vol. 34,7 (2018): 1235-1237. doi: https://doi.org/10.1093/bioinformatics/btx754
McIver LJ, Abu-Ali G, Franzosa EA, Schwager R, Morgan XC, Waldron L, Segata N, Huttenhower C. bioBakery: a meta'omic analysis environment. Bioinformatics. 2018 Apr 01;34(7):1235-1237. doi: 10.1093/bioinformatics/btx754. PMID: 29194469; PMCID: PMC6030947.
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Complex host genetics influence the microbiome in inflammatory bowel disease.

Genome medicine

Knights D, Silverberg MS, Weersma RK, Gevers D, Dijkstra G, Huang H, Tyler AD, van Sommeren S, Imhann F, Stempak JM, Huang H, Vangay P, Al-Ghalith GA, Russell C, Sauk J, Knight J, Daly MJ, Huttenhower C, Xavier RJ.
PMID: 25587358
Genome Med. 2014 Dec 02;6(12):107. doi: 10.1186/s13073-014-0107-1. eCollection 2014.

BACKGROUND: Human genetics and host-associated microbial communities have been associated independently with a wide range of chronic diseases. One of the strongest associations in each case is inflammatory bowel disease (IBD), but disease risk cannot be explained fully by...

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Knights D, Silverberg MS, Weersma RK, et al. Complex host genetics influence the microbiome in inflammatory bowel disease. Genome Med. 2014;6(12):107doi: 10.1186/s13073-014-0107-1.
Knights, D., Silverberg, M. S., Weersma, R. K., Gevers, D., Dijkstra, G., Huang, H., Tyler, A. D., van Sommeren, S., Imhann, F., Stempak, J. M., Huang, H., Vangay, P., Al-Ghalith, G. A., Russell, C., Sauk, J., Knight, J., Daly, M. J., Huttenhower, C., & Xavier, R. J. (2014). Complex host genetics influence the microbiome in inflammatory bowel disease. Genome medicine, 6(12), 107. https://doi.org/10.1186/s13073-014-0107-1
Knights, Dan, et al. "Complex host genetics influence the microbiome in inflammatory bowel disease." Genome medicine vol. 6,12 (2014): 107. doi: https://doi.org/10.1186/s13073-014-0107-1
Knights D, Silverberg MS, Weersma RK, Gevers D, Dijkstra G, Huang H, Tyler AD, van Sommeren S, Imhann F, Stempak JM, Huang H, Vangay P, Al-Ghalith GA, Russell C, Sauk J, Knight J, Daly MJ, Huttenhower C, Xavier RJ. Complex host genetics influence the microbiome in inflammatory bowel disease. Genome Med. 2014 Dec 02;6(12):107. doi: 10.1186/s13073-014-0107-1. eCollection 2014. PMID: 25587358; PMCID: PMC4292994.
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HMPDACC: a Human Microbiome Project Multi-omic data resource.

Nucleic acids research

Creasy HH, Felix V, Aluvathingal J, Crabtree J, Ifeonu O, Matsumura J, McCracken C, Nickel L, Orvis J, Schor M, Giglio M, Mahurkar A, White O.
PMID: 33305317
Nucleic Acids Res. 2021 Jan 08;49:D734-D742. doi: 10.1093/nar/gkaa996.

The Human Microbiome Project (HMP) explored microbial communities of the human body in both healthy and disease states. Two phases of the HMP (HMP and iHMP) together generated >48TB of data (public and controlled access) from multiple, varied omics...

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Creasy HH, Felix V, Aluvathingal J, et al. HMPDACC: a Human Microbiome Project Multi-omic data resource. Nucleic Acids Res. 2021;49:D734-D742doi: 10.1093/nar/gkaa996.
Creasy, H. H., Felix, V., Aluvathingal, J., Crabtree, J., Ifeonu, O., Matsumura, J., McCracken, C., Nickel, L., Orvis, J., Schor, M., Giglio, M., Mahurkar, A., & White, O. (2021). HMPDACC: a Human Microbiome Project Multi-omic data resource. Nucleic acids research, 49D734-D742. https://doi.org/10.1093/nar/gkaa996
Creasy, Heather Huot, et al. "HMPDACC: a Human Microbiome Project Multi-omic data resource." Nucleic acids research vol. 49 (2021): D734-D742. doi: https://doi.org/10.1093/nar/gkaa996
Creasy HH, Felix V, Aluvathingal J, Crabtree J, Ifeonu O, Matsumura J, McCracken C, Nickel L, Orvis J, Schor M, Giglio M, Mahurkar A, White O. HMPDACC: a Human Microbiome Project Multi-omic data resource. Nucleic Acids Res. 2021 Jan 08;49:D734-D742. doi: 10.1093/nar/gkaa996. PMID: 33305317; PMCID: PMC7778886.
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Sequencing and beyond: integrating molecular 'omics' for microbial community profiling.

Nature reviews. Microbiology

Franzosa EA, Hsu T, Sirota-Madi A, Shafquat A, Abu-Ali G, Morgan XC, Huttenhower C.
PMID: 25915636
Nat Rev Microbiol. 2015 Jun;13(6):360-72. doi: 10.1038/nrmicro3451. Epub 2015 Apr 27.

High-throughput DNA sequencing has proven invaluable for investigating diverse environmental and host-associated microbial communities. In this Review, we discuss emerging strategies for microbial community analysis that complement and expand traditional metagenomic profiling. These include novel DNA sequencing strategies for...

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Franzosa EA, Hsu T, Sirota-Madi A, et al. Sequencing and beyond: integrating molecular 'omics' for microbial community profiling. Nat Rev Microbiol. 2015;13(6):360-72doi: 10.1038/nrmicro3451.
Franzosa, E. A., Hsu, T., Sirota-Madi, A., Shafquat, A., Abu-Ali, G., Morgan, X. C., & Huttenhower, C. (2015). Sequencing and beyond: integrating molecular 'omics' for microbial community profiling. Nature reviews. Microbiology, 13(6), 360-72. https://doi.org/10.1038/nrmicro3451
Franzosa, Eric A, et al. "Sequencing and beyond: integrating molecular 'omics' for microbial community profiling." Nature reviews. Microbiology vol. 13,6 (2015): 360-72. doi: https://doi.org/10.1038/nrmicro3451
Franzosa EA, Hsu T, Sirota-Madi A, Shafquat A, Abu-Ali G, Morgan XC, Huttenhower C. Sequencing and beyond: integrating molecular 'omics' for microbial community profiling. Nat Rev Microbiol. 2015 Jun;13(6):360-72. doi: 10.1038/nrmicro3451. Epub 2015 Apr 27. PMID: 25915636; PMCID: PMC4800835.
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Ecological Structuring of Temperate Bacteriophages in the Inflammatory Bowel Disease-Affected Gut.

Microorganisms

Nishiyama H, Endo H, Blanc-Mathieu R, Ogata H.
PMID: 33121006
Microorganisms. 2020 Oct 27;8(11). doi: 10.3390/microorganisms8111663.

The aim of this study was to elucidate the ecological structure of the human gut temperate bacteriophage community and its role in inflammatory bowel disease (IBD). Temperate bacteriophages make up a large proportion of the human gut microbiota and...

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Nishiyama H, Endo H, Blanc-Mathieu R, et al. Ecological Structuring of Temperate Bacteriophages in the Inflammatory Bowel Disease-Affected Gut. Microorganisms. 2020;8(11)doi: 10.3390/microorganisms8111663.
Nishiyama, H., Endo, H., Blanc-Mathieu, R., & Ogata, H. (2020). Ecological Structuring of Temperate Bacteriophages in the Inflammatory Bowel Disease-Affected Gut. Microorganisms, 8(11), . https://doi.org/10.3390/microorganisms8111663
Nishiyama, Hiroki, et al. "Ecological Structuring of Temperate Bacteriophages in the Inflammatory Bowel Disease-Affected Gut." Microorganisms vol. 8,11 (2020). doi: https://doi.org/10.3390/microorganisms8111663
Nishiyama H, Endo H, Blanc-Mathieu R, Ogata H. Ecological Structuring of Temperate Bacteriophages in the Inflammatory Bowel Disease-Affected Gut. Microorganisms. 2020 Oct 27;8(11). doi: 10.3390/microorganisms8111663. PMID: 33121006; PMCID: PMC7692956.
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Showing 1 to 6 of 6 entries