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  1. Article: The Microbiome and Big Data.

    Navas-Molina, Jose A / Hyde, Embriette R / Sanders, Jon / Knight, Rob

    Current opinion in systems biology

    2017  Volume 4, Page(s) 92–96

    Abstract: Microbiome datasets have expanded rapidly in recent years. Advances in DNA sequencing, as well as the rise of shotgun metagenomics and metabolomics, are producing datasets that exceed the ability of researchers to analyze them on their personal computers. ...

    Abstract Microbiome datasets have expanded rapidly in recent years. Advances in DNA sequencing, as well as the rise of shotgun metagenomics and metabolomics, are producing datasets that exceed the ability of researchers to analyze them on their personal computers. Here we describe what Big Data is in the context of microbiome research, how this data can be transformed into knowledge about microbes and their functions in their environments, and how the knowledge can be applied to move microbiome research forward. In particular, the development of new high-resolution tools to assess strain-level variability (moving away from OTUs), the advent of cloud computing and centralized analysis resources such as Qiita (for sequences) and GNPS (for mass spectrometry), and better methods for curating and describing "metadata" (contextual information about the sequence or chemical information) are rapidly assisting the use of microbiome data in fields ranging from human health to environmental studies.
    Language English
    Publishing date 2017-07-11
    Publishing country England
    Document type Journal Article
    ISSN 2452-3100
    ISSN 2452-3100
    DOI 10.1016/j.coisb.2017.07.003
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article: Correcting for Microbial Blooms in Fecal Samples during Room-Temperature Shipping.

    Amir, Amnon / McDonald, Daniel / Navas-Molina, Jose A / Debelius, Justine / Morton, James T / Hyde, Embriette / Robbins-Pianka, Adam / Knight, Rob

    mSystems

    2017  Volume 2, Issue 2

    Abstract: The use of sterile swabs is a convenient and common way to collect microbiome samples, and many studies have shown that the effects of room-temperature storage are smaller than physiologically relevant differences between subjects. However, several ... ...

    Abstract The use of sterile swabs is a convenient and common way to collect microbiome samples, and many studies have shown that the effects of room-temperature storage are smaller than physiologically relevant differences between subjects. However, several bacterial taxa, notably members of the class
    Language English
    Publishing date 2017-03-07
    Publishing country United States
    Document type Journal Article
    ISSN 2379-5077
    ISSN 2379-5077
    DOI 10.1128/mSystems.00199-16
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Bringing the Dynamic Microbiome to Life with Animations.

    Vázquez-Baeza, Yoshiki / Gonzalez, Antonio / Smarr, Larry / McDonald, Daniel / Morton, James T / Navas-Molina, Jose A / Knight, Rob

    Cell host & microbe

    2017  Volume 21, Issue 1, Page(s) 7–10

    Abstract: Our bodies and natural environment contain complex microbial communities, colloquially termed microbiomes. We previously created a web-based application, EMPeror, for visualizing ordinations derived from comparisons of these microbiome communities. We ... ...

    Abstract Our bodies and natural environment contain complex microbial communities, colloquially termed microbiomes. We previously created a web-based application, EMPeror, for visualizing ordinations derived from comparisons of these microbiome communities. We have now improved EMPeror to create interactive animations that connect successive samples to highlight patterns over time.
    MeSH term(s) Clostridium difficile/genetics ; Enterocolitis, Pseudomembranous/microbiology ; Enterocolitis, Pseudomembranous/transmission ; Humans ; Internet ; Metagenome/genetics ; Microbiota/genetics
    Language English
    Publishing date 2017-01-17
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2278004-X
    ISSN 1934-6069 ; 1931-3128
    ISSN (online) 1934-6069
    ISSN 1931-3128
    DOI 10.1016/j.chom.2016.12.009
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article: Phylogenetic Placement of Exact Amplicon Sequences Improves Associations with Clinical Information.

    Janssen, Stefan / McDonald, Daniel / Gonzalez, Antonio / Navas-Molina, Jose A / Jiang, Lingjing / Xu, Zhenjiang Zech / Winker, Kevin / Kado, Deborah M / Orwoll, Eric / Manary, Mark / Mirarab, Siavash / Knight, Rob

    mSystems

    2018  Volume 3, Issue 3

    Abstract: Recent algorithmic advances in amplicon-based microbiome studies enable the inference of exact amplicon sequence fragments. These new methods enable the investigation of sub-operational taxonomic units (sOTU) by removing erroneous sequences. However, ... ...

    Abstract Recent algorithmic advances in amplicon-based microbiome studies enable the inference of exact amplicon sequence fragments. These new methods enable the investigation of sub-operational taxonomic units (sOTU) by removing erroneous sequences. However, short (e.g., 150-nucleotide [nt]) DNA sequence fragments do not contain sufficient phylogenetic signal to reproduce a reasonable tree, introducing a barrier in the utilization of critical phylogenetically aware metrics such as Faith's PD or UniFrac. Although fragment insertion methods do exist, those methods have not been tested for sOTUs from high-throughput amplicon studies in insertions against a broad reference phylogeny. We benchmarked the SATé-enabled phylogenetic placement (SEPP) technique explicitly against 16S V4 sequence fragments and showed that it outperforms the conceptually problematic but often-used practice of reconstructing
    Language English
    Publishing date 2018-04-17
    Publishing country United States
    Document type Journal Article
    ISSN 2379-5077
    ISSN 2379-5077
    DOI 10.1128/mSystems.00021-18
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article: Deblur Rapidly Resolves Single-Nucleotide Community Sequence Patterns.

    Amir, Amnon / McDonald, Daniel / Navas-Molina, Jose A / Kopylova, Evguenia / Morton, James T / Zech Xu, Zhenjiang / Kightley, Eric P / Thompson, Luke R / Hyde, Embriette R / Gonzalez, Antonio / Knight, Rob

    mSystems

    2017  Volume 2, Issue 2

    Abstract: High-throughput sequencing of 16S ribosomal RNA gene amplicons has facilitated understanding of complex microbial communities, but the inherent noise in PCR and DNA sequencing limits differentiation of closely related bacteria. Although many scientific ... ...

    Abstract High-throughput sequencing of 16S ribosomal RNA gene amplicons has facilitated understanding of complex microbial communities, but the inherent noise in PCR and DNA sequencing limits differentiation of closely related bacteria. Although many scientific questions can be addressed with broad taxonomic profiles, clinical, food safety, and some ecological applications require higher specificity. Here we introduce a novel sub-operational-taxonomic-unit (sOTU) approach, Deblur, that uses error profiles to obtain putative error-free sequences from Illumina MiSeq and HiSeq sequencing platforms. Deblur substantially reduces computational demands relative to similar sOTU methods and does so with similar or better sensitivity and specificity. Using simulations, mock mixtures, and real data sets, we detected closely related bacterial sequences with single nucleotide differences while removing false positives and maintaining stability in detection, suggesting that Deblur is limited only by read length and diversity within the amplicon sequences. Because Deblur operates on a per-sample level, it scales to modern data sets and meta-analyses. To highlight Deblur's ability to integrate data sets, we include an interactive exploration of its application to multiple distinct sequencing rounds of the American Gut Project. Deblur is open source under the Berkeley Software Distribution (BSD) license, easily installable, and downloadable from https://github.com/biocore/deblur.
    Language English
    Publishing date 2017-03-07
    Publishing country United States
    Document type Journal Article
    ISSN 2379-5077
    ISSN 2379-5077
    DOI 10.1128/mSystems.00191-16
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article: The Oral and Skin Microbiomes of Captive Komodo Dragons Are Significantly Shared with Their Habitat.

    Hyde, Embriette R / Navas-Molina, Jose A / Song, Se Jin / Kueneman, Jordan G / Ackermann, Gail / Cardona, Cesar / Humphrey, Gregory / Boyer, Don / Weaver, Tom / Mendelson, Joseph R / McKenzie, Valerie J / Gilbert, Jack A / Knight, Rob

    mSystems

    2016  Volume 1, Issue 4

    Abstract: Examining the way in which animals, including those in captivity, interact with their environment is extremely important for studying ecological processes and developing sophisticated animal husbandry. Here we use the Komodo dragon ( ...

    Abstract Examining the way in which animals, including those in captivity, interact with their environment is extremely important for studying ecological processes and developing sophisticated animal husbandry. Here we use the Komodo dragon (
    Language English
    Publishing date 2016-08-02
    Publishing country United States
    Document type Journal Article
    ISSN 2379-5077
    ISSN 2379-5077
    DOI 10.1128/mSystems.00046-16
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article: Open-Source Sequence Clustering Methods Improve the State Of the Art.

    Kopylova, Evguenia / Navas-Molina, Jose A / Mercier, Céline / Xu, Zhenjiang Zech / Mahé, Frédéric / He, Yan / Zhou, Hong-Wei / Rognes, Torbjørn / Caporaso, J Gregory / Knight, Rob

    mSystems

    2016  Volume 1, Issue 1

    Abstract: Sequence clustering is a common early step in amplicon-based microbial community analysis, when raw sequencing reads are clustered into operational taxonomic units (OTUs) to reduce the run time of subsequent analysis steps. Here, we evaluated the ... ...

    Abstract Sequence clustering is a common early step in amplicon-based microbial community analysis, when raw sequencing reads are clustered into operational taxonomic units (OTUs) to reduce the run time of subsequent analysis steps. Here, we evaluated the performance of recently released state-of-the-art open-source clustering software products, namely, OTUCLUST, Swarm, SUMACLUST, and SortMeRNA, against current principal options (UCLUST and USEARCH) in QIIME, hierarchical clustering methods in mothur, and USEARCH's most recent clustering algorithm, UPARSE. All the latest open-source tools showed promising results, reporting up to 60% fewer spurious OTUs than UCLUST, indicating that the underlying clustering algorithm can vastly reduce the number of these derived OTUs. Furthermore, we observed that stringent quality filtering, such as is done in UPARSE, can cause a significant underestimation of species abundance and diversity, leading to incorrect biological results. Swarm, SUMACLUST, and SortMeRNA have been included in the QIIME 1.9.0 release.
    Language English
    Publishing date 2016-02-09
    Publishing country United States
    Document type Journal Article
    ISSN 2379-5077
    ISSN 2379-5077
    DOI 10.1128/mSystems.00003-15
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article: Balance Trees Reveal Microbial Niche Differentiation.

    Morton, James T / Sanders, Jon / Quinn, Robert A / McDonald, Daniel / Gonzalez, Antonio / Vázquez-Baeza, Yoshiki / Navas-Molina, Jose A / Song, Se Jin / Metcalf, Jessica L / Hyde, Embriette R / Lladser, Manuel / Dorrestein, Pieter C / Knight, Rob

    mSystems

    2017  Volume 2, Issue 1

    Abstract: Advances in sequencing technologies have enabled novel insights into microbial niche differentiation, from analyzing environmental samples to understanding human diseases and informing dietary studies. However, identifying the microbial taxa that ... ...

    Abstract Advances in sequencing technologies have enabled novel insights into microbial niche differentiation, from analyzing environmental samples to understanding human diseases and informing dietary studies. However, identifying the microbial taxa that differentiate these samples can be challenging. These issues stem from the compositional nature of 16S rRNA gene data (or, more generally, taxon or functional gene data); the changes in the relative abundance of one taxon influence the apparent abundances of the others. Here we acknowledge that inferring properties of individual bacteria is a difficult problem and instead introduce the concept of balances to infer meaningful properties of subcommunities, rather than properties of individual species. We show that balances can yield insights about niche differentiation across multiple microbial environments, including soil environments and lung sputum. These techniques have the potential to reshape how we carry out future ecological analyses aimed at revealing differences in relative taxonomic abundances across different samples.
    Language English
    Publishing date 2017-01-17
    Publishing country United States
    Document type Journal Article
    ISSN 2379-5077
    ISSN 2379-5077
    DOI 10.1128/mSystems.00162-16
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article ; Online: Qiita: rapid, web-enabled microbiome meta-analysis.

    Gonzalez, Antonio / Navas-Molina, Jose A / Kosciolek, Tomasz / McDonald, Daniel / Vázquez-Baeza, Yoshiki / Ackermann, Gail / DeReus, Jeff / Janssen, Stefan / Swafford, Austin D / Orchanian, Stephanie B / Sanders, Jon G / Shorenstein, Joshua / Holste, Hannes / Petrus, Semar / Robbins-Pianka, Adam / Brislawn, Colin J / Wang, Mingxun / Rideout, Jai Ram / Bolyen, Evan /
    Dillon, Matthew / Caporaso, J Gregory / Dorrestein, Pieter C / Knight, Rob

    Nature methods

    2018  Volume 15, Issue 10, Page(s) 796–798

    Abstract: Multi-omic insights into microbiome function and composition typically advance one study at a time. However, in order for relationships across studies to be fully understood, data must be aggregated into meta-analyses. This makes it possible to generate ... ...

    Abstract Multi-omic insights into microbiome function and composition typically advance one study at a time. However, in order for relationships across studies to be fully understood, data must be aggregated into meta-analyses. This makes it possible to generate new hypotheses by finding features that are reproducible across biospecimens and data layers. Qiita dramatically accelerates such integration tasks in a web-based microbiome-comparison platform, which we demonstrate with Human Microbiome Project and Integrative Human Microbiome Project (iHMP) data.
    MeSH term(s) Computational Biology/methods ; Humans ; Internet ; Metagenomics ; Microbiota ; Software ; User-Computer Interface
    Language English
    Publishing date 2018-10-01
    Publishing country United States
    Document type Journal Article ; Meta-Analysis ; Research Support, N.I.H., Extramural ; Research Support, U.S. Gov't, Non-P.H.S.
    ZDB-ID 2169522-2
    ISSN 1548-7105 ; 1548-7091
    ISSN (online) 1548-7105
    ISSN 1548-7091
    DOI 10.1038/s41592-018-0141-9
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Article ; Online: Author Correction: Inflammation-induced IgA

    Shalapour, Shabnam / Lin, Xue-Jia / Bastian, Ingmar N / Brain, John / Burt, Alastair D / Aksenov, Alexander A / Vrbanac, Alison F / Li, Weihua / Perkins, Andres / Matsutani, Takaji / Zhong, Zhenyu / Dhar, Debanjan / Navas-Molina, Jose A / Xu, Jun / Loomba, Rohit / Downes, Michael / Yu, Ruth T / Evans, Ronald M / Dorrestein, Pieter C /
    Knight, Rob / Benner, Christopher / Anstee, Quentin M / Karin, Michael

    Nature

    2018  Volume 561, Issue 7721, Page(s) E1

    Abstract: In this Article, the sentence: "After 7 months of HFD, MUP-uPA mice developed ... ...

    Abstract In this Article, the sentence: "After 7 months of HFD, MUP-uPA mice developed HCC
    Language English
    Publishing date 2018-06-11
    Publishing country England
    Document type Journal Article ; Published Erratum
    ZDB-ID 120714-3
    ISSN 1476-4687 ; 0028-0836
    ISSN (online) 1476-4687
    ISSN 0028-0836
    DOI 10.1038/s41586-018-0304-y
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

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    Zs.MG 9: Show issues
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