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  1. Article ; Online: Determination of the Chromatin Openness in Bacterial Genomes.

    Al-Bassam, Mahmoud M / Zengler, Karsten

    Methods in molecular biology (Clifton, N.J.)

    2023  Volume 2611, Page(s) 63–69

    Abstract: The hyperactive Tn5 transposase in the ATAC-seq method has been widely used to determine the open DNA regions and understand the overall epigenomic regulation in the chromatins of eukaryotic cells. Here, we describe POP-seq (Prokaryotic chromatin ... ...

    Abstract The hyperactive Tn5 transposase in the ATAC-seq method has been widely used to determine the open DNA regions and understand the overall epigenomic regulation in the chromatins of eukaryotic cells. Here, we describe POP-seq (Prokaryotic chromatin Openness Profiling sequencing), an adaptation of the ATAC-seq method, to interrogate changes in the openness of prokaryotic nucleoids.
    MeSH term(s) Chromatin ; Sequence Analysis, DNA/methods ; High-Throughput Nucleotide Sequencing/methods ; DNA ; Genome, Bacterial
    Chemical Substances Chromatin ; DNA (9007-49-2)
    Language English
    Publishing date 2023-02-15
    Publishing country United States
    Document type Journal Article
    ISSN 1940-6029
    ISSN (online) 1940-6029
    DOI 10.1007/978-1-0716-2899-7_5
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  2. Article ; Online: Genome-scale metabolic modeling of the human gut bacterium Bacteroides fragilis strain 638R.

    Neal, Maxwell / Thiruppathy, Deepan / Zengler, Karsten

    PLoS computational biology

    2023  Volume 19, Issue 10, Page(s) e1011594

    Abstract: Bacteroides fragilis is a universal member of the dominant commensal gut phylum Bacteroidetes. Its fermentation products and abundance have been linked to obesity, inflammatory bowel disease, and other disorders through its effects on host metabolic ... ...

    Abstract Bacteroides fragilis is a universal member of the dominant commensal gut phylum Bacteroidetes. Its fermentation products and abundance have been linked to obesity, inflammatory bowel disease, and other disorders through its effects on host metabolic regulation and the immune system. As of yet, there has been no curated systems-level characterization of B. fragilis' metabolism that provides a comprehensive analysis of the link between human diet and B. fragilis' metabolic products. To address this, we developed a genome-scale metabolic model of B. fragilis strain 638R. The model iMN674 contains 1,634 reactions, 1,362 metabolites, three compartments, and reflects the strain's ability to utilize 142 metabolites. Predictions made with this model include its growth rate and efficiency on these substrates, the amounts of each fermentation product it produces under different conditions, and gene essentiality for each biomass component. The model highlights and resolves gaps in knowledge of B. fragilis' carbohydrate metabolism and its corresponding transport proteins. This high quality model provides the basis for rational prediction of B. fragilis' metabolic interactions with its environment and its host.
    MeSH term(s) Humans ; Bacteroides fragilis/genetics ; Bacteroides fragilis/metabolism ; Carrier Proteins/metabolism
    Chemical Substances Carrier Proteins
    Language English
    Publishing date 2023-10-30
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2193340-6
    ISSN 1553-7358 ; 1553-734X
    ISSN (online) 1553-7358
    ISSN 1553-734X
    DOI 10.1371/journal.pcbi.1011594
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  3. Article ; Online: Linking anaerobic gut bacteria and cardiovascular disease.

    Coker, Joanna / Zaramela, Livia S / Zengler, Karsten

    Nature microbiology

    2021  Volume 7, Issue 1, Page(s) 14–15

    MeSH term(s) Anaerobiosis ; Bacteria, Anaerobic ; Cardiovascular Diseases ; Gastrointestinal Microbiome ; Humans
    Language English
    Publishing date 2021-12-23
    Publishing country England
    Document type Journal Article ; Comment
    ISSN 2058-5276
    ISSN (online) 2058-5276
    DOI 10.1038/s41564-021-01009-4
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  4. Article ; Online: Metabolic engineering of Synechococcus elongatus 7942 for enhanced sucrose biosynthesis.

    Wang, Bo / Zuniga, Cristal / Guarnieri, Michael T / Zengler, Karsten / Betenbaugh, Michael / Young, Jamey D

    Metabolic engineering

    2023  Volume 80, Page(s) 12–24

    Abstract: The capability of cyanobacteria to produce sucrose from ... ...

    Abstract The capability of cyanobacteria to produce sucrose from CO
    MeSH term(s) Metabolic Engineering ; Sodium Chloride/metabolism ; Carbohydrate Metabolism ; Synechococcus/genetics ; Synechococcus/metabolism ; Sucrose/metabolism ; Photosynthesis
    Chemical Substances Sodium Chloride (451W47IQ8X) ; Sucrose (57-50-1)
    Language English
    Publishing date 2023-09-09
    Publishing country Belgium
    Document type Journal Article
    ZDB-ID 1470383-x
    ISSN 1096-7184 ; 1096-7176
    ISSN (online) 1096-7184
    ISSN 1096-7176
    DOI 10.1016/j.ymben.2023.09.002
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    In stock of ZB MED Cologne/Königswinter

    Zs.A 6288: Show issues Location:
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    bis Jg. 2021: Bestellungen von Artikeln über das Online-Bestellformular
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  5. Article ; Online: Biocontrol in built environments to reduce pathogen exposure and infection risk.

    Gottel, Neil R / Hill, Megan S / Neal, Maxwell J / Allard, Sarah M / Zengler, Karsten / Gilbert, Jack A

    The ISME journal

    2024  Volume 18, Issue 1

    Abstract: The microbiome of the built environment comprises bacterial, archaeal, fungal, and viral communities associated with human-made structures. Even though most of these microbes are benign, antibiotic-resistant pathogens can colonize and emerge indoors, ... ...

    Abstract The microbiome of the built environment comprises bacterial, archaeal, fungal, and viral communities associated with human-made structures. Even though most of these microbes are benign, antibiotic-resistant pathogens can colonize and emerge indoors, creating infection risk through surface transmission or inhalation. Several studies have catalogued the microbial composition and ecology in different built environment types. These have informed in vitro studies that seek to replicate the physicochemical features that promote pathogenic survival and transmission, ultimately facilitating the development and validation of intervention techniques used to reduce pathogen accumulation. Such interventions include using Bacillus-based cleaning products on surfaces or integrating bacilli into printable materials. Though this work is in its infancy, early research suggests the potential to use microbial biocontrol to reduce hospital- and home-acquired multidrug-resistant infections. Although these techniques hold promise, there is an urgent need to better understand the microbial ecology of built environments and to determine how these biocontrol solutions alter species interactions. This review covers our current understanding of microbial ecology of the built environment and proposes strategies to translate that knowledge into effective biocontrol of antibiotic-resistant pathogens.
    MeSH term(s) Humans ; Microbiota ; Bacteria/genetics ; Bacillus ; Anti-Bacterial Agents ; Built Environment
    Chemical Substances Anti-Bacterial Agents
    Language English
    Publishing date 2024-02-15
    Publishing country England
    Document type Review ; Journal Article
    ZDB-ID 2406536-5
    ISSN 1751-7370 ; 1751-7362
    ISSN (online) 1751-7370
    ISSN 1751-7362
    DOI 10.1093/ismejo/wrad024
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    In stock of ZB MED Bonn / Germany

    Z 7773: Show issues

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  6. Article: Guild and Niche Determination Enable Targeted Alteration of the Microbiome.

    Moyne, Oriane / Al-Bassam, Mahmoud / Lieng, Chloe / Thiruppathy, Deepan / Norton, Grant J / Kumar, Manish / Haddad, Eli / Zaramela, Livia S / Zengler, Karsten

    bioRxiv : the preprint server for biology

    2023  

    Abstract: Microbiome science has greatly contributed to our understanding of microbial life and its essential roles for the environment and human ... ...

    Abstract Microbiome science has greatly contributed to our understanding of microbial life and its essential roles for the environment and human health
    Language English
    Publishing date 2023-05-11
    Publishing country United States
    Document type Preprint
    DOI 10.1101/2023.05.11.540389
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  7. Article ; Online: The social network of microorganisms - how auxotrophies shape complex communities.

    Zengler, Karsten / Zaramela, Livia S

    Nature reviews. Microbiology

    2018  Volume 16, Issue 6, Page(s) 383–390

    Abstract: Microorganisms engage in complex interactions with other organisms and their environment. Recent studies have shown that these interactions are not limited to the exchange of electron donors. Most microorganisms are auxotrophs, thus relying on external ... ...

    Abstract Microorganisms engage in complex interactions with other organisms and their environment. Recent studies have shown that these interactions are not limited to the exchange of electron donors. Most microorganisms are auxotrophs, thus relying on external nutrients for growth, including the exchange of amino acids and vitamins. Currently, we lack a deeper understanding of auxotrophies in microorganisms and how nutrient requirements differ between different strains and different environments. In this Opinion article, we describe how the study of auxotrophies and nutrient requirements among members of complex communities will enable new insights into community composition and assembly. Understanding this complex network over space and time is crucial for developing strategies to interrogate and shape microbial communities.
    MeSH term(s) Bacteria/genetics ; Bacterial Physiological Phenomena ; Computer Simulation ; Genome, Bacterial ; Genomics/methods ; Microbiota/genetics ; Microbiota/physiology ; Models, Biological
    Language English
    Publishing date 2018-03-28
    Publishing country England
    Document type Journal Article ; Research Support, U.S. Gov't, Non-P.H.S. ; Review
    ZDB-ID 2139054-X
    ISSN 1740-1534 ; 1740-1526
    ISSN (online) 1740-1534
    ISSN 1740-1526
    DOI 10.1038/s41579-018-0004-5
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    In stock of ZB MED Cologne/Königswinter

    Zs.A 5865: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
    Jg. 1995 - 2021: Lesesall (2.OG)
    ab Jg. 2022: Lesesaal (EG)
    Zs.MG 74: Show issues

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  8. Article ; Online: Host DNA Depletion in Saliva Samples for Improved Shotgun Metagenomics.

    Marotz, Clarisse / Zuniga, Cristal / Zaramela, Livia / Knight, Rob / Zengler, Karsten

    Methods in molecular biology (Clifton, N.J.)

    2021  Volume 2327, Page(s) 87–92

    Abstract: Host DNA makes up the majority of DNA in a saliva sample. Therefore, shotgun metagenomics can be an inefficient way to evaluate the microbial populations of saliva since often <10% of the sequencing reads are microbial. In this chapter, we describe a ... ...

    Abstract Host DNA makes up the majority of DNA in a saliva sample. Therefore, shotgun metagenomics can be an inefficient way to evaluate the microbial populations of saliva since often <10% of the sequencing reads are microbial. In this chapter, we describe a method to deplete human DNA from fresh or frozen saliva samples, allowing for more efficient shotgun metagenomic sequencing of the salivary microbial community.
    MeSH term(s) DNA/genetics ; Humans ; Metagenome ; Metagenomics ; Microbiota/genetics ; Saliva ; Sequence Analysis, DNA
    Chemical Substances DNA (9007-49-2)
    Language English
    Publishing date 2021-08-19
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ISSN 1940-6029
    ISSN (online) 1940-6029
    DOI 10.1007/978-1-0716-1518-8_6
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  9. Article ; Online: Carbohydrates great and small, from dietary fiber to sialic acids: How glycans influence the gut microbiome and affect human health.

    Coker, Joanna K / Moyne, Oriane / Rodionov, Dmitry A / Zengler, Karsten

    Gut microbes

    2021  Volume 13, Issue 1, Page(s) 1–18

    Abstract: Gut microbiome composition depends heavily upon diet and has strong ties to human health. Dietary carbohydrates shape the gut microbiome by providing a potent nutrient source for particular microbes. This review explores how dietary carbohydrates in ... ...

    Abstract Gut microbiome composition depends heavily upon diet and has strong ties to human health. Dietary carbohydrates shape the gut microbiome by providing a potent nutrient source for particular microbes. This review explores how dietary carbohydrates in general, including individual monosaccharides and complex polysaccharides, influence the gut microbiome with subsequent effects on host health and disease. In particular, the effects of sialic acids, a prominent and influential class of monosaccharides, are discussed. Complex plant carbohydrates, such as dietary fiber, generally promote microbial production of compounds beneficial to the host while preventing degradation of host carbohydrates from colonic mucus. In contrast, simple and easily digestible sugars such as glucose are often associated with adverse effects on health and the microbiome. The monosaccharide class of sialic acids exerts a powerful but nuanced effect on gut microbiota. Sialic acid consumption (in monosaccharide form, or as part of human milk oligosaccharides or certain animal-based foods) drives the growth of organisms with sialic acid metabolism capabilities. Minor chemical modifications of Neu5Ac, the most common form of sialic acid, can alter these effects. All aspects of carbohydrate composition are therefore relevant to consider when designing dietary therapeutic strategies to alter the gut microbiome.
    MeSH term(s) Animals ; Bacteria/classification ; Bacteria/isolation & purification ; Bacteria/metabolism ; Dietary Carbohydrates/metabolism ; Dietary Fiber/metabolism ; Gastrointestinal Microbiome/physiology ; Humans ; Monosaccharides/metabolism ; Mucins/metabolism ; Polysaccharides/metabolism ; Sialic Acids/metabolism
    Chemical Substances Dietary Carbohydrates ; Dietary Fiber ; Monosaccharides ; Mucins ; Polysaccharides ; Sialic Acids
    Language English
    Publishing date 2021-02-21
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, U.S. Gov't, Non-P.H.S. ; Review
    ZDB-ID 2575755-6
    ISSN 1949-0984 ; 1949-0984
    ISSN (online) 1949-0984
    ISSN 1949-0984
    DOI 10.1080/19490976.2020.1869502
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  10. Article: synDNA-a Synthetic DNA Spike-in Method for Absolute Quantification of Shotgun Metagenomic Sequencing.

    Zaramela, Livia S / Tjuanta, Megan / Moyne, Oriane / Neal, Maxwell / Zengler, Karsten

    mSystems

    2022  , Page(s) e0044722

    Abstract: Microbiome studies have the common goal of determining which microbial taxa are present, respond to specific conditions, or promote phenotypic changes in the host. Most of these studies rely on relative abundance measurements to drive conclusions. ... ...

    Abstract Microbiome studies have the common goal of determining which microbial taxa are present, respond to specific conditions, or promote phenotypic changes in the host. Most of these studies rely on relative abundance measurements to drive conclusions. Inherent limitations of relative values are the inability to determine whether an individual taxon is more or less abundant and the magnitude of this change between the two samples. These limitations can be overcome by using absolute abundance quantifications, which can allow for a more complete understanding of community dynamics by measuring variations in total microbial loads. Obtaining absolute abundance measurements is still technically challenging. Here, we developed synthetic DNA (synDNA) spike-ins that enable precise and cost-effective absolute quantification of microbiome data by adding defined amounts of synDNAs to the samples. We designed 10 synDNAs with the following features: 2,000-bp length, variable GC content (26, 36, 46, 56, or 66% GC), and negligible identity to sequences found in the NCBI database. Dilution pools were generated by mixing the 10 synDNAs at different concentrations. Shotgun metagenomic sequencing showed that the pools of synDNAs with different percentages of GC efficiently reproduced the serial dilution, showing high correlation (
    Language English
    Publishing date 2022-11-01
    Publishing country United States
    Document type Journal Article
    ISSN 2379-5077
    ISSN 2379-5077
    DOI 10.1128/msystems.00447-22
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