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  1. Article ; Online: Engineered bacteria recycle tumor metabolic waste to boost immunotherapy.

    Cubillos-Ruiz, Juan R / Cubillos-Ruiz, Andres

    Cell host & microbe

    2021  Volume 29, Issue 12, Page(s) 1725–1727

    Abstract: A recent study published in Nature by Canale et al. (2021) shows that engineered probiotic bacteria can be used to augment the availability of nutrients required for optimal immune cell function in tumors. This approach enhances anti-tumor immunity and ... ...

    Abstract A recent study published in Nature by Canale et al. (2021) shows that engineered probiotic bacteria can be used to augment the availability of nutrients required for optimal immune cell function in tumors. This approach enhances anti-tumor immunity and improves the efficacy of immunotherapy in mouse models of cancer.
    MeSH term(s) Animals ; Bacteria/genetics ; Bacteria/metabolism ; Disease Models, Animal ; Immunization, Secondary ; Immunotherapy ; Metabolic Engineering ; Mice ; Neoplasms/metabolism ; Nutrients ; Probiotics ; Tumor Microenvironment/immunology
    Language English
    Publishing date 2021-12-09
    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.2021.11.008
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Draft genomes of three closely related low light-adapted Prochlorococcus

    Berta-Thompson, Jessie W. / Thomas, Elaina / Cubillos-Ruiz, Andrés / Hackl, Thomas / Becker, Jamie W. / Coe, Allison / Biller, Steven J. / Berube, Paul M. / Chisholm, Sallie W.

    BMC Genom Data. 2023 Dec., v. 24, no. 1 p.11-11

    2023  

    Abstract: OBJECTIVES: The marine cyanobacterium Prochlorococcus is a critical part of warm ocean ecosystems and a model for studying microbial evolution and ecology. To expand the representation of this organism’s vast wild diversity in sequence collections, we ... ...

    Abstract OBJECTIVES: The marine cyanobacterium Prochlorococcus is a critical part of warm ocean ecosystems and a model for studying microbial evolution and ecology. To expand the representation of this organism’s vast wild diversity in sequence collections, we performed a set of isolation efforts targeting low light-adapted Prochlorococcus. Three genomes resulting from this larger body of work are described here. DATA DESCRIPTION: We present draft-quality Prochlorococcus genomes from enrichment cultures P1344, P1361, and P1363, sampled in the North Pacific. The genomes were built from Illumina paired reads assembled de novo. Supporting datasets of raw reads, assessments, and sequences from co-enriched heterotrophic marine bacteria are also provided. These three genomes represent members of the low light-adapted LLIV Prochlorococcus clade that are closely related, with 99.9% average nucleotide identity between pairs, yet vary in gene content. Expanding the powerful toolkit of Prochlorococcus genomes, these sequences provide an opportunity to study fine-scale variation and microevolutionary processes.
    Keywords Prochlorococcus ; data collection ; ecology ; evolution ; genes ; models
    Language English
    Dates of publication 2023-12
    Size p. 11.
    Publishing place BioMed Central
    Document type Article ; Online
    ISSN 2730-6844
    DOI 10.1186/s12863-022-01103-4
    Database NAL-Catalogue (AGRICOLA)

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  3. Article ; Online: An engineered live biotherapeutic for the prevention of antibiotic-induced dysbiosis.

    Cubillos-Ruiz, Andrés / Alcantar, Miguel A / Donghia, Nina M / Cárdenas, Pablo / Avila-Pacheco, Julian / Collins, James J

    Nature biomedical engineering

    2022  Volume 6, Issue 7, Page(s) 910–921

    Abstract: Antibiotic-induced alterations in the gut microbiota are implicated in many metabolic and inflammatory diseases, increase the risk of secondary infections and contribute to the emergence of antimicrobial resistance. Here we report the design and in vivo ... ...

    Abstract Antibiotic-induced alterations in the gut microbiota are implicated in many metabolic and inflammatory diseases, increase the risk of secondary infections and contribute to the emergence of antimicrobial resistance. Here we report the design and in vivo performance of an engineered strain of Lactococcus lactis that altruistically degrades the widely used broad-spectrum antibiotics β-lactams (which disrupt commensal bacteria in the gut) through the secretion and extracellular assembly of a heterodimeric β-lactamase. The engineered β-lactamase-expression system does not confer β-lactam resistance to the producer cell, and is encoded via a genetically unlinked two-gene biosynthesis strategy that is not susceptible to dissemination by horizontal gene transfer. In a mouse model of parenteral ampicillin treatment, oral supplementation with the engineered live biotherapeutic minimized gut dysbiosis without affecting the ampicillin concentration in serum, precluded the enrichment of antimicrobial resistance genes in the gut microbiome and prevented the loss of colonization resistance against Clostridioides difficile. Engineered live biotherapeutics that safely degrade antibiotics in the gut may represent a suitable strategy for the prevention of dysbiosis and its associated pathologies.
    MeSH term(s) Ampicillin/pharmacology ; Animals ; Anti-Bacterial Agents/pharmacology ; Clostridioides difficile ; Dysbiosis/chemically induced ; Dysbiosis/drug therapy ; Dysbiosis/prevention & control ; Mice ; beta-Lactamases/metabolism
    Chemical Substances Anti-Bacterial Agents ; Ampicillin (7C782967RD) ; beta-Lactamases (EC 3.5.2.6)
    Language English
    Publishing date 2022-04-11
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
    ISSN 2157-846X
    ISSN (online) 2157-846X
    DOI 10.1038/s41551-022-00871-9
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Draft genomes of three closely related low light-adapted Prochlorococcus.

    Berta-Thompson, Jessie W / Thomas, Elaina / Cubillos-Ruiz, Andrés / Hackl, Thomas / Becker, Jamie W / Coe, Allison / Biller, Steven J / Berube, Paul M / Chisholm, Sallie W

    BMC genomic data

    2023  Volume 24, Issue 1, Page(s) 11

    Abstract: Objectives: The marine cyanobacterium Prochlorococcus is a critical part of warm ocean ecosystems and a model for studying microbial evolution and ecology. To expand the representation of this organism's vast wild diversity in sequence collections, we ... ...

    Abstract Objectives: The marine cyanobacterium Prochlorococcus is a critical part of warm ocean ecosystems and a model for studying microbial evolution and ecology. To expand the representation of this organism's vast wild diversity in sequence collections, we performed a set of isolation efforts targeting low light-adapted Prochlorococcus. Three genomes resulting from this larger body of work are described here.
    Data description: We present draft-quality Prochlorococcus genomes from enrichment cultures P1344, P1361, and P1363, sampled in the North Pacific. The genomes were built from Illumina paired reads assembled de novo. Supporting datasets of raw reads, assessments, and sequences from co-enriched heterotrophic marine bacteria are also provided. These three genomes represent members of the low light-adapted LLIV Prochlorococcus clade that are closely related, with 99.9% average nucleotide identity between pairs, yet vary in gene content. Expanding the powerful toolkit of Prochlorococcus genomes, these sequences provide an opportunity to study fine-scale variation and microevolutionary processes.
    MeSH term(s) Phylogeny ; Ecosystem ; Genome, Bacterial ; Prochlorococcus/genetics ; Ecology ; Bacteria/genetics
    Language English
    Publishing date 2023-02-24
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
    ISSN 2730-6844
    ISSN (online) 2730-6844
    DOI 10.1186/s12863-022-01103-4
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: Probiotic strains detect and suppress cholera in mice.

    Mao, Ning / Cubillos-Ruiz, Andres / Cameron, D Ewen / Collins, James J

    Science translational medicine

    2018  Volume 10, Issue 445

    Abstract: Microbiota-modulating interventions are an emerging strategy to promote gastrointestinal homeostasis. Yet, their use in the detection, prevention, and treatment of acute infections remains underexplored. We report the basis of a probiotic-based strategy ... ...

    Abstract Microbiota-modulating interventions are an emerging strategy to promote gastrointestinal homeostasis. Yet, their use in the detection, prevention, and treatment of acute infections remains underexplored. We report the basis of a probiotic-based strategy to promote colonization resistance and point-of-need diagnosis of cholera, an acute diarrheal disease caused by the pathogen
    MeSH term(s) Animals ; Cholera/therapy ; Lactococcus lactis/physiology ; Mice ; Probiotics/therapeutic use ; Quorum Sensing ; Vibrio cholerae/pathogenicity
    Language English
    Publishing date 2018-06-12
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
    ZDB-ID 2518854-9
    ISSN 1946-6242 ; 1946-6234
    ISSN (online) 1946-6242
    ISSN 1946-6234
    DOI 10.1126/scitranslmed.aao2586
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    Zs.A 6941: Show issues Location:
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  6. Article ; Online: Engineering living therapeutics with synthetic biology.

    Cubillos-Ruiz, Andres / Guo, Tingxi / Sokolovska, Anna / Miller, Paul F / Collins, James J / Lu, Timothy K / Lora, Jose M

    Nature reviews. Drug discovery

    2021  Volume 20, Issue 12, Page(s) 941–960

    Abstract: The steadfast advance of the synthetic biology field has enabled scientists to use genetically engineered cells, instead of small molecules or biologics, as the basis for the development of novel therapeutics. Cells endowed with synthetic gene circuits ... ...

    Abstract The steadfast advance of the synthetic biology field has enabled scientists to use genetically engineered cells, instead of small molecules or biologics, as the basis for the development of novel therapeutics. Cells endowed with synthetic gene circuits can control the localization, timing and dosage of therapeutic activities in response to specific disease biomarkers and thus represent a powerful new weapon in the fight against disease. Here, we conceptualize how synthetic biology approaches can be applied to programme living cells with therapeutic functions and discuss the advantages that they offer over conventional therapies in terms of flexibility, specificity and predictability, as well as challenges for their development. We present notable advances in the creation of engineered cells that harbour synthetic gene circuits capable of biological sensing and computation of signals derived from intracellular or extracellular biomarkers. We categorize and describe these developments based on the cell scaffold (human or microbial) and the site at which the engineered cell exerts its therapeutic function within its human host. The design of cell-based therapeutics with synthetic biology is a rapidly growing strategy in medicine that holds great promise for the development of effective treatments for a wide variety of human diseases.
    MeSH term(s) Cell Engineering/methods ; Cell- and Tissue-Based Therapy/trends ; Gene Regulatory Networks ; Genetic Engineering/methods ; Genetic Engineering/mortality ; Humans ; Synthetic Biology/methods ; Synthetic Biology/trends
    Language English
    Publishing date 2021-10-06
    Publishing country England
    Document type Journal Article ; Review
    ZDB-ID 2062954-0
    ISSN 1474-1784 ; 1474-1776
    ISSN (online) 1474-1784
    ISSN 1474-1776
    DOI 10.1038/s41573-021-00285-3
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  7. Article ; Online: Toward a genetic system in the marine cyanobacterium

    Laurenceau, Raphaël / Bliem, Christina / Osburne, Marcia S / Becker, Jamie W / Biller, Steven J / Cubillos-Ruiz, Andres / Chisholm, Sallie W

    Access microbiology

    2020  Volume 2, Issue 4, Page(s) acmi000107

    Abstract: As the smallest and most abundant primary producer in the oceans, the ... ...

    Abstract As the smallest and most abundant primary producer in the oceans, the cyanobacterium
    Language English
    Publishing date 2020-02-19
    Publishing country England
    Document type Journal Article
    ISSN 2516-8290
    ISSN (online) 2516-8290
    DOI 10.1099/acmi.0.000107
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  8. Article ; Online: Discovery of a structural class of antibiotics with explainable deep learning.

    Wong, Felix / Zheng, Erica J / Valeri, Jacqueline A / Donghia, Nina M / Anahtar, Melis N / Omori, Satotaka / Li, Alicia / Cubillos-Ruiz, Andres / Krishnan, Aarti / Jin, Wengong / Manson, Abigail L / Friedrichs, Jens / Helbig, Ralf / Hajian, Behnoush / Fiejtek, Dawid K / Wagner, Florence F / Soutter, Holly H / Earl, Ashlee M / Stokes, Jonathan M /
    Renner, Lars D / Collins, James J

    Nature

    2023  Volume 626, Issue 7997, Page(s) 177–185

    Abstract: The discovery of novel structural classes of antibiotics is urgently needed to address the ongoing antibiotic resistance ... ...

    Abstract The discovery of novel structural classes of antibiotics is urgently needed to address the ongoing antibiotic resistance crisis
    MeSH term(s) Animals ; Humans ; Mice ; Anti-Bacterial Agents/chemistry ; Anti-Bacterial Agents/classification ; Anti-Bacterial Agents/pharmacology ; Anti-Bacterial Agents/toxicity ; Deep Learning ; Methicillin-Resistant Staphylococcus aureus/drug effects ; Microbial Sensitivity Tests ; Staphylococcal Infections/drug therapy ; Staphylococcal Infections/microbiology ; Staphylococcus aureus/drug effects ; Neural Networks, Computer ; Algorithms ; Vancomycin-Resistant Enterococci/drug effects ; Disease Models, Animal ; Skin/drug effects ; Skin/microbiology ; Drug Discovery/methods ; Drug Discovery/trends
    Chemical Substances Anti-Bacterial Agents
    Language English
    Publishing date 2023-12-20
    Publishing country England
    Document type Journal Article
    ZDB-ID 120714-3
    ISSN 1476-4687 ; 0028-0836
    ISSN (online) 1476-4687
    ISSN 0028-0836
    DOI 10.1038/s41586-023-06887-8
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  9. Article ; Online: Analysis of the genetic variation in Mycobacterium tuberculosis strains by multiple genome alignments

    Morales Juan / Cubillos-Ruiz Andrés / Zambrano María

    BMC Research Notes, Vol 1, Iss 1, p

    2008  Volume 110

    Abstract: Abstract Background The recent determination of the complete nucleotide sequence of several Mycobacterium tuberculosis (MTB) genomes allows the use of comparative genomics as a tool for dissecting the nature and consequence of genetic variability within ... ...

    Abstract Abstract Background The recent determination of the complete nucleotide sequence of several Mycobacterium tuberculosis (MTB) genomes allows the use of comparative genomics as a tool for dissecting the nature and consequence of genetic variability within this species. The multiple alignment of the genomes of clinical strains (CDC1551, F11, Haarlem and C), along with the genomes of laboratory strains (H37Rv and H37Ra), provides new insights on the mechanisms of adaptation of this bacterium to the human host. Findings The genetic variation found in six M. tuberculosis strains does not involve significant genomic rearrangements. Most of the variation results from deletion and transposition events preferentially associated with insertion sequences and genes of the PE/PPE family but not with genes implicated in virulence. Using a Perl-based software islandsanalyser , which creates a representation of the genetic variation in the genome, we identified differences in the patterns of distribution and frequency of the polymorphisms across the genome. The identification of genes displaying strain-specific polymorphisms and the extrapolation of the number of strain-specific polymorphisms to an unlimited number of genomes indicates that the different strains contain a limited number of unique polymorphisms. Conclusion The comparison of multiple genomes demonstrates that the M. tuberculosis genome is currently undergoing an active process of gene decay, analogous to the adaptation process of obligate bacterial symbionts. This observation opens new perspectives into the evolution and the understanding of the pathogenesis of this bacterium.
    Keywords Medicine ; R ; Biology (General) ; QH301-705.5 ; Science (General) ; Q1-390
    Subject code 572
    Language English
    Publishing date 2008-11-01T00:00:00Z
    Publisher BMC
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  10. Article ; Online: Evolutionary radiation of lanthipeptides in marine cyanobacteria.

    Cubillos-Ruiz, Andres / Berta-Thompson, Jessie W / Becker, Jamie W / van der Donk, Wilfred A / Chisholm, Sallie W

    Proceedings of the National Academy of Sciences of the United States of America

    2017  Volume 114, Issue 27, Page(s) E5424–E5433

    Abstract: Lanthipeptides are ribosomally derived peptide secondary metabolites that undergo extensive posttranslational modification. Prochlorosins are a group of lanthipeptides produced by certain strains of the ubiquitous marine ... ...

    Abstract Lanthipeptides are ribosomally derived peptide secondary metabolites that undergo extensive posttranslational modification. Prochlorosins are a group of lanthipeptides produced by certain strains of the ubiquitous marine picocyanobacteria
    Language English
    Publishing date 2017-07-03
    Publishing country United States
    Document type Journal Article
    ZDB-ID 209104-5
    ISSN 1091-6490 ; 0027-8424
    ISSN (online) 1091-6490
    ISSN 0027-8424
    DOI 10.1073/pnas.1700990114
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