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  1. Article ; Online: Tracking humans and microbes.

    Lloréns-Rico, Verónica / Raes, Jeroen

    Nature

    2019  Volume 569, Issue 7758, Page(s) 632–633

    MeSH term(s) Female ; Humans ; Infant, Newborn ; Microbiota ; Pregnancy ; Premature Birth ; Vagina
    Language English
    Publishing date 2019-05-29
    Publishing country England
    Document type News ; Comment
    ZDB-ID 120714-3
    ISSN 1476-4687 ; 0028-0836
    ISSN (online) 1476-4687
    ISSN 0028-0836
    DOI 10.1038/d41586-019-01591-y
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  2. Article: Single-cell approaches in human microbiome research

    Lloréns-Rico, Verónica / Simcock, Joshua A. / Huys, Geert R.B. / Raes, Jeroen

    Cell. 2022 July 21, v. 185, no. 15

    2022  

    Abstract: Microbial culturing and meta-omic profiling technologies have significantly advanced our understanding of the taxonomic and functional variation of the human microbiome and its impact on host processes. The next increase in resolution will come by ... ...

    Abstract Microbial culturing and meta-omic profiling technologies have significantly advanced our understanding of the taxonomic and functional variation of the human microbiome and its impact on host processes. The next increase in resolution will come by understanding the role of low-abundant and less-prevalent bacteria and the study of individual cell behaviors that underlie the complexity of microbial ecosystems. To this aim, single-cell techniques are being rapidly developed to isolate, culture, and characterize the genomes and transcriptomes of individual microbes in complex communities. Here, we discuss how these single-cell technologies are providing unique insights into the biology and behavior of human microbiomes.
    Keywords genome ; humans ; microbiome ; transcriptome
    Language English
    Dates of publication 2022-0721
    Size p. 2725-2738.
    Publishing place Elsevier Inc.
    Document type Article
    ZDB-ID 187009-9
    ISSN 1097-4172 ; 0092-8674
    ISSN (online) 1097-4172
    ISSN 0092-8674
    DOI 10.1016/j.cell.2022.06.040
    Database NAL-Catalogue (AGRICOLA)

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  3. Article ; Online: Single-cell approaches in human microbiome research.

    Lloréns-Rico, Verónica / Simcock, Joshua A / Huys, Geert R B / Raes, Jeroen

    Cell

    2022  Volume 185, Issue 15, Page(s) 2725–2738

    Abstract: Microbial culturing and meta-omic profiling technologies have significantly advanced our understanding of the taxonomic and functional variation of the human microbiome and its impact on host processes. The next increase in resolution will come by ... ...

    Abstract Microbial culturing and meta-omic profiling technologies have significantly advanced our understanding of the taxonomic and functional variation of the human microbiome and its impact on host processes. The next increase in resolution will come by understanding the role of low-abundant and less-prevalent bacteria and the study of individual cell behaviors that underlie the complexity of microbial ecosystems. To this aim, single-cell techniques are being rapidly developed to isolate, culture, and characterize the genomes and transcriptomes of individual microbes in complex communities. Here, we discuss how these single-cell technologies are providing unique insights into the biology and behavior of human microbiomes.
    MeSH term(s) Bacteria/genetics ; Genome, Microbial ; Host Microbial Interactions ; Humans ; Microbiota ; Sequence Analysis, RNA ; Single-Cell Analysis
    Language English
    Publishing date 2022-07-19
    Publishing country United States
    Document type Journal Article ; Review ; Research Support, Non-U.S. Gov't
    ZDB-ID 187009-9
    ISSN 1097-4172 ; 0092-8674
    ISSN (online) 1097-4172
    ISSN 0092-8674
    DOI 10.1016/j.cell.2022.06.040
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  4. Article ; Online: Benchmarking microbiome transformations favors experimental quantitative approaches to address compositionality and sampling depth biases.

    Lloréns-Rico, Verónica / Vieira-Silva, Sara / Gonçalves, Pedro J / Falony, Gwen / Raes, Jeroen

    Nature communications

    2021  Volume 12, Issue 1, Page(s) 3562

    Abstract: While metagenomic sequencing has become the tool of preference to study host-associated microbial communities, downstream analyses and clinical interpretation of microbiome data remains challenging due to the sparsity and compositionality of sequence ... ...

    Abstract While metagenomic sequencing has become the tool of preference to study host-associated microbial communities, downstream analyses and clinical interpretation of microbiome data remains challenging due to the sparsity and compositionality of sequence matrices. Here, we evaluate both computational and experimental approaches proposed to mitigate the impact of these outstanding issues. Generating fecal metagenomes drawn from simulated microbial communities, we benchmark the performance of thirteen commonly used analytical approaches in terms of diversity estimation, identification of taxon-taxon associations, and assessment of taxon-metadata correlations under the challenge of varying microbial ecosystem loads. We find quantitative approaches including experimental procedures to incorporate microbial load variation in downstream analyses to perform significantly better than computational strategies designed to mitigate data compositionality and sparsity, not only improving the identification of true positive associations, but also reducing false positive detection. When analyzing simulated scenarios of low microbial load dysbiosis as observed in inflammatory pathologies, quantitative methods correcting for sampling depth show higher precision compared to uncorrected scaling. Overall, our findings advocate for a wider adoption of experimental quantitative approaches in microbiome research, yet also suggest preferred transformations for specific cases where determination of microbial load of samples is not feasible.
    MeSH term(s) Benchmarking/methods ; Classification ; Computational Biology/methods ; Dysbiosis/microbiology ; Electronic Data Processing/methods ; Humans ; Metagenome ; Metagenomics/methods ; Microbiota ; Selection Bias
    Language English
    Publishing date 2021-06-11
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2553671-0
    ISSN 2041-1723 ; 2041-1723
    ISSN (online) 2041-1723
    ISSN 2041-1723
    DOI 10.1038/s41467-021-23821-6
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  5. Article ; Online: Alternative transcriptional regulation in genome-reduced bacteria.

    Miravet-Verde, Samuel / Lloréns-Rico, Verónica / Serrano, Luis

    Current opinion in microbiology

    2017  Volume 39, Page(s) 89–95

    Abstract: Transcription is a core process of bacterial physiology, and as such it must be tightly controlled, so that bacterial cells maintain steady levels of each RNA molecule in homeostasis and modify them in response to perturbations. The major regulators of ... ...

    Abstract Transcription is a core process of bacterial physiology, and as such it must be tightly controlled, so that bacterial cells maintain steady levels of each RNA molecule in homeostasis and modify them in response to perturbations. The major regulators of transcription in bacteria (and in eukaryotes) are transcription factors. However, in genome-reduced bacteria, the limited number of these proteins is insufficient to explain the variety of responses shown upon changes in their environment. Thus, alternative regulators may play a central role in orchestrating RNA levels in these microorganisms. These alternative mechanisms rely on intrinsic features within DNA and RNA molecules, suggesting they are ancestral mechanisms shared among bacteria that could have an increased relevance on transcriptional regulation in minimal cells. In this review, we summarize the alternative elements that can regulate transcript abundance in genome-reduced bacteria and how they contribute to the RNA homeostasis at different levels.
    Language English
    Publishing date 2017-11-15
    Publishing country England
    Document type Journal Article ; Review
    ZDB-ID 1418474-6
    ISSN 1879-0364 ; 1369-5274
    ISSN (online) 1879-0364
    ISSN 1369-5274
    DOI 10.1016/j.mib.2017.10.022
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 5514: Show issues Location:
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  6. Article ; Online: Benchmarking microbiome transformations favors experimental quantitative approaches to address compositionality and sampling depth biases

    Verónica Lloréns-Rico / Sara Vieira-Silva / Pedro J. Gonçalves / Gwen Falony / Jeroen Raes

    Nature Communications, Vol 12, Iss 1, Pp 1-

    2021  Volume 12

    Abstract: Here, the authors use simulated quantitative gut microbial communities to benchmark the performance of 13 common data transformations in determining diversity as well as microbe-microbe and microbe-metadata associations, finding that quantitative ... ...

    Abstract Here, the authors use simulated quantitative gut microbial communities to benchmark the performance of 13 common data transformations in determining diversity as well as microbe-microbe and microbe-metadata associations, finding that quantitative approaches incorporating microbial load variation outperform computational strategies in downstream analyses, urging for a widespread adoption of quantitative approaches, or recommending specific computational transformations whenever determination of microbial load of samples is not feasible.
    Keywords Science ; Q
    Language English
    Publishing date 2021-06-01T00:00:00Z
    Publisher Nature Portfolio
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  7. Article ; Online: Endogenous IFNβ expression predicts outcome in critical patients with COVID-19.

    Menezes, Soraya Maria / Braz, Marcos / Llorens-Rico, Veronica / Wauters, Joost / Van Weyenbergh, Johan

    The Lancet. Microbe

    2021  Volume 2, Issue 6, Page(s) e235–e236

    MeSH term(s) COVID-19 ; Humans ; Interferon-beta/metabolism
    Chemical Substances Interferon-beta (77238-31-4)
    Language English
    Publishing date 2021-03-30
    Publishing country England
    Document type Letter
    ISSN 2666-5247
    ISSN (online) 2666-5247
    DOI 10.1016/S2666-5247(21)00063-X
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article: Insights into the Mechanisms of Basal Coordination of Transcription Using a Genome-Reduced Bacterium.

    Junier, Ivan / Unal, E Besray / Yus, Eva / Lloréns-Rico, Verónica / Serrano, Luis

    Cell systems

    2018  Volume 7, Issue 2, Page(s) 227–229

    Language English
    Publishing date 2018-09-05
    Publishing country United States
    Document type Published Erratum
    ISSN 2405-4712
    ISSN 2405-4712
    DOI 10.1016/j.cels.2018.08.006
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article ; Online: Distinguishing between productive and abortive promoters using a random forest classifier in Mycoplasma pneumoniae.

    Lloréns-Rico, Verónica / Lluch-Senar, Maria / Serrano, Luis

    Nucleic acids research

    2015  Volume 43, Issue 7, Page(s) 3442–3453

    Abstract: Distinguishing between promoter-like sequences in bacteria that belong to true or abortive promoters, or to those that do not initiate transcription at all, is one of the important challenges in transcriptomics. To address this problem, we have studied ... ...

    Abstract Distinguishing between promoter-like sequences in bacteria that belong to true or abortive promoters, or to those that do not initiate transcription at all, is one of the important challenges in transcriptomics. To address this problem, we have studied the genome-reduced bacterium Mycoplasma pneumoniae, for which the RNAs associated with transcriptional start sites have been recently experimentally identified. We determined the contribution to transcription events of different genomic features: the -10, extended -10 and -35 boxes, the UP element, the bases surrounding the -10 box and the nearest-neighbor free energy of the promoter region. Using a random forest classifier and the aforementioned features transformed into scores, we could distinguish between true, abortive promoters and non-promoters with good -10 box sequences. The methods used in this characterization of promoters can be extended to other bacteria and have important applications for promoter design in bacterial genome engineering.
    MeSH term(s) Genes, Bacterial ; Models, Theoretical ; Pneumonia, Mycoplasma/genetics ; Promoter Regions, Genetic
    Language English
    Publishing date 2015-03-16
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 186809-3
    ISSN 1362-4962 ; 1362-4954 ; 0301-5610 ; 0305-1048
    ISSN (online) 1362-4962 ; 1362-4954
    ISSN 0301-5610 ; 0305-1048
    DOI 10.1093/nar/gkv170
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Article ; Online: Assessing the hodgepodge of non-mapped reads in bacterial transcriptomes: real or artifactual RNA chimeras?

    Lloréns-Rico, Verónica / Serrano, Luis / Lluch-Senar, Maria

    BMC genomics

    2014  Volume 15, Page(s) 633

    Abstract: Background: RNA sequencing methods have already altered our view of the extent and complexity of bacterial and eukaryotic transcriptomes, revealing rare transcript isoforms (circular RNAs, RNA chimeras) that could play an important role in their biology. ...

    Abstract Background: RNA sequencing methods have already altered our view of the extent and complexity of bacterial and eukaryotic transcriptomes, revealing rare transcript isoforms (circular RNAs, RNA chimeras) that could play an important role in their biology.
    Results: We performed an analysis of chimera formation by four different computational approaches, including a custom designed pipeline, to study the transcriptomes of M. pneumoniae and P. aeruginosa, as well as mixtures of both. We found that rare transcript isoforms detected by conventional pipelines of analysis could be artifacts of the experimental procedure used in the library preparation, and that they are protocol-dependent.
    Conclusion: By using a customized pipeline we show that optimal library preparation protocol and the pipeline to analyze the results are crucial to identify real chimeric RNAs.
    MeSH term(s) Artifacts ; Bacteria/genetics ; Base Sequence ; Gene Expression Profiling/methods ; RNA Isoforms/genetics ; RNA, Bacterial/genetics ; Sequence Analysis, RNA/methods ; Software ; Statistics as Topic/methods
    Chemical Substances RNA Isoforms ; RNA, Bacterial
    Language English
    Publishing date 2014-07-29
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ISSN 1471-2164
    ISSN (online) 1471-2164
    DOI 10.1186/1471-2164-15-633
    Database MEDical Literature Analysis and Retrieval System OnLINE

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