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  1. Aminoglycoside tolerance in Vibrio cholerae engages translational reprogramming associated to queuosine tRNA modification

    This article has 19 authors:
    1. Louna Fruchard
    2. Anamaria Babosan
    3. Andre Carvalho
    4. Manon Lang
    5. Blaise Li
    6. Magalie Duchateau
    7. Quentin Giai-Gianetto
    8. Mariette Matondo
    9. Frédéric Bonhomme
    10. Isabelle Hatin
    11. Hugo Arbes
    12. Céline Fabret
    13. Guillaume Sanchez
    14. Virginie Marchand
    15. Yuri Motorin
    16. Olivier Namy
    17. Valérie de Crécy-Lagard
    18. Didier Mazel
    19. Zeynep Baharoglu
    This article has been curated by 1 group:
    • Curated by eLife

      eLife assessment

      This study investigates the role of queuosine (Q) tRNA modification in aminoglycoside tolerance in Vibrio cholerae and presents convincing evidence to conclude that Q is essential for the efficient translation of TAT codons, although this depends on the context. The absence of Q reduces aminoglycoside tolerance potentially by reprogramming the translation of an oxidative stress response gene, rxsA. Overall, the findings point to an important mechanism whereby changes in Q modification levels control the decoding of mRNAs enriched in TAT codons under antibiotic stress.

    Reviewed by eLife

    This article has 4 evaluationsAppears in 2 listsLatest version Latest activity
  2. MOB rules: Antibiotic Exposure Reprograms Metabolism to Mobilize Bacillus subtilis in Competitive Interactions

    This article has 7 authors:
    1. Yongjin Liu
    2. Sandra LaBonte
    3. Courtney Brake
    4. Carol LaFayette
    5. Adam P. Rosebrock
    6. Amy A. Caudy
    7. Paul D. Straight
    This article has been curated by 1 group:
    • Curated by eLife

      eLife assessment

      This paper reports on the transcriptional changes upon chloramphenicol-induced surface mobility of Bacillus subtilis, a phenomenon that can occur during co-incubation with Streptomyces venezuelae, a chloramphenicol producer. The work presented includes valuable and thorough transcriptomics data, which convincingly indicate that sub-lethal chloramphenicol triggers substantial changes in B. subtilis gene expression. There are, however, significant limitations and concerns whether the documented changes are causal for the phenotypes observed or simply correlated with these phenotypes; additionally, the notion that chloramphenicol triggers a 'division of labor' was incomplete and should be backed up experimentally.

    Reviewed by eLife

    This article has 3 evaluationsAppears in 2 listsLatest version Latest activity
  3. A packaging signal-binding protein regulates the assembly checkpoint of integrative filamentous phages

    This article has 7 authors:
    1. Ting-Yu Yeh
    2. Michael C. Feehley
    3. Patrick J. Feehley
    4. Vivian Y. Ooi
    5. Yi-Yung Hung
    6. Shao-Cheng Wang
    7. Gregory P. Contreras
    This article has been curated by 1 group:
    • Curated by eLife

      eLife assessment

      This valuable work describes a new protein factor that is required for filamentous phage assembly. Convincing evidence is provided for the binding of PSB15 to the packaging signal of the single-stranded DNA, Trx, and cardiolipin, and a mechanism for how the phage DNA is targeted to the assembly site in the bacterial inner membrane is presented. The work will be of interest to microbiologists.

    Reviewed by eLife

    This article has 3 evaluationsAppears in 2 listsLatest version Latest activity
  4. Purging viral latency by a bifunctional HSV-vectored therapeutic vaccine in chronically SIV-infected macaques

    This article has 11 authors:
    1. Ziyu Wen
    2. Pingchao Li
    3. Yue Yuan
    4. Congcong Wang
    5. Minchao Li
    6. Haohang Wang
    7. Minjuan Shi
    8. Yizi He
    9. Mingting Cui
    10. Ling Chen
    11. Caijun Sun
    This article has been curated by 1 group:
    • Curated by eLife

      eLife assessment

      In this useful study, the authors tested a novel approach to eradicate the HIV reservoir by constructing a herpes simplex virus (HSV)-based therapeutic vaccine. The approach was tested in experimental infections of chronically SIV-infected, antiretroviral therapy (ART)-treated macaques with extent of rebound after ART interruption as a measure of the size of the HIV reservoir. While mean viremia at rebound was lower in the HSV vaccine-treated group, the evidence presented appear to be be incomplete because the group size was small and the viral load at rebound was highly variable.

    Reviewed by eLife

    This article has 4 evaluationsAppears in 2 listsLatest version Latest activity
  5. Hosts Manipulate Lifestyle Switch and Pathogenicity Heterogeneity of Opportunistic Pathogens in the Single-cell Resolution

    This article has 13 authors:
    1. Ziguang Wang
    2. Shuai Li
    3. Sheng Zhang
    4. Tianyu Zhang
    5. Yujie Wu
    6. Anqi Liu
    7. Kui Wang
    8. Xiaowen Ji
    9. Haiqun Cao
    10. Eng-King Tan
    11. Yongcheng Wang
    12. Yirong Wang
    13. Wei Liu
    This article has been curated by 1 group:
    • Curated by eLife

      eLife assessment

      This valuable study examines the role of a host in conditions that shift pathogenicity of opportunistic microbes. The use of single-cell microbial transcriptomics and metabolomics to demonstrate the host's effects on pathogen dynamics is interesting and convincing. However, the connection to host antimicrobial peptides driving these effects is incomplete and would benefit from additional evidence and improved explanation in the text. This paper has the potential to be of broad interest to those working in host-microbe (microbiome and pathogen) interactions.

    Reviewed by eLife

    This article has 4 evaluationsAppears in 2 listsLatest version Latest activity
  6. Targeting plasmid-encoded proteins that contain immunoglobulin-like domains to combat antimicrobial resistance

    This article has 12 authors:
    1. Alejandro Prieto
    2. Llu√Įsa Mir√≥
    3. Yago Margolles
    4. Manuel Bernabeu
    5. David Salguero
    6. Susana Merino
    7. Joan Tom√°s
    8. Juan Alberto Corbera
    9. Anna Pérez-Bosque
    10. M√°rio H√ľttener
    11. Luis √Āngel Fern√°ndez
    12. Antonio Ju√°rez
    This article has been curated by 1 group:
    • Curated by eLife

      eLife assessment

      This important study addresses the challenge of antimicrobial resistance by targeting plasmid proteins that interfere with plasmid transfer as a novel strategy to limit the spread of antibiotic resistance genes. While the evidence presented is solid, the work would benefit from a clear integration of the approaches used and more thorough analyses to fully assess the effectiveness of this strategy. This study will interest those working on plasmid transfer and antimicrobial resistance.

    Reviewed by eLife

    This article has 3 evaluationsAppears in 2 listsLatest version Latest activity
  7. Discovery of the 1-naphthylamine biodegradation pathway reveals an enzyme that catalyzes 1-naphthylamine glutamylation

    This article has 7 authors:
    1. Shu-Ting Zhang
    2. Shi-Kai Deng
    3. Tao Li
    4. Megan E. Maloney
    5. De-Feng Li
    6. Jim C. Spain
    7. Ning-Yi Zhou
    This article has been curated by 1 group:
    • Curated by eLife

      eLife assessment

      This important work identifies a p. aeruginosa strain and enzyme that can degrade 1-naphthylamine, a harmful industrial pollutant. Data resulting from in vivo and structural approaches are compelling, but additional mutagenesis would further test and establish the broad substrate specificity of NpaA1. With this additional data, this paper would be of high interest to biologists and enzymologists studying biodegradation of industrial pollutants.

    Reviewed by eLife

    This article has 4 evaluationsAppears in 2 listsLatest version Latest activity
  8. Characterisation and comparison of semen microbiota and sperm function in men with infertility, recurrent miscarriage, or proven fertility

    This article has 19 authors:
    1. Shahriar Mowla
    2. Linda Farahani
    3. Tharu Tharakan
    4. Rhianna Davies
    5. Gonçalo DS Correia
    6. Yun S Lee
    7. Samit Kundu
    8. Shirin Khanjani
    9. Emad Sindi
    10. Raj Rai
    11. Lesley Regan
    12. Dalia Khalifa
    13. Ralf Henkel
    14. Suks Minhas
    15. Waljit S Dhillo
    16. Jara Ben Nagi
    17. Phillip R Bennett
    18. David A. MacIntyre
    19. Channa N Jayasena
    This article has been curated by 1 group:
    • Curated by eLife

      eLife assessment

      This valuable study reports a potential connection between the seminal microbiome and sperm quality/male fertility. The data are generally convincing, but the statistical methods employed need further justification. This study will be of interest to clinicians and biomedical researchers who work on microbiome and male fertility.

    Reviewed by eLife

    This article has 3 evaluationsAppears in 2 listsLatest version Latest activity
  9. The microbiome interacts with the circadian clock and dietary composition to regulate metabolite cycling in the gut

    This article has 4 authors:
    1. Yueliang Zhang
    2. Yongjun Li
    3. Sara B. Noya
    4. Amita Sehgal
    This article has been curated by 1 group:
    • Curated by eLife

      eLife assessment

      This study presents useful findings about daily rhythm changes of the Drosophila melanogaster adult gut metabolome, which is shown to be dependent on the fly microbiota, diet, and genotype. The phenomena observed are supported by solid experimental evidence, however, there are limitations regarding the analysis and a deeper interpretation of results would improve the manuscript. An absence of mechanistic functional investigation limits the power of the proposed conclusions. The experiments are currently incomplete as the effect of food intake timing was not directly addressed by measuring the quantity and timing of food consumption. The authors should strongly consider including the model organism used in the study in the title of the manuscript to reflect the work. This study will be of interest to physiologists of circadian biology and nutrition.

    Reviewed by eLife

    This article has 4 evaluationsAppears in 2 listsLatest version Latest activity
  10. The nanoscale organization of the Nipah virus fusion protein informs new membrane fusion mechanisms

    This article has 7 authors:
    1. Qian Wang
    2. Jinxin Liu
    3. Yuhang Luo
    4. Vicky Kliemke
    5. Giuliana Leonarda Matta
    6. Jingjing Wang
    7. Qian Liu
    This article has been curated by 1 group:
    • Curated by eLife

      eLife assessment

      This is a valuable paper that uses super-resolution microscopy to show the nanoclustering of the Nipah virus fusion protein on cell and viral membranes. Some of the conclusions regarding the clustering of viral fusion proteins is supported by solid biochemical and super-resolution imaging data while other conclusions such as significance for viral fusion mechanisms is not fully supported by the data provided.

    Reviewed by eLife

    This article has 4 evaluationsAppears in 2 listsLatest version Latest activity
  11. Polysaccharides induce deep-sea Lentisphaerae strains to release chronic bacteriophages

    This article has 4 authors:
    1. Chong Wang
    2. Rikuan Zheng
    3. Tianhang Zhang
    4. Chaomin Sun
    This article has been curated by 1 group:
    • Curated by eLife

      eLife assessment

      This manuscript presents useful findings on several phage from deep sea isolates of Lentisphaerae strains WC36 and zth2 that further our understanding of deep sea microbial life. The manuscript's primary claim is that phage isolates augment polysaccharide use in Pseudomonas bacteria via auxiliary metabolic genes (AMGs). However, the strength of the evidence is incomplete and does not support the primary claims. Namely, there are not data presented to rule out phage contamination in the polysaccharide stock solution, AMGs are potentially misidentified, and there is missing evidence of successful infection.

    Reviewed by eLife

    This article has 3 evaluationsAppears in 2 listsLatest version Latest activity
  12. Immunogenicity and safety of a live-attenuated SARS-CoV-2 vaccine candidate based on multiple attenuation mechanisms

    This article has 13 authors:
    1. Mie Suzuki-Okutani
    2. Shinya Okamura
    3. Tang Gis
    4. Hitomi Sasaki
    5. Suni Lee
    6. Akiho Yoshida
    7. Simon Goto
    8. Tatsuya Nakagawa
    9. Masahito Ikawa
    10. Wataru Kamitani
    11. Shiro Takekawa
    12. Koichi Yamanishi
    13. Hirotaka Ebina
    This article has been curated by 1 group:
    • Curated by eLife

      eLife assessment

      This is a valuable study on the efficacy of a live attenuated vaccine that was tested in different animal models. The evidence is convincing, but it could be further strengthened by comparing the efficacy of their platform with an mRNA vaccine and further investigating mucosal protection.

    Reviewed by eLife

    This article has 5 evaluationsAppears in 2 listsLatest version Latest activity
  13. Birnaviral Hijacking of Endosomal Membranes

    This article has 22 authors:
    1. Flavia A. Zanetti
    2. Ignacio Fern√°ndez
    3. Eduard Baquero
    4. Pablo Guardado-Calvo
    5. Sarah Dubois
    6. Etienne Morel
    7. Victoria Alfonso
    8. Milton O. Aguilera
    9. María E. Celayes
    10. Luis M. Polo
    11. Laila Suhaiman
    12. Vanesa V. Galassi
    13. María V. Chiarpotti
    14. Carolina Allende
    15. Javier M. Rodríguez
    16. José R. Castón
    17. Diego Lijavetzky
    18. Oscar Taboga
    19. María I. Colombo
    20. Mario G. Del Pópolo
    21. Félix A. Rey
    22. Laura R. Delgui
    This article has been curated by 1 group:
    • Curated by eLife

      eLife assessment

      This study presents valuable information on the mechanism of how birnavirus VP3 protein interacts with PI3P in early endosomes. Evidence supporting the proposed two-stage mechanism is incomplete and would benefit from additional supporting experiments, and additional experimentation would also address concerns about data consistency.

    Reviewed by eLife

    This article has 5 evaluationsAppears in 2 listsLatest version Latest activity
  14. Multimodal HLA-I genotype regulation by human cytomegalovirus US10 and resulting surface patterning

    This article has 14 authors:
    1. Carolin Gerke
    2. Liane Bauersfeld
    3. Valerie Oberhardt
    4. Christopher Sebastian J√ľrges
    5. Robbert M. Spaapen
    6. Claudio Mussolino
    7. Vu Thuy Khanh Le-Trilling
    8. Mirko Trilling
    9. Lars Dölken
    10. Florian Erhard
    11. Maike Hofmann
    12. Hartmut Hengel
    13. Frank Momburg
    14. Anne Halenius
    This article has been curated by 1 group:
    • Curated by eLife

      eLife assessment

      This study presents a useful finding on a virally encoded immune-evasin which differentially inhibits antigen presentation by cellular protein complexes called Major histocompatibility complex (MHC) class I, thereby diminishing the activation of cytotoxic T cells. The evidence supporting the claims of the authors is solid, although the addition of more mechanistic insights would strengthen the study. The work will be of interest to virologists and immunologists working on the adaptive immune response to herpesviral infection. Some conclusions would require additional experimental support.

    Reviewed by eLife

    This article has 5 evaluationsAppears in 2 listsLatest version Latest activity
  15. Released Bacterial ATP Shapes Local and Systemic Inflammation during Abdominal Sepsis

    This article has 9 authors:
    1. Daniel Spari
    2. Annina Schmid
    3. Daniel S√°nchez-Taltavull
    4. Shaira Murugan
    5. Keely Keller
    6. Nadia Ennaciri
    7. Lilian Salm
    8. Deborah Stroka
    9. Guido Beldi
    This article has been curated by 1 group:
    • Curated by eLife

      eLife assessment

      This fundamental study advances our understanding of the role of bacterial derived extracellular ATP in the pathogenesis of sepsis. The evidence supporting the conclusions is solid, particularly with the analysis of E. coli mutants to address different aspects of bacterial release of ATP. The work will be of broad interest to researchers on microbiology and infectious diseases.

    Reviewed by eLife

    This article has 4 evaluationsAppears in 2 listsLatest version Latest activity
  16. Merging Multi-OMICs with Proteome Integral Solubility Alteration Unveils Antibiotic Mode of Action

    This article has 9 authors:
    1. Ritwik Maity
    2. Xuepei Zhang
    3. Francesca Romana Liberati
    4. Chiara Scribani Rossi
    5. Francesca Cutruzzolà
    6. Serena Rinaldo
    7. Massimiliano Gaetani
    8. José Antonio Aínsa
    9. Javier Sancho
    This article has been curated by 1 group:
    • Curated by eLife

      eLife assessment

      This fundamental study provides insights into how pathogens respond, on a systemic level including several gene targets and clusters, to selected antimicrobial molecules. Compelling evidence is provided, through multi-omics and functional approaches, that very similar molecules originally designed to target the same bacterial protein act differently within the context of the whole set of cellular transcripts, expressed proteins, and pre-lethal metabolic changes. Given the incredibly fast accumulation of omics data to date and the much slower capacity of extracting biologically relevant insights from big data, this work exemplifies how the development of sensitive data analysis is still a major necessity in modern research.

    Reviewed by eLife

    This article has 3 evaluationsAppears in 2 listsLatest version Latest activity
  17. DNA Methylome Regulates Virulence and Metabolism in Pseudomonas syringae

    This article has 7 authors:
    1. Jiadai Huang
    2. Fang Chen
    3. Beifang Lu
    4. Yue Sun
    5. Youyue Li
    6. Canfeng Hua
    7. Xin Deng
    This article has been curated by 1 group:
    • Curated by eLife

      eLife assessment

      This valuable study presents findings on DNA methylation as an efficient epigenetic transcriptional regulating strategy in bacteria. The authors utilized single-molecule real-time sequencing to profile the DNA methylation landscape across three model pathovars of Pseudomonas syringae, identifying significant epigenetic mechanisms through the Type-I restriction-modification system, which includes a conserved sequence motif associated with N6-methyladenine. The evidence presented is solid and the study provides novel insights into the epigenetic mechanisms of P. syringae, expanding the understanding of bacterial pathogenicity and adaptation.

    Reviewed by eLife

    This article has 4 evaluationsAppears in 2 listsLatest version Latest activity
  18. Stratification of viral shedding patterns in saliva of COVID-19 patients

    This article has 16 authors:
    1. Hyeongki Park
    2. Raiki Yoshimura
    3. Shoya Iwanami
    4. Kwang Su Kim
    5. Keisuke Ejima
    6. Naotoshi Nakamura
    7. Kazuyuki Aihara
    8. Yoshitsugu Miyazaki
    9. Takashi Umeyama
    10. Ken Miyazawa
    11. Takeshi Morita
    12. Koichi Watashi
    13. Christopher B. Brooke
    14. Ruian Ke
    15. Shingo Iwami
    16. Taiga Miyazaki
    This article has been curated by 1 group:
    • Curated by eLife

      eLife assessment

      This useful work by Park attempts to use machine learning algorithms to identify correlates of different observed shedding patterns in two COVID-19 cohorts. The evidence supporting the study conclusions is incomplete due to the lack of uniformity in assays between the 2 cohorts, relevant metadata (previous infection/vaccination status, viral variant), early viral load data in the cohorts, and incomplete statistical analyses. With a strengthened analysis, the work may be of interest to virologists, clinicians, and public health scientists.

    Reviewed by eLife

    This article has 4 evaluationsAppears in 2 listsLatest version Latest activity
  19. A Modified BPaL Regimen for Tuberculosis Treatment replaces Linezolid with Inhaled Spectinamides

    This article has 15 authors:
    1. Malik Zohaib Ali
    2. Taru S. Dutt
    3. Amy MacNeill
    4. Amanda Walz
    5. Camron Pearce
    6. Ha Lam
    7. Jamie Philp
    8. Johnathan Patterson
    9. Marcela Henao-Tamayo
    10. Richard E. Lee
    11. Jiuyu Liu
    12. Gregory T. Robertson
    13. Anthony J. Hickey
    14. Bernd Meibohm
    15. Mercedes Gonzalez-Juarrero
    This article has been curated by 1 group:
    • Curated by eLife

      eLife assessment

      In this useful study, the authors report the efficacy, hematological effects, and inflammatory response of the BPaL regimen (containing bedaquiline, pretomanid, and linezolid) compared to a variation in which Linezolid is replaced with the preclinical development candidate spectinamide 1599, administered by inhalation in tuberculosis-infected mice. The authors provide convincing evidence that supports the replacement of Linezolid in the current standard of care for drug-resistant tuberculosis. However, a limitation of the work is the lack of control experiments with bedaquiline and pretomanid only, to further dissect the relevant contributions of linezolid and spectinamide in efficacy and adverse effects. Although the manuscript is well written overall, a re-formulation of some of the stated hypotheses and conclusions, as well as the addition of text to contextualize translatability, would improve its value.

    Reviewed by eLife

    This article has 4 evaluationsAppears in 2 listsLatest version Latest activity
  20. Staphylococcus aureus counters organic acid anion-mediated inhibition of peptidoglycan cross-linking through robust alanine racemase activity

    This article has 11 authors:
    1. Sasmita Panda
    2. Yahani P. Jayasinghe
    3. Dhananjay D. Shinde
    4. Emilio Bueno
    5. Amanda Stastny
    6. Blake P. Bertrand
    7. Sujata S. Chaudhari
    8. Tammy Kielian
    9. Felipe Cava
    10. Donald R. Ronning
    11. Vinai C. Thomas
    This article has been curated by 1 group:
    • Curated by eLife

      eLife assessment

      In this valuable study, the authors use Staphylococcus aureus to understand how organic acids inhibit bacterial growth. They provide convincing evidence that acetic acid specifically inhibits the activity of the Ddl enzyme and that S. aureus maintains a high intracellular D-ala concentration to circumvent acetate-mediated growth inhibition. This work will be of interest to researchers studying bacteria and antimicrobials.

    Reviewed by eLife, Arcadia Science

    This article has 4 evaluationsAppears in 3 listsLatest version Latest activity