Microbiology

The RND efflux pump EefABC is highly conserved within lineages of E. coli commonly associated with infection

1. Hannah L. Pugh
2. Elizabeth M. Darby
3. Leah Burgess
4. Abigail L. Colclough
5. Asti-Rochelle Meosa John
6. Steven Dunn
7. Christopher Connor
8. Eoughin A. Perry
9. Alan McNally
10. Vassiliy N. Bavro
11. Jessica M. A. Blair

Reviewed by PREreview

Architecture of genome-wide transcriptional regulatory network reveals dynamic functions and evolutionary trajectories in Pseudomonas syringae

1. Yue Sun
2. Jingwei Li
3. Jiadai Huang
4. Shumin Li
5. Youyue Li
6. Beifang Lu
7. Xin Deng

• Curated by eLife

  eLife assessment

  This work advances our understanding of transcriptional regulation of virulence and metabolic pathways in plant pathogenic bacteria. Solid evidence for the claims is provided by computational analysis of newly generated data on the genome-wide binding of 170 transcription factors to their target genes, together with experimental validation of the biological functions of some of these transcription factors. The findings and resources from this study will be valuable to researchers in the fields of systems biology, bacteriology, and plant-microbe interactions.

Reviewed by eLife

Temporal transcriptional response of Candida glabrata during macrophage infection reveals a multifaceted transcriptional regulator CgXbp1 important for macrophage response and fluconazole resistance

1. Maruti Nandan Rai
2. Qing Lan
3. Chirag Parsania
4. Rikky Rai
5. Niranjan Shirgaonkar
6. Ruiwen Chen
7. Li Shen
8. Kaeling Tan
9. Koon Ho Wong

• Curated by eLife

  Evaluation Summary:

  The paper by Rai and colleagues examines the transcriptional response of Candida glabrata, a common human fungal pathogen, during interaction with macrophages. They use RNA PolII profiling to identify not just the total transcripts but instead focus on the actively transcribing genes. By examining the profile over time, they identify particular transcripts that are enriched at each time point, building a hierarchical model for how a transcription factor, CgXbp1, may regulate part of this response. While the authors have generated a large and potentially impactful dataset, along with several interesting observations, it is important to be cautious as the direct targets of CgXbp1 were characterized under one particular condition and the transcriptional analyses were obtained in another condition, one shown to be highly dynamic as during macrophage infection.

  (This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. The reviewers remained anonymous to the authors.)

Reviewed by eLife

Hosts manipulate lifestyle switch and pathogenicity heterogeneity of opportunistic pathogens in the single-cell resolution

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. Yinglao Zhang
11. Eng King Tan
12. Yongcheng Wang
13. Yirong Wang
14. Wei Liu

• Curated by eLife

  eLife assessment

  The fundamental findings of this work substantially advance our understanding of the impact of the host on its gut microbes. The authors provided compelling evidence at single-cell resolution that the host can drive heterogeneity in the populations of gut microbes with significant consequences for the host physiology.

Reviewed by eLife

A modified BPaL regimen for tuberculosis treatment replaces linezolid with inhaled spectinamides

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

• 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. The work will be of interest to those studying tuberculosis treatment regimens.

Reviewed by eLife

Merging multi-omics with proteome integral solubility alteration unveils antibiotic mode of action

1. Ritwik Maity
2. Xuepei Zhang
3. Francesca Romana Liberati
4. Chiara Scribani Rossi
5. Francesca Cutruzzolá
6. Serena Rinaldo
7. Massimiliano Gaetani
8. José Antonio Aínsa
9. Javier Sancho

• 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 rapid accumulation of omics data 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

Growth consequences of the inhomogeneous organization of the bacterial cytoplasm

1. Johan H van Heerden
2. Alicia Berkvens
3. Daan H de Groot
4. Frank J Bruggeman

• Curated by eLife

  eLife assessment

  This important study examines E. coli growth and division, suggesting that inhomogeneous organization of ribosomes in the cytoplasm results in cell size-dependent growth rate perturbations. The work is conceptually appealing, but incomplete due to shortcomings in the experiments and modeling.

Reviewed by eLife

Machine learning approaches identify immunologic signatures of total and intact HIV DNA during long-term antiretroviral therapy

1. Lesia Semenova
2. Yingfan Wang
3. Shane Falcinelli
4. Nancie Archin
5. Alicia D Cooper-Volkheimer
6. David M Margolis
7. Nilu Goonetilleke
8. David M Murdoch
9. Cynthia D Rudin
10. Edward P Browne

• Curated by eLife

  eLife assessment

  Semenova et al. have studied a large cross-sectional cohort of people living with HIV on suppressive antiretroviral therapy and performed high dimensional flow-cytometry for analysis with data science/machine learning approaches to investigate associations of immunological and clinical parameters and intact/total HIV DNA levels (and categorizations). The study is useful in introducing these new methods and large data set and appears mostly solid, though some of the claims were incompletely supported by the modeling results. The authors have revised the text to fairly reflect their results, yet open questions remain about utility, particularly as to the value of categorical classification (vs continuous measurement) of reservoir size.

Reviewed by eLife

Competition and cooperation: The plasticity of bacterial interactions across environments

1. Josephine Solowiej-Wedderburn
2. Jennifer T. Pentz
3. Ludvig Lizana
4. Bjoern O. Schroeder
5. Peter A. Lind
6. Eric Libby

Reviewed by Arcadia Science

Secondary metabolite profiling of Pseudomonas aeruginosa isolates reveals rare genomic traits

1. Rachel L. Neve
2. Emily Giedraitis
3. Madeline S. Akbari
4. Shirli Cohen
5. Vanessa V. Phelan

Reviewed by Arcadia Science