Microbiology

Distinct bacterial and protist plankton diversity dynamics uncovered through DNA-based monitoring in the Baltic Sea area

1. Krzysztof T Jurdzinski
2. Meike AC Latz
3. Anders Torstensson
4. Sonia Brugel
5. Mikael Hedblom
6. Yue O O Hu
7. Markus Lindh
8. Agneta Andersson
9. Bengt Karlson
10. Anders F Andersson

Reviewed by Arcadia Science

Peptidoglycan-Chi3l1 interaction shapes gut microbiota in intestinal mucus layer

1. Yan Chen
2. Ruizhi Yang
3. Bin Qi
4. Zhao Shan

• Curated by eLife

  eLife assessment

  Supported by convincing data, this valuable study demonstrates that the Chitinase 3-like protein 1 (Chi3l1) interacts with gut microbiota and protects animals from intestinal injury in laboratory colitis model. The revised manuscript sufficiently addressed the reviewers' comments. The work will be of interest to scientists studying crosstalk between gut microbiota and inflammatory diseases.

Reviewed by eLife

A lytic transglycosylase connects bacterial focal adhesion complexes to the peptidoglycan cell wall

1. Carlos A Ramirez Carbo
2. Olalekan G Faromiki
3. Beiyan Nan

• Curated by eLife

  eLife assessment

  The manuscript by Carbo et al. reports a novel role for the MltG homolog AgmT in gliding motility in M. xanthus. The authors provide convincing data to demonstrate that AgmT is a cell wall lytic enzyme (likely a lytic transglycosylase), its lytic activity is required for gliding motility, and that its activity is required for proper binding of a component of the motility apparatus to the cell wall. The findings are valuable as they contribute to our understanding of the molecular mechanisms underlying the interaction between gliding motility and the bacterial cell wall.

Reviewed by eLife

Peptidoglycan-tethered and free forms of the Braun lipoprotein are in dynamic equilibrium in Escherichia coli

1. Yucheng Liang
2. Jean-Emmanuel Hugonnet
3. Filippo Rusconi
4. Michel Arthur

• Curated by eLife

  eLife assessment

  This useful study describes a single set of label-chase mass spectrometry experiments to confirm the molecular function of YafK as a peptidoglycan hydrolase, and to describe the timing of its attachment to the peptidoglycan. Confirmation of the molecular function of YafK is helpful for further studies to examine the function and regulation of the outer membrane-peptidoglycan link in bacteria. The evidence supporting the molecular function of YafK and that lpp molecules are shuffled on and off the peptidoglycan is solid, however, some of the other data still remain incomplete in the revised version. The work will be of interest to researchers studying lipoproteins in gram negative bacteria.

Reviewed by eLife

Cyclical MinD membrane affinity differences are not necessary for MinD gradient formation in Bacillus subtilis

1. Laura C Bohorquez
2. Henrik Strahl
3. Davide Marenduzzo
4. Martin J Thiele
5. Frank Bürmann
6. Leendert W Hamoen

• Curated by eLife

  eLife assessment

  This important study provides solid mechanistic and modeling data suggesting that the polar localization of MinCD in Bacillus subtilis is largely due to differences in diffusion rates between monomeric and dimeric MinD. This finding is exciting as it negates the necessity for a third, localization determinant, in this system as has been previously proposed. The work is generally strong but is incomplete without some additional quantitative analysis, as well as clarification of the underlying assumptions and details used for the modeling experiments.

Reviewed by eLife

Mechanistic Insights into MinD Regulation and Pattern Formation in Bacillus subtilis

1. Helge Feddersen
2. Marc Bramkamp

• Curated by eLife

  eLife assessment

  This useful study provides data suggesting that subcellular localization of the spatial regulator of cell division, MinD, is an intrinsic feature of the protein's ability to associate with the membrane as both a dimer and a monomer. These findings distinguish the behavior of MinD in B. subtilis from its counterpart in E. coli and suggest that there is not a need to invoke additional localization factors. However, all three reviewers agreed that the study is incomplete: experimentally, quantitation and assessment of MinD behavior in the presence of proteins previously implicated in its localization are missing, among other assays, and the molecular modeling necessary to support the authors' conclusion that their data support a reaction-diffusion model is completely absent. Finally, the manuscript itself is difficult to read with an overly long discussion and disorganized introduction and results sections, and it will require significant revision.

Reviewed by eLife

A metabolic modeling-based framework for predicting trophic dependencies in native rhizobiomes of crop plants

1. Alon Avraham Ginatt
2. Maria Berihu
3. Einam Castel
4. Shlomit Medina
5. Gon Carmi
6. Adi Faigenboim-Doron
7. Itai Sharon
8. Ofir Tal
9. Samir Droby
10. Tracey Somera
11. Mark Mazzola
12. Hanan Eizenberg
13. Shiri Freilich

• Curated by eLife

  eLife assessment

  By developing a framework to integrate metagenomic and metabolomic data with genome-scale metabolic models, this study establishes a toolkit to investigate trophic interactions between microbiota members in situ. The authors apply this method to the native rhizosphere bacterial communities of apple rootstocks, producing solid evidence and numerous detailed hypotheses on specific trophic exchanges and resource dependencies. The framework represents a valuable method to disentangle features of microbial interaction networks and will be of interest to microbiome scientists as well as plant and computational biologists.

Reviewed by eLife

Two newly cultivated eukaryotrophic flagellates represent distinct anaerobic lineages within Rhizaria

1. Yana Eglit
2. Maggie Lawton
3. Alastair G.B. Simpson
4. Ryan M.R. Gawryluk

Reviewed by Arcadia Science

Latent infection of an active giant endogenous virus in a unicellular green alga

1. Maria P. Erazo-Garcia
2. Uri Sheyn
3. Zachary K. Barth
4. Rory J. Craig
5. Petronella Wessman
6. Abdeali M. Jivaji
7. W. Keith Ray
8. Maria Svensson-Coelho
9. Charlie K. Cornwallis
10. Karin Rengefors
11. Corina P. D. Brussaard
12. Mohammad Moniruzzaman
13. Frank O. Aylward

Reviewed by Arcadia Science

Acute targeted induction of gut-microbial metabolism affects host clock genes and nocturnal feeding

1. Giorgia Greter
2. Claudia Moresi
3. Stefanie Oswald
4. Alice de Wouters d’Oplinter
5. Daria Künzli
6. Elisa Cappio Barazzone
7. Jiayi Lan
8. Emma Slack
9. Markus Arnoldini

• Curated by eLife

  eLife assessment

  Feeding, the circadian rhythm, and the gut microbiota are all intimately linked, motivating new approaches to identify causal relationships while minimizing confounding factors. The authors employ an innovative combination of the stool softener lactulose and a defined 3-member gut microbiota to acutely induce gut bacterial metabolism in mice during the daytime, resulting in changes in the ileal expression of clock genes and altered feeding behavior. Together, this study utilizes solid methods to provide important new insights into the role of gut microbiota in the circadian rhythm, setting the stage for follow-on studies aimed at better understanding the mechanisms responsible.

Reviewed by eLife