Depletion of microbiome-derived molecules in the host using Clostridium genetics
Authors: Kamir J Hiam
Curt R Fischer
Justin L Sonnenburg
Breanna M Allen
Kazuki Nagashima
Matthew H Spitzer
Dylan Dodd
Steven Higginbottom
Will Van Treuren
Michael A Fischbach
Chun-Jun Guo
Journal: Science (2019)
Discipline: Multidisciplinary
Keywords: gut microbiota; molecules; host circulation; Clostridium spp.; clean deletions
Affiliations: Department of Bioengineering and ChEM-H, Stanford University, Stanford, CA 94305, USA., Jill Roberts Institute for Research in Inflammatory Bowel Disease, Department of Medicine, Weill Cornell Medicine, NY 10021, USA., Graduate Program in Biomedical Sciences, Departments of Otolaryngology and Microbiology and Immunology, Helen Diller Family Comprehensive Cancer Center, Parker Institute for Cancer Immunotherapy, University of California, San Francisco, San Francisco, CA 94143, USA., Chan Zuckerberg Biohub, San Francisco, CA 94158, USA., Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA., Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA., Graduate Program in Biomedical Sciences, Departments of Otolaryngology and Microbiology and Immunology, Helen Diller Family Comprehensive Cancer Center, Parker Institute for Cancer Immunotherapy, University of California, San Francisco, San Francisco, CA 94143, USA.  ., Department of Bioengineering and ChEM-H, Stanford University, Stanford, CA 94305, USA.  .

Abstract:  The gut microbiota produce hundreds of molecules that are present at high concentrations in the host circulation. Unraveling the contribution of each molecule to host biology remains difficult. We developed a system for constructing clean deletions in Clostridium spp., the source of many molecules from the gut microbiome. By applying this method to the model commensal organism Clostridium sporogenes, we knocked out genes for 10 C. sporogenes-derived molecules that accumulate in host tissues. In mice colonized by a C. sporogenes for which the production of branched short-chain fatty acids was knocked out, we discovered that these microbial products have immunoglobulin A-modulatory activity. 

Retracted: No

PubPeer comments:
 Dear authors, We have with great interest and excitement discussed your paper u201cDepletion of microbiome-derived molecules in the host using *Clostridium genetics*u201d during our weekly literature meeting. Your paper not only provides a convincing way to deplete the organism of specific bacterial metabolites, but also provides an encouragement for scientists who would plan to use intestinal microbiota for therapeutical purposes. We especially appreciated the high readability of both the text and the figures. However, after reading your paper, we were left wondering about a few things that we think would be interesting to see explored or commented, either here, or in future publications: 1.tFig.3 - As we are not familiar with metabolomics, we have some basic questions about the chromatograms presented in Fig.3. There is a double peak present in (1) WT sample, which is not present in any other sample. Does the peaksu2019 composition matter? Peaks present in (9) differ in size in comparison with WT. Does peak size correspond to metabolite amount? Some peaks are slightly shifted between samples ((5) and (9) in particular). Does it mean anything in terms of the compound chemistry or is it just an acceptable variation between measurements? Again, we are not acquainted with the field, and thus unsure how to interpret these differences. 2.tFig.4 - Why arenu2019t all the metabolites measured in all bodily fluids at the same time? Even if the given metabolite should not be present in each excreta, it may have been useful if shown or commented upon. 3.tFig.5C - As we understand, your mass cytometry experiment analysed the cellular composition of small intestinal lamina propria. However, you have only shown the data for IgA plasma cells. Were any other cell types significantly different between mice? 4.tFig.5 - Did you measure plasma levels of IgA? Is the decreased IgA production a systemic phenomenon? We would greatly appreciate it if you could share your thoughts on our comments above, as this may aid us (and other readers) in better understanding of your work and thus help us all contribute to a fruitful scientific discussion. ,