In 2019, there have been substantial advances in our understanding of the gut microbiome. Key developments include an improved gut-on-a-chip system, a search for small proteins produced by the commensal gut microbiome and the publication of one of the most comprehensive multi-omic datasets for interrogating host–microorganism interactions in inflammatory bowel disease.
Key advances
Researchers successfully developed an improved gut-on-a-chip system that enabled sustained co-culture of gut epithelium with a complex anerobic microbial community that was recoverable and stable after 5 days3.
A metagenome-mining effort to discover small proteins produced by the commensal gut microbiome identified 4,539 protein families that have never before been described in the commensal gut microbiome4.
One of the most comprehensive multi-omic datasets for interrogating host–microorganism interactions in IBD identified a characteristic dysbiotic composition in patients with IBD that deviated from that of non-IBD controls, as well as large inter-individual differences7.
This is a preview of subscription content, access via your institution
Relevant articles
Open Access articles citing this article.
-
Enlightening the taxonomy darkness of human gut microbiomes with a cultured biobank
Microbiome Open Access 21 May 2021
Access options
Access Nature and 54 other Nature Portfolio journals
Get Nature+, our best-value online-access subscription
$29.99 /Â 30Â days
cancel any time
Subscribe to this journal
Receive 12 print issues and online access
$209.00 per year
only $17.42 per issue
Buy this article
- Purchase on Springer Link
- Instant access to full article PDF
Prices may be subject to local taxes which are calculated during checkout
References
Kim, H. J. et al. Human gut-on-a-chip inhabited by microbial flora that experiences intestinal peristalsis-like motions and flow. Lab Chip 12, 2165–2174 (2012).
Park, G.-S. et al. Emulating host-microbiome ecosystem of human gastrointestinal tract in vitro. Stem Cell Rev. 13, 321–334 (2017).
Jalili-Firoozinezhad, S. et al. A complex human gut microbiome cultured in an anaerobic intestine-on-a-chip. Nat. Biomed. Eng. 3, 520–531 (2019).
Sberro, H. et al. Large-scale analyses of human microbiomes reveal thousands of small, novel genes. Cell 178, 1245–1259.e14 (2019).
Bazzini, A. A. et al. Identification of small ORFs in vertebrates using ribosome footprinting and evolutionary conservation. EMBO J. 33, 981–993 (2014).
Aspden, J. L. et al. Extensive translation of small open reading frames revealed by Poly-Ribo-Seq. eLife 3, e03528 (2014).
Lloyd-Price, J. et al. Multi-omics of the gut microbial ecosystem in inflammatory bowel diseases. Nature 569, 655–662 (2019).
Author information
Authors and Affiliations
Corresponding author
Ethics declarations
Competing interests
The authors declare no competing interests.
Rights and permissions
About this article
Cite this article
Devkota, S. Big data and tiny proteins: shining a light on the dark corners of the gut microbiome. Nat Rev Gastroenterol Hepatol 17, 68–69 (2020). https://doi.org/10.1038/s41575-019-0243-6
Published:
Issue Date:
DOI: https://doi.org/10.1038/s41575-019-0243-6
