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Microbiome Gene Expression Study Reveals How Gut Bacteria Interact

The largest microbiome gene expression study to date, conducted by the members of the Clinical-Microbiomics team, reveals how gut bacteria behave when they interact with each other.  

 

By Sofia Popov


With data describing the expression of over 700,000 genes from hundreds of bacterial species, this new study, published in Nature Microbiology gives primary insights into the microbial community-wide transcriptional interactions. Carried out at the Technical University of Denmark, by our Director of Bioinformatics, Damian Rafal Plichta, and led by our CSO, Henrik Bjørn Nielsen, this study is the largest to characterise gene expression in the human gut microbiome.

Carried out at the Technical University of Denmark, by our Director of Bioinformatics, Damian Rafal Plichta, and led by our CSO, Henrik Bjørn Nielsen, this study is the largest to characterise gene expression in the human gut microbiome.

Numerous biological factors define the gut microbiota; in addition to symbiotic and antagonistic interactions between microbes, other important factors include host genetic effects, dietary habits and antibiotics. The gastrointestinal tract acts as a habitat for this ecosystem of hundreds of microbial species, yet few microbes can be readily cultivated. This is thought to be due to the dependencies between species, with other studies on microbial co-occurrence indicating that community substructures reflect the functional and metabolic interactions between cohabiting species in the gut. Since previous studies have focused on isolated microbes, this study sought to investigate how different gut microbes interact in their natural environment, particularly given their overlapping functional roles.

Since previous studies have focused on isolated microbes, this study sought to investigate how different gut microbes interact in their natural environment, particularly given their overlapping functional roles.

Using metagenomics and microarray-based metatranscriptomics data taken from over 230 stool samples, the team systematically identified transcriptional interactions between pairs of coexisting gut microbes. Among the significantly interacting pairs, results showed that the transcriptional changes led to a reduction in expression of orthologous functions between the coexisting species. The species-species transcriptional interactions were enriched for essential functions involved in the metabolism of carbohydrates and amino acids, butyrate biosynthesis and bacterial chemotaxis, to name a few. Moreover, the team was able to demonstrate that expression of certain functions, such as DNA replication, is less affected by coexistence, whilst central metabolism, including anaerobic respiration and environmental sensing, show more variation according to the specific community structure.

Rather than outcompeting one another, gut microbes manage the co-existence by differentiating at the level of transcriptional activity, which can promote a rich microbial community

These findings demonstrate that rather than outcompeting one another, gut microbes manage the co-existence by differentiating at the level of transcriptional activity, which can promote a rich microbial community. Using these insights, researchers will be able to see how bacterial behavior changes depending on which other bacteria are present, and to understand these influences outside their given context. In turn, these findings have potentially powerful applications in disease therapeutics, such as for inflammatory bowel disease, and in the future development of probiotics and faecal microbiota transplants.


 

REFERENCE 

Plichta D.R., et al. Transcriptional interactions suggest niche segregation among microorganisms in the human gut. Nature Microbiology, 1, p.16152. (2016). DOI: 10.1038/nmicrobiol.2016.152

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