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GENES AND GUT: EXPLORING THE RELATION BETWEEN GUT MICROBIOTA AND HUMAN GENE EXPRESSION

 

The bacteria that are associated with the human gastrointestinal tract, referred to as gut microbiota play an important role in the metabolism, nutrition, physiology, and immune function of the host human. This microbial community shows a high degree of variation among individuals based on their diet, medication, genetics etc., and their imbalance is strongly associated with diseases like inflammatory bowel syndrome, Crohn’s disease, colorectal cancer, and systemic metabolic diseases like obesity and diabetes.


Studies in mice have also suggested that gut microbiota are also involved in gene regulation influencing epigenetics and binding of transcription factors. In vivo studies in humans also suggested the influence on expression and RNA splicing by the gut microbiota but it is difficult to conduct large scale studies while accounting for environmental factors present in the host.


Using in vitro studies involving the inoculation of human colonic epithelial cells or colonocytes with live gut microbiota from five random, healthy individuals and analysis of gene expression and microbiota composition over a period of 1, 2, and 4 hours, it was found that 5413 genes showed expression levels different from the control consisting only colonocytes with genes PDLIM5 and DSE showing different expression levels consistently over the time of study and these genes are found to be associated with protein translation, and cell junctions such as adherens junctions indicating an interplay between gut microbiota and human gene expression.



The colonocytes were grown in hypoxic conditions in order to mimic the gut environment and the levels of responses of the host cell is measured by transcriptome sequencing or RNA-seq. It was noted that the microbial community did not change drastically over time and it maintained its individual characteristics but in the presence of colonocytes 13 out of 112 taxa showed various other levels of abundance with the rest of them showing no changes in composition.


Using a likelihood ratio test, the influence of microbiota composition on the host gene expression was studied by comparing the models in the presence or absence of the microbial community and found that 405 genes showed different expression levels in response to 5 different microbial communities. These results suggested that genes had different responses to the same treatment and no two microbiota had induced the same level of response in the genes.


Using DESeq it was also identified that the expression of 121 genes is associated with presence of 46 taxa and among these 35 were connected with expression of two or more genes which suggests that a single microbe may influence the expression of multiple genes and there is a mechanism by which these microbes may influence the host cells. These 121 genes are grouped into two clusters based on the association with different genera, first cluster includes 70 genes associated with genera Ruminococcus, Coprococcus, and Streptococcus and are involved in cell junction assembly and the remaining genes in the second cluster are associated with genera Odoribacter, Blautia, and Collinsella and involved in protein targeting of the endoplasmic reticulum. Among these, 21 genes were already found to be associated with colorectal cancer, obesity, type 2 diabetes and irritable bowel syndrome, with genus Collinsella found to be strongly connected with gene GLTP which is associated with these syndromes.



A representation of relationship between genes (in blue) with microbial taxa (in red)

For further demonstration of the influence of a particular microorganism on the host gene regulation, the colonocytes were treated with microbial sample containing no trace of Collinsella aerofaciens and samples containing known abundances of 0.01%, 0.1%, 1%, and 10% relative to the whole microbiota sample and using RNA-seq 1570 genes were identified whose expressions levels had changed in a manner dependent on the presence and abundance of Collinsella aerofaciens. It was also found that there is a positive correlation of effects on the gene expression between Collinsella and other microbes in the cluster and negative correlation in the cluster which does not contain Collinsella. These results suggest that the whole gut microbiota should be taken into consideration for the study of host-microbiota interactions.


Furtherly ATAC-seq was employed in the colonocytes inoculated with each of five microbial samples for 2 hours to elucidate the regulatory mechanism involved in the changes in gene expression in response to exposure to microbiota and was able to detect ATAC-seq peaks at the transcription start sites (TSS) of expressed genes. Using DESeq2 it was found that only a limited number of regions on chromatin were differently accessible across the five treatments. It was found that the enrichment of differently accessible regions at 2 hours within 50 kb of genes, were differentially expressed at 4 hours suggesting that the chromatin accessibility initially observed had led to changes in gene expression by 4 hours after inoculation of gut microbiota in the colonocytes. Also the directions of changes in chromatin accessibility and in gene expression were correlated  which indicated that access to the chromatin has led to upregulation of gene expression. Footprinting analysis of ATAC-seq data using CENTIPEDE had identified 397 transcription factors that were active under the treatment and control which may be involved in modulating the expression of these genes. Further enrichment analysis using a logistic model, 110 transcription factors were identified that may influence the gene expression in response to exposure the microbiota that may not require changes in chromatin accessibility which included  factors like AP1, RELB, NkFB, STAT1, STAT3, HFN4A and many others which are involved in immune response pathways, inflammation, and chemokine signaling.


These studies can pave a path for novel therapeutics aimed towards diseases connected with gut microbiota by manipulating the microbial population by supplementing with a specific microorganism with predictable influence on host genome expression in order to improve the human health.


REFERENCE:

  1. Richards AL, Muehlbauer ALAlazizi A, Burns MB, Findley A, Messina F, Gould TJCascardo C, Pique-Regi RBlekhman R, Luca F2019.Gut Microbiota Has a Widespread and Modifiable Effect on Host Gene Regulation. mSystems4:10.1128/msystems.00323-18. https://doi.org/10.1128/msystems.00323-18

  2. Bull MJ, Plummer NT. Part 1: The Human Gut Microbiome in Health and Disease. Integr Med (Encinitas). 2014 Dec;13(6):17-22. PMID: 26770121; PMCID: PMC4566439.




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