The BioInvestigationIndex (BII)

Title:

Xenobiotics shape the physiology and gene expression of the active human gut microbiome

Organism(s):

human gut metagenome

Description:

RNA-Seq transcriptional profiling of human gut metagenome after several days of incubation in the presence of various drugs. [original description: The human gut is colonized by trillions of microorganisms that influence human health and disease through the metabolism of xenobiotics, including therapeutic drugs and antibiotics. The diversity and metabolic potential of the human gut microbiome have been extensively characterized, but it remains unclear which microorganisms are active and which perturbations can influence this activity. Here, we use flow cytometry, 16S rRNA gene sequencing, and metatranscriptomics to demonstrate that the human gut contains distinctive subsets of active and damaged microorganisms, primarily composed of Firmicutes, which display marked temporal variation. Short-term exposure to a panel of xenobiotics resulted in significant changes in the physiology and gene expression of this active microbiome. Xenobiotic-responsive genes were found across multiple bacterial phyla, encoding novel candidate proteins for antibiotic resistance, drug metabolism, and stress response. These results demonstrate the power of moving beyond DNA-based measurements of microbial communities to better understand their physiology and metabolism. RNA-Seq analysis of the human gut microbiome during exposure to antibiotics and therapeutic drugs.]

Design(s):

RNA-seq of coding RNA

Experimental factor(s):

healthy adult 3 recorded
Individual B Individual A Individual C
incubation time 2 recorded
4 hours T0
treatment protocol of gut microbiome 20 recorded
digoxin tetracycline gDNA EtOH nizatidine norfloxacin chloramphenicol doxycycline sulfasalazine digitoxin kanamycin untreated (no incubation) ampicillin erythromycin pH5 ciprofloxacin tetramisole pH4 pH7 phenacetin
collection day 2 recorded
day1 day2

Publication(s):

Maurice CF, Haiser HJ, Turnbaugh PJ
Xenobiotics shape the physiology and gene expression of the active human gut microbiome. PubMed:23332745

Sample attribute(s):

healthy adult 3 recorded
Individual B Individual A Individual C
incubation time 2 recorded
4 hours 0
treatment protocol of gut microbiome 20 recorded
digoxin tetracycline gDNA ethanol nizatidine (CHEMBL653) norfloxacin chloramphenicol doxycycline sulfasalazine digitoxin kanamycin control condition ampicillin erythromycin pH5 ciprofloxacin tetramisole pH4 pH7 phenacetin
sex of host 2 recorded
female organism male organism
pH 3 recorded
5 4 7
collection day 2 recorded
day1 day2
organism 1 recorded
human gut metagenome