The term gut bacteria is chosen over the ancient word flora since the latter fails to account for the various nonbacterial components (such as archaea,viruses.fungi) that are now found to be common gut residents. The gut microbiome is a naturally occurring community of hundreds of distinct bacteria species that have a role in human health and disease. Bacterial species composition varies greatly between persons and has previously been linked to a variety of illnesses, including obesity, immunological response, and mental health. The human microbiome is made up of 100 trillion bacteria, viruses, and fungi, with the majority of them living in the human gut. The microbiome is important for protecting against pathogenic microbes, producing short-chain fatty acids as a source of energy, vitamin synthesis, fat storage, and central nervous system modulation. The first line of defence against bacterial infections is to use antibiotics.

Proton pump inhibitors, metformin, selective serotonin reuptake inhibitors, and laxatives are all medicines that affect the makeup and function of the gut microbiota. PPIs have been shown to alter specific taxa in the human gut microbiota, including increases in the abundance of Enterococcaceae, Streptococcaceae, Firmicutes, and Lactobacillus, as well as decreases in the abundance of Bacteroides and Clostridium cluster IV, resulting in a decrease in gut microbiota diversity. Metformin affects the gut microbiota composition by promoting the growth of some bacteria, such as Akkermansia muciniphila, Escherichia spp., or Lactobacillus, while decreasing the levels of others, such as Intestini bacter, according to several human and animal research. Hundreds of different bacteria species live in the human intestine in natural ecosystems.