Bacteria accounts for 99% of the gut microbiota, whereas archaea, fungi, viruses and protists compose the remaining 1%.

The establishment of a gut microbiota goes through colonization, succession and replacement, which increases abundance and diversity, and results in a relatively constant α-diversity microbial structure in the host. With the first use of high-throughput 16S rRNA sequencing to characterize fecal bacteria in 1996, microbiota-centric research related to health and diseases has grown tremendously ( 3). The developments of technologies in molecular biology, various omics, and computation allow efficient and accurate analysis of data derived from DNA sequence, metabolites and proteins from the gut microbiota.

The gut microbiota is the most complex and largest micro-ecosystem of archaea, bacteria, and eukaryotes residing in the lumen, and plays critical roles in growth, metabolism, immunity, environmental adaption, and behavior of the host.

The original observation that diarrhea caused by the use of antibiotics in human patients could be treated with intestinal bacteria from healthy donors led scientists to appreciate the roles of gut microbiome in the general health of the host ( 2). The meticulous skills and interest in lens making of Antonie van Leeuwenhoek eventually extended human observation capability beyond the edge of sight into the world of microbes that he called animalcules ( 1).

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