Debunking the myth of unculturable bacteria: recent advances and considerations in the culture of the gut microbiota

Abstract

The gut microbiota has a crucial function in human health. A disbalance in the microbiota composition can lead to a variety of diseases, including inflammatory bowel disease, neurodevelopmental disorders, and cancer. Therefore, it is important to study and identify the gut microbiota. In the past, the gut bacterial microbiota was studied using culture-based techniques. However, due to suboptimal methods and protocols, many bacteria were thought to be unculturable. Currently, new efforts to optimize culture-based techniques allowed the high-throughput cultivation of various previously uncultivated gut bacteria. This approach is called culturomics. The workflow of culturomics can roughly be divided into three steps: sample collection, culture, and bacteria identification. Here, we describe the recent advances and considerations in these culturomics processes, including sampling and preservation methods, the design of culture medium, and data collection and storage. Although there are many successful efforts in culturomics, there are still various aspects that need to be explored in the future. Further optimizing the culturomics protocol could potentially lead to the isolation and identification of novel, clinically relevant, bacterial species.