Culturomics for Gut Microbiota Research

The human microbiota is a complex combination of microbes living in human tissues and body fluids located in different parts of the body. Although little is known about its composition, it has been clearly shown that the human microbiome plays an important role in health and diseases. From basic culture techniques to sophisticated sequencing methods, many methods have been used to study and analyze the human microbiota. However, each technique stands alone with its pros and cons rendering none of it indispensable. Culturomics has been mainly used for the study of human microbiota, but increasingly extended to characterize the microbiota of other mammal species, including wildlife. Creative Biolabs focuses on live biotherapeutic product (LBP) development and our experienced R&D team will provide you with all the support you need during the development of your LBP products in the pipeline.

Culturomics Technology

Culturomics is a high-throughput culture method that uses MALDI-TOF mass spectrometry to identify bacterial species. Culturomics was originally designed to identify new bacterial species in the gut microbiota, but it has since been applied to other microbiota, such as those of the human vagina and urinary system. The first step in culturomics is to divide the samples and diversify them into different culture conditions. Culture conditions are designed to inhibit the culture of most populations and to promote the growth of fussy microorganisms at lower concentrations. An important feature of culturomics is the rapid (<1 hour) identification by MALDI- TOF mass spectrometry, which relies on the comparison of the protein mass spectra of the isolate with an upgradable database. If identification fails, the isolate will be sequenced by 16S ribosomal RNA (rRNA). If there is < 98.65% similarity to the closest official strain, the isolate could be a new species. The discovery of new taxa is confirmed by genome sequencing, and taxonogenomics is used to formally describe the bacterium. All identification results were compared with a database containing bacterial species recovered from humans. Culturomic identification of new species adds to the list of bacteria related to humans.

The culturomic workflow.Fig.1 The culturomic workflow. (Lagier, 2018)

Advantages of Culturomics for Gut Microbiota Research

Culturomics represents a novel approach to the study of complex microbial ecosystems, such as the human gut, that: (i) has the potential to detect minority populations; (ii) is not limited to eubacteria; and (iii) provides strains that allow extensive characterization of new species and study of interactions between different bacterial strains present in a given microbiome. Another advantage of using culture methods is additional information about the viability of detected microorganisms. Culturomics has not been developed to eliminate previous methods of adaptation, but to complement them by highlighting bacteria considered "unculturable" because they may play an important role in health balance and disease development. All of these microbiome analyses illustrate the need for a healthy gut microbiome. The next step in the regulation of the human gut microbiome may be to develop specific bacterial therapies aimed at restoring intestinal homeostasis. This has been tested in C. difficile infections by decreasing the number of recurrent episodes.

Comparison between metagenomics and culturomics.Fig.2 Comparison between metagenomics and culturomics. (Greub, 2012)

Culturomics allows for the conservation of bacterial strains and could be an innovative approach to developing bacteriotherapies based on the scientific observation of the composition of the gut microbiota. Creative Biolabs is a premier LBP development contract provider in the United States. We have accumulated a wealth of experience in the study of gut microbiota. If you are interested in our cluturomics services for gut microbiota research, please contact us for more information.


  1. Lagier, J.C.; et al. Culturing the human microbiota and culturomics. Nat Rev Microbiol. 2018 May 1; 16: 540-550.
  2. Greub, G. Culturomics: a new approach to study the human microbiome. Clin Microbiol Infect. 2012 Dec; 18(12): 1157-9.

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