Categories: Sanger Science5 May 20163.2 min read

Karma Bacterium: New additions to the Culture Club

DATE: 05/05/16
By Hilary Browne


Bacteria discovered from human faecal microbiota. Credit: Nature. DOI: 10.1038/nature17645

The bacteria that reside within our gut, termed the ‘intestinal microbiota’, play a vital role in human health and disease. They salvage energy for us from complex carbohydrates we can’t digest, they train our immune system to recognise ‘friend’ from ‘foe’ and they also help resist invasion by pathogens. Imbalances in this complex community are thought to contribute to disease and disorders such as obesity and inflammatory related conditions, though the mechanisms of this are not fully understood yet.

Much progress has been made in recent years to understand the role our intestinal residents play; however, there is still a barrier when it comes to culturing or growing these bacteria. This is due to the majority of the intestinal microbiota being strict anaerobes, growing only in the absence of oxygen. They therefore need to be cultured in an anaerobic environment and many of them require specific growth conditions and nutrients.

Our lab has recently developed a process to culture, identify and store these bacteria (Figure 1). Using both a complex growth medium containing lots of energy sources and our anaerobic growth cabinets we cultured over 130 different bacterial species from faeces (Figure 2). Interestingly, the dry weight of faeces is largely composed of bacteria shed from your large intestine. Many of these bacteria are novel and have never been grown and isolated before. We also used whole genome sequencing to determine the composition of the genes within these different species. This will help us understand the biological role they play within our gut.

Some members of the intestinal microbiota make spores which are small dormant structures that are extremely resistant to disinfectants, oxygen and other factors that would usually kill the bacterium. This form of bacterial hibernation allows survival outside of the gut of its host, once it is back in its normal environment, the spore can germinate and the bacterium can continue its life cycle. We found that the intestinal microbiota contains a large proportion of spore-forming bacteria. This changes the way we think about transmission and acquisition of our microbiota, it could now be a much more dynamic and active process as intestinal spore-formers are not limited by the outside aerobic environment.

The bacteria we isolated can be frozen at very cold temperatures and will grow again when thawed out; this allows them to be stored for long periods of time. We have sent these isolates to different public culture collections around the world where other researchers can buy them and use them for their work. This will facilitate research in this expanding field and will lead to a better understanding of how this essential group of bacteria function.

Our group is also interested in developing therapeutics to treat disorders associated with the intestinal microbiota. We know that the addition of particular mixes of intestinal bacteria missing from a person’s gut can help restore health. The bacteria we have isolated will provide a valuable starting point to developing a live bacterial medicine.

Hilary Browne is an Advanced Research Assistant in the Host-Microbiota Interactions Laboratory headed by Trevor Lawley. The group seek to understand the role our microbiota play in human health and disease and the interactions that take place between the host and the microbial community. This knowledge will facilitate development of therapeutics to treat disorders associated with imbalances in our microbiota.


  • Hilary P. Browne et al. (2016). Culturing of ‘unculturable’ human microbiota reveals novel taxa and extensive sporulation. Nature. DOI of paper: 10.1038/nature17645
  • Samuel C. Forster et al. (2016). HPMCD: the database of human microbial communities from metagenomic datasets and microbial reference genomes. Nucleic Acids Research. DOI of paper:10.1093/nar/gkv1216