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Genome analysis will reveal how bacteria in our guts make themselves at home

30 June 2011

Researchers from the Institute of Food Research and The Genome Analysis Centre, which are strategically funded by BBSRC, have published the genome sequence of a gut bacterium, to help understand how these organisms evolved their symbiotic relationships with their hosts.

The relationship between gut bacteria and the gastrointestinal tract is one of IFR's main research areas. Key to understanding the role of bacteria in establishing and maintaining gut health is knowledge of how the very close relationship between the bacteria and their hosts has evolved to be mutually beneficial to both.

One bacterial species, Lactobacillus reuteri, has been used as a model for studies in this area, and TGAC, a partner of IFR on the Norwich Research Park, has sequenced its genome, funded by the Biotechnology and Biological Sciences Research Council (BBSRC). The collaboration between the two institutes will provide new insights into the genomic basis for host adaptation of L. reuteri to the gut.

L. reuteri inhabits the gastrointestinal tract from a large host range, from humans to rodents and birds. Previous work had shown that each host species has its own subpopulation of L. reuteri strains. These strains differ slightly, and are host specific, and the differences between them are driven by evolutionary pressures from the host.

In close collaboration with IFR scientists, TGAC sequenced and assembled the genome of a L. reuteri strain obtained from pig to a high quality draft standard and also provided a full annotation. The annotation is needed to identify which genes carry out which functions in the sequence. Comparisons between different strains of L.reuteri, which have already been made available in the major international sequence databases, helped identify a set of genes unique to this particular strain.

The IFR and TGAC researchers are now hoping to use this information to elucidate exactly what it is that restricts certain L. reuteri strains to specific hosts.

L. reuteri confers certain health benefits, and has a role in modulating the immune system. A greater understanding of how L. reuteri host adaptation will help in efforts to exploit these health benefits, for example in the production of new probiotics.

The gastrointestinal tract contains many millions of bacteria, known collectively as the microbiota. IFR is also developing a model microbiota that is representative of the human colonic microbiota. This will become a powerful tool for investigating the function and interplay of the microbiota within the gastrointestinal system. It will also become an integral part of studies investigating the extent, diversity and function of metabolic diversity in the microbiota.

Reference: Genome sequence of a vertebrate gut symbiont Lactobacillus reuteri ATCC 53608, Heavens et al, Journal of Bacteriology doi:10.1128/JB.05282-11



BBSRC is the UK funding agency for research in the life sciences and the largest single public funder of agriculture and food-related research.

Sponsored by Government, BBSRC’s budget for 2011-12 is around £445M which it is investing in a wide range of research that makes a significant contribution to the quality of life in the UK and beyond and supports a number of important industrial stakeholders, including the agriculture, food, chemical, healthcare and pharmaceutical sectors.

BBSRC provides institute strategic research grants to the following:

  • The Babraham Institute
  • Institute for Animal Health
  • Institute of Biological, Environmental and Rural Sciences (Aberystwyth University)
  • Institute of Food Research
  • John Innes Centre
  • The Genome Analysis Centre
  • The Roslin Institute (University of Edinburgh)
  • Rothamsted Research

The Institutes conduct long-term, mission-oriented research using specialist facilities. They have strong interactions with industry, Government departments and other end-users of their research.

External contact

11 October 2005

The following stories appear in the October 2005 edition of Business, the quarterly magazine of research highlights from the Biotechnology and Biological Sciences Research Council (BBSRC).

Controlling 'superpests'
Scientists have developed a new technique that helps make pesticides more effective by removing insects’ ability to exhibit resistance. Their research will extend the effective life of current pesticides, reduce the amount that needs to be sprayed and remove the need for farmers to move to stronger and more harmful chemicals. The new technique relies on applying a chemical to block the insect’s processes that can degrade a pesticide. With the pests newly rendered helpless farmers can apply pesticide to kill them.
(Page 13)

Dr Graham Moores, Rothamsted Research, Tel: 01582 763133 ext 2483,

Fruit fly studies open new avenue in cancer research
Researchers have discovered a family of amino acid transporters that are powerful growth promoters in fruit flies. When the transporters were overexpressed in a fly, its cells became hypersensitive to insulin-like molecules in the body that have a long-term role in promoting cell growth in development and cancer, and the cells grew excessively. If the equivalent genes in humans have the same effect then this discovery could lead to new drugs or even dietary advice that could block their activity and slow down the growth of tumours.
(Page 20)

Dr Deborah Goberdhan, University of Oxford, Tel: 01865 282662, e-mail:

Gene delivery vehicle for skeletal regeneration
UK scientists are working on new methods to regenerate cartilage and bone by delivering genes to stem cells within the body to instruct them to turn into bone cells. The new research will use tiny nanoscopic systems that cross the surface of a stem cell and then deliver the genes into that prompt the cell to turn into a bone cell. This method of gene delivery could provide significant healthcare benefits as trauma, degenerative disease and bone loss with old age all lead to patients needing orthopaedic procedures that require new bone.
(Page 26)

Professor Richard Oreffo, University of Southampton, Tel: 023 8079 8502, e-mail:

'Ending up' with antibody production
Scientists are pioneering a new technique to produce large numbers of antibodies quickly and reliably and this is being used to help the study of dangerous bacteria. The new technique harnesses the unique properties of the C-terminus of a protein to produce a large number of antibodies that will only bind to a specific protein. The antibodies can then be used to identify, count and track the proteins. Proteins are central to many areas of bioscience research as they are often the targets for vaccines, the raw materials for bioprocessing or are employed as environmental biomarkers. Production of panels of antibodies that previously took years may now be possible in just weeks.
(Page 14)

Dr Rob Edwards, Imperial College Hammersmith Hospital, Tel: 020 8383 2055,

Building proteins on demand
A multidisciplinary team of researchers is developing new tools to direct the evolution of proteins, a move that will help the search for new anti-HIV drugs. The scientists have developed an efficient methodology for generating every possible mutation of a single protein and then assembling this into a library to identify which variations are resistant to drugs and which are not. This information can then be used to develop and validate new drugs.
(Page 9)

Dr Cameron Neylon, University of Southampton, e-mail:

Bringing physical forces to bear
World-leading laser facilities at the Rutherford Appleton Laboratory in Oxfordshire will be harnessed for biological studies thanks to joint funding from two Research Councils. A new laser system will study the bonds between atoms by looking at the unique frequency of their vibration. The new system will be able to take measurements of these ‘vibrational fingerprints’ at a scale so small that they will by able to study how cells repair damaged DNA, how proteins fold and develop new ways of detecting cancerous and pre-cancerous cells.
(Page 6)

Professor Tony Parker, CCLRC Rutherford Appleton Laboratory, Tel: 01235 445109, e-mail:

‘Model gut’ moves to commercialisation
Researchers at the Institute of Food Research in Norwich are moving closer to turning ten years of research on the workings of the human gut into a computer controlled model that will enable scientists to predict the digestive processes of human gut using real food and medicines. The result will be a revolutionary research tool that will enable researchers to examine the physical, chemical and biochemical functions of the gut as a whole.
(Page 3)

Zoe Dunford, Institute of Food Research, Tel: 01603 255111, e-mail:



The Biotechnology and Biological Sciences Research Council (BBSRC) is the UK funding agency for research in the life sciences. Sponsored by Government, BBSRC annually invests around £380 million in a wide range of research that makes a significant contribution to the quality of life for UK citizens and supports a number of important industrial stakeholders including the agriculture, food, chemical, healthcare and pharmaceutical sectors.