Poster Presentation Lorne Infection and Immunity 2020

Characterising microbiota diversity across the Australian community (#171)

Remy Young 1 , Tamblyn Thomason 1 , Jodee Gould 1 , Emily Gulliver 1 , Katherine Gibney 2 3 4 , Samuel Costello 5 6 , Samuel Forster 1 7
  1. Hudson institute, Clayton, VIC, Australia
  2. Communicable Disease Epidemiology and Surveillance, Victorian Department of Health, Melbourne, Victoria, Australia
  3. Doherty Institute, Melbourne, Victoria, Australia
  4. Victorian Infectious Diseases Service, Royal Melbourne Hospital, Parkville, Victoria, Australia
  5. Department of Gastroenterology and Hepatology, Queen Elizabeth Hospital, Woodville South, South Australia, Australia
  6. Basil Hetzel Institute, Woodville South, South Australia, Australia
  7. Wellcome Trust Sanger Institute, Cambridge, UK

The human gastrointestinal tract harbors one of the most diverse ecosystems of organisms currently known. The commensal microorganisms have important roles in carbohydrate metabolism, immune functions and essential human biology. Importantly, standardized western lifestyle, including diet, widespread sterilization and use of antibiotics, is driving the loss of diversity and extinction of many of these species. Disturbances to the microbial composition may also result in various pathological conditions, including inflammatory bowel disease, irritable bowel syndrome, obesity and diabetes.  Despite the essential role of these microorganisms, most of the current knowledge is skewed towards North American and European cohorts.

Until recently, it was generally accepted that the majority of the human gastrointestinal bacteria could not be cultured; however, we are now able to grow over 90% of these bacteria on a single culture medium1. Despite these advances, at least 2000 species remain to be purified and genome sequenced. Combining these culturing techniques, 16S rRNA sequencing, shotgun metagenomic sequencing and whole genome sequencing, this project aims to determine the variation in the microbiome by sampling from different individuals across Australia. Analysis of 18 faecal samples resulted in purification and 16S rRNA capillary sequence-based identification of 1858 isolates, of which 571 were putatively novel species. Parallel metagenomic sequencing suggests that substantial variation in community composition exists between individuals. Phenotypic whole genome sequencing analysis was performed on 82 candidate isolates to assess genomic differences in carbohydrate metabolism and antibiotic resistance, highlighting strain level variation between closely genetically linked isolates. Overall, substantial compositional and diversity differences were observed, as was a large percentage of unclassified reads in metagenomic sequencing, highlighting the need for further investigation into the microbiome in an Australian context.

  1. Browne, H. P. et al. Culturing of ‘unculturable’ human microbiota reveals novel taxa and extensive sporulation. Nature 533, 543-546 (2016).