Baby-Associated MicroBiota of the Intestine (BAMBI) — an example from the clinic

Necrotising enterocolitis (NEC) is one of the most devastating gastro-intestinal diseases affecting pre-term and low birth- weight babies¹. Microbial dysbiosis (imbalance) has been established as the most likely underlying cause of the disease². Previous studies have revealed that pre-term babies suffering from NEC had more potentially pathogenic bacteria and less of the beneficial Bifidobacterium bifidum².

Dr. Matthew Clark and Dr. Richard Leggett’s teams at the Earlham Institute in Norwich, UK, are utilising metagenomic nanopore sequencing to profile pre-term infant gut microbiota, identifying not just species but also quantifying them and profiling their antimicrobial resistance (AMR) genes³.

Nanopore sequencing allowed pathogen identification and AMR profiling within 1 hour of sequencing.

Through a time-course experiment, the team was able to observe the impact of probiotic and antibiotic treatments on microbiota composition³. As the probiotic was administered, the amount of B. bifidum (identified to the species level) in the baby’s gut increased, with both long read nanopore sequencing and short-read platforms giving similar profiles.

Interestingly, the researchers also noted that the nanopore metagenomic sequencing approach allowed more detailed taxonomic assignment when compared with 16S rRNA analysis using a short-read sequencing platform, which failed to differentiate members of the Enterobacteriaceae family³.

Utilising real-time analysis of a faecal sample from a critically ill infant, the team were able to confidently call the presence of the pathogen Klebsiella pneumoniae along with corresponding AMR profiles within 1 hour of sequencing³.

Nanopore sequencing data was found to be of similar quality to that provided by short-read sequencing technology but, critically, it could be generated in a fraction of the time, requiring just 5 hours as opposed to 39 hours for the short-read technology.

In conclusion, the researchers highlighted how nanopore technology could, in the future, be applied to clinical applications:

‘Our results demonstrate that MinION sequencers offer the ability to progress from clinical samples to a potential tailored patient antimicrobial treatment in just a few hours’³.

This case study is taken from the Microbiome white paper.