Microbe moments: favourite bacteria, career paths and lab coats
Lee Katz, Andrew Page and Nabil-Fareed Alikhan answer questions recorded for the Microbigals’ “Microbe Moment”. They discuss favourite organisms, microbes in food and medicine, and their different routes into microbial bioinformatics. Along the way, they challenge the idea that working in microbiology necessarily means wearing a white lab coat or watching a rotating DNA helix on screen.
Listen to Episode 59: Microbe Moment Micro Binfie on SoundCloud
In this episode
Favourite microbes and awkward taxonomy
Nabil-Fareed Alikhan chooses Thermus aquaticus, an extremophile he values for its contribution to PCR. The choice prompts an explanation of what an extremophile is: a microbe living in an extreme environment, rather than anything to do with political extremism.
Lee Katz chooses Neisseria gonorrhoeae, then broadens his answer to the genus Neisseria. He is interested in their ability to take up DNA from other Neisseria and recombine frequently, and connects his preference to his early work in public health. Andrew Page recalls encountering E. coli without initially knowing what it was. The conversation turns to microbial name recognition and the familiar taxonomic argument over whether Shigella deserves a separate name from E. coli.
Microbes in food and treatment
Nabil points out that microbes make many favourite foods possible. Alongside yeast for bread and beer and Lactobacillus for yoghurt, he highlights chocolate as a partially fermented product whose production involves yeast and bacterial species.
Lee describes how, over the last ten or so years, some pharmaceutical companies have been using Listeria’s ability to infect cells in cancer-vaccine research. His example involves adding cancer-related genes, including a mesothelioma gene, so that infection can lead to their presentation. He presents this use of a pathogen’s biology as one of his favourite microbial facts.
Andrew discusses faecal microbiome transplants (FMT), describing patients improving within hours after spending months on antibiotics. He emphasises the uncertainty about which microbes are responsible for the benefit. The hosts also discuss delivery through tubes, preparation involving a blender, and household members as donors; this is a conversational account rather than a treatment protocol.
Stool donations and nappy sequencing
Lee recalls donating a stool sample for internal research and says he would like to see or analyse the resulting sequence data, although he doubts the files remain accessible to him. Andrew then recalls Aaron Darling sequencing samples from every nappy during the first few months of his child’s life. Andrew thinks PGM was used. The hosts discuss whether the work was published, but do not identify a paper.
Three routes into microbial bioinformatics
Nabil wanted to work in genomics and bioinformatics. His adviser suggested bacterial genomes because their small size should make them easier to work with, and that argument brought him into the field.
Lee’s route began when someone at CDC contacted his lab about analysing four Neisseria meningitidis genomes sequenced on the 454 platform. He describes them as some of the first genomes sequenced at CDC. As the next PhD student available, he took on the work and stayed because it was interesting and had a useful impact.
Andrew entered as a computer scientist, doing infrastructure and back-end database work within a pathogen genomics team. Conversations over lunch about sexually transmitted infections and foodborne pathogens eventually made him realise that he had changed fields without noticing.
Beyond the white lab coat
The hosts contrast their computational work with publicity images of microbiologists in pristine white lab coats. Andrew recalls being photographed pipetting buffer into a used Nanopore flow cell. Lee distinguishes that kind of staged image from photographs taken while he was actually performing a miniprep. They also discuss everyday lab coats being blue, graffitied or washed many times to an off-grey colour rather than looking like publicity photographs.
The other stereotype is the rotating DNA double helix on a computer screen. Their real examples are less cinematic: recognising patterns in DNA sequences, watching a GFF file scroll past, or inspecting BAM files and read pileups. Familiarity with these representations can make features such as contamination recognisable by eye.
Highlights
- 00:01:26 — Thermus aquaticus, PCR and what an extremophile is
- 00:02:17 — Lee’s interest in Neisseria DNA uptake and frequent recombination
- 00:03:32 — Shigella, E. coli and the argument over separate names
- 00:04:05 — Using Listeria’s intracellular infection biology in cancer-vaccine research
- 00:04:42 — Microbes behind bread, beer, yoghurt and chocolate
- 00:05:13 — From chocolate fermentation to faecal microbiome transplants
- 00:06:45 — Recalling Aaron Darling’s sequencing of samples from his child’s nappies
- 00:07:12 — Nabil’s route into microbiology through small bacterial genomes
- 00:08:01 — Four Neisseria meningitidis genomes on 454 bring Lee into the field
- 00:08:30 — Andrew’s gradual move from computer science into pathogen genomics
- 00:09:28 — White lab coats and the mismatch between publicity photos and bioinformatics
- 00:11:54 — The rotating DNA helix stereotype versus real sequence inspection
In their own words
I think some microbes have slightly better marketing budgets than others, really.
— Nabil-Fareed Alikhan, 00:03:25
Who is talking
- Lee Katz (host)
- Andrew Page (host)
- Nabil-Fareed Alikhan (host)
Also mentioned: Aaron Darling.
Tools and resources mentioned
PCR, 454, PGM, Nanopore flow cell, Miniprep.
Questions this episode answers
What are the hosts’ favourite microbes?
Nabil-Fareed Alikhan chooses Thermus aquaticus because of its contribution to PCR. Lee Katz chooses Neisseria gonorrhoeae and the wider Neisseria genus, particularly their DNA uptake and recombination. Andrew Page recalls E. coli as an early encounter rather than naming a clear favourite.
What does the episode say about microbes in chocolate?
Nabil describes chocolate as a partially fermented product. He explains that yeast and bacterial species help process the cocoa, placing chocolate alongside bread, beer and yoghurt as foods that depend on microbes.
How did Lee Katz get into microbial bioinformatics?
Someone at CDC contacted his lab for help analysing four Neisseria meningitidis genomes sequenced on 454. Lee was the next PhD student available to take on the work, and he stayed because of its scientific interest and impact.
What misconceptions about bioinformatics do the hosts discuss?
They challenge the expectation that bioinformaticians routinely wear pristine white lab coats or analyse rotating DNA double helices. Their examples of actual computational work include inspecting DNA sequences, GFF files, BAM files and read pileups.
This page was written from a machine transcript of the episode and checked against it. Listen to the episode for the whole conversation.
Show notes
Andrew, Nabil, and Lee answer the Microbigal’s questions for the “Microbe Moment.” You can find the Microbigals at https://www.microbigals.com