The art of exploring the fecal-ome

The community of bacteria living inside our own guts is about as local an ecosystem as we’re likely to find. So you’d think navel-gazing biologists would already know all about it. But several barriers have made this ecosystem nearly as inaccessible as the forests of the Amazon River were for 18^th century naturalists.

One problem has been that bacteria have traditionally been studied by growing them in glass or plastic dishes containing a “culture medium,” typically a sort of gelatin concoction containing mystery ingredients like calf serum. Lots of bacteria grow well on this stuff, but even more don’t. And most of what we know about bacteria comes from studies of the short of list bacteria that will grow in the lab.

Advances in genomics have revealed the presence of new species of bacteria everywhere biologists have looked. But, apparently, even that diversity is just the tip of the iceberg.

Computer scientists and geneticists at Stanford recently collaborated on a technique and uncovered an amazing amount of diversity in the gut contents of a human male, who volunteered a fecal sample. In the sample, the Stanford team found not just lots of species, but also lots of sub-strains — as many as five different strains of a single species. You can read more about the technique in the press release I wrote about the study, which appeared today in Nature Biotechnology.

The work's similarity to an incredibly tough jigsaw puzzle captured my imagination.

Geneticist Michael Snyder, PhD, who is a senior author on the paper, explained to me that it’s now pretty easy to assemble the genome of a single person or bacterium from the short strands of DNA in a sample.

But when you have a mix of lots of different species, he said, it’s like assembling 100 jigsaw puzzles from a single pile of pieces from all those different jigsaw puzzles. Not only do you have to fit the pieces together, but you have to know which puzzle or species each piece came from.

If the jigsaw puzzles are as different as, say, a Van Gogh Sunflowers painting and Ansel Adams’ "Moonrise, Hernandez, New Mexico", you wouldn’t have much trouble separating the pieces. But what if you’ve got several strains of the same bacterial species? That’s the equivalent of a mix of puzzles all depicting different versions of Monet’s paintings of Cathedral Rouen.

Previously: Microbiome explorations stoke researcher's passion, At TEDMED 2015: How microbiome studies could improve the future of humanity, Investigating the human microbiome: “We’re only just beginning and there is so much more to explore
Monet image courtesy of KnightSerbia