3.5 Camping

How does my microbiome change after camping?

Here are the genus-level organisms in my gut after camping that weren’t there before:

New after camping (%)
Sutterella 0.25
Thalassospira 0.15
Methanomassiliicoccus 0.07
Asaccharospora 0.07
Catenibacterium 0.06
Gordonibacter 0.05
Enterobacter 0.05
Herbaspirillum 0.04
Leuconostoc 0.03
Hydrogenoanaerobacterium 0.02

Interesting to note the very large increase in the formerly-non-existent Kluyvera. This is a branch of microbes that includes E. Coli and the pathogen Shigella. Unfortunately, 16S doesn’t have enough resolution to distinguish between harmless and pathogenic versions of these taxa, but it is intriguing that they would show up.93

Here are the ones I lost on the trip:

Before Camping (%)
Hespellia 0.30
Succiniclasticum 0.02
Eisenbergiella 0.02

Odd that I lost all my remaining Bifidobacterium, though it’s important to note that the Before sample has a low read count (10275) compared to the “After” one (67794).

Let’s look at a different camping trip, one in which I sampled daily including on the trail.

In this case, I left on a Wednesday, staying overnight on the trail on Wednesday night (“Before”), then Thursday night. I took a sample on Friday morning (“Day 1”) and another one after I arrived home (“After”)

Before Trail Home After
Firmicutes 63.64 45.56 51.84 61.80
Bacteroidetes 22.74 44.88 38.12 25.94
Verrucomicrobia 7.85 4.17 3.63 3.97
Euryarchaeota 3.50 0.51 1.40 1.42
Actinobacteria 2.75 3.39 4.49 3.29
Proteobacteria 2.02 1.00 0.80 4.18