9.6 Lab Tests Compared

When I tested the same sample from two labs, the similarities and differences are in the tables below.

9.6.1 Thryve

uBiome vs Thryve: Table 9.2.

Table 9.2: Phylum-level abundances from the sample sample.
Phylum Thryve (%) uBiome (%)
Firmicutes 68.34 72.65
Bacteroidetes 18.12 19.06
Verrucomicrobia 4.72 2.79
Actinobacteria 4.33 3.86
Proteobacteria 1.85 1.33
Euryarchaeota 0.48 2.58
Tenericutes 0.08 0.00
Synergistetes 0.05 0.17
Cyanobacteria 0.02 0.00
Lentisphaerae 0.02 0.14

and genus-level comparisons are in Table 9.3.

Table 9.3: Genus-level abundances from the sample sample.
Genus Thryve (%) uBiome (%)
Faecalibacterium 13.97 22.24
Bacteroides 10.33 11.83
Eubacterium 8.51 0.00
Oscillibacter 5.08 0.39
Akkermansia 4.57 2.22
Hydrogenispora 4.55 NA
Clostridium 3.96 0.45
Bifidobacterium 3.88 1.29
Erysipelatoclostridium 2.23 1.34
Lactobacillus 2.17 0.50
Casaltella 1.94 NA
Parabacteroides 1.85 1.16
Ruminococcus 1.85 0.00
Blautia 1.52 4.89
Coprococcus 1.46 0.00

9.6.2 DayTwo

At the phylum level, the samples are remarkably similar (Table 9.4), though less so at the genus level (Table 9.5).

Table 9.4: Phylum-level abundances from the sample sample.
Phylum DayTwo (%) uBiome (%)
Firmicutes 49.16 50.17
Bacteroidetes 45.53 35.14
Proteobacteria 3.99 8.21
Actinobacteria 1.01 4.50
Verrucomicrobia 0.01 1.47
Acidobacteria NA 0.00
Armatimonadetes NA 0.00
Basidiomycota NA 0.00
Candidatus Saccharibacteria NA 0.00
Chlamydiae NA 0.00
Table 9.5: Phylum-level abundances from the sample sample.
Genus DayTwo (%) uBiome 2 (%)
Bacteroides 24.45 19.96
Faecalibacterium 16.24 3.62
Odoribacter 9.31 4.16
Subdoligranulum 7.38 0.27
Lachnospira 5.13 0.70
Ruminococcus 4.53 0.00
Barnesiella 4.51 2.18
Parabacteroides 3.86 2.33
Roseburia 2.24 8.59
Alistipes 2.23 3.74
Coprococcus 1.52 0.00
Bacteroidales 1.13 NA
Dorea 1.11 0.94
Blautia 1.10 5.90
Bifidobacterium 0.96 2.46
Table 9.5: Genus-level abundances from the sample sample.
Genus DayTwo (%) uBiome 1 (%)
Bacteroides 24.45 14.91
Faecalibacterium 16.24 5.71
Odoribacter 9.31 3.39
Subdoligranulum 7.38 0.27
Lachnospira 5.13 0.62
Ruminococcus 4.53 0.00
Barnesiella 4.51 1.38
Parabacteroides 3.86 1.71
Roseburia 2.24 6.44
Alistipes 2.23 4.04
Coprococcus 1.52 0.00
Bacteroidales 1.13 NA
Dorea 1.11 1.21
Blautia 1.10 7.08
Bifidobacterium 0.96 0.38

9.6.3 Viome

Instead of looking at the bacterial DNA, which at best only tells which organisms are present, this company looks at the genes that those microbes are using. Called “metatranscriptomics”, the process is much more expensive because it requires looking at the RNA that are used while transcribing genes into proteins, but the result is a better look at what is actually happening.

I submitted the same sample to two labs, one to Viome and the other to the uBiome 16S lab. The results are quite different (see Table 9.6 and 9.7 Species details in Table ??. ).

Table 9.6: Phylum-level abundances from the sample sample.
Phylum Viome (%) uBiome (%)
Verrucomicrobia 53.15 3.24
Proteobacteria 25.58 2.50
Firmicutes 8.88 64.54
Synergistetes 8.12 0.29
Actinobacteria 1.63 1.99
Bacteroidetes 0.81 27.20
Euryarchaeota NA 2.39
Fibrobacteres NA 0.00
Lentisphaerae NA 0.24
Tenericutes NA 0.01
Table 9.7: Genus-level abundances from the sample sample.
Genus Viome (%) uBiome (%)
Parasutterella 19.36 0.93
Serratia 11.79 0.00
Romboutsia 9.86 0.95
Eubacterium 8.41 0.00
Akkermansia 8.31 3.22
Lactococcus 5.23 0.36
Turicibacter 3.65 0.22
Acinetobacter 3.58 0.00
Enterococcus 3.58 0.00
Blautia 2.37 7.84
Escherichia 2.31 NA
Bilophila 1.25 0.38
Ruminococcus 1.03 0.00
Eggerthella 0.97 0.01
Parabacteroides 0.93 1.14
Species % (16s)
Faecalibacterium prausnitzii 9.04
Bacteroides plebeius 7.60
Faecalibacterium sp. canine oral taxon 147 5.18
Roseburia faecis 3.47
Odoribacter laneus 2.65
Bacteroides massiliensis 2.29
Methanobrevibacter smithii 2.26
Subdoligranulum variabile 1.76
Blautia luti 1.56
Fusicatenibacter saccharivorans 1.55 
##         Observed Chao1 se.chao1 ACE se.ACE Shannon  Simpson InvSimpson   Fisher
## X378005       43    43        0 NaN    NaN 2.33002 0.854334    6.86502 3.420956

9.6.4 Gencove

Another company offering microbiome (and other genomic) testing is Gencove.

I tested a Gencove kit on the same cheek sample I used for a uBiome mouth test. Gencove’s directions ask me to spit into a vial. I then dipped a uBiome swab into the vial. Using a separate uBiome test kit, I sampled my cheek microbiome in my normal way – just a swab against the inside of my mouth, on the right and left cheeks, carefully avoiding other parts of the mouth like the tongue or lips. See Table 9.8 for results.

Table 9.8: Phylum-level comparisons of the same sample. Units are percentage abundance.
Phylum uBiome Vial uBiome Cheek Gencove
Firmicutes 51.26 38.70 37
Proteobacteria 34.92 18.99 22
Bacteroidetes 6.01 22.69 23
Fusobacteria 5.39 14.60 1
Actinobacteria 2.15 3.89 16

It makes sense that the uBiome results would differ from one another: one is a mixed sample taken from a distributed mix of saliva within the mouth and the other is a simple swab along the cheek – a very different ecosystem from the rest of the mouth. If you squint a little, the Gencove top results look similar to the uBiome cheek sample, with similar abundances across the board – with one major exception, the phylum Actinobacteria. Unfortunately this exception is too big to ignore. Besides, it’s not really fair to compare the cheek sample – you have to compare the vial samples with each other.

The bottom line is that different labs show different results, sometimes with such a major difference that you can’t really compare them.