Table 3. Comparisons of alpha diversity measurements between Hodgkin lymphoma cases and co-twin controls, in 13 pairs discordant for Hodgkin lymphoma.

Measurements of alpha diversitya	Mean (cases)	Mean (unaffected co-twins)	Mean difference (unaffected co-twin−case difference)	P-valueb
Initial analysis
No. of unique OTUs	338	369	31	0.015
Shannon index	5.6	5.8	0.2	0.27
Chao1	533	574	41	0.066
PD_whole tree	21.2	22.8	1.6	0.051
Conservative analysis
No. of unique OTUs	183	196	13	0.10
Shannon index	5.2	5.4	0.2	0.40
Chao1	230	237	7	0.47
PD_whole tree	13.7	14.6	0.9	0.045

^aOTUs, species-level operational taxonomic units; number of unique OTUs is also referred to as ‘richness' Shannon index, which is a conservative alpha diversity estimate that adjusts for relative abundance of each OTU, is defined as (negative) the sum over OTUs of the product of the relative abundance of the OTU times the natural logarithm of the relative abundance; Chao1 is a presence/absence of alpha diversity indicator that is bias-corrected for rare taxa; PD, phylogenetic distance; PD_whole tree is an alpha diversity estimate that reflects phylogenetic divergence among OTUs present within an individual. The initial analysis included all 16S rRNA sequence reads. The conservative analysis restricted to reads with a minimum relative abundance of 0.1%.

^bP-value by paired t-tests.