Relative abundance data can misrepresent heritability of the microbiome

Bruijning, Marjolein; Ayroles, Julien F.; Henry, Lucas P.; Koskella, Britt; Meyer, Kyle M.; Metcalf, C. Jessica E.

doi:10.1186/s40168-023-01669-w

Microbiome

Table 1 Summary of the studies estimating heritabilities of the abundance of microbial taxa, sorted by sample size. More details in Additional file 1: Appendix S4 on methodology per study

From: Relative abundance data can misrepresent heritability of the microbiome

Number	Host system	# Samples	# Taxa	# Heritable taxa	Average non-zero heritability	Host genetic relatedness based on^a	Normalization/transformation	Reference
1	Mice	32	43	NA^b	0.47^b	Lineage	Total sum scaling	[15]
2	Chickens	56	23	0	NA	Pedigree	Log-transformation and scaling	[16]
3^c	Humans	93	116	14	0.35	SNPs	Quantile normalization	[17]
		91	104	10	0.37
		127	102	13	0.26
4	Humans	108	221	0	NA	Twins	Box-Cox transformation	[5] data from [18]
5	Humans	126	2,933	0	NA	Twins	Box-Cox transformation	[5] data from [19]
6^d	Humans	244	3	1	0.35	Twins	Arcsine square root transformation	[20]
		88	3	0	NA		Arcsine square root transformation
7	Humans	250	109	11	NA^e	Twins	Box-Cox transformation	[21]
8	Humans	270	249	26	0.58	Pedigree	Inverse normal transformation	[22]
9	Switchgrass	383	110	21	0.24	SNPs	Total sum scaling	[23]
10^f	Cows	650	512	39	NA^e	SNPs	Quantile normalization	[24]
		200	512	3			Quantile normalization
11	Humans	485	91	42	0.34	Twins	Log transformation and scaling	[25]
12	Humans	542	369	85	0.27	Twins	Inverse normal transformation	[26]
13	Mice	592	43	NA^b	0.51^b	SNPs	Total sum scaling	[27]
14	Sorghum	600	1189	443	0.22	Lineage	Cumulative sum scaling	[28]
15	Humans	655	85	52	0.24	Twins	Inverse normal transformation	[29]
16	Humans	1068	21	6	0.40	SNPs	Box-Cox transformation	[30]
17	Humans	1081	909	10	0.29	Twins	Box-Cox transformation	[5]
18	Humans	1176	209	11	0.31	Twins	Inverse rank-sum transformation	[31]
19^g	Pigs	1205	1678	170	0.056	Lineage	Total sum scaling	[32]
		1295	1678	261	0.078
		1283	1678	366	0.099
20^h	Maize	4866	792	143	0.17	Lineage	Log transformation	[33]
		45	2557	5	0.45		Log transformation
21	Humans	3261	945	52	0.30	Twins	Box-Cox transformation	[6]
22	Humans	4745	242	31	0.20	Pedigree	Centered log-ratio transformation	[34]
23	Baboons	16,234	283	273	0.068	Pedigree	Total sum scaling	[13]

^aType of host genetic data to estimate heritability. Pedigree: take into account pedigree to estimate narrow-sense h². SNPs: incorporate genetic relatedness matrix based on SNPs, to calculate SNP heritability. Lineage: genotype/lineage as random effect, estimates broad-sense H². Twins: compare MZ with DZ twins, to estimate broad-sense H²
^bNo significance measures are provided. Average heritability is therefore calculated using all estimates
^cAnalyses are done for winter, summer and both seasons combined
^dEuropean and African ancestry
^eHeritability estimates per taxon are not provided
^fTwo different breeds
^gThree time points during host development
^h2010 and 2015 field study

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ISSN: 2049-2618

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