Community recovery dynamics in yellow perch microbiome after gradual and constant metallic perturbations

Cheaib, Bachar; Seghouani, Hamza; Ijaz, Umer Zeeshan; Derome, Nicolas

doi:10.1186/s40168-020-0789-0

Microbiome

Table 4 Phylogenetic divergence in host and water microbiomes

From: Community recovery dynamics in yellow perch microbiome after gradual and constant metallic perturbations

	Time	Groups	Permanova	Multiple test correction	Betadisper	Mrpp
	Time	Groups	p value ADONIS	p values B-H	p values dispersion	p value MRPP
Ctrl = control regime; CC = concentration is constant; CV = concentration is variable
Gut	T0	All groups	0.052		0.079	0.279
		CC-Ctrl	0.042 *	0.077	0.048*	0.033 *
		CC-CV	0.051	0.077	0.141	0.049 *
		Ctrl-CV	0.280*	0.280	0.302	0.234
	T3	All groups	0.001**		0.367	0.647
		CC-Ctrl	0.001**	0.002 **	0.916	0.001***
		CC-CV	0.006 **	0.006 **	0.145	0.008 *
		Ctrl-CV	0.001***	0.002 **	0.295	0.001 ***
	T5	All groups	0.006 *		0.217	0.199
		CC-Ctrl	0.135	0.135	0.923	0.104
		CC-CV	0.005 **	0.012 *	0.084	0.009**
		Ctrl-CV	0.008 **	0.012 *	0.130	0.008 **
Skin	T0	All groups	0.016 *		0.540	0.500
		CC-Ctrl	0.166	0.166	0.649	0.154
		CC-CV	0.081	0.122	0.256	0.075
		Ctrl-CV	0.026 *	0.078	0.599	0.020 *
	T3	All groups	0.008 **		0.820	0.580
		CC-Ctrl	0.035*	0.049 *	0.619	0.049 *
		CC-CV	0.049 *	0.049 *	0.586	0.045 *
		Ctrl-CV	0.021*	0.049 *	0.872	0.009 **
	T5	All groups	0.001***		0.380	0.001 ***
		CC-Ctrl	0.011 *	0.011 *	0.749	0.008 **
		CC-CV	0.001***	0.002 **	0.307	0.002 **
		Ctrl-CV	0.001 ***	0.002 **	0.236	0.001 **
Water	T0	All groups	0.001 ***		0.656	0.886
		CC-Ctrl	0.018 *	0.027 *	1.000	0.009 **
		CC-CV	0.002 **	0.006 **	0.291	0.002 **
		Ctrl-CV	0.036 *	0.036 *	0.519	0.038 *
	T3	All groups	0.001 ***		0.036 *	0.596
		CC-Ctrl	0.002 **	0.002**	0.068	0.002 **
		CC-CV	0.001 **	0.002 **	0.020 *	0.001 ***
		Ctrl-CV	0.001 ***	0.002 **	0.546	0.001 ***
	TR1	All groups	0.001 ***		0.214	0.108
		CC-Ctrl	0.001 ***	0.002 **	0.305	0.002 **
		CC-CV	0.001 ***	0.002 **	0.064	0.001 ***
		Ctrl-CV	0.007 **	0.007 **	0.653	0.007 **
	TR2	All groups	0.001 ***		0.639	0.381
		CC-Ctrl	0.003 **	0.005 **	0.395	0.003 **
		CC-CV	0.096	0.096	0.892	0.077
		Ctrl-CV	0.001 ***	0.003 **	0.391	0.001 ***
	TR3	All groups	0.001 ***		0.561	0.629
		CC-Ctrl	0.001 ***	0.003 **	0.343	0.001 ***
		CC-CV	0.003 **	0.005 **	0.536	0.002 **
		Ctrl-CV	0.007 **	0.007 **	0.620	0.006 **
	TR4	All groups	0.001 ***		0.498	0.031 *
		CC-Ctrl	0.009 **	0.009 **	0.536	0.007 **
		CC-CV	0.006 **	0.009 **	0.179	0.009 **
		Ctrl-CV	0.004 **	0.009 **	0.578	0.002 **
	T5	All groups	0.001 ***		0.408	0.027 *
		CC-Ctrl	0.002 **	0.002 **	0.331	0.001 **
		CC-CV	0.001 ***	0.002 **	0.578	0.003 **
		Ctrl-CV	0.002 **	0.002 **	0.438	0.001 **

The phylogenetic distances between OTUs were computed using Gunifrac distance (see “Methods” section). The divergence between treatments and control was assessed using PERMANOVA and the homogeneity for group dispersions (distance from centroid) was evaluated using two multivariate tests, BETADISPER and multi-response permutation procedure (MRRP) of within versus among group dissimilarities. The significance of divergence between groups was measured by applying multiple correction tests with Benjamini-Hochberg BH (p value < 0.05)
p value < = 0.001 : “***”, p value < = 0.01 : “**”, p value < = 0.05 : “*”

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ISSN: 2049-2618

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