Table 2.

DESeq2 supports LEfSe results at the ASV level

Pair-wise	base mean	Log2 fold change	lfcSE	stat	p value	p adjusted	Genus
High	33.90	11.12	2.85	3.90	9.74E-05	0.0093	Klebsiella
	16.16	23.66	5.92	4.00	9.74E-05	0.0067	Veillonella*
	2.59	23.04	5.92	3.89	9.93E-05	0.009345	Veillonella*
Decreased	68.40	−2.89	0.84	−3.45	0.0005576	0.03653	Romboutsia
	40.17	−4.74	1.24	−3.83	0.000128	0.011178	Enterococcus
	36.80	−3.37	0.75	−4.49	7.13E-06	0.001006	Intestinibacter
High	91.95	19.79	5.84	3.39	0.0007063	0.023203	Veillonella*
	33.90	9.69	2.87	3.37	0.0007523	0.024312	Klebsiella
	16.16	35.34	5.97	5.92	3.14E-09	5.95E-07	Veillonella*
Neutral	68.40	−2.88	0.84	−3.40	0.0006627	0.021951	Romboutsia
	40.17	–4.42	1.25	−3.55	0.0003914	0.013917	Enteroccocus
	36.80	−3.86	0.76	−5.10	3.43E-07	4.40E-05	Intestinibacter
High	91.95	23.27	5.98	3.89	9.97E-05	0.003386	Veillonella
	33.90	11.17	2.94	3.79	0.0001484	0.00458	Klebsiella
	17.77	13.94	4.43	3.15	0.0016554	0.035626	Phascolarctobacterium
Increased	40.17	−4.61	1.27	−3.62	0.0002916	0.007681	Enterococcus
	20.27	−2.43	0.64	−3.81	0.0001388	0.004329	Lachnoclostridium
	17.55	−2.33	0.63	−3.72	0.0002009	0.005902	Erysipelatoclostridium
Increased	9.15	30.00	3.85	7.78	7.03E-15	3.26E-12	Escherichia/Shigella*
	6.86	16.40	3.86	4.25	2.10E-05	0.000638	Escherichia/Shigella*
	5.84	9.63	2.42	3.98	6.90E-05	0.002038	Bacteroides
Decreased	19.75	−19.63	3.86	−5.09	3.53E-07	2.00E-05	Veillonella
	13.36	−29.79	3.86	−7.72	1.12E-14	4.15E-12	Megasphaera
	6.97	−6.55	1.70	−3.85	0.0001173	0.003287	Klebsiella
Increased	14.13	7.69	1.71	4.49	6.96E-06	0.000299	Citrobacter
	5.84	10.89	2.44	4.47	8.00E-06	0.00034	Bacteroides
	3.06	27.04	3.89	6.95	3.61E-12	3.02E-10	Escherichia/Shigella
Neutral	267.32	−2.30	0.68	−3.39	0.0007071	0.026723	Bifidobacterium
	19.75	−16.58	3.89	−4.26	2.01E-05	0.000822	Veillonella
	6.97	−7.24	1.71	−4.23	2.38E-05	0.000964	Klebsiella
Neutral	9.15	18.37	3.56	5.16	2.48E-07	3.18E-05	Escherichia/Shigella*
	6.86	15.09	3.56	4.24	2.24E-05	0.001983	Escherichia/Shigella*
	5.81	14.73	3.56	4.14	3.50E-05	0.002961	Anaeroglobus
Decreased	13.36	−28.66	3.56	−8.05	8.41E-16	8.83E-13	Megasphaera
	6.20	−12.57	3.56	−3.53	0.0004112	0.02818	Sarcina
	2.59	−27.94	3.56	−7.84	4.33E-15	3.45E-12	Veillonella

The top three ASVs by base mean from each group in the pair-wise comparison are listed and described taxonomically at the genus level (n = 403 individual stool samples). Genera indicated with an asterisk (*) represent bacteria shared at the taxonomic level but are actually unique sequences. Breastfeeding status at the time of sample collection was corrected for in the DESeq2 model design. Source data are provided in the source data file