Succession and determinants of the early life nasopharyngeal microbiota in a South African birth cohort

Claassen-Weitz, Shantelle; Gardner-Lubbe, Sugnet; Xia, Yao; Mwaikono, Kilaza S.; Mounaud, Stephanie Harris; Nierman, William C.; Workman, Lesley; Zar, Heather J.; Nicol, Mark P.

doi:10.1186/s40168-023-01563-5

Microbiome

Table 2 Early life exposures associated with nasopharyngeal bacterial alpha (Shannon) diversity

From: Succession and determinants of the early life nasopharyngeal microbiota in a South African birth cohort

Covariate	Interval A: M01-M03	P value	Interval B: M04-M06	P value	Interval C: M07-M12	P value
Specimen collection season	Summer > Autumn	0.008**	Summer > Autumn	0.315	Summer > Autumn	0.150
	Summer > Winter	0.261	Summer > Winter	0.925	Summer > Winter	0.083*
	Summer > Spring	0.415	Summer < Spring	0.358	Summer > Spring	0.570
	Summer > Autumn	0.268	Summer > Autumn	0.005**	Summer > Autumn	0.071*
	Summer < Winter	0.388	Summer > Winter	0.009**	Summer > Winter	< 0.001**
	Summer < Spring	0.525	Summer > Spring	0.891	Summer > Spring	0.004**
Gestational age	More than 40 weeks > Less than 37 weeks	0.903	More than 40 weeks < Less than 37 weeks	0.057*	More than 40 weeks < Less than 37 weeks	0.241
	More than 40 weeks < 37–40 weeks	0.439	More than 40 weeks < 37–40 weeks	0.093*	More than 40 weeks < 37–40 weeks	0.372
	More than 40 weeks > Less than 37 weeks	0.659	More than 40 weeks < Less than 37 weeks	0.097*	More than 40 weeks < Less than 37 weeks	0.211
	More than 40 weeks < 37–40 weeks	0.339	More than 40 weeks < 37–40 weeks	0.254	More than 40 weeks < 37–40 weeks	0.114
Duration of exclusive breastfeeding	None/less than 1 month < Until 1 month	0.437	None/less than 1 month < Until 1 month	0.789	None/less than 1 month < Until 1 month	0.599
	None/less than 1 month < Until 2 months	0.905	None/less than 1 month < Until 2 months	0.671	None/less than 1 month < Until 2 months	0.325
	None/less than 1 month < Until 3 months	0.426	None/less than 1 month > Until 3 months	0.182	None/less than 1 month < Until 3 months	0.658
			None/less than 1 month < Until 4 months	< 0.001**	None/less than 1 month < Until 4 months	0.049**
			None/less than 1 month > Until 5 months	0.905	None/less than 1 month > Until 5 months	0.762
			None/less than 1 month > Until 6 months	0.581	None/less than 1 month < Until 6 months	0.499
	None/less than 1 month < Until 1 month	0.740	None/less than 1 month > Until 1 month	0.691	None/less than 1 month < Until 1 month	0.004**
	None/less than 1 month < Until 2 months	0.697	None/less than 1 month > Until 2 months	0.927	None/less than 1 month < Until 2 months	0.006**
	None/less than 1 month < Until 3 months	0.912	None/less than 1 month > Until 3 months	0.809	None/less than 1 month < Until 3 months	0.358
			None/less than 1 month < Until 4 months	0.008**	None/less than 1 month < Until 4 months	0.050*
			None/less than 1 month > Until 5 months	0.918	None/less than 1 month < Until 5 months	0.815
			None/less than 1 month > Until 6 months	0.279	None/less than 1 month < Until 6 months	0.425
Maternal smoking	Yes > No	0.350	Yes > No	0.317	Yes > No	0.420
Maternal smoking	Yes > No	0.089*	Yes > No	0.113	Yes > No	0.209
Pets in the home during the 1st 3 months of life	Yes < No	0.116	Yes > No	0.651	Yes > No	0.095*
Pets in the home during the 1st 3 months of life	Yes < No	0.491	Yes > No	0.279	Yes > No	0.084*
Older siblings	Yes > No	0.405	Yes > No	0.764	Yes > No	0.090*
Older siblings	Yes > No	0.600	Yes > No	0.030**	Yes > No	0.362
Maternal educational attainment	Primary level education < Secondary level education	0.936	Primary level education < Secondary level education	0.003**	Primary level education < Secondary level education	0.779
Maternal educational attainment	Primary level education < Secondary level education	0.918	Primary level education < Secondary level education	0.198	Primary level education < Secondary level education	0.346
Antibiotics prior to specimen collection	Not tested	-	Yes > No	0.991	Yes > No	0.239
Antibiotics prior to specimen collection	Not tested	-	Yes < No	0.623	Yes > No	0.077*
HIV-exposure	HIV-unexposed > HIV-exposed, uninfected	0.560	HIV-unexposed > HIV-exposed, uninfected	0.050*	HIV-unexposed > HIV-exposed, uninfected	0.341
HIV-exposure	HIV-unexposed < HIV-exposed, uninfected	0.423	HIV-unexposed > HIV-exposed, uninfected	0.281	HIV-unexposed > HIV-exposed, uninfected	0.071*
Height-for-age z-score (HAZ) at 12 months	High^a HAZ scores < Low^b HAZ scores	0.026**	High^a HAZ scores < Low^b HAZ scores	0.381	High^a HAZ scores < Low^b HAZ scores	0.202
	High^a HAZ scores < Medium^c HAZ scores	0.009**	High^a HAZ scores < Medium^c HAZ scores	0.694	High^a HAZ scores < Medium^c HAZ scores	0.250
	High^a HAZ scores < Low^b HAZ scores	0.068*	High^a HAZ scores > Low^b HAZ scores	0.851	High^a HAZ scores < Low^b HAZ scores	0.461
	High^a HAZ scores < Medium^c HAZ scores	0.058*	High^a HAZ scores > Medium^c HAZ scores	0.505	High^a HAZ scores < Medium^c HAZ scores	0.689

Within-specimen (alpha) diversity p values were adjusted for specimen collection age and season
HIV Human immunodeficiency virus, TB-INH Tuberculosis isoniazid
^*p values < 0.10; ^**p values < 0.05
^aHigh HAZ: > 1 standard deviation above the mean HAZ score
^bLow HAZ: ≤ 1 standard deviation below the mean HAZ score
^cMedium HAZ score: − 1 to 1 standard deviation of the mean HAZ score

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