Evaluation of stool microbiota signatures in two cohorts of Asian (Singapore and Indonesia) newborns at risk of atopy

Gaik Chin Yap; Kok Keong Chee; Pei-Ying Hong; Christophe Lay; Cahya D Satria; Sumadiono; Yati Soenarto; Ekawaty L Haksari; Marion Aw; Lynette Pei-Chi Shek; Kaw Yan Chua; Yudong Zhao; Doreen Leow; Bee Wah Lee

doi:10.1186/1471-2180-11-193

BMC Microbiology

Table 3 Shannon and Simpson diversity index determined from T-RFLP profiles

From: Evaluation of stool microbiota signatures in two cohorts of Asian (Singapore and Indonesia) newborns at risk of atopy

Time	Index of diversity		Location		Mode of delivery
			Indonesia (n = 19)	Singapore (n = 29)	Vaginal (n = 32)	Caesarean (n = 16)
3 month	Shannon AluI	mean (SD)	1.648 (0.658)*	1.211 (0.643)*	1.350 (0.706)	1.452 (0.635)
		median (range)	1.714 (0.211-2.723)*	1.224 (0-2.371)*	1.424 (0-2.723)	1.415 (0.211-2.647)
	Simpson AluI	mean (SD)	0.685 (0.222)	0.530 (0.261)	0.579 (0.268)	0.617 (0.237)
		median (range)	0.768 (0.085-0.914)	0.568 (0-0.882)	0.667 (0.914)	0.669 (0.085-0.908)
	Shannon MspI	mean (SD)	1.474 (0.647)	1.402 (0.503)	1.408 (0.544)	1.477 (0.605)
		median (range)	1.412 (0.522-2.801)	1.379 (0.228-2.131)	1.378 (0.228-2.672)	1.508 (0.523-2.801)
	Simpson MspI	mean (SD)	0.634 (0.198)	0.627 (0.193)	0.626 (0.190)	0.638 (0.207)
		median (range)	0.652 (0.220-0.916)	0.692 (0.085-0.851)	0.662 (0.085-0.905)	0.697 (0.220-0.916)
	Shannon RsaI	mean (SD)	1.689 (0.597)	1.552 (0.497)	1.621 (0.517)	1.577 (0.591)
		median (range)	1.709 (0.339-2.635)	1.539 (0.643-2.507)	1.664 (0.643-2.514)	1.659 (0.339-2.635)
	Simpson RsaI	mean (SD)	0.711 (0.185)	0.697 (0.177)	0.718 (0.159)	0.671 (0.214)
		median (range)	0.760 (0.162-0.898)	0.737 (0.317-0.979)	0.745 (0.384-0.979)	0.734 (0.162-0.898)
			Indonesia (n = 29)	Singapore (n = 41)	Vaginal (n = 46)	Caesarean (n = 24)
1 year	Shannon AluI	mean (SD)	2.102 (0.594)*	1.861 (0.423)*	2.089 (0.409)*	1.715 (0.601)*
		median (range)	2.107 (0.558-2.822)*	1.976 (0.803-2.574)*	2.089 (0.940-2.822)*	1.708 (0.558-2.697)*
	Simpson AluI	mean (SD)	0.785 (0.168)	0.759 (0.120)	0.804 (0.104)*	0.704 (0.179)*
		median (range)	0.837 (0.226-0.925)	0.796 (0.434-0.905)	0.824 (0.434-0.925)*	0.742 (0.226-0.917)*
	Shannon MspI	mean (SD)	1.910 (0.753)*	1.740 (0.430)*	1.992 (0.456)*	1.462 (0.658)*
		median (range)	1.929 (0.252-3.199)*	1.8 (0.777-2.478)*	1.961 (1.137-3.199)*	1.473 (0.252-2.919)*
	Simpson MspI	mean (SD)	0.744 (0.186)	0.747 (0.101)	0.795 (0.086)*	0.650 (0.175)*
		median (range)	0.788 (0.160-0.951)	0.766 (0.462-0.882)	0.806 (0.614-0.951)*	0.686 (0.160-0.935)*
	Shannon RsaI	mean (SD)	2.026 (0.600)	1.965 (0.379)	2.148 (0.334)*	1.688 (0.572)*
		median (range)	2.020 (0.376-2.890)	1.985 (0.874-2.561)	2.181 (1.533-2.890)*	1.765 (0.376-2.868)*
	Simpson RsaI	mean (SD)	0.772 (0.170)	0.797 (0.097)	0.829 (0.064)*	0.706 (0.183)*
		median (range)	0.806 (0.165-0.925)	0.820 (0.459-0.902)	0.846 (0.681-0.925)*	0.776 (0.165-0.925)*

16S rRNA gene amplicons from infant fecal sample were digested with three restriction enzymes (AluI, MspI and RsaI).
*Statistically significant differences were indicated (adjusted p < 0.05). Linear regression for location and mode of delivery were performed with adjustment for confounding factors (Location, mode of delivery, weaning age, sibling number, total breastfeeding up to 6 month, eczema and prenatal antibiotics). Missing data was reported due to lack of availability of DNA samples for certain subjects.

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