Table 3

Shannon and Simpson diversity index determined from T-RFLP profiles

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.

Yap et al. BMC Microbiology 2011 11:193   doi:10.1186/1471-2180-11-193

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