Figure 8. Microbial community composition, community complexity, and an overview of binning for samples from infant #2.
The diagrams are unit repeats of a tetranucleotide emergent self organizing map; points coded to reflect the bin assignment of the scaffold verify the binning (see ‘Materials and methods’ section). Vertical red lines separate samples before and after antibiotic administration to treat necrotizing enterocolitis (NEC) (two instances). Organisms are listed primarily in order of abundance in the first sample. Note that, with the exception of the dominant member, Enterobacter cloacae, species representation changed dramatically following antibiotic administration. The Veillonella strain varied (numbers differentiate areas that represent different populations).
Figure 8—figure supplement 1. Rank abundance curves describing the microbial community (exclusive of phage and plasmids) in infant #2.
Colors correspond with those used in emergent self organizing maps (see
Figure 8 and Supplementary file
3). Details are available in Supplementary file
3. NEC: necrotizing enterocolitis.
Figure 8—figure supplement 2. An overview of the microbial communities from infant #3.
The red line separates samples collected before and after antibiotic
treatment for necrotizing enterocolitis. Shown are rank abundance curves
for all samples and time series emergent self organizing maps for two
samples, which were used to refine the binning (see ‘Materials and
methods’ section). Note the prominence of Veillonella
parvula, Enterococcus faecalis, and Citrobacter
KTE32 in samples prior to diagnosis, and the loss of
Veillonella and other less abundant species following
antibiotic administration. E. faecalis and
Citrobacter KTE32 strains persist through treatment,
but the Staphylococcus epidermidis-related strains
before (7) and after treatment (7′) are distinct. DOL: day of
life.
Figure 8—figure supplement 3. Overview community composition for infant #8, who developed necrotizing enterocolitis 1 day after collection of the last sample.
(A) Time series + GC content emergent self organizing
maps (ESOMs) were used to fine-tune binning and provide an overview of
community composition. Points in the ESOM are color coded to indicate
genome bin, the name for which is given to the right. (B)
Time series abundance patterns for the relatively well-sampled bacteria;
brown shading over numbers indicates sample pairs collected on the same
day. The communities were dominated by bacteria closely related to
Enterobacter cloacae (yellow) and Klebsiella
pneumoniae (brown). (C) Expanded view of the low
abundance part of B. Several organisms were present at low
abundance; some appeared a few days prior to the necrotizing
enterocolitis diagnosis. Clostridium was detected but the genome sampling
was so low that it was not included in the figure (see Supplementary file
3). DOL: day of life.