A Review of Dynamics and Stabilization of the Human Gut

Microbiome during the First Year of Life

Background

Dynamics and Stabilization of the Human Gut Microbiome during the First Year of Life
was first published on Cell Host &Microbe in 2015. Authors include Fredrik Bckhed and
Jovanna Dahlgren.

Experiment Design

Sample: intestinal microbes of 98 mothers and newborn babies (mostly Swedish)

Sequencing strategy: using metagenomic sequencing, a total of 1.52Tb of data, an

average of 3.99Gb/sample

Analysis Procedures

1. Based on the metagenomic data, the gene catalog was established at each time
point by de novo assembly, and the KEGG database was used to generate the gene
functional annotation.

2. According to the abundance of different samples, contigs were assembled by

binning, and 4356 genomes (>0.9Mb) were obtained by co-assembly. These
assembled genomes are supplemented by 1147 genomes in NCBI.

3. All genomes were subsequently clustered to obtain 690 unique metagenomic OTUs
(MetaOTUs), which was equivalent to the classification of species.
Analysis Content

The Phylum Firmicutes and Bacteroides were the most abundant among all detected
microorganisms, followed by actinomycetes and proteobacteria. According to the
metagenomic data species annotations, a total of 373 MetaOTUs were annotated to
the species, and the remaining 317 represented new species that were associated with
known species. Most of the MetaOTUs obtained from newborns are also found in
mothers, and the abundance is gradually increasing. As revealed by Figure 1, the red
area is Novel MetaOTUs, the outer circle is the species annotated to the door level,
the inner circle is the species that is gazing to the genus level, and the middle circle
represents the abundance of each MetaOTUs of different samples.

Figure 1. MetaOTUs phylogenetic tree

By using unweighted UniFrac distance PCoA analysis of all samples, the samples were
clustered according to age. The 12-month neonatal situation was most similar to that
of the mother, because the neonatal intestinal microflora structure had stabilized.

With age growing, the alpha diversity in the neonatal intestinal flora gradually increased,
while the beta diversity gradually decreased, indicating that the microbial species in
the community became more complex, and the differences between communities
became smaller.
Next, the authors performed a comparison of the gut microbiota structure of neonates
with C-section and vaginally born. The result turned out to be consistent with the PCoA
results. As the age increases, the bacterial composition tends to approach mothers.
However, due to the absence of maternal birth canal, the number of maternal
microorganisms obtained at the time of birth is small. Compared with the vaginally
newborn, their establishment of microorganisms in the intestine is slow and some of
the flora is missing.
 Figure 2. A comparison of the gut microbiota structure of neonates with C-section
and vaginally born

The metagenomic analysis also reveals the energy utilization of the neonatal intestinal
flora over time. The function of the fecal flora in the first year of delivery is improved,
and the phosphotransferase system (PTS) gene related to carbohydrate absorption is
rich in the neonatal intestinal flora.

The gut flora of neonatal and 4-month-old neonatal is enriched with the gene that
digests the sugar in the breast milk, at which point the sugar is the main source of
energy. The β-glucose-specific transporter is the most abundant in newborns at 4
months and 12 months of age. The intestinal flora of 12-month-old newborns is
enriched with genes that break down polysaccharides and starch and is associated
with an increase in Bacteroides variabilis, which has all the enzymes involved in
polysaccharide digestion.
 Figure 3. KO pathway

Bacteria in the gut of virginally newborns include: Enterococcus, Escherichia/Shigella,

Streptococcus, and Rothia Geory and Brown, indicating a relatively oxygen-rich
intestinal environment. The 4-month neonatal gut flora is characterized by
Bifidobacterium, Lactobacillus, Collins, Granulicatella, and Vesococcus, indicating a
gradual decrease in intestinal oxygen concentration and an increase in the ability to
produce and utilize lactic acid. The diet at this time is mainly breast milk.

The characteristics of the 12-month neonatal gut flora include: bacteria found in
newborns and in 4-month old newborns (as previously listed), and only present in 12
months Bacteria, such as the genus Eichhornia.
 Figure 4. Characteristics of intestinal flora in different periods of caesarean section

Summary

As an important research tool, metagenomics can get a lot of high-value information

in the process of microbial population research. It is of great significance for further
research on microbial-related metabolism and immunity.

Features of CD Genomics Metagenomic Sequencing

1. Rich experience in sample processing

Such as soil, sediment, intestinal contents, manure, water, air, dairy products...CD
Genomics has rich experience in various sample extraction;
2. High quality data

CD Genomics has a wide range of technical platforms to obtain high quality data;

3. Satisfactory analysis report

More database annotations for more analysis results

4. Deep data mining capacity and comprehensive follow-up customer services

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and sequencing platform to provide microbial genome de novo resequencing,
16S/18S/ITS, metagenomics, transcriptome sequencing and other micro-site one-
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