A Review of Dynamics and Stabilization of the Human Gut Microbiome during the First Year of Life


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


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;

  1. High quality data

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

  1. Satisfactory analysis report

More database annotations for more analysis results

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

CD Genomics has professional bioinformatics analysis team, powerful experimental and sequencing platform to provide microbial genome de novo resequencing16S/18S/ITS, metagenomics, transcriptome sequencing and other micro-site one-stop sequencing analysis services.