Succession of microbial consortia in the developing infant gut microbiome
Open accessAbstract
The colonization process of the infant gut microbiome has been called chaotic, but this view could reflect insufficient documentation of the factors affecting the microbiome. We performed a 2.5-y case study of the assembly of the human infant gut microbiome, to relate life events to microbiome composition and function. Sixty fecal samples were collected from a healthy infant along with a diary of diet and health status. Analysis of >300,000 16S rRNA genes indicated that the phylogenetic diversity of the microbiome increased gradually over time and that changes in community composition conformed to a smooth temporal gradient. In contrast, major taxonomic groups showed abrupt shifts in abundance corresponding to changes in diet or health. Community assembly was nonrandom: we observed discrete steps of bacterial succession punctuated by life events. Furthermore, analysis of ≈500,000 DNA metagenomic reads from 12 fecal samples revealed that the earliest microbiome was enriched in genes facilitating lactate utilization, and that functional genes involved in plant polysaccharide metabolism were present before the introduction of solid food, priming the infant gut for an adult diet. However, ingestion of table foods caused a sustained increase in the abundance of Bacteroidetes, elevated fecal short chain fatty acid levels, enrichment of genes associated with carbohydrate utilization, vitamin biosynthesis, and xenobiotic degradation, and a more stable community composition, all of which are characteristic of the adult microbiome. This study revealed that seemingly chaotic shifts in the microbiome are associated with life events; however, additional experiments ought to be conducted to assess how different infants respond to similar life events.
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As the infant matures, strict anaerobes gradually take over as the dominant taxa, and overall diversity increases to adult-like levels by around 1-3 years of age, coinciding with weaning and a shift to solid food intake.
“As the infant matures, strict anaerobes gradually take over as the dominant taxa, and there is an increase in overall diversity to adult-like levels by around 1-3 years of age, coinciding with weaning and a shift to solid food intake (Koenig et al., 2011;Palmer et al., 2007;Yatsunenko et al., 2012).”
From The Microbiota-Gut-Brain Axis (2019) · cites this paper as Koenig et al., 2011
In the months to years after birth, gut microbial communities shift in response to life events such as solid food exposure, illnesses, and antibiotics, with gradual diversity increases and convergence to an adult-like microbiota.
“In the subsequent months to years, gut microbial communities continue to shift in response to key life events (e.g., exposure to solid foods, illnesses, antibiotics) with gradual increases in diversity and convergence to an “adult-like” microbiota9–11.”
From The gut Microbiome in adult and pediatric functional gastrointestinal disorders (2019) · cites this paper as [9]
In a single infant followed for 2.5 years, bacterial taxa changed with life events such as illness, dietary changes, and antibiotic treatment.
“Characterization of the intestinal microbiota in a single infant, over a period of 2.5 years, showed how the bacterial taxa changed with life events such as illnesses, dietary changes, and antibiotic treatment.”
From Diet and the Intestinal Microbiome: Associations, Functions, and Implications for Health and Disease (2014) · cites this paper as [3]
In that infant, weaning was accompanied by a shift toward a more stable, adult-like microbiota.
“There was also a shift towards a more stable, adult-like microbiota with weaning3.”
From Diet and the Intestinal Microbiome: Associations, Functions, and Implications for Health and Disease (2014) · cites this paper as [3]
In that infant, the greatest change in intestinal microbiota composition occurred when solid foods were introduced.
“Interestingly, the greatest change in the composition of the infant's intestinal microbiota occurred with the introduction of solid foods.”
From Diet and the Intestinal Microbiome: Associations, Functions, and Implications for Health and Disease (2014) · cites this paper as [3]
After primary inoculation, infants are regularly exposed to microbes and their microbial diversity increases rapidly.
“After this primary inoculation, infants are regularly exposed to microbes, and diversity increases rapidly3.”
From Diet and the Intestinal Microbiome: Associations, Functions, and Implications for Health and Disease (2014) · cites this paper as [3]
Most critical events in education of host immunity may take place during the first years of life, when microbiota composition displays the highest intra- and inter-individual variability before reaching a more stable adult-like configuration at the age of ~3 years.
“Most critical events in education of host immunity may take place during the first years of life, in which microbiota composition displays the highest intra- and inter-individual variability before reaching a more stable adult-like configuration at the age of ~3 years.18–20”
From Interaction between microbiota and immunity in health and disease (2020) · cites this paper as [19]
While the inflammation characteristics of gingivitis are mostly reversible, periodontitis results in long-term, irreversible damage to the periodontal tissues and alveolar bone that manifests as tissue detachment from the tooth, formation of a pocket wherein pathogenic bacteria can proliferate further, and eventual tooth loss in advanced stages of the disease.
“While the inflammation characteristics of gingivitis are mostly reversible, periodontitis results in long‐term, irreversible damage to the periodontal tissues and alveolar bone that manifests as tissue detachment from the tooth, formation of a pocket wherein pathogenic bacteria can proliferate further, and eventual tooth loss in advanced stages of the disease.192, 193, 194, 195”
From The oral microbiome: Role of key organisms and complex networks in oral health and disease (2021) · cites this paper as [192]
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- Authors
- Koenig, J. E., Spor, A., Scalfone, N., Fricker, A. D., Stombaugh, J., Knight, R., Angenent, L. T., & Ley, R. E.
- Affiliations
- Cornell University (US)
- University of Colorado Boulder (US)
- Howard Hughes Medical Institute (US)
- Venue
- Proceedings of the National Academy of Sciences
- Publisher
- National Academy of Sciences
- Published
- 2010-07-28
- Volume
- 108
- Issue
- supplement_1
- Pages
- 4578-4585
- ISSN
- 0027-8424 (ISSN-L)
- 1091-6490
- PMC
- PMC3063592
- OpenAlex
- W2139884694
- Cited by
- 2,540
- References
- 44
- Citations by year
- 2026: 67 · 2025: 94 · 2024: 143 · 2023: 161 · 2022: 182 · 2021: 186 · 2020: 201 · 2019: 201 · 2018: 191 · 2017: 203 · 2016: 218 · 2015: 210 · 2014: 161 · 2013: 157 · 2012: 105
- FWCI
- 41.59
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- Proceedings of the National Academy of Sciences (publishedVersion)
- Europe PMC (PubMed Central) (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gut microbiota and health
- Health Sciences › Nursing › Nutrition and Dietetics › Infant Nutrition and Health
- Physical Sciences › Environmental Science › Ecology › Microbial Community Ecology and Physiology
- Keywords
- infant gut microbiota, microbial succession, microbial community assembly, life events, lactate utilization, Bacteroidetes, short-chain fatty acids, carbohydrate utilization, vitamin biosynthesis, xenobiotic degradation, phylogenetic diversity, metagenomics, 16S rRNA gene
- MeSH terms
- Age Factors, Base Sequence, Feces, Humans, Infant, Infant, Newborn, Molecular Sequence Data, RNA, Ribosomal, 16S, Species Specificity, Cluster Analysis, Sequence Analysis, DNA, DNA Primers, Gastrointestinal Tract, Metagenome, DNA Barcoding, Taxonomic
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