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Table 1 Postnatal development of the microbiota and effects of obesity and IBD

From: Metagenomic cross-talk: the regulatory interplay between immunogenomics and the microbiome

Physiologic or pathologic status Involved taxa Phenotypic manifestation References
Early microbial colonization Breastfed individuals: low species diversity, most abundant phyla are Actinobacteria and Firmicutes. Formula-fed individuals: low species diversity, most abundant phyla are Actinobacteria and Bacteriodetes. All individuals: facultative anaerobic bacteria including Staphylococcus species, Streptococcus species, Escherichia coli and other Enterobacteriaceae are thought to be the first colonizers of the gut Several factors can control microbial colonization after birth, including delivery mode, hygiene, feeding, and antibiotics use [122, 123]
  Weissella, Leuconostoc, Staphylococcus, Streptococcus, and Lactococcus species predominate Human colostrum and breast milk contains more than 700 species of bacteria, including species typically found in the oral cavity [124]
  Major phyla: Bacteriodetes and Firmicutes From 18 months, the diet influences the bacterial composition, and this composition is stabilized, with increased diversity [125]
  Enterococcaceae, Streptococcaceae, Lactobacillaceae, Clostridiaceae, and Bifidobacteriaceae The newborn gut microbiota is similar to the maternal skin and vaginal microbiota [123]
  Cesarean‐born infants featured lower relative abundance of Bifidobacterium and Bacteroides species compared to vaginally born children The delivery mode determines early colonization through modulating the type of bacteria that the child is exposed to at birth [126, 127]
Obesity Reduced abundance of Bacteroidetes species in obese individuals Transfer of microbiota with a composition characteristically found in obese mice into germ-free mice results in weight gain [12]
  Firmicutes were dominant in normal-weight individuals and in those with obesity, but substantially less abundant in individuals who had undergone gastric bypass surgery, who had a proportional increase in abundance of Gammaproteobacteria. Prevotellaceae were highly enriched in individuals with obesity Treatment with antibiotics results in weight gain [128]
  Increased relative abundance of Faecalibacterium prausnitzii in children with obesity Treatment of children with antibiotics before the age of 6 months results in weight gain [129]
  Bacteroides and Clostridium were the most prevalent genera Colonization of adult germ-free mice with a microbial community harvested from the distal gut of conventionally raised mice produces a dramatic increase in body fat content within 10–14 days [130]
  The relative abundance of Bacteroidetes in obese mice is 50 % lower than that in normal-weight mice, whereas the relative abundance of Firmicutes is proportionally higher A low-calorie, fat-restricted or carbohydrate-restricted diet leads to an increase in relative abundance of Bacteroidetes [13]
IBD Higher relative abundance in CD: Proteobacteria, Fusobacterium, Haemophilus influenzae and other Haemophilus species, Neisseriaceae, E. coli. Lower relative abundance in CD: Bacteroides, Bifidobacterium, and Blautia The intestinal microbiota is disturbed in children with IBD [115, 131]
  1. CD Crohn’s disease, IBD inflammatory bowel disease, UC ulcerative colitis