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 | |
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 | ||
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 |