Architecture and Composition of the Intestinal Flora

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This entry is adapted from the peer-reviewed paper 10.3390/ijms23158343

Intestinal microorganisms are composed of bacteria, archaea, eukaryotes, and viruses, and more than 99% of them are bacteria. Approximately 10¹⁴ bacteria are known to constitute the intestinal flora in the adult gut, and this number is 10 times the number of human somatic cells.

intestinal flora homeostatic imbalances diseases

1. Introduction

The intestinal flora co-exists harmoniously with the host, participate in the digestion and the absorption of nutrients, and also help to maintain the integrity of the host's immune system so as to prevent pathogen colonization ^[1]. Additionally, intestinal flora consists of various bacteria in low or high abundance, which co-evolve with the host. While the host provides nutrients and a suitable survival place for the intestinal flora, the intestinal flora assists the host in absorbing nutrients, such as vitamins and short-chain fatty acids, in a more efficient manner in order to drive growth processes and to support the functions of the intestinal system and the immune system ^[2]。

2. Architecture and Composition of the Intestinal Flora

The gut microbiota exists throughout the life of the host. The diversity of bacteria in the intestines of infants is very low at first, and it gradually accelerates during the course of early development. The intestinal floras in newborn babes are mainly of the Enterobacteriaceae and Staphylococcus species, and the intestinal flora during lactation are mainly of the Bifidobacterium species. After the consumption of a solid diet, the bacteria colonizing the intestine are found to be mostly the anaerobic strains ^[3]^[4]^[5]. A low level of Bacteroidetes and a high level of Bifidobacterium are also found in adolescence, followed by the formation of intestinal microbial communities dominated by Bacteroidetes and Firmicutes, which are involved in carbohydrate and amino acid metabolism, fermentation, and oxidative phosphorylation ^[6]^[7]. Studies have shown that aging is associated with a number of important changes, including a decrease in the diversity of the intestinal flora; decreases in the proportions of Firmicutes and Bacteroidetes; decreases in the abundances of Ruminococcaceae, Lachnospiraceae, and Bacteroidaceae; increases in the abundances of opportunistic pathogens; and decreases in the populations of the bacteria crucial for producing short-chain fatty acids required for the maintenance of structural integrity and the prevention of inflammation in the intestine ^[8]^[9]^[10]。

The composition of the intestinal microbiota varies throughout the digestive tract. Food is mixed with saliva before entering the stomach and intestine. The oral microbiota is complex and diverse: ~1000 species of bacteria have been identified to date ^[11]^[12]. Esophageal microbial communities mainly include Firmicutes, Bacteroidetes, Actinobacteria, Proteobacteria, and Fusobacteria ^[13]^[14]. Most of the bacteria in the host's body are localized in the gastrointestinal tract, and there are significant differences in bacterial diversity and quantity between the stomach and the intestine. There are 10 to 10³ bacteria per gram of stomach content, mainly including Firmicutes, Bacteroidetes, Clostridium, Actinobacteria, along with Streptococcus and Haemophilus. Helicobacter pylori is the dominant bacterium in the stomach ^[15]^[16]. The small intestine consists of the duodenum, jejunum, and ileum. There are 10³ bacteria per gram of duodenal content, and Firmicutes and Actinobacteria are the main bacteria ^[8]. The bacterial density in the jejunum is high; there are 10⁴–10⁷ bacteria per gram of content—mainly Gram-positive aerobic bacteria and facultative anaerobic bacteria, such as Lactobacillus, Enterococcus, and Streptococcus. The numbers of ileal anaerobic bacteria close to the ileocecal valve, gradually exceed those of aerobic bacteria, and Streptococcus is the dominant bacteria in this segment of the intestine ^[17]. The colon, located in the lower part of the large intestine, contains 10¹¹–10¹² bacteria per gram of content, which are mainly anaerobic bacteria, including Firmicutes and Bacteroidetes. There is a high population density and diversity. The ratio of Firmicutes to Bacteroidetes is related to the susceptibility to diseases. In the large intestine, Bacteroides, Bifidobacterium, Streptococcus, Enterobacteriaceae, Enterococcus, Clostridium, Lactobacillus, and Ruminococcus are the dominant bacteria. In addition, the colon also contains several pathogenic bacteria, such as Campylobacter jejuni, Salmonella enteritidis, Vibrio cholerae, Escherichia coli, and Bacteroides fragilis ^[15]. The distribution of bacteria in the digestive tract is shown in Figure 1.

Figure 1. Distribution of gastrointestinal bacteria: The distribution of intestinal bacteria in the digestive tract varies, and there are many types and quantities of bacteria in the oral cavity. Following their entry into the esophagus, the colonization of bacteria is reduced. Due to the secretion of gastric acid, most bacteria in the stomach cannot survive, allowing more acid-tolerant bacteria, such as Prevotella, Roche, and Streptococcus, to dominate. The number of bacteria increases from the duodenum to jejunum and ileum. These bacteria include Clostridium, Lactobacillus, and Enterococcus. A large number of bacteria exist in the colon, including Bifidobacterium, Clostridium, Ruminococcus, Bacteroides, Streptococcus, and Prevotella.

The intestinal flora is mainly classified according to natural attributes, including Firmicutes, Bacteroidetes, Proteobacteria, Actinobacteria, Verrucomicrobia, Fusobacteria, and Cyanobacteria. Approximately 98% of the intestinal flora are composed of four main types of bacteria—Firmicutes, Bacteroidetes, Proteobacteria, and Actinomycetes—and the classification of the bacteria is shown below in Table 1. The most common bacterial genera are Bacteroides, Clostridium, Peptococcus, Bifidobacterium, Eubacterium, Ruminococcus, Enterococcus faecalis, and Peptostreptococcus ^[9]. Furthermore, most of the bacteria in Bacteroidetes belong to Bacteroidetes and Prevotella, and the Firmicutes are mainly Clostridium, Eubacteria, and Ruminococcus.

Table 1. Classification of bacterial species in the intestinal flora: According to classification by natural properties, intestinal bacteria can be divided into six categories for the most part: Firmicutes, Bacteroidetes, Proteobacteria, Actinobacteria, Fusobacteria, and Verrucomicrobia. Each category includes bacterial species.

Phylum	Class	Order	Family	Genus	Species
Firmicutes	Clostridia	Clostridiales	Clostridiaceae	Faecalibacterium	Faecalibacterium prausnitzii
			Clostridiaceae	Clostridium	Clostridium spp.
			Lachnospiraceae	Coprocococcus	Coprococcus eutactus
			Peptostreptococcaceae	Peptostreptococcus	Peptostreptococcus anaerobius
			Veillonellaceae	Veillonella	Veillonella parvula
	Bacilli	Lactobacillales	Lactobacillaceae	Lactobacillus	Lactobacillus acidophilus
		Lactobacillales	Enterococcaceae	Enterococcus	Enterococcus faecalis
		Bacillales	Listeriaceae	Listeria	Listeria iuanuii
Bacteroidetes	Flavobacteria	Flavobacteriales	Flavobacteriaceae	Flavobacterium
	Bacteroidetes	Bacteroidales	Bacteroidaceae	Bacteroides	Bacteroides fragilis
					Bacteroides caccae
					Bacteroides pyogenes
			Porphyromonadaceae	Porphyromonas
			Porphyromonadaceae	Parabacteroides	Parabacteroides distasonis
			Rikenellaceae	Alistipes	Alistipes finegoldii
			Prevotellaceae	Prevotella	Prevotella spp.
Proteobacteria	Gamma proteobacteria	Enterobacteriales	Enterobacteriaceae	Escherichia	Escherichia coli
	Gamma proteobacteria	Enterobacteriales	Enterobacteriaceae	Enterobacter	Enterobacter areogenes
	Delta proteobacteria	Desulfovibrionales Desulfobacterales	Desulfovibrionaceae Desulfobacteraceae	Desulfovibrio	Desulfovibrio intestinalis
	Delta proteobacteria	Desulfovibrionales Desulfobacterales	Desulfovibrionaceae Desulfobacteraceae	Desulfobacter
	Epsilon proteobacteria	Campylobacterales	Helicobacteraceae	Helicobacter	Helicobacter pylori
Actinobacteria	Actinobacteria	Actinomycetales	Actinomycetaceae	Actinobaculum
		Actinomycetales	Corynebacteriaceae	Corynebacterium	Corynebacterium glutamicum
		Bifidobacteriales	Bifidobacteriaceae	Bifidobacterium	Bifidobacterium adolescentis
		Bifidobacteriales	Bifidobacteriaceae	Bifidobacterium	Bifidobacterium longum
Fusobacteria	Fusobacteria	Fusobacteriales	Fusobacteriaceae	Fusobacterium	Fusobacterium nucleatum
Verrucomicrobia	Verrucomicrobiae	Verrucomicrobiales	Verrucomicrobiaceae	Akkermansia	Akkermansia muciniphila

In addition to the classification according to natural properties, intestinal flora can be classified according to their relationships with the host. The relationship with the host can be mutually beneficial (i.e., symbiotic), conditionally pathogenic, or exclusively pathogenic. The beneficial bacteria mainly promote intestinal peristalsis, prevent constipation and diarrhea, promote the synthesis of vitamins, discharge exogenous harmful substances, and occlude the invasion of pathogens, including Bifidobacterium, Lactobacillus, Lactococcus, Enterococcus faecalis, Eubacterium, Peptococcus, Clostridium, and Rothia ^[18]^[19]. Under certain conditions, conditionally pathogenic bacteria are invasive and cause harm to the human body. The conditionally pathogenic microorganisms often include Escherichia coli, Enterococcus, Ruminococcus, Bacteroides, Vibrio desulphurization, Candida albicans, and Pseudomonas aeruginosa as well as Proteobacteria ^[20]. Pathogenic bacteria generate toxic metabolites, which increase the reabsorption of harmful substances in the intestine, thereby causing abnormalities in intestinal peristalsis and heightened invasion of the intestinal tract by pathogenic bacteria, including Escherichia coli, Staphylococcus, Proteobacteria, Streptococcus, Peptostreptococcus, Fusobacteria, Clostridium, Klebsiella, Prevotella, Clostridium tetanus, and Veillonellaceae ^[21]^[22]。

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1. Introduction

2. Architecture and Composition of the Intestinal Flora

References