Architecture and Composition of the Intestinal Flora

Architecture and Composition of the Intestinal Flora: Comparison

Please note this is a comparison between Version 1 by Guo Xiaohua and Version 3 by Peter Tang.

Intestinal microorganisms are composed of bacteria, archaea, eukaryotes, and viruses, and more than 肠道微生物由细菌、古细菌、真核生物和病毒组成，其中99% of them are bacteria. Approximately 以上是细菌。已知大约有 10 ¹⁴种细菌构成成人肠道中的肠道菌群，这个数量是人体体细胞数量的 bacteria are known to constitute the intestinal flora in the adult gut, and this number is 10 times the number of human somatic cells.10 倍。

intestinal flora
homeostatic imbalances
diseases

1. Introduction

一、简介

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 肠道菌群与宿主和谐共存，参与营养物质的消化吸收，也有助于维持宿主免疫系统的完整性，防止病原体定植^{[ 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 。此外，肠道菌群由低或高丰度的各种细菌组成，它们与宿主共同进化。在宿主为肠道菌群提供营养和合适的生存场所的同时，肠道菌群帮助宿主以更有效的方式吸收维生素和短链脂肪酸等营养物质，以驱动生长过程并支持肠道菌群的生长。肠道系统和免疫系统的功能^{[ 2 ]}。

2. Architecture and Composition of the Intestinal Flora肠道菌群的结构和组成

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 肠道微生物群存在于宿主的整个生命周期。婴儿肠道内细菌的多样性起初很低，在早期发育过程中逐渐加速。新生儿肠道菌群以肠杆菌科和葡萄球菌为主，哺乳期肠道菌群以双歧杆菌为主。食用固体饮食后，发现肠道中的细菌主要是厌氧菌株^{[ 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 。低水平的拟杆菌和高水平的双歧杆菌也发现在青春期，随后形成以拟杆菌门和厚壁菌门为主的肠道微生物群落，参与碳水化合物和氨基酸的代谢、发酵和氧化磷酸化^{[ 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。研究表明，衰老与许多重要变化有关，包括肠道菌群多样性的减少；厚壁菌门和拟杆菌门的比例降低；瘤胃球菌科、毛螺菌科和拟杆菌科的丰度下降; 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 机会性病原体的丰度增加；和减少对产生维持结构完整性和预防肠道炎症所需的短链脂肪酸至关重要的细菌数量^{[ 8 ] [ 9 ] [ 10 ]}。

The肠道微生物群的组成在整个消化道中各不相同。食物在进入胃和肠之前与唾液混合。口腔微生物群复杂多样：迄今为止已鉴定出约 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 1000 种细菌^{[ 11 ] [ 12 ]}. Esophageal microbial communities mainly include Firmicutes, Bacteroidetes, Actinobacteria, Proteobacteria, and Fusobacteria 。食道微生物群落主要包括厚壁菌门、拟杆菌门、放线菌门、变形菌门和梭杆菌门^{[ 13 ] [ 14 ]}.。宿主体内的细菌大多局限在胃肠道内，胃和肠之间的细菌多样性和数量存在显着差异。有 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 to10 到 10 ³ 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 每克胃内容物的细菌主要包括厚壁菌门、拟杆菌门、梭状芽孢杆菌、放线菌，以及链球菌和嗜血杆菌。幽门螺杆菌是胃中的主要细菌^{[ 15 ] [ 16 ]}. The small intestine consists of the duodenum, jejunum, and ileum. There are 。小肠由十二指肠、空肠和回肠组成。每克十二指肠内含细菌10 ³ bacteria per gram of duodenal content, and Firmicutes and Actinobacteria are the main bacteria ，其中厚壁菌门和放线菌门是主要细菌^{[ 8 ]}. The bacterial density in。空肠细菌密度高；有 the jejunum is high; there are 10 ⁴ –10 ⁷ bacteria per gram of content每克含量的细菌——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 主要是革兰氏阳性需氧菌和兼性厌氧菌，如乳酸杆菌、肠球菌和链球菌。靠近回盲瓣的回肠厌氧菌数量逐渐超过需氧菌，而链球菌是该段肠道的优势菌^{[ 17 ]}.。结肠位于大肠下部，含有 The colon, located in the lower part of the large intestine, contains 10 ¹¹ –10 ¹²每克含量的细菌，主要是厌氧菌，包括厚壁菌门和拟杆菌门。人口密度高，多样性高。厚壁菌门与拟杆菌门的比例与疾病的易感性有关。在大肠中，拟杆菌属、双歧杆菌属、链球菌属、肠杆菌科、肠球菌属、梭菌属、乳酸杆菌属和瘤胃球菌属是优势菌。此外，结肠还含有多种致病菌，如空肠弯曲杆菌、肠炎沙门氏菌、霍乱弧菌、大肠杆菌和脆弱拟杆菌 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 。消化道细菌分布见图1.。

Figure 图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.

.胃肠道细菌分布：消化道肠道细菌的分布各不相同，口腔内的细菌种类和数量很多。进入食道后，细菌的定植减少。由于胃酸的分泌，胃中的大部分细菌无法存活，让更多的耐酸细菌，如普氏菌、罗氏菌、链球菌等占据主导地位。细菌的数量从十二指肠到空肠和回肠增加。这些细菌包括梭菌属、乳杆菌属和肠球菌属。结肠中存在大量细菌，包括双歧杆菌属、梭菌属、瘤胃球菌属、拟杆菌属、链球菌属和普氏菌属。

The肠道菌群主要按自然属性分类，包括厚壁菌门、拟杆菌门、变形菌门、放线菌门、疣微菌门、梭杆菌门和蓝细菌门。大约 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 bacteria98% 的肠道菌群由四种主要类型的细菌组成——Firmicutes, 、Bacteroidetes, 、Proteobacteria, and 和 Actinomycetes—and the classification of the bacteria is shown below in——细菌的分类如下表 Table 1. The most common bacterial genera are Bacteroides, Clostridium, Peptococcus, Bifidobacterium, Eubacterium, Ruminococcus, Enterococcus faecalis, and Peptostreptococcus 所示。最常见的细菌属是拟杆菌属、梭菌属、消化球菌属、双歧杆菌属、真杆菌属、瘤胃球菌属、粪肠球菌属和消化链球菌属^{[ 9 ]} . Furthermore, most of the bacteria in Bacteroidetes belong to Bacteroidetes and Prevotella, and the Firmicutes are mainly Clostridium, Eubacteria, and Ruminococcus.此外，拟杆菌门中的细菌大部分属于拟杆菌门和普氏菌，厚壁菌门主要是梭菌、真细菌和瘤胃球菌。

Table 表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.

, Clostridium, and Rothia ^[

门	班级	命令	家庭	属	物种
厚壁菌门	梭状芽孢杆菌	梭菌目	梭菌科	粪杆菌	粪杆菌
			梭菌科	梭菌属	梭菌属
			毛螺菌科	粪球菌	真球菌
			消化链球菌科	消化链球菌	厌氧消化链球菌
			韦荣菌科	韦永内拉	韦荣内拉小
	杆菌	乳酸杆菌目	乳酸杆菌科	乳酸杆菌	嗜酸乳杆菌
		乳酸杆菌目	肠球菌科	肠球菌	粪肠球菌
		杆菌目	李斯特科	李斯特菌	李斯特菌
拟杆菌门	黄杆菌	黄杆菌目	黄杆菌科	黄杆菌属
	拟杆菌门	拟杆菌目	拟杆菌科	拟杆菌属	脆弱拟杆菌
					拟杆菌
					化脓性拟杆菌
			卟啉单胞菌科	卟啉单胞菌
			卟啉单胞菌科	副拟杆菌属	拟杆菌属
			理科	阿里斯蒂佩斯	细金螟
			普氏菌科	普雷沃泰拉	普氏菌属
变形菌门	伽玛变形菌	肠杆菌	肠杆菌科	大肠埃希菌	大肠杆菌
	伽玛变形菌	肠杆菌	肠杆菌科	肠杆菌属	产肠杆菌
	三角洲变形菌	脱硫弧菌目脱硫杆菌目	脱硫弧菌科脱硫杆菌科	脱硫弧菌	肠脱硫弧菌
	三角洲变形菌	脱硫弧菌目脱硫杆菌目	脱硫弧菌科脱硫杆菌科	脱硫杆菌
	ε变形菌	弯曲杆菌目	幽门螺杆菌科	幽门螺杆菌	幽门螺杆菌
放线菌	放线菌	放线菌目	放线菌科	放线杆菌
		放线菌目	棒状杆菌科	棒状杆菌	谷氨酸棒杆菌
		双歧杆菌	双歧杆菌科	双歧杆菌	青春双歧杆菌
		双歧杆菌	双歧杆菌科	双歧杆菌	长双歧杆菌
梭杆菌	梭杆菌	梭杆菌目	梭杆菌科	梭杆菌属	具核梭杆菌
疣微菌	疣微菌	疣状微生物	疣微菌科	阿克曼西亚	阿克曼氏菌

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

肠道菌群中菌种分类：根据自然特性分类，肠道细菌大部分可分为六类：厚壁菌门、拟杆菌门、变形菌门、放线菌门、梭杆菌门和疣微菌门。每个类别都包括细菌种类。

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

肠道菌群除按自然特性分类外，还可按与宿主的关系分类。与宿主的关系可以是互利的（即共生的）、条件致病的或完全致病的。有益菌主要促进肠道蠕动，预防便秘和腹泻，促进维生素的合成，排出外源性有害物质，阻断双歧杆菌、乳酸杆菌、乳球菌、粪肠球菌、真杆菌、消化球菌、梭状芽孢杆菌和罗氏菌等病原体 ^{的入侵。 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

。在一定条件下，有条件的病原菌具有侵入性，对人体造成伤害。条件致病微生物通常包括大肠杆菌、肠球菌、瘤胃球菌、拟杆菌、脱硫弧菌、白色念珠菌和铜绿假单胞菌以及变形菌

^{[ 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

. 致病菌产生有毒代谢物，增加肠道对有害物质的重吸收，从而导致肠道蠕动异常，致病菌对肠道的侵袭增加，包括大肠杆菌、葡萄球菌、变形杆菌、链球菌、消化链球菌、梭杆菌、梭菌、克雷伯氏菌、普雷沃氏菌、破伤风梭菌和韦荣氏菌科

^{[ 21 ] [ 22 ]}。

。

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