# Microbes in Health and Disease: Human Gut Microbiota
## 1 Introduction  
Microbes (bacteria, archaea, fungi, protists, and microalgae) are microscopic organisms that are distributed ubiquitously in various aquatic, terrestrial, and air environments (e.g., freshwater lakes, seawater, hot springs, soil, sand, rock, disserts, and glaciers), and they also live in and on the bodies of organisms [1]. Microbes maintain the global biogeochemical cycles and flow of energy [2], and they find wide applications in industry [3], agriculture [4; 5], and pharmaceutics and therapy [6] as well as bioremediation [7]. Particularly, they play important roles in determining the state of human health, disease, and well-being [8] (Figure 1). These are discussed below. Specifically, over 1 trillion (10\({}^{12}\)) microbial species [1], \(\sim\)10\({}^{30}\) bacteria, \(\sim\)10\({}^{27}\) fungi, \(\sim\)10\({}^{29}\) archaea, and \(\sim\)10\({}^{27}\) protists live in the earth's ecosystem [9]. And \(\sim\)3.8 \(\times\) 10\({}^{13}\) bacteria live in and on an adult human body [10]. Microbes account for \(\sim\)17% of the global carbon biomass [9]. Additionally, microalgae (cyanobacteria and eukaryotic microalgae) are important photosynthesizing microbes that convert sunlight and carbon dioxide into  
Figure 1: Illustration of (**A**) distribution and classification of microbes and their roles in various fields and (**B**) the causes and therapies for the dysbiosis of human gut microbiota and associated disorders in digestion, metabolism, immunity, heart and vessels, and mental state. oxygen and biomass [11]. Cyanobacteria alone contribute more than 50% of atmospheric oxygen, 10% of global photosynthetic primary production [12], and at least 2.32 \(\times\) 10\({}^{14}\) g of carbon biomass [13]. In nature, bacteria, archaea, and fungi serve as key decomposers and break down non-living matter into simple, bioavailable compounds so that living organisms utilize them as nutrients [2]. Certain prokaryotes are the only organisms on earth that are capable of performing nitrogen fixation, nitrification, and denitrification as well as dissimilatory sulfate reduction and anaerobic sulfide oxidation, which are the key biochemical processes in the global nitrogen and sulfur cycles [14]. For example, nitrogen gas is inaccessible for all but nitrogen-fixing prokaryotes [15]. Under the catalysis of nitrogenases, these nitrogen-fixing prokaryotic specialists (e.g., rhizobia and certain species of cyanobacteria and Actinobacteria) convert nitrogen gas into ammonia, which is subsequently utilized as nutrients by organisms [16]. Additionally, the biological oxidation of reduced inorganic sulfur compounds (e.g., sulfides) is exclusively executed by archaea and bacteria that can be aerobic and anaerobic [17]; phototrophic purple and green sulfur bacteria are the common anaerobic sulfur-oxidizing prokaryotes [18]. Therefore, microbes constitute important primary producers and decomposers, and they maintain the carbon, nitrogen, and sulfur cycles as well as the flow of energy on the earth. Additionally, microbes play crucial roles in the food and beverage industry [3], agriculture [4], and pharmaceutics and therapy [6] as well as bioremediation [7]. For example, some special microbes, including the fungal baker yeast _Saccharomyces cerevisiae_, fungal molds (e.g., _Aspergillus_ and _Mucor_), and bacteria (e.g., _Streptococcus_ and _Lactobacillus_), are involved in the manufacturing of some internationally and locally common fermented foods (e.g., bread, wine, yogurt, and Chinese soybean curd) [3; 19; 20]. In the process of making bread, baker yeasts are added to the dough and convert sugar to alcohol and CO\({}_{2}\) as the products of alcoholic fermentation; they simultaneously synthesize other metabolites under anaerobic conditions, resulting in an increase in the volume of dough and a change in flavor [3]. In the process of manufacturing yogurt, lactic acid-producing bacteria (e.g., _Streptococcus thermophilus_ and _Lactobacillus bulgarcicus_) are added to heat-processed milk [20].