A complete guide to human microbiomes: Body niches, transmission, development, dysbiosis, and restoration

Abstract

Humans are supra-organisms co-evolved with microbial communities (Prokaryotic and Eukaryotic), named the microbiome. These microbiomes supply essential ecosystem services that play critical roles in human health. A loss of indigenous microbes through modern lifestyles leads to microbial extinctions, associated with many diseases and epidemics. This narrative review conforms a complete guide to the human holobiont-comprising the host and all its symbiont populations- summarizes the latest and most significant research findings in human microbiome. It pretends to be a comprehensive resource in the field, describing all human body niches and their dominant microbial taxa while discussing common perturbations on microbial homeostasis, impacts of urbanization and restoration and humanitarian efforts to preserve good microbes from extinction.

Keywords: body niches; dysbiosis; evolution; human microbiome; restoration.

FIGURE 1

Human microbiome development and transmission. Panel (A) Representation of humans’ first contact with microbes during birth and a comparison of how delivery mode (vaginal delivery and C-section) impacts infant microbiota. Panel (B) Human microbial transmission and development from pre-birth to adulthood. Microbes that colonize newborns will form a variety of niches in different body sites, adult diversity is attained at ~3 years old. Elder people have a decrease in microbial diversity leading to dysbiosis that may be associated with neurodegenerative disorders. Panel (C) Practices of breastfeeding and/or formula feeding play an important role in shaping the intestinal microbiome. Formula feeding is associated with intestinal inflammation, with an increase in Enterobacteriaceae and Clostridium spp. and reduced levels of probiotic Bifidobacterium and Lactobacillus spp. acquired via lactation. Image created with BioRender.com.

FIGURE 2

Microbiome in human epithelial and mucosal sites other than the gut. Panel (A) Representation of biofilm formation in dental plaque, periodontal disease progression and risk factors associated with periodontitis and oral cancer at each progression stage. Disease development is associated oral dysbiosis. Disease stages are identified by colors; green represents healthy gums, yellow represents gingivitis, orange represents periodontitis and red represents oral squamous cell carcinoma. Panel (B) Characteristic microbiome of the skin, ear, eyes and the nasopharyngeal tract. Homeostatic microbiome are identified in green, and microorganisms that increase in abundance during dysbiosis are identified in red. Alterations of microbial populations can lead to the development of different health conditions which could be irreversible. Image created with BioRender.com.

FIGURE 3

Complexity of the human gut microbiota. Panel (A) Representation of the most characteristic and predominant organisms found in each gastrointestinal site. Panel (B) Representation of the differences between individuals with a healthy lifestyle compared to obese individuals. Normal/lean microbiota are dominated by Bacteroidetes, Firmicutes, Proteobacteria, and Actinobacteria (1B). Obesity, diabetes, and gut inflammation are characterized by an increase in Firmicutes and Lipopolysaccharides (LPS), and a reduction in Bacteroidetes and short-chain fatty acids (2B). The production of LPS is recognized by Toll-Like receptor four which produces inflammatory interleukins (IL-6) and phosphorylation of Insulin Receptor-1 which is associated with insulin resistance (3B). Panel (C) Represents how bacterial antigens enter the Peyer’s patches through M cells and are captured by dendritic cells (DCs). Lymphocytes interact with antigen-loaded DCs and they migrate to the lymph nodes causing expansion, differentiation and proliferation. In addition, antigens can be transported to the spleen by circulation. Antigens are processed and presented to T cells, initiating an immune response. Finally, effector T cells return to the gut lamina propria where they reside. Panel (D) shows how alterations in gut microbiota can cause stress and anxiety-like disorders. Image created with BioRender.com.

FIGURE 4

Changes in the gut microbiome across urbanization and human lifestyles. Panel (A) shows the impact of modernization on the gut microbial diversity due to changes in diet, healthcare, sanitation, and lifestyle associated to modernity. Ancient microbiomes have higher microbial diversity and may even include taxa such as Treponema, that is no longer a component of the modern human microbiota. Panel (B) outlines the effects of urbanization on the gut microbiome. Increase in the consumption of refined sugars, antibiotics, chemical antimicrobials, exposure to air pollution and water chlorination, can have detrimental effects on the gut microbiota leading to the development of metabolic conditions, colorectal cancer, and antibiotic resistance. Image created with BioRender.com.

FIGURE 5

Restoration of the gut microbiome. Panel (A) Probiotics provide live microorganisms in the form of food or supplements that directly colonize the gut, while prebiotics provide fiber and carbohydrates that stimulate the growth of healthy bacterial colonies that already reside in the gut. Together, probiotics and prebiotics compose synbiotics which can be obtained commercially. Panel (B) displays two ways of microbial seeding, vaginal transfer for C-section born babies and fecal matter transplants. Image created with BioRender.com.