Ch. 33 The Microbe-Human Ecosystem

• Microbiome

  All the genes found in one's microbiota
• Microbiota


  All the microorganisms that live in and on an organism
• Holobionts


  Hosts and microbes live together and evolve together
• Humans cannot live a normal life without their microbial partners
• 16S ribosomal RNA sequencing reveal these microorganisms (Holobionts)
• Each microbial niche is related to a variety of factors such as body location, age, sex, diet and environment
• More than half of your body is not human, say scientists
• Human Microbiome Project (HMP)


  The goal of the first phase was to characterize the human microbiome, the second phase seeks to explore three microbiome-related conditions: pregnancy and preterm birth, irritable bowel syndrome, and type 2 diabetes
• The microbiota community is not static, it begins developing at birth and changes as we age
• A stable community of microbes is adopted by age 3
• It is important to develop a diverse microbiome
• Newborn colonization


  • Vaginal birth provides exposure to microbes from the mother's birth canal, whereas cesarean delivery provides microbe exposure from initial caretakers
  • Bifidobacteria transport polymeric sugars found in human breast milk directly across their plasma membrane, fermentation of these sugars produces acetate and lactate, which provides the infant with calories and lowers the gut pH, limiting growth of pathogens
• The adult human microbiota is relatively stable over time, only changing due to physical or lifestyle changes
• Bacteria common to human skin, the intestinal tract, and the other mucosal surfaces

  • Actinobacteriota
  • Bacteroidota
  • Firmicutes
  • Fusobacteriota
  • Proteobacteria
  • Verrucomicrobiota
• Internal organs and tissues are normally free of microorganisms, while surface tissues are constantly in contact with the environment and are colonized by various microbes
• Skin environment


  • Slightly acidic pH
  • High concentration of NaCl
  • Some areas lack moisture
  • Some bathed in oily lubricant sebum and antimicrobial peptides
  • Some microbes are temporarily present and are typically unable to multiply on the skin
  • Dry areas (forearms, buttocks, hands) harbor greatest microbial diversity, moist areas exhibit less diversity, sebaceous areas (forehead, behind the ear, and the back) exhibit lowest bacterial diversity
• Staphylococcus epidermidis


  Colonize the skin and generally nonpathogenic, key component of healthy skin, modulate keratinocyte gene expression stimulating antimicrobial peptide release, secrete short chain fatty acids, bind to the pattern recognition receptor TLR-2, inhibit growth of pathogens through bacterial interference
• The upper respiratory tract is colonized by a diverse group of microbes, while the lower respiratory tract was previously thought to be sterile but is not
• Microbes in the upper respiratory tract

  • Staphylococcus, Corynebacterium, and Cutibacterium in areas closest to the environment
  • Streptococcus and Dolosigranulum, Moraxella and Haemophilus spp. in the deeper nasal cavity
  • Neisseria, Rothia, Veillonella, Prevotella, and Leptotrichia in the oropharynx
• Microbes in the lower respiratory tract are introduced principally from the oropharynx and stay temporary, being expelled and replaced by new transients
• Eye

  A small number of bacteria, predominantly Staphylococcus epidermidis, are found on the conjunctiva
• External ear

  Similar to skin flora, with nonpathogenic staphylococci and Corynebacterium spp. predominating
• Mouth colonization


  • Soon after birth, the mouth is colonized by microorganisms from the surrounding environment
  • Anaerobes (Porphyromonas, Prevotella, and Fusobacterium spp.) become dominant due to the anoxic nature of the space between the teeth and gums
  • As teeth grow, Streptococcus parasanguinis and S. mutans attach to enamel surfaces, S. salivarius attaches to the buccal and gum epithelial surfaces and colonizes the saliva
  • They produce a glycocalyx and various other adherence factors that enable them to attach to oral surfaces, contributing to dental plaque, caries, gingivitis, and periodontal disease
• Stomach


  Most microbes are killed by the acidic conditions (pH of 2 to 3), usually containing less than 10 viable bacteria per milliliter of gastric fluid, but Streptococcus, Staphylococcus, Lactobacillus, Peptostreptococcus spp., and yeasts such as Candida spp. can survive if they pass through the stomach very quickly or are ingested with food particles and are resistant to the gastric pH
• Small intestine


  • Duodenum (first 25 cm) contains few organisms due to stomach acid, bile, and pancreatic secretions, with Gram-positive bacteria comprising most of the microbiota
  • Jejunum contains Enterococcus faecalis, lactobacilli, diphtheroids, and the yeast Candida albicans
  • Ileum has a flora similar to that in the colon, with a more alkaline pH and anaerobic Gram-negative bacteria and members of the Enterobacteriaceae becoming established
• Large intestine (colon)


  One of the most densely packed microbial ecosystems on Earth, with people living in industrialized nations having a different core microbiome from those who consume a plant-based diet, and the gut microbiome having metabolic, immunological, and endocrine roles
• Roles of the gut microbiome

  • Ferment foods that we cannot digest
  • Synthesize micronutrients including vitamins
  • Metabolize dietary toxins and carcinogens
  • Ensure immune system maturation
  • Protect against enteric pathogens
  • Convert steroids such as cholesterol and bile acids to other compounds
• Genitourinary tract

  Kidneys, ureter, and urinary bladder are normally free of microbes, while the distal portions of the urethra contain a few microbes like S. epidermidis, Enterococcus faecalis, and Corynebacterium spp., and the female genital tract has a complex microbiota dominated by acid-tolerant lactobacilli that ferment glycogen and form lactic acid, maintaining a pH between 4.4 and 4.6
• Functional core microbiome

  Microbes that provide essential functions for host homeostasis
• Core microbiome


  Microbes that provide the host with a suite of activities required for health and homeostasis
• Individuals who consume a plant-based diet have a different core microbiome from that of other nations
• Gut microbiome


  • Has metabolic, immunological, and endocrine roles
  • Ferments foods that we cannot digest
  • Synthesizes micronutrients including vitamins
  • Metabolizes dietary toxins and carcinogens
  • Ensures immune system maturation
  • Protects against enteric pathogens
  • Converts steroids such as cholesterol and bile acids to other compounds
• Primary bile acids

  Chemically modified by gut microbes to secondary bile acids, which impact the growth of other microbes in the gut
• Genitourinary tract


  • Kidneys, ureter, and urinary bladder are normally free of microbes
  • Distal portions of urethra have few microbes (S. epidermidis, Enterococcus faecalis, and Corynebacterium spp.)
  • Female genital tract has a complex microbiota that changes due to menstrual cycle
  • Acid-tolerant lactobacilli predominate and ferment glycogen, forming lactic acid - pH of the vagina and cervix is between 4.4 and 4.6
• Functional core microbiome


  Microbes that provide the host with a suite of activities required for health and homeostasis
• Provision of vitamin K by E. coli is an example of the functional core microbiome
• Gut microbiota has an emerging role in human behavior, which is a rapidly advancing field
• Metabolome

  The products these microorganisms secrete
• Overweight people

  Have higher concentrations of gut bacteria belonging to the phylum Firmicutes compared to bacteria belonging to the phylum Bacteroidota
• Several other gut microbiota population changes have refocused attention from the individual species in the gut microbiome to the metabolome