MCB 150 Animals as Habitat

• Animals, encompassing humans and other fauna, serve as crucial habitats for diverse microorganisms
• Conducive internal environment for microbial growth


  • Abundant nutrients
  • Consistent moisture levels
  • Tightly regulated temperature and pH
• The various anatomical surfaces and specialized niches within an animal provide a multitude of unique microenvironments for microbial colonization
• The byproducts of animal metabolism further contribute to the suitability of this habitat, acting as a readily available source of nutrients for resident microbial communities
• Normal flora


  Indigenous microorganisms such as bacteria, archaea, fungi, and viruses, which are typically harmless to the host
• Characteristics of normal flora


  • They should be abundant at any given anatomical site
  • They should maintain a positive host-microbe relationship
  • They should have protective functions, which include microbial antagonism and competitive exclusion
• Suitable sites for microbial colonization in humans and animals


  • Gastrointestinal tract
  • Oral cavity
  • Skin
  • Respiratory tract
  • Urogenital tract
• Herbivores


  • They have evolved specialized gut structures that allow them to form a mutualistic-symbiotic relationship with microorganisms
  • These microorganisms are crucial in degrading and catabolizing plant fibers, which are the structural components of plant cell walls
• Mammals and other animals cannot metabolize and digest cellulose and other plant polysaccharides due to the absence of genes encoding for enzymes required to hydrolyze to decompose the complex polysaccharide chains
• Digestive patterns in herbivores


  • Foregut fermentation
  • Hindgut fermentation
• Foregut fermentation


  Microbial fermentation chamber precedes the small intestine
• Hindgut fermentation


  They do not have a chamber and only have one stomach, but they utilize an organ called the cecum, located between the small and large intestines, as their fermenting vessel
• Rumen


  A specialized foregut digestive organ wherein cellulose and other plant polysaccharides are digested and broken down by microorganisms
• The rumen hosts many prokaryotes and eukaryotes more significantly than those in fertile soils
• Rumen microbiota


  • Bacteria, Archaea, various fungi, and nonphototrophic protists constitute a harmonious and integrated microbial community
  • Anaerobic bacteria and archaea dominate the rumen due to anoxic conditions
  • Cellulose is converted to fatty acids, CO2, and CH4 (methane) in a multistep and integrated microbial food chain
  • Various rumen bacteria hydrolyze cellulose into sugars and ferment the sugars into Volatile Fatty Acids (VFAs)
  • Fibrobacter succinogenes, Ruminococcus albus (dominant cellulolytic anaerobes), and ciliated protists are also present in the rumen at a 106 cells/mL density
• Rumen fermentation


  1. The cow eats the plant material and swallows it

  2. The food enters the first chamber of the four-compartment stomach, the reticulum

  3. Large food particles are regurgitated, chewed, and mixed with saliva containing bicarbonate before being transported back to the reticulo-rumen

  4. In the rumen, cellulolytic microorganisms hydrolyze cellulose, liberating glucose molecules

  5. The free glucose can then be fermented by bacteria, producing VFAs such as acetic acid, propionic, and butyric acids, and the gases CO2 and CH4 are released through belching

  6. The digested bacterial cells become a significant source of protein and vitamins for the animal
• Previously, knowledge about the adult human gut microbiota relied on labor-intensive culture-based methods
• Recent advancements in culture-independent approaches, such as high-throughput sequencing, have greatly enhanced our understanding of the human gut microbiota
• Sequencing the bacterial 16S ribosomal RNA gene has become a popular method for studying gut microbiota
• Whole-genome shotgun metagenomics is also being utilized for more reliable microbiota composition and diversity estimates
• The gut microbiota is less diverse than other microbial communities in the body and exhibits functional redundancy
• The functional capacity of the human gut microbiome has been extensively cataloged, revealing country-specific microbial signatures influenced by environmental factors and possibly host genetics
• The human gut microbiota is relatively stable at the phylum level, with Bacteroidetes and Firmicutes being conserved in almost all individuals
• The variation in interindividual microbial communities is more significant than at the phylum level due to deep functional redundancy in the gut microbiota
• Bacterial cells are unevenly distributed along the Gut-Intermediate Tissue (GIT), with varying numbers of bacteria per gram
• The microbial community varies among sites, with different bacterial phyla enriched in the small intestine and colon
• The lumen microbiota differs significantly from those close to and attached to the epithelium
• Factors affecting gut microbiota


  • Age
  • Diet
  • Antibiotics
• Age and gut microbiota


  • Microbial colonization of the gut starts at birth and is influenced by the vaginal microbiota of the mother
  • In the 1st year of life, microbiota composition is simple and shows wide interindividual variations
  • Starting at 2.5 years, the infant microbiota's composition, diversity, and functional capabilities resemble those of adults
  • The microbial community in individuals over 65 undergoes a shift, with an increase in Bacteroidetes phyla and Clostridium cluster IV
  • The diversity of the microbiota in the elderly is linked to living arrangements
  • The capacity of the elderly microbiota to carry out metabolic processes is reduced while proteolytic activity is increased
• Diet and gut microbiota


  • Specific dietary components, such as fibers, proteins, fats, vitamins, and minerals, can promote the growth of beneficial bacteria while suppressing harmful ones
  • Prebiotics and probiotics can positively impact gut microbiota composition
  • The importance of a balanced and diverse diet rich in plant-based foods, fibers, and fermented products to maintain a healthy gut microbiome and prevent gastrointestinal diseases
• Antibiotics and gut microbiota


  Antibiotics are designed to target harmful bacteria but do not discriminate between pathogenic and beneficial bacteria, leading to disruption of the gut microbiome
• Dietary patterns


  Highly influence gut microbiome composition
• Dietary components that promote beneficial bacteria and reduce harmful ones


  • Fibers
  • Proteins
  • Fats
  • Vitamins
  • Minerals
• Prebiotics


  Nondigestible food components that stimulate the growth of beneficial bacteria
• Probiotics


  Live beneficial bacteria
• Postbiotics


  Beneficial substances gut microbes produce during fermentation
• A balanced and diverse diet rich in plant-based foods, fibers, and fermented products is important to maintain a healthy gut microbiome and prevent gastrointestinal diseases
• Antibiotics can lead to a significant reduction in microbial diversity and the elimination of beneficial microbes
• Disruption of the microbiome can lead to increased susceptibility to infections, chronic diseases, antibiotic resistance, and impacts on metabolic, immune, and neurological functions
• The human intestinal microbiota has been linked to various diseases, syndromes, and functional aberrations, with the most significant associations being the link between chronic gastrointestinal diseases like IBS and IBD and systemic metabolic diseases like type 2 diabetes and obesity