Lesson 9 - Microbial Ecology and Microbial Technology

Microbial Ecology

• Study of the numerous interrelationships between microbes and the world around them

  • Studies their interactions between microorganisms and their environment, including interactions with nonliving and living components.

• Importance

  • Influences health (e.g., diseases by pathogens and beneficial relationships with microbes).

  • Microbes play roles in agriculture, industry, waste management, sewage treatment, and water purification.

  • Essential in biotechnology, genetic engineering, bioremediation, and gene therapy

Symbiosis (symbiotic Relationship)

• Refers to a close association between two different species.

  • The organisms in this relationship are called symbionts, which interact in various ways:

    • Neutralism

    • Commensalism

    • Parasitism

Symbionts

Organisms that live in a symbiotic relationship

Symbiotic Relationship | Commensalism

• Benefits one symbiont while having no effect on the other.

  • Many of the organisms in the indigenous microbiota of humans are commensals

  • E.g., Demodex mites living in human hair follicles benefit from the environment but do not affect the host.

Symbiotic Relationship | Neutralism

• Neither symbiont affects the other.

  • E.g., Microorganisms coexisting in the same niche without impacting each other.

Symbiotic Relationship | Mutualism

• Beneficial to both symbionts.

  • Humans have a ______ relationship with many of the microorganisms of their indigenous microbiota

  • Examples:

    • Escherichia coli in the human gut:

      • E. coli derives nutrients while producing Vitamin K for the host.

    • Protozoa in termites:

      • Protozoa digest wood into nutrients, and termites provide shelter and food.

    • Lichens:

      • A partnership between algae (or cyanobacteria) and fungi; the alga

Symbiotic Relationship | Parasitism

• Beneficial to one symbiont (the parasite) and harmful to the other (the host).

  • Certain parasites always cause disease, and some cause the death of the host

  • Examples:

    • Trypanosoma gambiense, the protozoan causing African sleeping sickness, harms humans.

    • "Smart" parasites minimize harm, while "dumb" parasites may kill their host, risking their own survival.

Host

Living organism that harbors (accommodates) another living organism

Dysbiosis (Dynamic Symbiotic Relationships)

• Conditions can cause a mutualistic or commensalistic relationship between humans and their indigenous microbiota to shift to a parasitic, disease-causing (pathogenic) relationship (mutualistic/commensalistic to parasitic)

  • Shifts can occur due to changes in environmental or host conditions

Opportunistic Pathogens

Normally harmless microbes may become pathogenic if the host's defenses are weakened (e.g., due to surgery, burns, or immunosuppression).

Indigenous Microflora

• Consists of all microorganisms—bacteria, fungi, protozoa, and viruses—that live on and within the human body.

  • “Normal flora”

  • Humans have an estimated 100 trillion microbes, outnumbering the body’s cells by tenfold.

  • Composed of 10,000 different species

  • This microbiota plays a crucial role in health by aiding digestion, synthesizing vitamins, and preventing colonization by harmful pathogens.

  • The types of resident microbiota differ from one anatomic site to another

Development of Microflora | Fetal Stage

The fetus is sterile.

Development of Microflora | Post-Birth

• Microbial colonization begins as the newborn is exposed to microorganisms from the mother, environment, food, and air.

  • These microbes establish themselves on skin, mucous membranes, and the digestive and genitourinary tracts.

Characteristics of Microflora

• Microbial composition varies by body site, determined by conditions like moisture, pH, salinity, and nutrient availability.

  • Some body parts, like blood, lymph, and internal organs, are typically sterile.

Transient Microflora

These are short-lived microbes unable to compete with resident flora or survive body defenses like acidic environments or secretions.

Impact of Microflora Imbalance

Disruptions, such as from antibiotics, can lead to conditions like diarrhea or superinfections caused by opportunistic microbes, e.g., Candida albicans, leading to candidiasis.

Microflora by Body Region | Skin

• A relatively inhospitable environment for microorganisms

  • Consists primarily of bacteria and fungi

  • Many that lives are anaerobes

  • Hosts about 300 species, influenced by moisture, temperature, and anatomical location.

  • Common microbes:

    • Staphylococcus epidermidis

    • Corynebacterium spp.

    • Propionibacterium spp.

    • Anaerobes dominate deeper skin layers

Microflora by Body Region | Outer Ear and Auditory Canal

Similar to skin microflora.

Microflora by Body Region | Inner Ear and Middle Ear

Sterile; infections occur via the eustachian tube

Microflora by Body Region | Eyes

• External surface is lubricated, cleansed, and protected by tears, mucus, and sebum

  • Protected by tears containing lysozyme, reducing microbial growth.

Microflora by Body Region | Respiratory Tract (Upper Tract - Nose and Pharynx)

• Harbors diverse microbes, including harmless ones and opportunistic pathogens.

• Have an abundant and varied population of microbes because these areas provide moist

Microflora by Body Region | Respiratory Tract (Lower Tract)

• Usually sterile due to defense mechanisms.

  • Consists of the larynx (voice box), trachea, bronchi, bronchioles, and lungs

Hygiene

Frequent washing removes transient microbes and reduces infections.

Healthy Carriers

• Harbor virulent (disease-causing) pathogens in their nasal passages or throats, but do not have the diseases associated with them

  • Some people harbor pathogens like Streptococcus pneumoniae or Neisseria meningitidis without symptoms.

Microflora by Body Region | Oral Cavity

• Supports anaerobic and aerobic bacteria, thriving in gum margins and tooth crevices.

  • Common microbes:

    • Streptococcus mutans (causes dental caries)

    • Actinomyces spp.

    • Poor hygiene can lead to diseases like gingivitis and periodontitis.

    • Most common indigenous microbiota: α-hemolytic streptococci

Oral Cavity | Anaerobic Microorganisms

Flourish in gum margins, crevices between the teeth, and deep folds (crypts) on the surface of the tonsils

Microflora by Body Region | Gastrointestinal Tract (GI) or Digestive Tract

• Consists of a long tube with many expanded areas designed for digestion of food, absorption of nutrients, and elimination of undigested materials

  • Includes esophagus, stomach, small intestine, large intestine (colon), and anus

  • Many are removed as a result of defacation

Microflora by Body Region - Gastrointestinal Tract (GI) or Digestive Tract | Stomach

• Minimal microbes due to acidic pH (~1.5).

  • Exceptions include Helicobacter pylori, linked to ulcers.

Microflora by Body Region - Gastrointestinal Tract (GI) or Digestive Tract | Small Intestine

Fewer microbes in the upper portion (duodenum) because bile inhibits their growth; more in the ileum.

Microflora by Body Region - Gastrointestinal Tract (GI) or Digestive Tract | Colon

• Contains the largest number and variety of microorganisms of any colonized area of the body

  • Houses 500–600 species, primarily anaerobes like Bacteroides and Clostridium.

  • Anaerobic

  • Many are opportunists

  • Role:

    • Aid digestion.

  • Prevent pathogen overgrowth.

    • Example: E. coli—harmless in the colon but can cause UTIs elsewhere.

Microflora by Body Region | Genitourinary Tract (GU)

• Consists of the urinary tract (kidneys, ureters, urinary bladder, and urethra) and the various parts of the male and female reproductive systems

  • Healthy kidney, ureters, and urinary bladder are thought to be sterile

Microflora by Body Region | Genitourinary Tract (GU) - Urinary Tract

Sterile except for the distal urethra, which hosts bacteria and yeasts.

Microflora by Body Region | Genitourinary Tract (GU) - Reproductive Tract

• Male: Mostly sterile.

• Female: Varies by life stage:

  • Childbearing Years

    • Acidic vaginal secretions (~pH 4.0–5.0) favor Lactobacillus spp., which suppress harmful bacteria and yeast.

  • Puberty/Menopause

    • Alkaline secretions promote different microflora.

Distal Urethra and External Opening of the Urethra

Harbor many microbes, including bacteria, yeasts, and viruses

Beneficial Role of Microflora | Nutrient Production

• Intestinal bacteria synthesize essential vitamins, such as:

  • Vitamin K

    • Important for blood clotting.

  • Vitamin B12, pantothenic acid, pyridoxine, and biotin

    • Essential for various metabolic processes.

Beneficial Role of Microflora | Immune System Stimulation

Indigenous microbes provide constant exposure to antigens and irritants, priming the immune system to respond more effectively to pathogens.

Beneficial Role of Microflora | Microbial Antagonism

• Microbes versus microbes

  • Indigenous microflora inhibit colonization by harmful pathogens through:

    • Space and Nutrient Competition

    • Production of Antimicrobial Substances

Beneficial Role of Microflora |

Microbial Antagonism | Space and Nutrient Competition

Large populations of beneficial bacteria occupy niches, denying resources to invaders.

Microbial Antagonism | Production of Antimicrobial Substances - Antibiotics

Substances like penicillin produced by certain microbes kill or inhibit other microorganisms.

Microbial Antagonism | Production of Antimicrobial Substances - Bacteriocins

Proteins such as colicin, produced by E. coli, are lethal to other bacteria.

Beneficial Role of Microflora | Biotherapeutic Agents (Probiotics)

Beneficial bacteria and yeasts, such as Lactobacillus and Bifidobacterium, help restore microbial balance, preventing overgrowth of harmful organisms like Clostridium difficile or Candida albicans.

Harmful Roles of Microflora | Opportunistic Pathogens

• Indigenous microbes can become pathogenic under certain conditions, such as:

  • E. coli: Normally harmless in the gut, but can cause infections if it enters the urinary tract, bloodstream, or wounds.

  • Other opportunistic pathogens: Staphylococcus aureus, Enterococcus spp., and members of Enterobacteriaceae.

Harmful Roles of Microflora | Biofilms

• Complex and persistent communities of assorted microbes

  • Virtually everywhere

  • Microbial communities organized into persistent biofilms can:

    • Form on natural and artificial surfaces (e.g., heart valves, catheters).

    • Cause diseases such as endocarditis, cystic fibrosis, and periodontal disease.

    • Exhibit resistance to antibiotics and immune responses due to:

      • Reduced penetration of antimicrobials.

      • Protection provided by neighboring organisms within the biofilm.

  • Very difficult to treat and require long-term antibiotics and occasionally surgery for eradication

Harmful Roles of Microflora | Synergistic Infections

• Two or more microorganisms may “team up” to produce a disease that neither could cause by itself

  • Multiple species of microbes may collaborate to cause diseases, such as:

    • Acute necrotizing ulcerative gingivitis (ANUG).

    • Bacterial vaginosis (BV).

Harmful Roles of Microflora | Disruption of Microbial Balance

• Antibiotics or chemotherapy can disrupt the balance of indigenous microflora, leading to overgrowth of harmful microbes like:

  • Clostridium difficile: Causes pseudomembranous colitis.

  • Candida albicans: Causes yeast infections.

Microbial Technology (Application and Significance) | Medical Applications - Therapeutic Proteins

• Genetically engineered bacteria and yeasts produce vital proteins like:

  • Human insulin.

  • Human growth hormone.

  • Tissue plasminogen activator.

  • Interferons and vaccines (e.g., Hepatitis B).

Microbial Technology (Application and Significance) | Medical Applications - DNA Vaccines

Experimental vaccines where genes encoding a pathogen’s proteins are inserted into plasmids to stimulate the immune system.

Microbial Technology (Application and Significance) | Medical Applications - Antibiotics and Therapeutic Agents

• Microbial metabolites include:

  • Antibiotics (e.g., penicillins, cephalosporins, tetracycline).

  • Anticancer drugs, immunosuppressants, and herbicides.

Microbial Technology (Application and Significance) | Agricultural Applications - Transgenic Plants

Genes from microbes (e.g., Bacillus thuringiensis) are introduced into crops to enhance resistance to pests and pathogens.

Microbial Technology (Application and Significance) | Agricultural Applications - Biocontrol

Microbial products are used as herbicides, insecticides, or nematocides to protect crops.

Microbial Technology (Application and Significance) | Food Technology - Fermented Foods

Microbes play a key role in producing yogurt, cheese, sauerkraut, soy sauce, and alcoholic beverages.

Microbial Technology (Application and Significance) | Food Technology - Amino Acid Production

Microbial production of amino acids like lysine and methionine for food and feed supplements.

Microbial Technology (Application and Significance) | Food Technology - Single-Cell Protein (SCP)

Algae and fungi are cultivated as protein sources for animal feed and human nutrition.

Microbial Technology (Application and Significance) | Environmental Applications - Bioremediation

• Microbes clean up pollutants, including:

  • Oil spills (e.g., genetically engineered bacteria).

  • Toxic solvents like trichloroethylene in soils.

Microbial Technology (Application and Significance) | Environmental Applications - Composting and Waste Treatment

Microorganisms decompose organic waste in composting and sewage treatment.

Microbial Technology (Application and Significance) | Industrial Applications - Chemical Production

• Large-scale microbial production of:

  • Acetic acid, ethanol, citric acid, lactic acid, and glycerol.

  • Biofuels like hydrogen and methane.

Microbial Technology (Application and Significance) | Industrial Applications - Biomining

Microbes extract metals like copper, uranium, and zinc through bioleaching.

Microbial Technology (Application and Significance) | Industrial Applications - Enzymes for Industry

Microbial enzymes (e.g., amylase, protease, lactase) are used in textiles, detergents, and food processing.

Impact and Future Potential of Microbial Technology

• Microbial biotechnology has revolutionized many industries by offering sustainable and efficient solutions. Its future lies in:

  • Developing advanced biotherapeutics.

  • Enhancing crop resilience.

  • Innovating eco-friendly bio-based processes to replace synthetic chemicals.

Ecology

Systematic study of the interrelationships that exist between organisms and their environment

Microbiota

Refers to microorganisms that make up our indigenous microflora

Microbiome

Consists of not only the microorganisms but also the genes they possess and their effect on the local environment within the body

Superinfection

Overgrowth or population explosion of an organism that is usually present in low numbers

Helicobacter pylori

Live in some people’s stomachs and is a common cause of ulcers

Metabolic by-products of lactobacilli

Inhibit growth of the bacteria associated with bacterial vaginosis (BV)

Microcolonies

Bacteria that grow in tiny clusters that are separated by a network of water channels

Planktonic Bacteria

Released from the surface of the biofilm, have a normal metabolism, and can colonize other surfaces to initiate further biofilm formation

Frustrated Phagocytes

When leukocytes and macrophages become activated and secrete toxic compounds that cause damage to nearby healthy host tissues

Endosymbionts

Bacteria found inside other microorganisms

Saprophytes

Bacteria that decompose dead organic matter into inorganic materials

Biogeochemical Cycling

Cycling of elements by microorganisms

Biotechnology

Any technological application that uses biological systems, living organisms, or derivatives thereof, to make or modify products or processes for specific use