Ch. 27 and 33: Microbial Interactions

what are the 2 types of microbial interactions

symbiosis and consortium

symbiosis

how organisms interact with each other

types of symbiosis

ectosymbiont: organism located on surface

endosymbiont: organism located within another

consortium

host with more than 1 associated symbiont

• intermittent and cyclic

• or permanent

positive microbial interactions

• mutualism

• cooperation

• commensalism

negative microbial interactions

• predation (killing)

• parasitism (exploitation)

• amensalism

• competition

mutualism

• some reciprocal benefit to both partners

  • some degree of obligation

• microorganism-insect relationship

  • aphids (insect) and B. aphidicola (bacteria) have coevolved

    • B. aphidicola helps aphids digest, aphids provide food for bacteria

• protozoan-termite relationship

  • lignocellulose is broken down by Trichonympha (protist)

  • termite provides food for protozoan

  • protist itself may harbor its on endosymbiont nitrogen fixing bacteria (Elusimicrobium)

cooperation

• A positive symbiosis that benefits both organisms

  • relationship is not obligatory; can survive w/o each other

• Bacteria and nematode relationship

• Bacteria and human relationship

  • Probiotics maintain intestinal lining

• Next-Generation Beneficial Microbes: The Case of Akkermansia muciniphila

  • Helps in production of mucus for intestinal lining, prevents inflammation

commensalism

• One organism benefits (commensal) and the other is neither harmed nor helped

  • unidirectional relationship

• Often syntrophic (cross-feeding)

  • modification of environment

• Examples:

  • Nitrification (NH3 → NO2 → NO3)

    • Nitrosomonas (first step), Nitrobacter (second step) 

  • Microbial succession during spoilage of milk

  • Formation of biofilms

  • Skin or surface microbes on plants or animals

predation

• Obtain biochemical precursors and energy after the prey is dead

  • Bdellovibrio penetrates cell wall, grows outside plasma membrane

  • Vampirococcus uses an epibiotic mode of attacking the prey

  • Daptobacter penetrates the prey then directly consumes the cytoplasmic contents

  • Myxococcus “wolf pack” cells use gliding motility to creep, overtake their prey, and release degradative enzymes

    • facultative predator

parasitism

• One organism gains (parasite) and the other is harmed (host)

• Obtain biochemical precursors and energy while the prey is still alive

• Always some co-existence

  • successful parasites have evolved to co-exist in equilibrium

• Genomic reduction

  • Parasite may not need some genes d/t depending on host for it

amensalism

• Negative impact of one organism on another based on release of a specific compound

• Examples:

  • antibiotic production

  • bacteriocin production

competition

• Occurs when two organisms try to acquire or use the same resource

• Two possible outcomes:

  • one organism dominates

  • two organisms share the resource

microbiome

• normal microbiota

• human body is diverse environment - specific niches present

• dynamic relationships exist

superorganisms

when gene-encoded metabolic processes of the host become integrated with those of the microbes

what helps to make a reducing environment in the gut

• E. coli and streptococci

• enhances growth of bifidobacteria

• milk also helps select for non-pathogenic bacteria

bifidobacteria is found in

breastfed babies

• helps in selection of non-pathogenic bacteria by promoting growth of intestinal bacteria

bifidobacteria

• Can synthesize all amino acids (prototrophic)

  • can’t synthesize all nitrogenous bases

• Can do fermentation → calories and lowers the gut pH (helps in digestion)

• Used as probiotics

• Helps in immune response ~~ enhances vaccination efficacy

• Born vaginally - baby gets bacteria from mother

• decreases throughout lifetime

• endosymbiont

germfree animals (gnotobiotic)

• Study effects of microbes

  • compare germfree and normal animals

  • introducing a single microbe

• Coupled with genomic studies for maximum benefit

• Gut-brain connection is important through microbiota

human-microbe interactions: human microbiome project

• Initiated in December 2007 by the National Institutes of Health (NIH)

• As of 2014

  • whole metagenomic sequencing data for ~800 healthy human cohort samples obtained

  • 16S sequence data from ~5,000 healthy human cohort samples

• Information gained may shed light on complex interactions

• Five phyla present in most humans: Actinobacteria, Bacteroidetes, Firmicutes, Fusobacteria, and Proteobacteria

  • Actinobacteria decreases through age, firmicutes increases

skin

• Resident and transient microbiota - ectosymbiont

• Inhospitable environment

• Inhibitory substances 

  • lysozyme and cathelicidins by macrophages and granulocytes

    • Lysozyme breaks beta 1,4 glycosidic bond between NAM-NAG of cell wall

    • Cathelicidins have broad antimicrobial activity, fight against viruses and fungi

  • oleic acid produced by Gram-positive C. acnes to inhibit Gram-negatives

• Deodorants have antibacterials 

why is skin an inhospitable environment

• slightly acidic pH

• high concentration of NaCl

• many areas low in moisture

Acne vulgaris

• caused in part by Cutibacterium (formerly known as Propionibacterium) acnes

  • → sebum accumulation, becomes an opportunistic pathogen, feeding on sebum

what are natural bacterias on skin

staph aureus and staph epidermis

• staph aureus is opportunistic

• staph epidermis is normal part of flora

eye

• small number of commensal bacteria found on the conjunctiva of the eye

• predominant bacterium is Staphylococcus epidermidis

ear

• similar to skin flora, containing staph aureus

• also has fungi

  • C. auris

mouth

• Bacteria thriving; imbalance → dental plaque, dental caries, gingivitis, and periodontal disease

• oral cavity is colonized by microorganisms from the surrounding environment

• after teething, obligate anaerobes become dominant d/t anoxic nature of mouth

  • Initially aerobes

stomach

• acidic environment

• Some microbes can survive if ingested in food particles

• H. pylori releases molecules to be able to survive in stomach

intestines is made up of

small intestine and large intestine

small intestine

duodenum

jejunum

ileum

duodenum

• contains few organisms

• Slightly lower pH compared to jejunum and ileum bc closer to stomach

jejunum

• similar organisms to those in ileum

ileum

• flora similar to colon

• pH becomes more alkaline; higher pH than stomach

  • pH increasing from duodenum → ileum

• anaerobic Gram-negative and Enterobacteriaceae

large intestine

• Largest microbial population of body

  • replaced rapidly because of their high reproductive rate

  • most microbes are anaerobes

upper respiratory tract is made up of

nose, nasopharynx and oropharynx

nose and nasopharynx

• S. aureus and S. epidermidis

  • predominant bacteria

  • found just inside nostrils

• Nasopharynx may contain low numbers of potential pathogens

  • Streptococcus pneumoniae, Neisseria meningitidis, and Haemophilus influenzae

oropharynx

• Division of the pharynx lying between the soft palate and the upper edge of the epiglottis

  • α-hemolytic streptococci

  • diphtheroids (Gram-positive)

  • Gram-negative cocci

  • anaerobes in tonsillar crypts

    • Crypts inhibit fungus (yeast) and other bacterias, prevent ear ifx

lower respiratory tract

• No normal microbiota in the lower respiratory tract

• Microbes moved by:

  • continuous stream of mucous generated by ciliated epithelial cells

  • phagocytic action of alveolar macrophages

  • lysozyme in mucus

GU tract

• Unfavorable environment for foreign microbes

  • low pH of urine and vagina

  • vagina has lactobacilli

    • Goes through fermentation, lowering pH

  • urea and other toxic metabolic end products in urine

  • hypertonic nature of kidney medulla

• Flushing with urine and mucus

• Distance barrier of male urethra - less frequent UTIs

normal flora of GU tract

• Kidneys, ureter, and bladder

  • normally free of microbes

• Distal portions of urethra

  • few microbes found

• Female genital tract

  • complex microbiota in a state of flux due to menstrual cycle

  • acid-tolerant lactobacilli predominate (pH 4.4-4.6)

functional core microbiome is required for

homeostasis

• We rely on our gut microbiota

• Research has refocused attention from individual species to metabolome 

  • products these microorganisms secrete

immunity

• Antibiotics disrupt the gut microbial community

• Colonization resistance is based on competitive exclusion

• Releases toxic peptides to target pathogens

  • bacteriocins, microcins, colicins

indirect mechanisms of gut microbiota

• induction of host cell response

  • → peptidoglycan, SCFAs → stimulates host to make antimicrobial peptides

    • targets Enterococcus, Listeria

  • → SCFAs, bile acid modification → boosts host immune cell response

    • targets C. diff, E. coli

direct mechanisms of gut microbiota

• interactions between gut microbes

  • → nutrient consumption - outcompete pathogens for food

    • targets E. coli, salmonella, C. diff

  • → bacteriocins, type VI secretion system-dependent toxins - release toxins to kill pathogens

    • targets Pseudomonas, Vibrio, Bacteriocides

gut-brain axis

• Gut microbiota may affect CNS

• Specific behavioral traits: inquisitiveness, sociability, anxiety, depression

• Ways the microbiome can influence the CNS:

  • microbiome effect on the immune system

  • Microbes signal enteric nervous system, connected to the CNS by the Vagus nerve

    • If connection is disrupted, can lead to dysbiosis

  • soluble microbial products (short-chain fatty acids – SCFAs)

    • Affect how we react

    • Prevents inflammation

dysbiosis

• Metabolic syndrome has at least three of the following: 

  • Large waist circumference

  • High blood triglyceride level

  • High blood pressure

  • Elevated low-density lipoprotein and fasting blood glucose levels

inflammatory bowel disease (IBD) patients

• disproportionate number of bacteria in the Proteobacteria (Gram-negative) phylum

• promote inflammation via production of long-chain fatty-acid instead of SCFA

diet of someone with cardiovascular disease

• lots of red meat and high-fat foods

• little fiber for gut microbes to use to produce anti-inflammatory short-chain fatty acids

cancer

• Microbes are involved in about 20% of malignancies

• Host cells become cancerous 

  • human viruses and bacterial products alter the host cell cycle to favor proliferation

  • prevent host cells from repairing DNA damage

• Helicobacter pylori dysregulate host cell cycling

  • Causes ulcers, no DNA repair → stomach cancer

• Bacteria can be involved in metastasis of tumors to distant sites

• Many cancers linked to microbes are driven by the inflammatory state associated with dysbiosis

synbiotics

foods or supplements that include both a prebiotic and a probiotic

western diet

• High fat and low fiber → dysbiosis of gut microbiota

  • Decrease in SCFA-producing bacteria

• Less mucus layer

• Decrease in tight junction protein, AMPs, and SCFAs

• Induce intestinal inflammation

prebiotic/probiotic diets

• Low fat and high fiber →

  • Increase in SCFA-producing bacteria

  • Increase in Lactobacillus and Bifidobacterium

• Maintained mucus layer

• Increase in tight junction proteins, AMPs, and SCFAs

• Protects from intestinal inflammation