Bacterial Growth and Normal Flora

organs should be sterile in healthy people

-Brain, muscle, bone, fluids (CSF, Synovial, Lymph, membrane fluids, blood) -blood becomes transiently bacteriemic after brushing your teeth -if it is made of epithelial cells, it is most likely colonized, even if microbial numbers are low.

skin microbiome

-Colonized, but hostile environment: Variable temperature Acidic Salt Lysozyme Sebaceous secretions Composition highly dependent upon site Diseases associated with flora Impetigo, acne Gangrene, necrotizing fasciitis, cellulitis

human micobiome project

-an offshoot of Human Genome Project -number revisions: more human cells than we intially thought -our microbes are vital part of our genetic makeup and evolution: 10,000 species; 81-99% of genera identified As of 2014, it was often reported in popular media and in the scientific literature that there are about 10 times as many microbial cells in the human body than there are human cells; this figure was based on estimates that the human microbiome includes around 100 trillion bacterial cells and an adult human typically has around 10 trillion human cells.[3] In 2014 the American Academy of Microbiology published an FAQ that emphasized that the number of microbial cells and the number of human cells are both estimates, and noted that recent research had arrived at a new estimate of the number of human cells at around 37 trillion cells, meaning that the ratio of microbial to human cells is probably about 3:1.[3][4] In 2016 another group published a new estimate of ratio as being roughly 1:1 (1.3:1, with "an uncertainty of 25% and a variation of 53% over the population of standard 70 kg males"). -surprises: the HMP project also discovered several "surprises", which include: Microbes contribute more genes responsible for human survival than humans' own genes. It is estimated that bacterial protein-coding genes are 360 times more abundant than human genes. Microbial metabolic activities; for example, digestion of fats; are not always provided by the same bacterial species. The presence of the activities seems to matter more. Components of the human microbiome change over time, affected by a patient disease state and medication. However, the microbiome eventually returns to a state of equilibrium, even though the composition of bacterial types has changed.

how can you make your microbiome more diverse

-dairy bacteria found in samples from subjects with dairy rich diets, strongly indicating that a persons diet has a direct effect on gut bacteria -ppl who drank more coffee or tea had more diverse micobiomes, while ppl who drank more soda had less bacterial diversity. -drinking red wine gives you anti inflammatory bacteria which can combat illness like irritable bowel syndrome

flora in mouth

-highly variable (600 different species described and anaerobes dominate 3:1-10:1) -the rate of infection secondary to human bites is estimated to be about 10%. Bite wounds inflicted by children are known to have lower rates of infection owing to less diseased teeth or a lower incidence of gingivitis in children as compared with adults. ubiquitous conditions of mouth: -plaque -dental caries -gingivitis diet and hygiene influence composition

what happens when microbiome goes wrong?

-not healthy -enlargement of cecum due to lack of mucus degradation -thin intestinal walls: mult defects in differentiation of intestinal epithelium -immunological defects in gut: associated with lymphoid tissue -low antibody titers -low metabolic rate -susceptibility to super infection with pathogens -vitamin deficiencies

RBC and hemoglobin concentration

-one study found a microbiome correlation with RBC count and hemoglobin concentration, suggesting that certain species of gut bacteria could be connected to how the body processes O2. But we dont know for sure, not enough studies.

species that regularly live in the stomach

-only a few bc of high acid content -include helicobacter, lactobacilli, staphylococci, streptococci, candida. They interact tightly with epithelial cells for protection from acid. -transient flora acquired by eating

urogenital tract

-only the anterior urethra and vagina are permanently colonized -composition influenced by hormonal state -lactobacilli are dominant and protective -UTIs are associated with decreased bacterial diversity in men and women. Urine/bladder is NOT normally sterile, even if labs say it is (numbers below detection).

neutrophiles

-range of pH 5-8; optimum near pH 7 -food can be preserved by increasing acidity -H pylori grows in stomach (makes urease to split urea into CO2 and ammonia to decrease acidity of surroundings)

a) areas with least similarities between ppl in species b)areas with least similarities between ppl in species

-spaces between fingers, spaces between toes, axillae, umbilical cord b)nostril, nares and back

fecal microbial transplant (FMT)

-the process of transplantation of fecal bacteria from a healthy individual into a recipient. FMT involves restoration of the colonic microflora by introducing healthy bacterial flora through infusion of stool, e.g. by enema, orogastric tube or by mouth in the form of a capsule containing freeze-dried material, obtained from a healthy donor.

endogenous infections

-when your normal good flora makes you sick -in immunocompromised patients -in healthy ppl when normal flora is introduced to unusual location -when bacteria are present in unusually large numbers There is concern that some anaerobic infections are not being detected due in part to a decline in the appropriate testing in microbiology laboratories, reflecting economic realities, outsourcing, and reliance on empiric antibiotics. In addition, the incidence of anaerobic infections appears to be rising, which is likely the result of an increase in the number of patients with complex underlying illnesses.

small intestine

-where most nutrient absorption happens; pH of 8.5 bc of influx of basic bile. Bacterial density of small intestine is lowest in duodenum, higher in jejunum and ileum -the natural flora of the small intestine protects the host by metabolizing carcinogens in dietary foods. -the natural flora of small intestine protects the host by metabolizing carcinogens in dietary foods -the natural flora of the small intestine protects teh host by metabolizing carcinogens in dietary foods -help produce Vitamin K, which is absorbed and used by host -the bacteria are important even for the muscular activity of the small intestine, without bacteria, there is reduced muscular activity. -streptococci, lactobacilli

large intestine

-where most water absorption happens. pH varies from 5.5 to 7. This environment is relatively stable due to slower movement of materials through the large intestine. Bacteria account for 60% of fecal dry weight. -lactobacilli, bifidiobacteria, methanogens, bacteroides, enterococci, E coli, clostridia, fungi -bacteria account for 60% of fecal dry weight -mostly anaerobes , densely populated

function of normal flora

1. protects you from pathogens by taking up space, competing for nutrients, making antimicrobial substances 2. do some food processing for you. Make vitamins that we cant make 3. stimulate the immune system; induce production of antibodies

the way infants were delivered and their flora

1. vaginally derived infants more likely become colonized with flora of mother's birth canal 2. infants by C section get bacteria from moms skin and hospital environment -Breastfed infants less likely to have pathogenic C. they have a lower risk of obesity, in preemies lower risk for NEC (Necrotizing enterocolitis). Breast milk has sugars that can selectively promote the growth of Bifidobacterium in gut. -most kids have gut flora composition similar to adults by the time theyre 2-3.

what is skin pH

4.7

optimal pH of bacteria

6.5-7.5

what does FMT treat

Currently, FMT is the approved treatment only for recurrent C. diff diarrhea Studies currently in progress are testing FMT for: Inflammatory Bowel Disease Metabolic Syndrome: Obesity, Diabetes & Cardiovascular Disease Allergies, Asthma

julius wagner jauregg

His work involved the treatment of mental disease by inducing a fever, an approach known as pyrotherapy.

why would anyone do FMT?

In 2013 a randomized, controlled trial of FMT from healthy donors showed it to be highly effective in treating recurrent C. difficile in adults, and more effective than vancomycin alone. FMT has been used experimentally to treat other gastrointestinal diseases, including colitis, constipation, irritable bowel syndrome, and neurological conditions such as multiple sclerosis and Parkinson's. In the United States, the Food and Drug Administration (FDA) has regulated human feces as an experimental drug since 2013. Trial was stopped early because the treatment arm reached significance before the end. And it's unethical to withhold a better treatment from study participants.

shotgun sequencing

In the begining microbes were characterized by culture -then there was PCR so they were defined by positive PCR with known primers DNA is broken up randomly into numerous small segments, which are sequenced using the chain termination method to obtain reads. Multiple overlapping reads for the target DNA are obtained by performing several rounds of this fragmentation and sequencing. Computer programs then use the overlapping ends of different reads to assemble them into a continuous sequence.[1]

anaerobes as pathogens

So most of the time your normal flora is harmless and good for you, but sometimes it can make you sick. Many of the medically important anaerobes are part of the normal human flora. As such, they are nonpathogens in their normal habitat and cause disease only when they leave those sites. The two prominent exceptions to this are Clostridium botulinum and Clostridium tetani, the agents of botulism and tetanus, respectively, which are soil organisms. Clostridium perfringens, another important human pathogen, is found in the colon and in the soil. Diseases caused by members of the anaerobic normal flora are characterized by abscesses, which are most frequently located in the brain, lungs, female genital tract, biliary tract, and other intra-abdominal sites. Most abscesses contain more than one organism, either multiple anaerobes or a mixture of anaerobes plus facultative anaerobes. It is thought that the facultative anaerobes consume sufficient oxygen to allow the anaerobes to flourish. Three important findings on physical examination that arouse suspicion of an anaerobic infection are a foul-smelling discharge, gas in the tissue, and necrotic tissue. In addition, infections in the setting of pulmonary aspiration, bowel surgery, abortion, cancer, or human and animal bites frequently involve anaerobes.

tertiary syphilis

Your core temp is ~37C. Your extremities are not that warm. This allows certain microbes to reproduce in different areas. Leprosy hits the same areas you have to worry about for frostbite. The same thing happens for syphilis. Tertiary syphilis may occur approximately 3 to 15 years after the initial infection, and may be divided into three different forms: gummatous syphilis (15%), late neurosyphilis (6.5%), and cardiovascular syphilis (10%). Without treatment, a third of infected people develop tertiary disease. Doctors had observed that some patients who develop high fevers could be cured of syphilis. Thus, from 1917 to the mid 1940s, malaria induced by the least aggressive parasite, Plasmodium vivax, was used as treatment for tertiary syphilis because it produced prolonged high fevers. The technique was known as malariotherapy; however, it was dangerous, killing about 15% of patients, so it is no longer in use. In 1927 he won the Nobel Prize for "his discovery of the therapeutic value of malaria inoculation in the treatment of dementia paralytica".

antibiotics

a type of antimicrobial drug used in the treatment and prevention of bacterial infections. May either kill of inhibit the growth of bacteria. -short courses of antibiotics can leave normal gut bacteria harboring antibiotic resistant genes for up to two years after treatment. Researchers think this increases the chances of resistance genes being surrendered to pathogenic bacteria, aiding their survival and suggesting that the long term effects of antibiotic therapy are more sig than previously thought. After the antibiotic, until the body recovers, the disturbed microbiome is susceptible to super infection by pathogenic organisms, leading to more antibiotic use, a vicious cycle.

oxygen requirements: a) obligate aerobe b) facultative anaerobe c) obligate anaerobe d) microaerophile e) aerotolerant anaerobe

a) only grows when O2 is available (at top of flask). Micrococcus luteus b) grows best when O2 is available, but also grows without it. Grows throughout tube but concentrated at top. E. coli c) Canot grow when O2 is present. At bottom of flaskClostridium botulinum e) grows only if small amounts of O2 available. Close to top of flas. Heliobacter pylori. f) grows equally well with or without O2. Spread throughout tube. Streptococcus pyogenes. Boil nutrient agar to drive off O2; cool to just above solidifying temperature; innoculate; gently swirl

microanimals

animals so small that they can only be seen under a microscope. Microscope arthropods include dust mies, spider mites, crustaceans such as copepods and the cladocera

diagnosis of C. difficile

by stool culture or testing for the bacterias DNA or toxins. If a person tests pos but has not symptoms it is known as C. difficile colonization than an infection. Asymptomatic C. difficile carriage happens in 20% of hospitalized adults; these patients shed C. difficile in stool but dont have diarrhea or other clinical symptoms. In long term care facilities; the rate of asymptomatic colinization may approach 50%. These individuals serve as a reservoir for environmental contamination -best signs are significant diarrhea, recent antibotic exposure, abdominal pain, fever and a distinctive foul odor to the stool resembling horse manure. Ppl with a severe infection also may dev serious inflammation of the colon and have little or no diarrhea. Recurrance after successful initial therapy happens in 10-40% of cases, this reps relapse rather than reinfection regardless of interval between episodes.

Flora in nose

corynebacteria, staphylococci, streptococci

predominant phyla in lower GI tract

firmicutes, bacteroides, proteobacteria, actinobacteria FABP

what predominates skin microbiome?

gram pos, halotolerant bacteria. Most come from our phyla: actinobacteria (51.8%), frimicutes (22.4%), proteobacteria (16.5%), bacteroidetes (6.3%)

alkaliphiles

grow optimally at pH above 8.5

acidophiles

grow optimally at pH below 5.5 -picrophilus oshimae has optimum pH of less than 1

transient microbia

nonpathogenic or potentially pathogenic microorganisms that inhabit the skin or mucous membranes for hours, days, or weeks. The transient microbiota is derived from the environment, does not produce disease, and does not establish itself permanently on the surface. Members are generally of little significance so long as the normal resident flora remains intact. However, if the resident microbiota is disturbed, transient microorganisms may colonize, proliferate, and produce disease.

temperature range of: a) psychrophile b) psychrotroph c) mesophile d) thermophiles e) hyperthermophiles

optimum growth close to upper end a) 5-15C. In arctic and antarctic regions. b) 20-30C. Important for food spoilage c) 25-45C. Adapted to body temp (37C). Have a narrow range. Fever is effective in inhibiting their bacterial growth. E coli and most common bacteria are mesophiles. Pathogens adapted to be in human body have temp range from 35-40. Mesophiles in soil have lower optimum temp, closer to 30. d) thermophiles: 45-70. Common in hot springs. Resist denaturing. Thermostability comes form AA sequence. number and position of bonds, which det structure hyperthermophiles: 70-110C. usually members of archaea. Found in hydrothermal vents.

microbiodata

organisms. human microbiota is the aggregate of microorganisms, a microbiome that resides on or within a number of tissues and biofluids, including the skin, mammary glands, placenta, seminal fluid, uterus, ovarian follicles, lung, saliva, oral mucosa, conjunctiva, and gastrointestinal tracts. They include bacteria, fungi, and archaea. Micro-animals which live on the human body are excluded.

temperature and food preservation

refrigeration (4C) slows spoilage by limiting growth of otherwise fast growing mesophiles. Psychrophiles, psychrotrophs can still grow, but slowly. Freezing preserves food; not effective at killing microbes. Almost all are incabale of growth below freezing.

resident microbiodata

relatively fixed types of microorganisms regularly found in a given area at a given age; if disturbed, it promptly reestablishes itself.

esophagus flora

resident flora similar to mouth, but fewer species -transient flora acquired by eating

3 main ecological areas

sebaceous (propionibacteria and staphylococci), moist (corynebacteria and staphylococci), dry (b-Proteobacteria and flavobacteriales) -ecologically, sebaceous areas have greater species richness than moist and dry ones!!

what is acid mantle made of

sebum secreted from sebaceous glands which mixes with lactic and AAs from sweat. An acid skin pH (4-4.5) keeps resident bacterial flora attached to the skin, whereas alkaline pH (8-9) promotes dispersal from the skin.

clostridium difficile

spore forming, toxin-producing, gram pos anaerobic bacterium that causes antibiotic associated colitis. it colonizes the human intestinal tract after the normal gut flora has been altered by antibiotic therapy. -one of the most common healthcare associated infections and a significant cause of morbidity and mortality among older adult hospitalized patients. people are most often infected in hospitals, nursing homes or other medical institutions, although infection outside medical setting is increasing. The rate of C. difficile acquisition is 13% in patients with hospital stays of up to 2 weeks, and 50% with stays longer than 4 weeks.

flora in pharynx and trachea

streptococci, neisseriae predominant -staphylococci, diptheroids, pneumococci ect.,also common

next generation sequencing

technologies produce shorter reads (anywhere from 25-500bp) but many hundreds of thousands or millions of reads in a relatively short time (on the order of a day).[16] This results in high coverage, but the assembly process is much more computationally intensive. These technologies are vastly superior to Sanger sequencing due to the high volume of data and the relatively short time it takes to sequence a whole genome.

factors influencing bacterial growth

temperature, oxygen availability, pH, water availability, atmospheric or osmotic pressure, radiation, nutrient availability