Microbiology Chapter 24

Major genera of skin

Corynebacterium Propionibacterium Staphylococcus

Small intestine made up of

Duodenum: fairly acidic normal microbiota resembles the stomach Ileum: gradually less acidic so bacterial numbers increase, 10^5-10^7 micorbial numbers Anoxic environment Fusifrom anaerobic bacteria are present Jejunum: is similar to Ileum

Formula fed infants

Elevated numbers of Clostridium difficile, Granulicatella adiacens, Citrobacter, Enterobacter cloacae, Bilophila wadsworthia

Gut Enterotype 1

Enriched in Bacteroides

Gut Enterotype 2

Enriched in Prevotella

Gut Enterotype 3

Enriched in Ruminococcus

C-section

Enterobacter hormachei, Haemophilus parainfluenzae, Staohylococcus saprophticus, S. aureus, Streptococcus australis, and Veillonella dispar. Indicating that skin and oral microbes as well as environmental populations were the first colonizers. Bacteroides are less prevalent or missing.

bacteria in jejunum

Enterococci Lactobacilli

Vaginal delivery newborns

Escherichia Bifidobacterium Enterococcus Bacteroides Bilophila

Most abundant genera in oral cavity

Firmicutes

Vast majority of human gut phylotypes

Firmicutes (dominate) Bacteroidtes (dominate) Proteobacteria Top to dominating vary depending on an individual's health. Large species variety one individual harbors a total of 160 species

Significantly less stable

Firmicutes and Proteobacteria

Bacteria is the stomach

Firmicutes, Bacteroidetes, and Actinobacteria dominate gastric fluid smaples whereas Firmicutes and Proteobacteria are more abundant in gastric mucosal samples. H. pylori accounts for the vast majority of stomach's microbial mass

bacteria in Liver Esophagus duodenum and stomach

Helicobacter Proteobacteria Bacteroidtes Actinobacteria Fusobacteria Firmicutes

Single most abundant species in the oral cavity

(Veillonella parvula) and obligate anaerobe.

Mice vs Humans microbiome

High abundance in human gut: Prevotella, Faecalibacterium, and Ruminococcus In mice: Lactobacillus, Alistpes, and Turicibacter. Colon and Cecum in much larger proportionally in mice than in humans.

International Human Genome Consortium Questions

1. Do individuals share a core human microbiome? 2. Is there a correlation between the composition of microbiota colonizing a body site and host genotype? 3. Do differences in the human microbiome correlate with differences in human health? 4. Are differences in the relative abundance of specific bacterial population important to either health or disease?

Well studied examples that link gut microbiota an clinical disease

1. Inflammatory bowel disease 2. Obesity

Frality of elderly correlates with two major microbial factors

1. Overall decrease in gut bacterial diversity 2. Reduced abundance of Firmicutes and increased abundance of Bacteroides

Other related Firmicute genera of the mouth

Abiotrophia Gemella Granulicatella

Major phyla of skin

Actinobacteria Firmicutes Proteobacteria Bacteroidetes

Fecal matter

Bacteria compose one third of the weight. A person sheds 10^13 bacterial cells each day in the feces.

Most stable species

Bacteriodetes and Actinobacteria

Mice study

Bacteroides fragilis part of the normal microbiota of mouse gut has a symbiosis factor which enables production of polysaccharide A which signals the host immune system to promote tolerance needed for successful colonization by this bacterium. Has shown protect mice from Helicobacter hepaticus. In experiment where mice were with mutant B. fragilis H. hepaticus colonizes the gut.

Most prevalent bacteria in gastrointestinal tract

Bacteroidetes

Dry skin

Betaproteobacteria Corynebacteria Flavobaceriales

4 month infants

Bifidobacterium, Lactobacillus, Collinsella, Granulicatella, and veillonella reflecting reduced oxygen availability and increased production and utilization of lactose.

bacteria in Esophagus

Prevotella Streptococcus Veillonella

Most prevalent bacteria on skin

Propionibacterium

Sebaceous skin

Propionibacterium

Skin of adults

Propionibacterium Corynebacterium

Global Gut Project

Sampled three distinct populations (Malawians, US citizens, and Venezula) of various ages

Bacteria commonly present in upper respiratory tract

Staphylococci Streptococci Diphtheroid bacilli Gram negtaive cocci

Potentially pathogenic bacteria present in upper respiratory tract

Staphylococcus aureus Sterptococcus pneumoniae in the nasopharynx of healthy individuals may be carriers but don't develop disease because other bacteria inhibit the growth.

Most abundant genus of the mouth is

Streoptococcus comprising 25% of the cells

Most prevalent bacteria in Saliva

Streptococcus

Skin of young children

Streptococcus Betaproteobacteria Gammaproteobacteria

bacteria in small and large intestine

Streptococcus Staphylococcus Ruminococcus Proteus Peptostreptoccus Peptococcus Methanobrevibacter Lactobacillus Klebsiella Eubacterium Escherichia Enterococcus Enterobacteria Clostridium Bifidobacterium Bacteroides

Primary colonizers of clean teeth

Streptococcus obligate anaerobes (Veillonella and Fusobacterium) colonize habitats below the gum line. Prevent pathogenic bacteria from adhering to mucosal surfaces.

Benefits of knowing the human microbiome

development of biomarkers for predicting predisposition to diseases designing targeted therapies personalized drug therapies and probiotics However we are only in the early stages of mapping because of the diversity that exists.

adult microbiome

early life experiences that govern or influence microbial colonization may be an important factor in adult health and predisposition to disease.

B. longum

enrichment of this species is related to the composition of human milk. Because it contains oligoscacharides humans wouldn't ordinarily be able to digest. Also leads to production of short chain fatty acids creating a environment favoring the growth of commensal normal microbiota important for educating the immune system.

Oral microbiome

essentially as diverse as the gut but humans share greater proportion of taxa in the mouth than the gut. Streptococcus Haemophilus Veillonella Actinomyces Fusobacterium

Corynebacterium matruchotii

exclusively found in the supragingival plaque

Enterococcus and Escherichia

facultative microbes indicative of aerobic state of early gut system

Treponema socranskii

found mostly in the subgingival plaque

Microbiome

functional collection of different microbes in a particular environment

Human Microbiome Project

funded by the US National Institute of Health collected samples from 242 individuals all American medical students in good health sampling different body sites and then evaluated bacterial diversity based of 16S rRNA gene sequencing and limited metagenomic analyses. Object was to develop baseline information for what constituted a healthy microbiome. Wasn't very diverse

Difference of vaginal and C-section babies

greatly reduced after 12 months

Roof of the mouth

harbors a low diversity of microbiota than does the gingival plaque and this is because of the high turn over of cells

Lumen

in large intestine where most of the bacteria lives and are restricted to. Growth rate here is one to two doublings per day.

Breast fed infants

increased levels of probiotics Lactobacillus johnsonii, L. Gasseri, Bifidobacterium longum. to name a few.

vaginosis

major changes in the balance of microbes in the vagina is characterized by increased bacterial diversity, elevated pH, and vaginal discharge.

Colon

makes up the rest of the large intestine and is whee bacteria is present in enormous amounts. Essential an in vivo fermentation mechnanism. Facultative anaerobes consume any extra oxygen leaving the environment anoxic so Clostrium and Bacteriodes mainly grow. 10^10 to 10^11 are the cell counts. Eukaryic microbes are present but only in small amounts are mainly yeasts; (Canidad albicans). Two major families of Firmicutes (Lachnospiraceae and Ruminococcacea) are important in the digestion of plant polysaccharides.

human micorbiome

massive assemblage of microorganisms, comprised of different microbiota that colonize different habitats of the body

Normal microbiata

microorganisms that are usually found associated with healthy body tissue. What the chapter focuses on.

inflammatory bowel disease (IBD)

not caused by a specific pathogen but by imbalance between the immune system and normal gut microbiota. Can occur from taking antibiotics too early. Probably not a strong genetic connection as may not infect both indentical twins. Strong correlation between this and diet as those with high animal protein diet and carbohydrates are more likely to be infected. Possible transmission seen in mice. may follow the disruption of mucosal barrier.

Proteus

notorius urinary tract pathogen is a strong urease producer generates ammonia and uses it as nitrogen source. Also causes urine pH to become alkaline and triggers other urinary tract conditions such as formation of kidney stones.

Corynebacterium argentortense

occurs mostly in the saliva

Helicobacter pylori

pathogenic proteobacterium typically transmitted orally and can persist for decades in the gastric mucosa. 20% of people with this bacteria will suffer from upper gastrointestinal tract symptoms, development of ulcers and gastric malignancies may occur. Recognized as a definite carcinogen.

Goblet cells

produce various antimicrobial peptides that help prevent microbial contact with the underlying epithelium

Microbiota

references the type of organisms present in an environmental habitat.

Major physiological process of stomach

secretion of acid (HCl) digestion of macromolecules pH 2

Lautropia mirabilis

selectively colonizes the supragingival plaque

Termination of breast feeding results in

shift towards more adult like composition Bacteroides, Bilophila, Roseburia, Clostridium, Anaerostipes, and Eikenella.

human gastrointestinal tract

stomach, small intestine, and large intestine. has 400 m^2 of surface area and is home to 10^13 microbial cells. Total bacterial numbers are 10^4/ g in the stomach to 10^8/g in the small intestine to 10^11-10^12 per g in the large intestine.

Mucin

thick liquid secretion containing water soluble proteins and glycoproteins in prouduced by goblet cells (specialized class of epithelial cells) in the intestinal epithelium forms a protective layer immediately adjacent to the intestinal epithelium, inner mucous layer is rarely colonized by bacteria.

upper respiratory tract

throat/tonsils, nasopharynx, oral cavity, oropharynx, and larynx. Microbes live in areas bathed with secretion from the mucus membranes.

Host microbiome supraorganism

together the human body as the host and its associated microbes are increasingly recognizied to constitute this

lower respiratory tract

trachea, bronchi, and lungs has no resident microbiota in healthy adults despite the large number of organisms potentially able to reach this region during normal breathing. Ciliated epithelial cells beat upwards expelling dust particles.

Stomach

was thought to be sterile or minimally populated until the discovery of Helicobacter pylori in 1983 colonizes the stomach of 50% of the world's population. Home of the most vibrant bacterial community. Dominant bacteria: Bacteroidetes (Prevotella), Firmicutes (Streptococcus, Veillonella, Lactobacillus), Actinobacteria (Rothia, Propionibacterium), Fusobacteria, and Proteobacteria (Haemophilus, Methylobacterium)

Vagina

weakly acidic ph 5 and contains significant amounts of glycogen. fermented by Lactobacillus acidophilus which produces lactic acid maintain pH, is absent befoe puberty and after menopasue is both cases pH of returns to neutral. Less complex culture of bacteria is present mainly composed of lactobacilli

Environmental and host factors influence the composition of normal skin microbiota

weather: temperature and moisture can increase microbiota age: young children have more varied microbiota and carry more pathogenic gram negative species than adults. personal hygiene: poor hygiene results in higher microbial population density Dog owners: human and their dogs have more microbiota in common than their dogs and other dogs.

Bacteria found in mouth during first year of life

when teeth are absent are mostly aerotolerant anaerobes such as streptococci and lactobacilli and a few aerobes.

Factors determining the early assembly of gut microbiome

whether the birth was vaginal or by C-section Vaginal birth the microbiome is very similar while C-section the micrbiome is significantly different. 72% vs 41%

Early microbial colonizers are important source of amino acids and vitamins

K2 B6 B7 As the gut matures B1 B5 B2

Urogenital tracts

Kidneys and bladders are sterile, epithelial cells lining distal urethra are colonized by facultatively aerobic gram negative Bacteria. Escherichia coli and Proteus micrabilis can multiply in urethra if changes in pH occur and cause disease.

Lowest and highest pH of vagina based of bacteria

L. crispatus and heterogeneous respectively

Most prevalent bacteria in Urogenital tract

Lactobacillus

4-ethylphenylsulfate

affect behavior in mice Gut bacteria helps to produce gut-brain-axis likely connected

Lysozyme

an enzyme in saliva that cleaves glycosidic linkages in peptidoglycan of the bacterial cell wall weakening the cell and causing lysis.

Lactoperoxidase

another enzyme found in both milk and saliva kills bacteria by a reaction that generates singlet oxygen (toxic form)

Gut enterotypes

are functionally distinct and can influence diet and vitamin production

Monogastric

are omnivorous human have only the stomach positioned before the intestines.

uncircumcised penis

bacterial abundance is typically much greater

Microbes in the human microbiome

between 10^13 and 10^14 roughly ten times the number of human cells in a person

Propionibacterium acnes

colonization is promoted by its ability to hydrolyze triglycerides present in sebum resulting in release of free fatty acids that produce adherence of this bacterium which sometimes cause the disease acne.

Skin microbiota

consists of a rich community of microorganisms that associate intimately with host's hormonal, nervous, and immunological systems. Approximately one million resident bacteria per square inch centimeter of skin for a total of 10^10 covering the average adult.

Major physiological process of Small intestine

continuation of digestion absoprtion of monosaccharides, amino acids, fatty acids, water pH 4-5

Four dominate types of Lactobacillus present in vagina

crispatus iners reuteri jensenii

Bacteroides thetaiotaomicron

bacteria encoding a diverse set of glycan-degrading enzyme is associated with the increase in pectin in solid foods

Elderly vs Young

Increasing proportion of Bacteroidetes vs higher proportion of firmicutes

Bifidobacterium

Infant gut is dominated by this fermented class of Actinobacteria

Experimental Protocols for comparing human Microbiome

Megasequencing allows for comparison to resolve dynamic relationships. The microbial diversity has been mapped using 16S rRNA gene sequencing. In comparing they have found great microbial diversity not even a microbial species present in the greatest abundance.

Metabolism of microorganism in the oral cavity

Most are facultatively anaerobic (Bacteroidetes) Obligately anaerobic (Neisseria, Acinebacter, and Moraxella) genera in the Proteobacteria

Sites of human body inhabited by microorganisms

Mouth, nasal cavities, throat, stomach, intestines, urogenital tracts, and skin.

Children with IBD

Veillonella Prevotella Lactobacillus Parasporobacterium Above in high levels Below in low levels Bifidobacerium and Virrucomicrobium

Products of gut microbial metabolism

Voltile fatty acids: microbial fermentation of plant material. H2, CO2, and CH4 B12 9 of the 20 amino acids such as lysine

Tryptamines

a trytophan metabolite thought to function as a biogenic neurotransmitter that signals he enteric nervous system. Gut bacteria helps to produce

Major physiological process of Large intestine

absorption of bile acids, vitamin b12 pH 7