Bio Microbiology - Spring 2013 Study Guide 20 Normal Flora - Normal Responses - Disease

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1 Bio Microbiology - Spring 2013 Study Guide 20 Normal Flora - Normal Responses - Disease

2 It has been calculated that the normal human houses about bacteria on the skin, in the mouth, and in the gastrointestinal tract. The latter number is far in excess of the number of eukaryotic cells in all organs which comprise the human host (10 13 ).

3 Numbers of bacteria that colonize different parts of the body. Numbers represent the number of organisms per gram of homogenized tissue or fluid or per square centimeter of skin surface.

4 Normal Flora Tissue Tropism - The normal flora exhibit a tissue preference or predilection for colonization. Certain species of bacteria are invariably in one locale and never in another. BACTERIUM TISSUE Corynebacterium diphtheriae Throat Neisseria gonorrhoeae Urogenital epithelium Streptococcus mutans Tooth surfaces Streptococcus salivarius Tongue surfaces Vibrio cholerae Small intestine epithelium Escherichia coli Small intestine epithelium Staphylococcus aureus Nasal membranes Staphylococcus epidermidis Skin

5 BACTERIA COMMONLY FOUND ON THE SURFACES OF THE HUMAN BODY TABLE 1. BACTERIA COMMONLY FOUND ON THE SURFACES OF THE HUMAN BODY BACTERIUM Skin Conjunctiva Nose Pharynx Mouth Lower Intestine Anterior urethra Vagina Staphylococcus epidermidis Staphylococcus aureus + +/ /- + Streptococcus mitis /- + + Streptococcus salivarius Streptococcus mutans + ++ Enterococcus faecalis +/ Streptococcus pneumoniae +/- +/ /- Streptococcus pyogenes +/- +/ /- +/- Neisseria sp Neisseria meningitidis Veillonellae sp. + +/- Enterobacteriaceae (Escherichia coli) +/- +/- +/ Proteus sp. +/ Pseudomonas aeruginosa +/- +/- + +/- Haemophilus influenzae +/ Bacteroides sp /- Bifidobacterium bifidum ++ Lactobacillus sp Clostridium sp. +/- ++ Clostridium tetani +/- Corynebacteria Mycobacteria + +/- +/- + + Actinomycetes + +

6 Normal Flora Some of the indigenous bacteria are able to construct bacterial biofilms on a tissue surface, or they are able to colonize a biofilm built by another bacterial species.

7 Normal Flora of the Skin.

8 Count per square cm Skin Site Contact Method Scrub Method Forehead X 10 5 Armpit X 10 6 Back X 10 2 Forearm X 10 2 W.C Noble and D.A. Somerville, 1974 Microbiology of Human Skin

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10 Fig. 2. Collector's curves of observed and estimated SLOTU richness of pooled forearm skin samples from six healthy subjects Copyright 2007 by the National Academy Gao, of Sciences Zhan et al. (2007) Proc. Natl. Acad. Sci. USA 104,

11 Fig. 1. Phylogenetic analysis of bacterial 16S rdna detected in normal skin from six subjects Copyright 2007 by the National Academy of Sciences

12 Fig. 3. Distribution of 2,038 16S rdna clones from left and right forearm, by phylum Gao, Zhan et al. (2007) Proc. Natl. Acad. Sci. USA 104, Copyright 2007 by the National Academy of Sciences

13 A diversity profile of the human skin microbiota Elizabeth A. Grice, et al. Genome Res : A cross-section of the skin and the regions sampled by each collection method.

14 A Venn diagram that illustrates observed overlap of OTUs with 97% similarity according to sampling method Grice E. A. et.al. Genome Res. 2008;18: by Cold Spring Harbor Laboratory Press

15 Interpersonal and intrapersonal variation Grice E. A. et.al. Genome Res. 2008;18: by Cold Spring Harbor Laboratory Press

16 Comparison of relative abundance of bacteria in mouse ear punch and human punch biopsy libraries. 16S rdna sequences are first grouped into division 2008 by Cold Spring Harbor Laboratory Press Grice E. A. et.al. Genome Res. 2008;18:

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18 Streptococcus mutans. Gram stain. CDC. Actinomyces israelii

19 Normal flora of the Urogenital Tract

20 Intestinal Bacteria BACTERIUM Incidence Bacteroides fragilis 100 Bacteroides melaninogenicus 100 Bacteroides oralis 100 Lactobacillus Clostridium perfringens Clostridium septicum 5-25 Clostridium tetani 1-35 Bifidobacterium bifidum Staphylococcus aureus Enterococcus faecalis 100 Escherichia coli 100 Salmonella enteritidis 3-7 Salmonella typhi 0 Klebsiella sp Enterobacter sp Proteus mirabilis 5-55 Pseudomonas aeruginosa 3-11 Peptostreptococcus sp. common Peptococcus sp. moderate Methanogens (Archaea) common

21 NUMBERS OF VIABLE BACTERIA FOUND IN THE FECES OF ADULT ANIMALS (Log # viable cells per gram feces) Animal E. coli C. perfringens Enterococci Bacteroides Lactobacilli Cattle Sheep Horses Pigs Chickens Rabbits Dogs Cats Mice Humans Modified from Rosebury, T. : Microorganisms Indigenous to Man. McGraw-Hill. New York. 1962

22 Metagenomic Analysis of the Human Distal Gut Microbiome Science 2 June 2006: Vol. 312 no pp DOI: /science The human intestinal microbiota is composed of to microorganisms whose collective genome ( microbiome ) contains at least 100 times as many genes as our own genome. We analyzed 78 million base pairs of unique DNA sequence and 2062 polymerase chain reaction amplified 16S ribosomal DNA sequences obtained from the fecal DNAs of two healthy adults. Using metabolic function analyses of identified genes, we compared our human genome with the average content of previously sequenced microbial genomes. Our microbiome has significantly enriched metabolism of glycans, amino acids, and xenobiotics; methanogenesis; and 2-methyl-D-erythritol 4-phosphate pathway mediated biosynthesis of vitamins and isoprenoids. Thus, humans are superorganisms whose metabolism represents an amalgamation of microbial and human attributes.

23 COG analysis reveals metabolic functions that are enriched or underrepresented in the human distal gut microbiome (relative to all sequenced microbes). Color code: black, subject 7; gray, subject 8. Bars above both dashed lines indicate enrichment, and bars below both lines indicate underrepresentation (P < 0.05).

24 KEGG pathway reconstructions reveal metabolic functions that are enriched or underrepresented in the human distal gut microbiome as follows: both samples compared with all sequenced bacterial genomes in KEGG (blue), the human genome (red), and all sequenced archaeal genomes in KEGG (yellow). Asterisks indicate enrichment (odds ratio > 1,P < 0.05) or underrepresentation (odds ratio < 1, P < 0.05).

25 Isoprenoid biosynthesis via the MEP pathway and methanogenesis are highly enriched in the distal gut microbiome. (A) MEP pathway for isoprenoid biosynthesis. (B) Odds ratio for each COG in the MEP pathway. All enzymes necessary to convert DXP to IPP and thiamine are enriched (P < relative to all sequenced microbes). (C) Location and role of key enzymes in methanogenesis. (D) Odds ratio for each COG highlighted in (C).

26 Figure 1. The intestinal microbiota promotes three levels of protection against enteric infection. (I) Saturation of colonization sites and competition for nutrients by the microbiota limit pathogen association with host tissue. (II) Commensal microbes prime barrier immunity by driving expression of mucin, immunoglobulin A (IgA) and antimicrobial peptides (AMPs) that further prevents pathogen contact with host mucosa. (III) Finally, the microbiota enhances immune responses to invading pathogens. This is achieve by promoting IL-22 expression by T cells and NKp46+ cells, which increases epithelial resistance against infection, as well as priming secretion of IL-1β by intestinal monocytes (MФ) and dendritic cells (DCs), which promotes recruitment of inflammatory cells into the site of infection. In conditions in which the microbiota is absent, such as following antibiotic treatment, there is reduced competition, barrier resistance and immune defense against pathogen invasion. Arya Khosravi, Sarkis K Mazmanian Current Opinion in Microbiology null 2013 null Disruption of the gut microbiome as a risk factor for microbial infections

27 Figure 2. The commensal microbiota primes barrier immunity. Direct stimulation of epithelial Toll-like receptors (TLRs) by commensal microbial associated molecular patterns (MAMPs) primes expression of RegIIIγ (a). Production of RegIIIγ is essential to limit microbial contact with host mucosa. As such, defects in TLR function results in deficient RegIIIγ expression resulting in an increased association of commensal microbes with host tissue as well as a heighten risk of infection with enteric pathogens (b). Additionally, reduced TLR stimulation as a consequence of the depletion of the microbiota is sufficient to reduce RegIIIγ expression and render the host susceptible to infection (c).

28 Figure 3. Disruption of host microbial symbiosis as a risk factor for infectious disease. Exposure to pathogenic microorganisms is often insufficient to cause disease. Rather, susceptibility to infectious disease reflects deficient immune resistance to pathogen challenge. As such, exogenous and endogenous factors that directly compromise individual immune function (including genetic immune defects and chemotherapy) are significant risk factors for infection. We extend this model by proposing that the factors that disrupt the protective benefits of the commensal microbiota similarly compromise individual immune integrity and predispose to infectious disease.

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