1. Normal Microbiota: Characterization, Origin and Role in Health


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Group Communications

Project By: Emily Roy, Alice Tran, Kawinthi Fernando

2/15/11 Hey guys, How do we design the page so it looks more organized, like the other groups? Does that sound like a good idea to you?

2/16/11 Sounds good, I added headings but go ahead and organize it more as you see fit. To make it like a Wikipedia page you can update references at the bottom of the page if you think it's a good idea. And this section is for notes to each other. We can date sequential comments just to keep them organized. :)

Topics within Characterization that I thought of included:

  • where (on/in body)
  • why they colonize where they do
  • how some bacteria adapt to different sites
  • what kinds
  • variety person to person
  • flux throughout life or even day to day (early life?)


2/17/11 I found this interesting article (http://www.ncbi.nlm.nih.gov/pubmed/20664075), but it seems from the abstract that it might have more to do w/ the role of normal microbiota so, just a heads up for Kawinthi if you're interested :) -Alice

2/23/11 Terms to keep in mind for role and origin, respectively: Function: “an activity or behavior associated with a community” Invasion: “an ecological event characterized by the establishment of a foreign organism in a new community and the persistence and spread of this organism” -Alice, Emily

3/2/11 Hey guys. If you check out the class website, we have only 20-25 minutes to present. So keep that in mind when you are getting your information together. We only have about 6-8 minutes to present each. -Emily

3/3/11 So I am finding a lot of research for the microbes that originated in the GI tract, so I think I am going to focus my part of the presentation if you are okay with that. I think it will take up the whole 8 minutes that I have to present anyway.

Normal Microbiota


Alice Tran

1. Source: Todar, Kenneth. "The Normal Flora." Todar's Online Textbook of Bacteriology. Kenneth Todar, PhD, 2011. Web. 16 Feb. 2011. <http://www.textbookofbacteriology.net/normalflora.html>.

This webpage is an overview of normal microbiota in humans, just a very broad starting point. Some points I'd like to bring to your attention:

  • "A recent experiment that used 16S RNA probes to survey the diversity of bacteria in dental plaque revealed that only one percent of the total species found have ever been cultivated." Just something to keep in mind as we'll be characterizing mostly those bacterial types that have been better studied.
  • Sites normally colonized by microbes include the skin, upper respiratory (nasopharynx), mouth, lower GI, ant. urethra, and vagina.
  • This source described "many" types of indigenous microbes as opportunistic pathogens. (So I'd be looking into whether other sources agree.) It also identified some specific examples of well-known beneficial normal flora, including Bifidobacterium ("predominant bacterial species in intestine of breast-fed infants, where it may prevent colonization by potential pathogens") and Lactobacillus acidophilus, which colonizes the vaginal epithelium during child-bearing years and establishes low pH that inhibits pathogen growth.
  • The idea that tissue tropism helps determine bacterial preference for certain tissues seemed important in characterization. The host provides essential nutrients/growth factors including suitable oxygen levels, pH, temp. Also, specific adherence occurs between bacterial surface components (ligands, adhesins, parts of capsules, fimbriae, cell walls) and receptors (glycoprotein molecules on host cell surface). Just something to keep in mind as one possible bacterial property to explore.
"Gram-positive bacteria, such as the Streptococcus and Lactobacillus, are thought to adhere to the gastrointestinal epithelium using polysaccharide capsules or cell wall teichoic acids to attach to specific receptors on the epithelial cells. Gram-negative bacteria such as the enterics may attach by means of specific fimbriae which bind to glycoproteins on the epithelial cell surface
  • "The makeup of the normal flora may be influenced by various factors, including genetics, age, sex, stress, nutrition and diet of the individual." Events identified in the text as consistently effecting substantial changes in the makeup of normal flora included weaning, eruption of teeth, and onset/cessation of ovarian functions.
  • About 10^12 bacteria on skin, 10^10 in mouth, 10^14 in gastrointestinal tract; so, we're carrying more bacterial than human eukaryotic cells? (I'll try to check that out!) Specific sites include:
  • Low-density in most sites of skin, with high density at more moist sites; most skin bacteria sequestered in sweat glands
  • Nostrils have lots of bacteria but not healthy sinsuses (sterile)
  • Healthy lower respiratory tract virtually free of microbes b/c efficient cleansing action of ciliated epithelium lining tract
  • Anterior urethra may be colonized, but not lots of bacteria. (urine normally sterile)
  • Vagina colonized soon after birth.
  • Oral cavity has nutrients, epithelial debris, secretions, so it's a favorable habitat for great variety of microbes.
  • Lots of GI normal flora. Also, "composition of the flora of the gastrointestinal tract varies along the tract (at longitudinal levels) and across the tract (at horizontal levels) where certain bacteria attach to the gastrointestinal epithelium and others occur in the lumen."

2. Source: Lawson, R. Daniel, and Walter J. Coyle. "The Noncolonic Microbiome: Does It Really Matter?" Current Gastroenterology Reports Aug. 2010: 259-62. PubMed. Web. 17 Feb. 2011. <http://www.springerlink.com/content/2456264281182n44/fulltext.pdf>.

This article is a review of recent work with characterizing the microbiome of the upper GI, previously thought to be mostly sterile in healthy individuals. It emphasized the importance of molecular techniques in detection of microbes in this area. Interesting points included:

  • GI tract "is home to about 100 trillion microorganisms; most bacteria are found in the colon and are thought to outnumber those in the stomach and esophagus combined by about 10 orders of magnitude."
  • The body of work on colonic microbes suggests that they "may play a key role in maintaining health, host immunity, and supporting human metabolism and when perturbed can contribute to colonic disease (irritable bowel syndrome, inflammatory bowel disease, cancer) and, perhaps, systemic disease (type 2 diabetes, insulin resistance, obesity)."
  • PCR amplification of rRNA genes (16S-rDNA) extracted from biopsy specimens "contradict prior notions of a relatively sterile environment within the upper gastrointestinal tract." Statistical estimates suggest species diversity at likely over 200 in upper GI.
  • "About 97% of all unique sequences belong to Firmicutes, Bacteroidetes, Proteobacteria, and Actinobacteria."
  • Firmicutes makes up about "70% of clones isolated from the esophagus, and between 22% and 31% of those from the gastric mucosa." The article also has more specific breakdowns of types of upper GI bacteria.
  • "[E]sophageal and gastric mucosal microbiomes reflect the intermittent yet persistent migrations of oropharyngeal flora," which are dominated by strict aerobic Streptococcus species as well as anaerobic species.
  • In addition, there seems to be "an indigenous population of organisms nestled in the seqeuestered mucosal environment of the upper GI tract resistant to mechanical erosion via complex virulence factors (adhesins)."
  • Relatively few bacteria in esophagus and stomach due to physical barriers like the gelatinous mucus film coating GI tract, acidic

environment (pH 2) of gastric lumen limits to only acidophilic species. However, some bacteria demonstrate close physical association with the mucosal surface.

  • "[H]ost genetic make-up and immune system influence environmental interactions that govern each area's microbiome."
  • "[I]n the absence of disease, similar patterns in communities, at least at the phyla level, can be seen among these studies, regardless of ethnicity or gender.... There may be a core microbiome...in the esophagus and stomach, as has been postulated in the colon."

3. Source: Robinson, Courtney J., et al. "From structure to function: the ecology of host-associated microbial communities." Microbiology and Molecular Biology Reviews" Sep. 2010:453-76. PubMed. Web. 17 Feb. 2011. <http://mmbr.asm.org.silk.library.umass.edu/cgi/reprint/74/3/453>.

Emphasizes conceptual connections between environmental microbiology and studies of the human microbiome. Discusses the importance of the "application of approaches from environmental microbiology to study of the human body," especially culture-independent methods of microbial community characterization. Introduced me to the Human Microbiome Project and its questions (can we determine the true diversity of the human microbiome, is there a core microbiome, does its structure impact health and disease and if so, how) as well as a listing of terms (Table 1) used to characterize microbiobial communities that may be useful to direct the parameters of our project. Really cool review, broad, very informative, and fairly recent. Also, tons of references we can check out.

  • "[C]loning and sequencing of 16S rRNA-encoding genes have been considered the gold standard for the characerization of microbial communities."
  • Other methods mentioned included in situ hybridization using group-specific 16S rRNA probes, community fingerprinting (terminal restriction fragment length polymorphism analyses).
  • Metagenomics, "the functional and sequence-based analysis of total environmental DNA" which involves "direct cloning of DNAs extracted from environmental samples," has been useful in exploring the "genetic capacity and activity of microbes."
  • Though huge data sets have resulted from sequencing efforts, "the controversy surrounding microbiologists' inability to define a species nowextends to sequence data" and subsequent estimates of community richness.


Emily Roy

Source: Biasucci, Giacomo, Belinda Benenati, Lorenzo Morelli, Elena Bessi, and Gu¨ Nther Boehm. "Cesarean Delivery May Affect the Early Biodiversity of Intestinal Bacteri." The Journal of Nutrition. Web. 13 Feb. 2011. <http://jn.nutrition.org/content/138/9/1796S.full.pdf>.

Summary: The bacterial colonies in the gut vary depending on the mode of birth. In vaginal birth, the mouth of the infant touches the inside of the vagina on its way out. In a C-section birth, the baby is not exposed to those bacteria. Also, there may be a delay in lactating, so the babies may not benefit by the antibodies in the mother's milk. When studying the bacteria, there were different densities of the colonies and in some cases, entire colonies were absent in the C-section babies.

Source: FOOD MICROBIOLOGY. Marina Elli, Maria Luisa Callegari, Susanna Ferrari, Elena Bessi, Daniela Cattivelli, Sara Soldi, Lorenzo Morelli, Nathalie Goupil Feuillerat, and Jean-Michel Antoine Survival of Yogurt Bacteria in the Human Gut Appl. Envir. Microbiol., July 2006; 72: 5113 - 5117

Summary: This study showed that bacteria that are present in yogurt and other probiotics can be found in the feces of a healthy individual several days later. This proves that bacteria can survive the various defenses in the human gut. It is believed that these microbes need the assistance of "molecular tools" in order to survive. It has not been discovered what helps these microbes to survive, yet.

Source: MICROBIAL ECOLOGY. Sylvia H. Duncan, Karen P. Scott, Alan G. Ramsay, Hermie J. M. Harmsen, Gjalt W. Welling, Colin S. Stewart, and Harry J. Flint. Effects of Alternative Dietary Substrates on Competition between Human Colonic Bacteria in an Anaerobic Fermentor System Appl. Envir. Microbiol., Feb 2003; 69: 1136 - 1142.

Summary: This article did not prove as relevant as I thought it would be. It studied what changes in bacterial colonies in the gut have the largest effect on human health. It also touched upon the idea that some of these bacteria can be grown and placed into the gut to improve health. More studies would need to be conducted first, however.


Kawinthi Fernando

Source: Fujimura, Kei. "Role of the gut microbiota in defining human health." Expert Reviews. (2010): 435-446. Print.[1]

Mainly a general article on why microbiota is present in the human body, and what altering the norm may do. A few interesting quotations:

"Disruption of the gut microbiome, termed dysbiosis, is frequently accompanied by overgrowth of pathogenic bacteria or fungi, in conjunction with significant loss of microbial diversity or key functional groups and an inflammatory response by the host, which contributes to disease development" (439).

"While antibiotics have revolutionized our ability to combat infectious diseases, their widespread use has led to a dramatic rise in the prevalence of antibiotic-resistant microbes, and recent concerns have been raised regarding the potential for adverse effects on host microbiota" (443).

This article is also really interesting on it's commentary of the origin of microbiota- Emily, you might find it helpful! There are some neat graphs and tables regarding the origin, as well.

Source: Foxman, Betsy. "Conceptualizing Human Microbiota: From Multicelled Organ to Ecological Community." Interdisciplinary Perspectives on Infectious Disease. 2008. (2008): 1-5. Print.[2]

Some very interesting insight of microbiota and how they could be characterized in the human body.

"...conceptualizing the microbiota as an organ leads us to consider that the microbiota on he skin or intestinal lumen might form physical structures, such as biofilms. This structure might vary in size and composition, being a thick lawn in some areas and thin islands in others and act as an additional physical barrier to colonization by pathogens. Disrupting these protective biofilms chemically or physically may lead to invasion by pathogens" (2-3).

This article strikes the surface of conceptualizing microbiota. This actually might help Alice with her research. The potential characterization of the microorganisms living in a human host is thoroughly discussed, as well as a brief overview of the Human Genome Project at the very end.

Source: Mazmanian, Sarkis. "Has the Microbiota Played a Critical Role in the Evolution of the Adaptive Immune System?." Science Magazine. 330. (2010): 1768-1773. Print.[3]

This is a fantastic article, very general information, but still very in-depth in regard to what the normal microbes actually do both for the immune system and in other parts of the human body.

"Although microbes have been classically viewed as pathogens, it is now well established that the majority of host-bacterial interactions are symbiotic. During development and into adulthood, gut bacteria shape the tissues, cells, and molecular profile of our gastrointestinal immune system. This partnership, forged over many millennia of coevolution, is based on a molecular exchange involving bacterial signals that are recognized by host receptors to mediate beneficial outcomes for both microbes and humans" (1768).

"Symbionts are not the only microbes the host encounters, however. An important challenge faced by the host immune system is to distinguish between beneficial and pathogenic microbes, because they share similar molecular patterns that are recognized by the innate immune system" (1768).

Great image explaining the human microbiome, genome, and T(reg) profiles: [4]

Source: Wall, R. "Role of Gut Microbiota in Early Infant Development." Clinical Medicine: Pediatrics. 3. (2009): 45-54. Print. [5]

  • This link allows you to download the full text, but I can't get a direct link to the full text itself.

This article focuses a great deal on the infant development of microbiota, but also delves into specific description of the function of enteric microbiota of the adult. The very end goes into details of infant probiotics. The article is very short, and basic, but still very informative.

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