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More recently, scientists have begun to further classify gram-negative and gram-positive bacteria. They have added a special group of deeply branching bacteria based on a combination of physiological, biochemical, and genetic features. They also now further classify gram-negative bacteria into Proteobacteria , Cytophaga-Flavobacterium-Bacteroides (CFB) , and spirochetes .

The deeply branching bacteria are thought to be a very early evolutionary form of bacteria (see Deeply Branching Bacteria ). They live in hot, acidic, ultraviolet-light-exposed, and anaerobic (deprived of oxygen) conditions. Proteobacteria is a phylum of very diverse groups of gram-negative bacteria; it includes some important human pathogens (e.g., E. coli and Bordetella pertussis ). The CFB group of bacteria includes components of the normal human gut microbiota, like Bacteroides . The spirochetes are spiral-shaped bacteria and include the pathogen Treponema pallidum , which causes syphilis. We will characterize these groups of bacteria in more detail later in the chapter.

Based on their prevalence of guanine and cytosine nucleotides, gram-positive bacteria are also classified into low G+C and high G+C gram-positive bacteria . The low G+C gram-positive bacteria have less than 50% of guanine and cytosine nucleotides in their DNA. They include human pathogens, such as those that cause anthrax ( Bacillus anthracis ), tetanus ( Clostridium tetani ), and listeriosis ( Listeria monocytogenes ). High G+C gram-positive bacteria, which have more than 50% guanine and cytosine nucleotides in their DNA, include the bacteria that cause diphtheria ( Corynebacterium diphtheriae ), tuberculosis ( Mycobacterium tuberculosis ), and other diseases.

The classifications of prokaryotes are constantly changing as new species are being discovered. We will describe them in more detail, along with the diseases they cause, in later sections and chapters.

  • How do scientists classify prokaryotes?

Human microbiome project

The Human Microbiome Project was launched by the National Institutes of Health (NIH) in 2008. One main goal of the project is to create a large repository of the gene sequences of important microbes found in humans, helping biologists and clinicians understand the dynamics of the human microbiome and the relationship between the human microbiota and diseases. A network of labs working together has been compiling the data from swabs of several areas of the skin, gut, and mouth from hundreds of individuals.

One of the challenges in understanding the human microbiome has been the difficulty of culturing many of the microbes that inhabit the human body. It has been estimated that we are only able to culture 1% of the bacteria in nature and that we are unable to grow the remaining 99%. To address this challenge, researchers have used metagenomic analysis , which studies genetic material harvested directly from microbial communities, as opposed to that of individual species grown in a culture. This allows researchers to study the genetic material of all microbes in the microbiome, rather than just those that can be cultured. National Institutes of Health. “Human Microbiome Project. Overview.” http://commonfund.nih.gov/hmp/overview. Accessed June 7, 2016.

One important achievement of the Human Microbiome Project is establishing the first reference database on microorganisms living in and on the human body. Many of the microbes in the microbiome are beneficial, but some are not. It was found, somewhat unexpectedly, that all of us have some serious microbial pathogens in our microbiota. For example, the conjunctiva of the human eye contains 24 genera of bacteria and numerous pathogenic species. Q. Dong et al. “Diversity of Bacteria at Healthy Human Conjunctiva.” Investigative Ophthalmology&Visual Science 52 no. 8 (2011):5408–5413. A healthy human mouth contains a number of species of the genus Streptococcus , including pathogenic species S. pyogenes and S. pneumoniae . F.E. Dewhirst et al. “The Human Oral Microbiome.” Journal of Bacteriology 192 no. 19 (2010):5002–5017. This raises the question of why certain prokaryotic organisms exist commensally in certain individuals but act as deadly pathogens in others. Also unexpected was the number of organisms that had never been cultured. For example, in one metagenomic study of the human gut microbiota, 174 new species of bacteria were identified. J.C. Lagier et al. “Microbial Culturomics: Paradigm Shift in the Human Gut Microbiome Study.” Clinical Microbiology and Infection 18 no. 12 (2012):1185–1193.

Another goal for the near future is to characterize the human microbiota in patients with different diseases and to find out whether there are any relationships between the contents of an individual’s microbiota and risk for or susceptibility to specific diseases. Analyzing the microbiome in a person with a specific disease may reveal new ways to fight diseases.

Key concepts and summary

  • Prokaryotes are unicellular microorganisms whose cells have no nucleus.
  • Prokaryotes can be found everywhere on our planet, even in the most extreme environments.
  • Prokaryotes are very flexible metabolically, so they are able to adjust their feeding to the available natural resources.
  • Prokaryotes live in communities that interact among themselves and with large organisms that they use as hosts (including humans).
  • The totality of forms of prokaryotes (particularly bacteria) living on the human body is called the human microbiome, which varies between regions of the body and individuals, and changes over time.
  • The totality of forms of prokaryotes (particularly bacteria) living in a certain region of the human body (e.g., mouth, throat, gut, eye, vagina) is called the microbiota of this region.
  • Prokaryotes are classified into domains Archaea and Bacteria.
  • In recent years, the traditional approaches to classification of prokaryotes have been supplemented by approaches based on molecular genetics.

True/false

Among prokaryotes, there are some that can live in every environment on earth.

True

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Fill in the blank

When prokaryotes live as interacting communities in which one population benefits to the harm of the other, the type of symbiosis is called ________.

parasitism

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The domain ________ does not include prokaryotes.

Eukarya

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Pathogenic bacteria that are part of the transient microbiota can sometimes be eliminated by ________ therapy.

antibiotic

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Nitrogen-fixing bacteria provide other organisms with usable nitrogen in the form of ________.

ammonia

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Short answer

Compare commensalism and amensalism.

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Give an example of the changes of human microbiota that result from medical intervention.

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Questions & Answers

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Source:  OpenStax, Microbiology. OpenStax CNX. Nov 01, 2016 Download for free at http://cnx.org/content/col12087/1.4
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