Notes for Bio 2- Bacteria

Microbes & Diversity

A

microbe (or microorganism) is a microscopic organism. Organisms that fall into this category include those from all three domains of life—

Bacteria, Archaea, and Eukarya—as well as non-living entities like viruses (which are not classified into the three domains).

Difficulty in Estimating Microbial Diversity

Estimating the total diversity of microbes and bacteria on Earth is difficult for several reasons:

• Undiscovered Species: Up to 99.99% of bacteria species may remain undiscovered and undescribed. Billions of species are thought to exist, but only an estimated 30,000–40,000 have been identified.

• Methodology: Scientists primarily rely on genetic tools to understand evolutionary relationships among bacteria, but these tools are not perfect.

Bacterial Diversity on the Human Body

On humans, bacteria are found everywhere. A single square inch of your skin can have about 8 million cells , and there are about 500–1000 different species in or on your body.

• The

  highest diversity of bacteria is found in the gut and on the skin.

• The types of bacteria found on the body

  differ greatly between regions, as shown by the pie charts for various anatomical sites.

Small Size and Essential Life Functions

The small size of single-celled microbes allows them to carry out essential life functions without complex adaptations:

• Gas exchange, movement of materials, and acquisition of nutrients are all possible through diffusion across the cell membrane due to the cell's high surface area-to-volume ratio.

What are Bacteria?

Domains of Life and Relatedness

The three domains of life are

Bacteria, Archaea, and Eukarya.

• The two domains that are most closely related are

  Archaea and Eukarya (Eucaryota).

Common Bacterial Shapes

Bacterial species are commonly classified by their shape. The three most common shapes are:

• Cocci: Spherical bacteria.

• Bacilli: Rod-shaped bacteria.

• Spirilla: Spiral-shaped bacteria.

Function of Bacterial Structures

The functions of key structures in a bacterial cell (which is prokaryotic) are:

Arrangement by Size

Arranging the following from small to large :

1. Atom

2. Small Molecules

3. Lipids

4. Viruses

5. Bacteria cell (≈1 μm to 10 μm)

6. Mitochondria (Organelles) (≈1 μm to 10 μm)

7. Eukaryotic cell (≈10 μm to 100 μm)

Note: Bacteria cells and mitochondria are similar in size (both around the 1 μm to 10 μm range).

Bacterial Classification and Gram Staining

Traits for Identification

Humans identify or classify bacteria based on several traits, including:

• Shape: Classified as cocci (spherical), bacilli (rod-shaped), or spirilla (spiral-shaped).

• Appearance in Culture: The colors and shapes of their colonies when grown on a plate can be used for identification.

• Gram Staining: Determining if they are gram-negative or gram-positive based on their cell wall structure.

Gram-Negative vs. Gram-Positive

The difference between gram-negative and gram-positive bacteria lies in the structure of their

cell walls.

• Gram-Positive Bacteria: The glycoprotein layer (peptidoglycan) is on the outside of the cell wall.

• Gram-Negative Bacteria: The glycoprotein layer lies beneath an additional outer membrane (composed of lipopolysaccharide and protein).

How to Tell Them Apart (Gram Staining):

Scientists and medical personnel use Gram staining to differentiate them:

• Gram-Positive Bacteria: Can be stained with a purple dye because the glycoprotein layer is exposed.

• Gram-Negative Bacteria: Cannot be stained with the dye because the glycoprotein layer is shielded beneath the additional outer membrane.

Bacterial Evolution

Features Contributing to Fast Evolution

Bacteria evolve very quickly due to two primary factors:

1. High Mutation Rate: Bacteria generally have a high mutation rate.

2. Ability to Share DNA (Horizontal Gene Transfer): They can obtain outside sources of genetic diversity.

Mutation Rate and Genome Size

In general, organisms with

smaller genomes (like most bacteria and viruses) tend to have higher rates of mutation per site per year than those with larger genomes (like eukaryotes). Most bacteria have a higher mutation rate than humans (eukaryotes).

Methods of Genetic Exchange (Horizontal Gene Transfer)

Bacteria can exchange genetic material within the same generation via three primary mechanisms:

Bacteria and Humans

Impact of Bacteria on Human Lives

Human lives are affected by bacteria in numerous ways, both helpful and harmful:

Microbiome and its Roles

A

microbiome is the community of microbes that live in and on a human or other organism.

• Size: There are slightly more microbial cells than human cells in or on the human body, with an estimated total of about 68 trillion microbial cells.

• Roles: Our microbiome potentially plays a role in physical health, mental health ,

  digestion , and influencing

  behavior, appetite, and mood. Less diverse microbiomes may be associated with chronic illnesses.

Scientific Data/Data Literacy Exercises

Interpreting Bar Graphs

• Stacked Bar Graphs: Used to represent the total quantity and how that total is made up of different components. In the "Total Number of Cells in the Human Body" graph , the total bar height represents the total cells, and the stacked sections show the relative proportion of human cells versus microbial cells.

• Side-by-Side Bar Graphs: Used to compare the values of different, independent categories (e.g., comparing microbial diversity in different body regions) or the results of different experimental groups (like the mouse experiment results).

Pie Charts

Pie charts are usually used to represent parts of a whole, specifically the proportions or percentages of different categories within a total. In the bacterial diversity image, they show the relative abundance of different bacterial divisions (like Actinobacteria, Firmicutes, etc.) at specific locations on the human body.

Variables in an Experiment

In an experiment, the variables are:

• Independent Variable (IV): The factor that is manipulated or changed by the experimenter. In the mouse microbiome experiment, the independent variable is the

  source of the microbiome transplant (from a "normal" mouse or a "depressed" mouse).

• Dependent Variable (DV): The factor that is measured or observed to see if it changes in response to the independent variable. It is the result of the experiment. In the mouse microbiome experiment, the dependent variables are the measures of depressive behavior in the mice, such as:

  • Latency to groom (s) in the

    Splash test.

  • Time immobile (s) in the

    Tail suspension test.

  • Time immobile (s) in the

    Forced swim test.

Interpreting Mouse Microbiome Experiment Results

The hypothesis was: If microbiome composition can cause depressive behavior, then "normal" mice who receive a microbiome transplant from "depressed" mice will exhibit depressed behavior.

Taking longer to react (higher time values) indicates depressive behavior for all three tests.

Results Description

The graphs compare four groups:

• Black bars: Normal mice (Control)

• Red bars (solid): "Depressed" mice

• White bars: Normal mice with transplant from normal mice

• Red bars (outline): Normal mice with transplant from depressed mice

Important Patterns and Differences:

• In all three tests (

  Splash test, Tail suspension test, and Forced swim test), the "Depressed" mice (solid red bars) showed the highest levels of depressive behavior (longest reaction times/time immobile) compared to the Control mice (black bars).

• In the

  transplant groups, the Normal mice with a transplant from depressed mice (outlined red bars) consistently showed higher depressive behavior (longer reaction times/time immobile) than the Normal mice with a transplant from normal mice (white bars).

• The level of depressive behavior in the mice with the depressed microbiome transplant (outlined red bars) was significantly

  higher than the normal controls (black bars and white bars), and in some cases, statistically similar to the original depressed mice (solid red bars).

Support for the Hypothesis

Yes, the data support the idea that microbiomes can influence behavior.

• The crucial finding is that

  normal mice receiving a microbiome transplant from depressed mice exhibited a significant increase in depressive behavior compared to the normal mice receiving a transplant from normal mice. This change in behavior is directly linked to the change in their microbial community, suggesting a

  causal link between the gut microbiome composition and depressive behavior.

Why Transplants Were Necessary

The microbe transplants were necessary to test the idea that microbes

cause depressed behavior.

• Simply comparing the microbiomes of control mice to depressed mice (the original black vs. solid red groups) would only show a

  correlation (a difference in microbiome is associated with a difference in behavior).

• By

  transplanting the "depressed" microbiome into healthy, normal mice and observing the subsequent development of depressive behavior, researchers could establish a potential causal link—that the microbiome composition itself is a factor that causes the behavioral change.