Microbiology Cells Module 4

Goals of Human Microbiome Project

To develop a reference set of microbial genome sequences and to perform preliminary characterization of the human microbiome

To explore the relationship between disease and changes in the human microbiome

To develop new technologies and tools for computational analysis

To establish a resource repository

To study the ethical, legal, and social implications of human microbiome research

Microbiome Definition

The complete collection of microorganisms, and their genes, within a particular environment.

Microbiota

Individual microbial species in a biome

HMP Aim

characterize microbial communities found at multiple human body sites and to look for correlations between changes in the microbiome and human health.

Human microbiome

Strong niche specialization both within and among individuals = different sites, different microbes

Diversity and abundance of each habitat’s signature microbes vary widely even among healthy subjects

10,000 microbial species in human microbiome

Everyone has ~160 species (57 were really common)

500-1,000 bacterial species just in the gut

Human microbiome functions

Prevent Pathogens from being successful

Block colonization niches

Competing for nutrients

Modifying environment to change virulence factor expression

Making environment actively hostile: Producing bacteriocins (antimicrobial) & short chain fatty acids (SCFA)

Lowering pH

Cause host to thicken mucus layer

Cause host to upregulate antimicrobial peptides (defensin, IgA)

Primes host neutrophils and macrophages

Human Gut Microflora

92 bacterial and 26 archaeal groups exist, but human microbial communities are dominated by 4:

Firmicutes

Bacteroidetes

Actinobacteria

Proteobacteria

Microbiome main functions

Synthesise vitamins

modulate immune response

alter drug delivery

Functional foods

food claimed to have a healthpromoting or disease-preventing property beyond the basic function of supplying nutrients.

Most common probiotics and potential benefits

Lactic acid bacteria and bifidobacteria

chronic intestinal inflammatory diseases, prevention and treatment of pathogen-induced diarrhea, urogenital infections.

Prebiotics

an ingredient that beneficially nourishes the good bacteria already in the large bowel or colon. Prebiotics stimulate the growth of probiotics

Human-microbe interactions

We are a colonized ecosystem

Colonizing microbes can be: Good, Bad. Neutral

All are simply extracting Carbon and energy

Good vs bad microflore

Two gut species: C. difficile and Lactobacillus

Both use sialic acids from mucins (the main structural component of the mucus layer in the gut) as carbon/energy source, heterotrophs

Speed of growth and presence of accessory genes are the only factors making C. difficile a pathogen

Fecal matter transplants

highly successful treatment for multiple recurrences of Clostridium difficile infection (CDI)

Natural microbial environments

Most organisms cannot be or have not been isolated in pure culture

Identification now done using genetic ‘fingerprints’

Uncultured microbial world is greater than the cultured world

Microbial ecology definition

The study of the interrelationships among microorganisms and their environment

Catabolism

involves breaking down complex molecules releasing energy in the process

Anabolism

utilizes that released energy to synthesize larger, more complex molecules from smaller building blocks

Redox

NADH/NADPH is an intermediate to transfer energy within a cell, they are recycled

Photoautotrophs

Uses light energy and Carbon dioxide

Photoheterotrophs

Use light energy and organic compounds from a different organism

Chemoautotrophs

Use Chemical energy and Carbon Dioxide

Chemoheterotrophs

Uses Chemical energy and organic compounds from a different organism

Hetero

Need fixed cardon so dependant on primary producers

Chemo

Uses chemical energy from either C compounds, organic glucose, or Non C compounds, inorganic H2S

How can so many different microbes share the same metabolisms?

Occupy the same niche but different areas of the environment

What areas the human microbiome focus on

Oral, skin, vaginal, gut, nasal/lung