1.  Overview

2.  Structural & Functional Features

3.  Taxonomy

4.  Communities

Bacteria Outline

PHYLUM

Bacteria - Taxonomy

CLASS

ORDER

FAMILY

GENUS

SPECIES

SUB-SPECIES & STRAINS

FirmicutesBacteroidetes

ProteobacteriaActinobacteria

TenericutesVerrucomicrobia

FusobacteriaCyanobacteria

etc.

Bacteria - Phyla

90%

Do we really need to learn taxonomy?

Yes. (if you want to interpret

functional labs and understand the microbiome

in depth)

§  Interpreting functional microbiome test results (stool tests, organic acid tests, etc.)

§  Understanding probiotics and interaction with microbiome

§  Understanding importance / relevance of scientific and clinical microbiome research

Taxonomy + FunctionImportant for …

Be patient! Mastering technical terminology takes time and familiarity.

PHYLUM

CLASS

ORDER

FAMILY

GENUS

SPECIES

STRAIN

Firmicutes

Bacilli

Lactobacillales

Lactobacillaceae

Lactobacillus

L. acidophilus

DDS-1

Actinobacteria

Actinobacteria

Bifidobacteriales

Bifidobacteriaceae

Bifidobacterium

B. bifidum

ATCC 29521

1. Lactobacillus acidophilus 2. Bifidobacterium bifidum

§  Mostly gram-positive (“strong skin”)

§  Tend to be associated closely with intestinal mucosa (vs. lumenal)

§  Mostly coccus and bacillus forms

§  Many can produce endospores

§  Common groups:•  Lactobacillus (commensal and probiotic)•  Bacillus (commensal and probiotic)•  Clostridia (commensal)

Firmicutes

§  Gram-negative & anaerobic

§  Tend to be located lumenally (vs. mucosal)

§  Rod-shaped

§  Do not form endospores

§  Common groups:•  Bacteroides•  Prevotella

Bacteroidetes

§  Gram-negative

§  Facultative & obligate anaerobes

§  Very diverse forms (“protean” = capable of assuming many forms)

§  Includes a variety of well-known pathogens / pathobionts

•  Escherichia coli, Salmonella, Helicobacter pylori, Yersinia pestis (plague)

Proteobacteria

§  Actinobacteria•  Gram-positive

•  Long rods & filaments

•  Example: Bifidobacteria

§  Verrucomicrobia•  Verruca = “wart”

•  Anaerobic, gram-negative

•  Example: Akkermansia muciniphila

Other Phyla

A few notable groups and species …

(commensals, pathobionts, and pathogens)

Clostridia§  Firmicutes > Clostridia

§  Abundant (10-40% of total gut bacteria) and complex group

§  Very important group; some perform many beneficial functions

§  Strictly anaerobic, gram-positive

§  Colonizes near the epithelial barrier in the colon

Clostridia§  Major butyrate producers (feed colon epithelial

cells)

§  Also produce secondary bile acids from primary bile acids

§  Form endospores

§  Includes some pathogens: C. difficile, C. tetani, C. botulinum, etc.

COMMENSALS

§  Faecalibacterium prausnitzii

§  Roseburia intestinalis

§  Eubacterium rectale

§  Coprococcus eutactus

§  Clostridium scindens

§  Butyrivibrio crossotus

Clostridia Examples

PATHOGENS

§  Clostridium difficile (diarrhea, severe colitis)

§  Clostridium tetani (tetanus)

§  Clostridium botulinum (botulism, botox)

§  Clostridium perfringens (food poisoning, gangrene)

§  Phylum: Verrucomicrobia

§  Relatively abundant: up to 3.0% of gut bacterial population on average

§  Strictly anaerobic, gram-negative

§  Colonizes the mucus layer; produces propionate and acetate from mucus

§  SCFAs modulate gene expression via epigenetics

§  Improves epithelial barrier function

Akkermansia Muciniphila

Pathobionts & Pathogens

Dysbiosis & Pathobionts

Commensals (Symbionts)

Pathogens & Parasites

EXTERNAL (Transient)

Beneficial Microbes

INTERNAL (Long-term)

§  Bacteroidetes•  Bacteroides fragilis

§  Proteobacteria•  Helicobacter pylori: Can cause ulcers and stomach cancer

but may reduce esophageal cancer risk

•  Bilophila wadsworthia: normal commensal but may contribute to colitis with high-fat diet

•  Klebsiella: normal commensal but can cause infections (sometimes serious)

Pathobiont Examples

§  Obligate anaerobe, gram-negative

§  Polysaccharide A: stimulates anti-inflammatory response (induces Treg cells)

§  BUT, it can be a pathobiont•  Can produce a capsule (virulence factor)•  Common opportunistic pathogen in internal

abdominal infections (leaky gut)•  Underscores importance of barrier integrity for both

commensals and pathogens

Bacteroides fragilis

§  Proteobacteria•  Salmonella enterica (typhimurium)

•  Escherichia coli (pathogenic strains)

•  Vibrio cholerae

•  Campylobacter jejuni

•  Klebsiella pneumoniae

§  Firmicutes > Bacilli > Lactobaciallales•  Enterococcus faecalis•  Enterococcus faecium

Pathogenic Bacteria

§  Taxonomy important for working with microbiome

§  Commensals: some groups and species play a special positive role•  Immune function, intestinal barrier, motility, many others …

•  Keeping pathobionts and pathogens in check

§  Pathobionts & pathogens•  Can cause disease

•  Depends on context, including the health of the individual, the overall health of the microbiome, and environmental factors

Taxonomy: Take-Homes

1.  Overview

2.  Structural & Functional Features

3.  Taxonomy

4.  Communities

Bacteria Outline

§  Flexibility in using different substrates (depending on genes within each bacteria)

§  Ability to tolerate variable physiological factors (oxygen, pH, bile, etc.)

§  Rapid evolution of DNA

§  Horizontal gene transfer (via plasmids)

§  Replication rate, formation of endospores

§  Community interactions, biofilms

Adaptibility & Resilience

§  Complex ecological communities of microbes

§  Composition depends on local factors (physiological conditions, available substrates, other microbes, etc.)

§  Highly interdependent, complex functional relationships (with each other & with us)

§  Cooperate and compete

§  Relatively stable & resilient

Microbiome Communities

§  Location •  Digestive tract region &

microenvironment / niche •  Mucus layer vs. lumen

§  Available substrates §  pH §  Oxygen §  Transit time / flow rate §  Barriers & immune factors §  Attachment sites §  Others: Redox status, bile salts, etc.

Physiological Factors

§  Sources & types (diet, secretions, microbe metabolites)

§  Availability§  Competition with other microbes§  Digestion / absorption by GI tract§  Concentration, flow rate, etc.

§  Position in community “food chain”

Substrates (Nutrients)

Cross-Feeding & Competition

SPECIES 1

A Resistant starch

B SPECIES 3

C

Acetate

Butyrate

SPECIES 2

SPECIES 4

§  Direct§  Substrates (nutrients / metabolites)

§  Space / attachment sites (mucus / epithelial later)

§  Antimicrobial factors: organic acids, bacteriocins, lactocillin, etc.

§  Indirect§  Suppress immune response to themselves

§  Enhance immune response to competitors

§  Others, including possibly affecting eating behavior

Competition

§  Cross-feeding / food web (mutualism)•  Metabolites produced by one species can be used as a

substrate for another

§  Coordination via “quorum sensing”•  Molecules used to coordinate activities•  Depends on density

§  Sharing DNA•  e.g. - antibiotic resistance genes

§  Biofilms

Cooperation

§  Bacteria + EPS (extracellular polymeric substance – polysaccharides, proteins & nucleic acids)

§  Normal part of many communities, but can contribute to pathogenicity (resistance to treatments)

§  More stable, protected microenvironment

§  Enables greater synergy & cooperation within community

§  Contains extracellular enzymes – external “shared” digestion

Biofilms

§  Capacity of microbiome communities to resist new colonization by pathogens and other transients (e.g., probiotics, foodborne microbes)

§  Key to preventing GI infections: “First line of defense”

§  Main factors contributing:•  Lack of niches (competition - space, available substrates)•  Hostile environment (pH, antimicrobial factors, immune factors)•  Biofilms•  Coordination (quorum sensing)

Colonization Resistance

§  Above factors contribute to stability & resilience •  Stability: resistance to change, ability to maintain homeostasis

•  Resilience: capacity to return to homeostasis after disturbance

§  Diverse ecosystems are generally more stable & resilient

§  Microbiome stability, resilience, & functional capacity contribute to human health & resilience •  Less prone to disruption of our homeostasis & health

•  Contributes to tolerance of a wider range of foods and conditions •  Makes it challenging to change the microbiome

•  BUT less diverse (less stable) microbiomes may be easier to change

Stability & Resilience

1.  Overview

2.  Structural & Functional Features

3.  Taxonomy

4.  Communities

Bacteria Outline

1.  Microbiome overview: getting a sense of the microbiome, research, what we know

2.  Bacteria: features, functions, communities & taxonomy

3.  Other microbes: archaea, fungi, viruses, parasites (protozoa & helminths)

Module 1 Overview