Lecture 30 - Symbiosis-II - 2023

30 – Symbiosis II:
Mammalian Microbiota
BioMi 2900
Facultative mutualism
Source: Science in the News, Harvard University

Which definition best fits a facultative commensal
symbiotic relationship between two organisms?
A. Both benefit from the relationship, but each can also live
independently
B. Only one benefits from the relationship, and this organism is
also dependent upon it for survival
C. Only one benefits from the relationship, and both organisms
can also live independently
D. One benefits from the relationship to the other’s detriment
Symbiosis II – Mammalian Microbiota
1. Gastrointestinal tracts
2. Ruminants
3. A census of microbes
4. Microbial habitats of the human body
5. Human GI tract
6. Microbiota of the human colon
During the bamboo shoot growing season, the giant panda
needs to eat 84 pounds of bamboo shoots a day! How can a
giant panda get enough nutrition from bamboo shoots?
A. Panda shifts its gut microbiota between the bamboo shoot

abundance seasons and scarce seasons
B. Panda supplements its diet with meat and insects
C. Panda bears can hibernate through the bamboo shoot
scarce season
D. I don’t know!
1. Gastrointestinal tracts
• Gastrointestinal tracts of mammals,

particularly herbivores (plant diet)
and omnivores (plant and animal
diet), are highly evolved and
specialized to aid in the access,
digestion and absorption of
nutrients ALSO accommodate
microbes
Stevens and Hume
• Compare/contrast parts of the GI tract of two large herbivores

– Stomach – acidic environment, proteases, other degradative enzymes
– Small intestine – site of absorption of nutrients (amino acids)
– Large intestine – microbial fermentation
– The rumen!
Foregut vs. hindgut fermenting
mammalian herbivores
• Rumen: 84L
• Abomasum (acid stomach): 27L • Stomach: 8 - 18L
• Small intestine: 66L • Small intestine: 64L
• Cecum: 10L • Cecum: 26 - 34L
• Large intestine:28L • Large intestine: 81L
Digestion of hay by a cow is more efficient than digestion of hay by a horse
2. Ruminants
• 180 species worldwide – highly successful herbivores
• Foregut fermentation chamber – the rumen – followed by foregut
chambers to sieve particles, regurgitate fiber for further mastication
(chewing cud)
• Rumen
– houses a complex community of microbes, representing all domains of life,
specialized for the digestion of plants (access to cellulose and other plant
polysaccharides that the ruminant could not digest by itself)
– Allows long retention time of food – more time for microbial processes to
work on breakdown
– Gases (methane, CO2) removed by burping
Some important groups in the rumen
• Cellulose-degrading and sugar fermenting bacteria: Phylum
Firmicutes (e.g. Ruminococcus spp.) and Fibrobacteres
(Fibrobacter), also Bacteriodetes
• Protists (anaerobic)– abundant but contributions are poorly
understood, some with methanogen endo- and epi-symbionts
• Fungi – also degrade plant PS
• Methanogens
• Viruses
Microbial contributions to ruminant nutrition
• Digest complex polysaccharides into
simple sugars (glucose)
• Fermentation products (VFAs, SCFAs)
provide C and energy to host
(syntrophy is important!)
• What about N? Proteins are degraded
quickly in the rumen and removed as
waste (NH3 => urea=>urine)
• You can think of the rumen like a
chemostat: some microbes leave the
rumen, enter the true stomach
(abomasum) and are lysed. Microbial
protein and vitamins can be absorbed in
the small intestine.
Fistulated cow
Behind every successful cow are millions of gut
microorganisms
cannula
What would happen if there were no microbes in the rumen? “porthole”
A. Nothing would happen

B. Cow would get sick or maybe die
C. Cow would burp even more
D. Cow would jump over the moon
Source: https://modernfarmer.com/2014/09/holey-cow-wonderful-world-fistulated-cow/
Herbivores’ dietary dilemma
Unbalanced diet – high organic C relative to N

• Microbial partners help gain access to inaccessible C
• How to get enough N (essential amino acids) when
you don’t have a rumen?
• Consume a lot of food to obtain enough of the little
that’s available
• Consume some of the microbes from your GI tract!
Rodents and Lagomorphs…
• Coprophagy
• Cecotrophy
During the bamboo shoot growing season, the giant panda needs to
eat 84 pounds of bamboo a day! How can a giant panda get enough
nutrition from bamboo shoots?
Chlostridium butyricum: VFAs produced
Highlights
•Giant pandas gain more body mass when eating shoots compared with leaves
•More SCFAs are produced by the giant panda gut microbiome in the shoot-eating season
•Germ Free mice receiving the panda microbiota from the shoot-eating season gain more fat
•Butyrate can synchronize host hepatic circadian rhythm to increase lipid production
Seasonal shift of the gut microbiome

synchronizes host peripheral circadian rhythm
for physiological adaptation to a low-fat diet
in the giant panda. Cell Reports, January, 2022
https://www.technologynetworks.com/immunology/news/pandas-
gut-bacteria-may-help-them-fatten-up-while-eating-bamboo-357615
3. A census of microbes
• High throughput sequence analysis – allows for deep studies
• Amplify a portion of the small subunit rRNA genes (16S rRNA, 18S rRNA) from
diverse, uncultured organisms
• Or sequence all DNA or RNA (meta-genomics, -transcriptomics)
Note: like any census

you won’t get
everyone’s info
A few definitions…
• Microbiota – the microbes that live in a particular

environment includes bacteria, archaea, microbial
eukaryotes, viruses
• Microbiome – the collection of genomes and all genes
of the microbiota; metabolic potential
4. Microbial habitats of the human body
Conditions dictate the kinds of microbes that predominate.

An estimated 500 – 1000 species of microbes inhabit the adult human at any one time!
(for more details see chapter 24)
Commensals or Mutualists?
• We each have our own unique microbiome composition
• Microbes associated with sites on the human body are different
from environmental microbes or even microbes in our food –
selection for symbionts
• Microbes benefit from a constant temp, predictable environment,
regular access to nutrients – we even feed some microbes
polysaccharides (mucus, breast milk)!
• We benefit from products of microbial metabolism (vitamins, VFAs)
• Normal microbiota may prevent invasion from potential pathogens
• Microbes are kept in their proper place by immune defenses
5. Human GI Tract
• Omnivore – but we eat really processed foods

• Chemostat
• Lifestyle, stress, antibiotics, environment, exposure to animals
impact adult microbiota.
Cross-section view of human intestine
lumen
IgA –
antibodies
mucus
AMPs –
antimicrobial
peptides
epithelium
6. Microbiota of the human colon
• Similarities with other animals, such as cows…

– Major Phyla: Firmicutes, Bacteriodetes, Proteobacteria, Actinobacteria
– Diverse bacterial populations
• Differences compared to the cow:
– Not a well-developed community of protists in humans (usually)
– More limited diversity in Archaeal populations
Benefits of a healthy gut microbiome
• Discourage colonization or overgrowth of pathogens. (C.diff)
• Provide 10 -15% of calories from food, especially access to complex
carbohydrates.
• Produce vitamins and other metabolic co-factors.
• Help educate the immune system and trigger maturation of the gut.
• Microbial metabolic byproducts modulate inflammatory response.
• Impacts on diabetes; obesity/leanness; cardiac function; autism;

development of allergies; behavior, body odor…
Which infant gut microbiota would have the
greatest diversity:
A. Breast milk and vaginal (natural) birth

B. Formula milk and Cesarean (C-section) birth
C. Vaginal birth and formula milk
D. C-section birth and breast milk
E. All have the same amount of gut microbe diversity
Where do we get our gut microbes?
First, contacts with mom…

then the environment
Community assembly is influenced by diet – formula vs. breast milk

Community will be altered by antibiotics
Composition changes dramatically during the first ~2 years but
eventually stabilizes into our adult microbiota (early conditions
influence adult microbiota)
Host genetics… not so important
We are colonized rapidly with inoculum mainly from our
mothers
Label
Fig 24.22
• One of the oligosaccharides in breast milk

that select for desirable organisms like
• Bifidobacterium is an Bifidobacterium and Lactobacillus
Actinobacterium that has metabolism • Termination of breast feeding leads to a
similar to LAB more adult-like microbiota
• It is considered a desirable probiotic
Fig 4.20
The gut microbiota matures in about 3 yrs*
Diversity is higher in less westernized cultures
OTU: Operational Taxonomic Unit
“number of species of microbes”
• *Don’t feed babies honey until they’re

>2-4 yrs old
• Honey contains Clostridium botulinum
spores that can colonize an immature GI
tract
Amazonians
Can the microbiome play a role in obesity?
Transfer of
obesity to
mice
through
microbiota
Germ free
Fig 24.25b
The gut microbiota is influenced by our diets
Bruno Senghor, Cheikh Sokhna, Raymond Ruimy, Jean-Christophe Lagier, Gut microbiota diversity according to
dietary habits and geographical provenance, Human Microbiome Journal, Volumes 7–8, 2018, Pages 1-9,
https://doi.org/10.1016/j.humic.2018.01.001.
Dysbiosis: disruption of homeostasis between gut microbiota and host
Dysbiosis: disruption of homeostasis between gut
microbiota and host
Can your gut microbiota affect your mood?
Science Journal
Could gut microbes regulate appetite and body temperature?
Bacterial cell wall molecules that travel to the brain could trigger a host of behaviors
14 APR 2022, BYELIZABETH PENNISI
Gut bacteria can influence the brain’s temperature controls and stimulate nest -building in mice
For example:
Serotonin is produced in the
gut and is associated with
happiness
Horn, J., Mayer, D.E., Chen, S. et al. Role of diet and its effects on the gut
microbiome in the pathophysiology of mental disorders. Transl Psychiatry 12,
164 (2022). https://doi.org/10.1038/s41398-022-01922-0
Summer
reading!
What’s on the horizon?
• Better living through (microbial bio)chemistry: working with our
microbes to preserve/improve the effectiveness of drugs and
identify gut microbiomes that make a drug toxic (e.g.
acetaminophen – specific microbial activities associated with
elevated liver toxicity)
• Human behavior and microbiota, the gut/brain axis (the production
of the neurotransmitter serotonin in the gut is regulated by gut
bacteria)
• Probiotics – live microbes consumed to provide a health benefit
beyond a nutritional gain (e.g. to alter cell-cell communication
systems, alter our immune response), prebiotics – foods that
enhance growth of good microbes

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30 – Symbiosis II:

Source: Science in the News, Harvard University

A. Panda shifts its gut microbiota between the bamboo shoot

• Gastrointestinal tracts of mammals,

• Compare/contrast parts of the GI tract of two large herbivores

A. Nothing would happen

Unbalanced diet – high organic C relative to N

Chlostridium butyricum: VFAs produced

Seasonal shift of the gut microbiome

Note: like any census

• Microbiota – the microbes that live in a particular

Conditions dictate the kinds of microbes that predominate.

• Omnivore – but we eat really processed foods

• Similarities with other animals, such as cows…

• Impacts on diabetes; obesity/leanness; cardiac function; autism;

A. Breast milk and vaginal (natural) birth

First, contacts with mom…

Community assembly is influenced by diet – formula vs. breast milk

• One of the oligosaccharides in breast milk

• *Don’t feed babies honey until they’re

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