Microbe-Host & Microbe-Microbe Interactions
Chapter 1. Human Microbiome
- Microbiota: sum of all microbes that reside in or on a host or a specified part of a host. Includes
bacteria, archaea, eukaryotes, and viruses.
- Metagenome: genes and genomes of the microbiota. Provides informa>on about the func>onal
gene>c poten>al of the popula>on.
- Microbiome: the totality of microbes, their gene>c informa>on, their products, and the milieu in
which they interact.
Tradi>onally, normal microbiota: black box – many (99%) bacteria uncul>vable and focus on the role of specific
microbes in disease. In the past 15 years, the field of microbiota research has exploded. DNA-based analyses:
enormous new data sets. Apprecia>on of the beneficial influence of microbiota on human health
Man is super organism, ra>o microbes/human cells: 1,3/1 (number of bacteria in reference man: 3,9·1013;
number of human cells 3·1013), ra>o microbial genes/human genes: 100 (25 000 human genes, 2-20 million
microbial genes).
Microbiome composi,on of ‘healthy’ humans
The human microbiome project (HMP):
- By US Na>onal Ins>tutes of Health ($175M; 2007 - …) - ~250 researchers.
- Study of composi>onal range of the normal microbiome of healthy individuals.
- 4,788 samples – 300 US individuals – 18 body habitats (5 major areas).
- 16S rRNA gene analysis & shotgun metagenomic sequencing (subset of 681 samples).
Varia%on in microbiome composi%on
Varia%on among anatomical sites
<10 of 50 phyla represented. No taxa are universally present among all habitats and individuals at the
sequencing depth employed here, unlike several pathways, although several clades demonstrated broad
prevalence and rela>vely abundant carriage paderns.
Instead, as suggested by individually focused studies, each body habitat in almost every subject was
characterized by one or a few signature taxa making up the plurality of the community.
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,Signature clades at the genus level formed on average anywhere from 17% to 84% of their respec>ve body
habitats, completely absent in some communi>es (0% at this level of detec>on) and represen>ng the en>re
popula>on (100%) in others.
Notably, less dominant taxa were also highly personalized, both among individuals and body habitats; in the
oral cavity, for example, most habitats are dominated by Streptococcus, but these are followed in abundance
by Haemophilus in the buccal mucosa, Ac1nomyces in the supra-gingival plaque, and Prevotella in the
immediately adjacent (but low oxygen) sub-gingival plaque.
- Anatomical site: primary determinant of microbiome composi>on.
- Microbial a-diversity is dependent on anatomical site, oral cavity: high diversity; vagina: low.
Interpersonal varia%on
Inter-individual varia>on in the microbiome proved to be specific, func>onally relevant, and personalized.
Varia>on in rela>ve abundance of Streptococcus spp. in the oral cavity (tongue).
The genus dominates the oropharynx, with different species
abundant within each sampled body habitat and, even at
the species level, marked differences in carriage within each
habitat among individuals. As the ra>o of pan-to-core
genomes is high in many human-associated microbes, this
varia>on in abundance could be due to selec>ve pressures
ac>ng on pathways differen>ally present among
Streptococcus species or strains.
Other func>onally relevant inter-individual varia>on at the
species and strain levels occurred throughout the microbiome. In the gut, Bacteroides fragilis has been shown
to prime T-cell responses in animal models via the capsular polysaccharide A18, and in the HMP stool samples
this taxon was carried at a level of at least 0.1% in 16% of samples (over 1% abundance in 3%).
On the skin, S. aureus, of par>cular interest as the cause of methicillin-resistant S. aureus (MRSA) infec>ons,
had 29% nasal and 4% skin carriage rates, roughly as expected. Close phylogene>c rela>ves such as
Staphylococcus epidermidis (itself considered commensal) were, in contrast, universal on the skin and present
in 93% of nares samples, and at the opposite extreme Pseudomonas aeruginosa (a representa>ve Gram - skin
pathogen) was completely absent from both body habitats (0% at this level of detec>on).
These and the data above suggest that the carriage padern of some species in the human microbiome may be
analogous to gene>c traits, where recessive alleles of modest risk are maintained in a popula>on. In the case
of the human micro-biome, high-risk pathogens remain absent, whereas species that pose a modest degree
of risk also seem to be stably maintained in this ecological niche.
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,Temporal varia%on
131 individuals sampled at addi>onal >me point o within-subject
varia>on over >me is consistently lower than between-subject
varia>on. The uniqueness of each individual’s microbiome is
stable over >me. Day-to-day varia>on of gut microbiome (stool)
of two healthy individuals:
- Clear dis>nc>on between individuals.
- Temporal stability.
- Only strong perturba>ons caused changes:
• Travelling/dietary changes.
• Infec>ons.
• An>bio>cs.
Taxonomic versus func%onal diversity
Unlike taxa, several core func>ons are ubiquitous among individuals and body habitats, ribosome and
transla>onal machinery, nucleo>de charging and ATP synthesis, and glycolysis. Unlike taxa, only few core
func>ons are highly variable among subjects within any body habitat. Greater variability in niche-specific
func>ons of rare but consistently present pathways long tail’ of low-abundance genes and pathways probably
encodes much of the uncharacterized biomolecular func>on and metabolism of these metagenomes.
Our metagenome is more unique than our genome:
• Any 2 humans: 99,9% iden>cal genomes, 2 E. coli cells can have genomes that are 40% different.
• Strong and stable interpersonal varia>on in metagenome composi>on.
Zoom in on the gut microbiome
The ‘normal’ gut microbiota is dominated by anaerobic bacteria, which outnumber aerobic and faculta>ve
anaerobic bacteria by 100- to 1,000-fold. In total, the intes>nal microbiota consists of approximately 500–
1,000 species that, interes>ngly, belong to only a few of the known bacterial phyla. By far the most abundant
phyla in the human gut are Firmicutes and Bacteriodetes, but other species present are members of the phyla
Proteobacteria, Verrumicrobia, Ac>nobacteria, Fusobacteria and Cyanobacteria. Two gradients of microbial
distribu>on can be found in the gastrointes>nal tract. Microbial density increases both from the proximal to
the distal gut.
Many bacterial species are present in the lumen, whereas fewer, but well-adapted species, including several
proteobacteria and Akkermansia muciniphila, adhere and reside within the mucus layer close to the >ssue.
Coloniza>on of the host begins during birth, and the composi>on of the microbiota changes throughout host
development. In the adult intes>ne, a total of about 1014 bacterial cells are present, which is ten >mes the
number of human cells in the body. Their combined genomes contain more than 5 million genes, thus
outnumbering the host’s gene>c poten>al by two orders of magnitude. This large arsenal of gene products
provides a diverse range of biochemical and metabolic ac>vi>es to complement host physiology. In fact, the
metabolic capacity of the gut microbiota equals that of the liver, and the intes>nal microbiota can therefore
be considered as an addi>onal organ. These bacteria are essen>al for several aspects of host biology.
- 500-1000 species
- Anaerobes: 100 to 1000-fold more abundant than aerobes/faculta>ve anaerobes.
- Firmicutes and Bacteroidetes are most abundant phyla; inverse associa>on.
- Adult intes>ne 1014 bacterial cells – more than 5 million genes.
- Enormous metabolic capacity: considered as addi>onal organ.
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, Dis%nct gut enterotypes
Enterotypes: classifica>on of living organisms based on the bacteriological composi>on of their gut microbiota.
By combining 22 newly sequenced
faecal metagenomes of individuals
from four countries with previously
published data sets, here we iden>fy
three robust clusters (referred to as
enterotypes hereaoer) that are not
na>on or con>nent specific. We also
confirmed the enterotypes in two
published, larger cohorts, indica>ng
that intes>nal microbiota varia>on is
generally stra>fied, not con>nuous.
This indicates further the existence of
a limited number of well-balanced
host-microbial symbio>c states that
might respond differently to diet and drug intake.
The enterotypes are mostly driven by species composi>on, but abundant molecular func>ons are not
necessarily provided by abundant species, highligh>ng the importance of a func>onal analysis to understand
microbial communi>es. Although individual host proper>es such as body mass index, age, or gender cannot
explain the observed enterotypes, data-driven marker genes or func>onal modules can be iden>fied for each
of these host proper>es. For example, twelve genes significantly correlate with age and three func>onal
modules with the body mass index, hin>ng at a diagnos>c poten>al of microbial markers.
Well-balanced, defined microbial community composi>ons of which only a limited number exist.
A mutualis%c associa%on
Mutualism is a mode of symbiosis which is beneficial for both organisms. Host offers to the microbiota: o
nutrient-rich environment o maintained at constant temperature.
Bacteria are essen>al for several aspects of host biology. For example, they facilitate the metabolism of
otherwise indiges>ble polysaccharides and produce essen>al vitamins; they are required for the development
and differen>a>on of the host’s intes>nal epithelium and immune system; they confer protec>on against
invasion by opportunis>c pathogens; and they have a key role in maintaining >ssue homeostasis. Recent
studies have also revealed that the human microbiota influences the development and homeostasis of other
host >ssues, including the bone. The microbiota also benefits from this mutualis>c associa>on, as the
mammalian intes>ne is a nutrient-rich environment that is maintained at a constant temperature. However, it
is also a dynamic habitat that undergoes constant and rapid changes in its physiological parameters owing to
varia>ons in, for example, host diet, lifestyle, hygiene or use of an>bio>cs, all of which affect gut microbial
composi>on.
Microbial impact on host physiology
Important role of compara>ve studies between germ-free and conven>onally raised mice. The gut microbiota
has been shown to affect several aspects of host physiology; arrows represent either s>mulatory or inhibitory
effects of the gut microbiota on host physiological processes. The microbiota has been shown to influence
intes>nal func>on in the host, promo>ng gut-associated lymphoid >ssue (GALT) matura>on, >ssue
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