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topic 4: bacterial communities/microbiomes and metagenomics - Coggle…
topic 4: bacterial communities/microbiomes and metagenomics
human health and the microbiome
the power of the community as an ecological bucket brigade rathe than of individual species
different taxa are interdependent and the overall ecological function of the community is relating on many different individual functions performed by different members
the end product from a function carried out by one member is the start product for another function carried out by a different member
HUMAN MICROBIOME
similar number of bacteria cells on you and in you than human cells
microbial communities are very much a part of us and their genes are part of out genome
basic questions
is there a human microbiome 0e. one shared by all humans but distinct from close relatives
how do changes in the microbiome affect susceptibility to different diseases?
can we optimise diet for the overfed and underfed based on a knowledge of gut microbiota
microbiome plays a protective - or contributory - role in many human diseases eg. obesity diabetes eczema, and gut flora also impacts on mood disorders, cognition and pain
the hygiene hypothesis
states that lack of early childhood exposure to infectious agents, symbiotic microorganisms (eg. gut flora, probiotics) and parasites increases susceptibility to chronic inflammatory diseases by suppressing development of the immune system
asthama, type 1 diabetes, cancer, ms, depression, autism
the microbiome at key body sites: gut, skin, vagina
maternal provisioning of the microbiome
the microbiome of insects
insects display a wide range of dependence on gut bacteria for basic functions
most insect guts contain relatively few microbial species as compared to mammalian guts, but some insects harbour large gut communities of specialised bacteria. honeybee adult contains c. 10^9 bacterial cells, also very compartmentalised - whereas an adult drosophila only has about 10^5 bacteria
other are colonised only opportunistically and sparsely by bacteria common in the environemnt
intimate (co-evolutionary) associated are much more likely in cases where there are dependable transmission routes such as the social insects
the most abundant gut communities are found in some detritivores and wood feeders, including termites, crickets, cockroaches ad wood boring and detritivorous beetles
these larger gut communtieisare usually associated with more compartmentalised guts
however even in asocial insect species, gut bacteria can contribute to nutrition, protection from parasites and pathogens, modulation of immune responses and communication
known functions of bacteria in insect guts
colonisation resistance against pathogens or parasites has been described for bumble bee and various mosquitos
the diet of honey bees derives solely from plants (nectar + pollen)
pollen is an important source of vitamins and amino cids, but pollen grains are tough and hard to digest (bees are one of the few insects that produce cellulase)
to get around this, bees process pollen by packing it in cells and adding various glandular secretions, sealing the cell with honey, leaving it to mature to become 'bee bread'
bee bread has more vitamins, and a different amino acid composition than pollen
a bacterial community is responsible for this transformation
bee bread is used as food throughout the hive - idea of a communal stomach
in drosophila commensal gut microbiota has been shown to be involved in intestinal cell renewal and growth
diet breakdown is byt eh characteristic gut microbiota in the handgun of termites. gut bacteria have also been shown to degrade toxins such as insecticides ingested with the diet
in a number of insects, gut bacteria produced molecules involved in infraspecific and interspecific communication such as pheromones and kairomones
the gut microbiome and behaviour in insects
certain molecular mechanisms governing behaviour in humans and insets are analogous
dor social insects, little is known about how microbial community structure impacts host Brian and behaviour, and how social interactions shape the assembly o microbial communities in return
in the lower termite reticulitermes sprats, conspecific intruders are more easily recognised when they are colonised by foreign gut bacteria promoting unfamiliar scents
the production of the pheromone guaiacol by gut microbes mediates the aggregation of lucsts into swarms
when bactrocera dorsals oriental fruit flies are depleted of their gut microbes, they prefer food containing a full complement of amino acids over other less nutrient rich options, even when this food is less readily accessible
social immunity in social insects
when a pathogen is detected within a colony, interactions change so that the degree of modularity increases - this limits the transmission of the pathogen
in some ant species infected individuals will leave the colony voluntarily to prevent further infection
dampwood termites that are infected with fungal spores exhibit a shaking behaviour that alerts other individuals to stay clear
environmental metagenomics
the nitrogen cycle
no single bacteria is completely capable of nitrification (oxidising ammonia to nitrate) - a key step in nitrogen cycle
carried out in two stages
a. degradation of ammonia to nitrite: performed by ammonia oxidising bacteria
beta-proteobacteria
gammaproteobacteria
and ammonia oxidant archae
nitrosopumilus maritimus
b. oxidisation of nitrite into nitrate is done mainly by
Nitrobacter
bacteria
bacteriophages as probiotics
competitive displacement
allows probiotic bacteria to establish a correct niche
phage probiotics
can target specific members of the microbiome without causing massive dysbiosis
lytic phages physically lyse cells
decrease pro inflammatory microbiota members and increase population of anti inflammatory bacteria
why do we need phage probiotics
gut microbiome is a fully established niche
decolonising microbiome is different from specifically removing a strain
phage specificity is great for MDR residential gut bacteria and AMR strains
phage cocktail
multiple phage use to enhance anti inflammatory activity of Bifidobacterium animalis
resistance evolved quite quickly for MDR strains - study had a high proportional of phage homology
main aim is that they recognise different receptors - using similar phages defeats that purpose
the impact of the covid-19 pandemic on the infant microbiome
before the age of three the infant microbiome is universe, dynamic and very sensitive to disturbances
pandemic impacts
decreased social interaction
decerease in commensal exposure and pathogen exposure that would normally train the immune system
increased c sections (mostly covid patients)
47% covid patients had preterm deliveries
increased exposure to pets also alters the microbiom
altered feeding patterns as virus could be passed through breast milk so decreased
increased broad spectrum antibiotic use that can be really significant in wiping out entire taxonomic groups in infant microbiomes
hygiene hypothesis
early life exposure to infectious agents has a significant impact on the immune system - updated to incorporate microbiome and the overly hygienic western culture impacts
role of microbiome in immune development
lymphatic system
training Ig groups
window for proper immune training to occur
e gallinarum as a gut pathobiont
enterococcus gallinarum
gram positive non spore forming motile
tends to be vancomycin resistant
yang et al 2022 - pathogenic potential due to within host solution featuring liver translocation
within host evolution can lead to acquisition of pathogenic behaviour
isolated species from diverse sources of autoimmune prone mice (known to translocate there initially)
isolates very tightly clustered, likely from same lineage
high resolution results using further sequencing methods
how have transitions to agriculture shaped our oral microbiomes - perspectives from filipino hunter gatherer communities and ancient microbiomes
oral microbiome
2nd most diverse human microbiome
1000+ species present
limited physiological function
inhibits pathogen colonisation
nitrate metabolism potential implication in blood pressure
oral dysbiosis
extremely common
linked to lots of common oral disease
dental caries
periodontitis
human dietary trnaisionts
neolithic transition to agriculture
19th century Industrial Revolution
key concepts of metagenomics
the application of modern genomics techniques to the study of communities of microbial organisms directly in their natural environments, bypassing the need for isolation and lab cultivation of individual species
first culture independent studies performed using universal 16S rRNA PCR primers from environmental samples
it is not possible to grow ~99% of soil bacteria in laboratory
human gut bacteria ~50-60% of taxa are culturable
the use of 16S rRNA for metagenomics was adopted due to its establishment as a universal phylogenetic marker
a number of limitations
universal primers may not be universal
multiple copies of 16s rRNA exist in a single genome - results are at best semi quantitative
only hints at species diversity, providing no evidence as to metabolic diversity
more recently metagenomics has utilised
sequencing of total community DNA
sequencing short random reads of the DNA then trying to piece it all back together -
shotgun metagenomics
crucial first step in organising metagenomics data is
binning
involves the subdivision of the data into different phylogenetic groups
depending on quality of the data, the read length of the data, and how exotic the community is, phylogenetic resolution can range from genus to kingtom
three broad categories used
similarity based (eg. BLASTing sequencing against Pfam (protein) or NCBI (nucleotide) databases. reliant on reference genomes in the existing databases which are heavily biased towards pathogenic and cultivatable organisms
composition based methods
gc content
codon bias
oligonucleotide frequences
methods based on read frequency
metagenomic approaches are important because
evolution and biodiversity
understand the degree of co-evolution between eukaryotes and their associated microbiome
metagenomics has transformed our view on biodiversity - eg. led to the discovery of the CPR bacteria (candidate phyla radiation)
35 new phyla, encompassing >15% of bacterial domain, exhibiting endosymbiont like features
public health
understanding the role of the microbiome in human development and health
ecology
understand and compare species richness and community ecology
alpha diversity within habitat
beta diversity between habitats
agriculture
understand how bacterial soil communities can protect plants against pathogens (suppressive soils)
industry
discover new genes and proteins of relevance to industry, eg. bioremediation
biochemical cycles
the role of bacterial communities in the carbon and nitrogen cycles
most metagenomics studies have revealed a massive amount of diversity in natural bacterial communtiies
it is very unusual to be able to assemble complete genome sequences as this would require a very large number of reads for a single "species"
if there are 1000s of species the overall size of the dataset required is prohibitive as the most abundant species will be sequenced over and over again and the rare species missed entirely
recent advances in 'Long Read' platforms have made it much easier to generate complete assembles from metagenomics data (metagenome-assembled genomes (MAGs))
environmental metagenomics
examples of metagenomics studies
environmental samples
acid mine drainage
focus of one of the first metagenomics studies in 2004
one of the main discoveries was nitrogen fixation
not carried out by any of the main five taxa, but by a previously unknown "keystone" species (one of a disproportionately large ecological significance given its low abundance_
Leptospirillum ferrodiaztrophum
carried the
nif
gene for nitrogen fixation and was cultured by providing N2 as the only nitrogen source (so non-nitrogen fixers would not grow)
the presence of a gene doesn't tell you that it is being expressed in the sampled environment
metaproteomic analysis off these biofilms have now also been carried out, and about half of the proteins predicted from the DNA sequences are confirmed to be produced
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metal mining exposes sulphide minerals. microbial communities then oxidise these minerals to result in highly acidic solutions collectively known as acid mine dtainage
often contains toxic metals, such as copper or iron. these combined with reduced pH have a detrimental impact on aquatic environemnts
microbial communities in AMD have been characterised using metagenomics in order to understand:
the metabolic processes leading to acidification (eg. nitrogen fixation, sulphur oxidation and iron oxidation)
how these communities tolerate such highly acidic conditions
bacterial community is very simple - provides a perfect entry level system into metagenomics
consists of 5 major taxa - three bacterial and two archaean. same 5 taxa form a biofilm in multiple AMD sites
simplicity of the community meant that "shotgun sequence" data was sufficient to fully assemble two of these genomes, and partially complete the other three
carried out using initial binning procedures based on composition and frequency of recovery
geochemistry of habitat is also very well characterised prior to the study
ocean
the microbiome of the oceans
each microbe is separated by about 100-200 body lengths from the nearest neighbour
not a soup - highly structured according to
temperature
pH
salinity
organic matter
light availability
broadly Marine microbes can be divided into planktonic cells and cells associated with a surface (organic matter or another cell) - these can be crudely separated by size fractionation
between 20-50% of all bacterial cells in the ocean are lysed every day by phage
microbial communities have essential roles in ocean ecology and planetary health
participate in nutrient cycles, remove huge quantities of carbon dioxide from the air and support ocean food webs
Better understanding of the ocean microbiome could underpin strategies to address environmental and societal challenges, including achievement of multiple SUSTAINABLE DEVELOPMENT GOALS
metagenomic data has identified 200000 different types of virus, 35,000 different taxa of bacteria and archaea and 150,000 taxa of micro eukaryotes
responsible for almost half of the global primary production
high abundance of genes encoding rhodopsin proteins
rhodopsin allows cells without photosynthetic machinery to harvest energy through sunlight-driven proton pumping
previously only found in microbes living in extreme enviornments
now known that >40% of bacterial cells in the surface ocean have the capability of proteorhodopsin-based energy transduction
study on genetic diversity rather than community function
size fractionation and shotgun sequencing survey of the Sargasso Sea (previously thought to be relatively low in diversity)
one of the more controversial claims from the study was the identification of genes corresponding to a burholderia genome
genus was not thought to be one that thrived in the marine environment
sequences identical to a widespread clone of B cepacia
clone does not grow in sea water, but is known to be a common contaminant of medical devices
likely explanation is contamination during the sampling on the boat via the use of a Vicks stick
reported 1,214,207 putative protein coding genes
1412 different rRNA genes in microbial plankton in reasonable agreement with the diversity of protein coding genes which suggested ~1800 species (148 of which were new to science)
however the complexity of the data meant that no complete genomes and very few large contains could be assembled
wastewater
also contains antibiotics, and their presence in the environment can lead to more resistant bacteria
represents a key route by which antibiotic resistant (or otherwise dangerous) bacteria might enter the environment
metagenomics is increasingly used to understand and monitor the type and quantity of bacteria that are released into the environment, and also the type and quantity of individual genes (such as resistance genes)
outstanding questions relating to wastewater and AMR
how efficient are wastewater treatment plants at removing
antibiotics in the wastewater
antibiotic resistant bacteria in the wastewater
could the concentration of bacteria/antibiotics at wastewater treatment plants be acting to drive the evolution of more resistance?
how well does resistance data from sewage correlate with data from clinical surveillance?
does the abundance of resistance genes in wastewater correlate with the concentration of antibiotics?
how do we gauge the risks to public health and develop an informed regulatory framework?
use metagenomics to analyse wastewater at different steps of the treatment process in three different treatment plants in Sweden - also measured concentrations of antibiotics, biocides and metals
they found that there was already a major shift in bacterial community (compared to face samples) in the wastewater pipes before they reached the treatment plants (represented by a shift from obligate anaerobes such as bactericides to facultative anaerobes such as acinetobacter)
treatment process is not efficient at removing resistance genes but it can be quite good at removing resistant bacteria
some resistance genes were even enriched - notably the plasmid borne OXA-48 which encodes a carbapenemase and is commonly carried by Klebsiella, E coli and other enterobacteriacae
a high prevalence of
bla
OXA48 in
Klebisella ornithinolytica
and related species in hospital wastewater in south west England
looked at the abundance of different antibiotic resistance genes over different stages of water treatment
they found that the relative abundance of total ARGs decreased by ~50% from the influent to the effluent, with each sampling lcoation defined by a unique resistor (ie. total ARG) composition. however, 90% of the ARGs found in the influent were also detected in the effluent.
global monitoring of AMR based on metagenomics analyses of urban sewage
metagenomic analysis of untreated sewage from 79 sites in 60 countries
differences in abundance and diversity of AMR genes between different continents
differences not correlated with antimicrobial use but with socio-economic, health and environmental factors
soil
thermal vents
hot springs
whale fall
host associated
humans
mouth
skin
gut
respiratory
female genital tract
termites, bees, aphids
earthworms
coral
the holobiont and the human microbiome
host associated microbiomes and "the holobiont"
the whole host-microbiome ecosystem has been referred to as the
holobiont
with all genes from the host and the microbiota consituting the
hologenome
proponents of the holobiont view argue that the composite phenotype of both host and microbiota consistutes a single "selective unit"
however selection can operate over multiple levels simultaneously. the holobiont, the individual host organism, each of the diverse microorganisms, and the multitude of genes present in the hologenome all represent units of selection
holobiont should not be thought of as a "superorganism"
it is not obvious where the boundaries of the hologenome lie
microbiome communities fall in to three types
well defined, host controlled populations of relatively low diversity
complex assemblages that, to some degree, persist through time
entirely transient, diet-controlled populations
one view is to equate host genes with individual components ("species") of the microbiota, such that key obligate species are analogous to conserved genes and more transient symbiotic species are more like weakly selected genes
morris JJ. what is the hologenome concept of evolution
also holobionts themselves can interact eg. pollinators and flowers - should these then be combined into a single hologbiont?
but how far can a single holobiont realistically extend? a whole forest?
human microbiome
similar number of bacterial cells on you and in you than human cells
human gab consists of at least 1800 genera and approximately 15,000 - 36,000 species of bacteria (100x more genes than human genome)
humans plus their microbial communities have been considered as a holob8ont
remains unclear if there is a standard core human microbiome
main foci for studying the human microbiome have been on 5 main body sites
mouth
skin
vagina
gut
respiratory tract
key questions relating to the human microbiome and health
how do changes in the microbiome affect susceptibility to different diseases?
can a better understanding of the human microbiome lead to better therapies and interventions?
key concepts relating to the human microbiome
body sites characterised by signature taxa eg. oral cavity dominated by
Streptococcus
considerable variation between healthy individuals, but the functional relevance of this variation is largely unknown. even identical twins share less than 50% of their bacterial taxa at the species lebel
HGT within gut microbiota occurs frequently - this may have implications for the host (eg. the emergence of new antibiotic resistant strains via plasmid transfer)
structure and functional variation of a microbial community may associated with disease susceptibility or other phenotypic characteristics (although this association is not necessarily causal)
first metagenomics study on the human microbiome was published in 2006 and involved sequencing the bacterial communities from the colons of two healthy adults
high proportion of bacterial genes discovered for
breakdown of plant-derived polysaccharides eg. cellulose, starch, pectin
detoxification of xenobiotics eg. something produced by a different organism such as antibiotics
synthesis of essential vitamins and amino-acids
10% of the metabolites in the mammalian blood flow are of bacterial origin
many species of the human microbiome remain uncharacterised, particularly within non western regions
large scale metagenomic assembly uncovered thousands of new human microbiome species
non westernised populations harbour a large fraction of the newly discovered species
microbiome and disease
: obesity
2006: 16S rRNA cloning based studies looked at the human gut microbes: relative proportion of bacteroidetes lower in obese people, suggesting that a high abundance of this taxon is associated with weight loss
2010: confirmed in studies of mice: obese mice found to have more
firmicutes
and fewer
bacteroidetes
than their genetically-lean siblings
germ free mice colonised with microbiota from oases mice gained more weight than those colonised with microbiota from lead mice
2018: the proportion of firmicutes in the gut of obese children was found to be increased, and the proportion of bacterioidetes was decreased
the identification of a microbial component to obesity leads to potential therapeutic implications, although it is often unclear whether association between a change in the microbiome and a clinical state is causal
a possible link between a high abundance of Firmicutes and Obesity
the action of gut microbiota is needed to digest some polysaccharides
firmicutes convert polysaccharides into monosaccharides and short chain fatty acids
these SCFAs are able to bind and activate two GPCRs of the gut epithelial cells
the activation of these receptors induces peptide YY which decreases gut motility, slowing intestinal transit and increasing nutrient uptake
type 1 diabetes
an autoimmune disease associated with unstable gut communities and decreased diversity
there appears to be large scale replacement of firmicutes species with bacteroidetes species
irritable bowel disease (IBD)
is associated with decreases in members of anti inflammatory clostridia and increases in e coli
clostridium difficile
infection
CDI is a bacterial infectious disease of the gastrointestinal tract caused by c.dif
occurs when patients receive antibiotics which eradicate their normal enteric gut bacteria and allow the opportunistic pathogen to proliferate
stool from patients with recurrent cdi showed a dramatic loss of microbial diversity compared to healthy group
increasingly treated using FMT - up to 90% success rates
metagenomics to check the persistence of transplanted microbiota in the human gut
donor and native microbial strains coexist for at least 3 months after faecal microbiota transplantation (FMT)
outocmes varied across donor-recipient pairs - individual patterns of establishment and donor-recipient compatibilities
introduced strains more likely to establish if the species were already present in the resident gut microbiota than if the donor species were novel
dividing gut communities into "enterotypes"
combining 33 newly sequenced faecal metagenomes of individuals from four countries with previously published data sets, three robust clusters were identified that are not nation or continent specific
three distinct robust clusters driven by discriminative genera
bacteroides
prevotella
ruminococcus
communities vary by function - unclear on explanation - may be as important to medicine as blood groups
more on the human microbiome
- what's there and what is it doing
human microbiome sample
extract dna
which organisms are present?
Amplify 16S rRNA gene by PCR and sequence
bin similar sequences into OTUs
compare OTUs to databases
identify OTUs in sample and relative frequencies
phylogenetic view of community composition
what are the functions of the community?
sequence total DNA
compare sequences to reference genomes
identify microbial sequences, variants and polymorphisms in sample
compare sequences to databases
identify genes, pathways and relative frequencies in sample
assemble into contigs (or try to)
the gut microbiome also plays a role in
development
lifespan and aging
immunity
mood and behaviour
the gut microbiome, stress and behaviour: the brain-gut axis
recent studies using germ free (gnotobiotic) animals indicate a role for the gut microbiota in the regulation of mood cognition and pain
modulation of the gut microflora may represent a novel strategy for developing therapeutics for complex stress related CNS disorders
specifically the brain gut axis describes the complex bidirectional communication between the ins and the go treats - is responsible for regulation of digestive function, satiety and hunger
communication between gut and brain occurs via neuronal routes, humour signalling molecules and hormonal components
impairements in brain-gut axis signaling are associated with gut inflammation, chronicle abdominal pain syndromes, easting disorders, stress and altered behaviour
vagus nerve
major nerve of the parasympathetic division of the ANS and has been shown to be an important pathway for bidirectional communication between the gut microbes and the brain
treatment with lactobacillus rhamnosus in rodents induced alterations in GABA receptor expression in the Brian and reduced stress induced corticosterone and anxiety and depression related behavious
effects dependent on vagus nerve integrity
the role of serotonin
important function in mood and cognition
95% of the serotonin in the body is found not in the brain but in the gut, where it plays a role in the regulation of GI secretion, motility (smooth muscle contraction and relaxation) and pain perception
alteration of the functioning of this neurotransmitter may explain the high rate of comorbidity between pathological symptoms of the gut and mood disorders, and why SSRIs (which alter the functioning of serotonin) can alleviate the symptoms of irritable bowel syndrome as well as depression
serotonin is synthesised from tryptophan and the gut microbiota (in particular bifidobacteria) plays a key role in tryptophan metabolism
this provides a direct link between gut microbiota and mood disorders
germ-free mice/.mice treated with antibiotics, show decreased anxiety in stressful environments (which is detrimental to the host). colonisation with healthy microbiota, particularly lactobacillus and bifidobacterium can reverse these effects
microbiome of the vagina
mutualistic interactions with bacteria that provide protection against disease (first line of defence)
lactic acid bacteria produce lactic acid resulting in a low pH environment that restricts the growth of pahtogens
conserved community function despite high levels of community diversity
composition of vaginal microbial communities is influenced by oestrogen levels and by aging, the menstrual cycle, pregnancy and possible stress
variation of the vaginal microbiome in women of different ethnic groups
bacterial communities were characterises (16S rRNA) from 396 healthy women of four ethnic groups
five different types of community were found, four of which were dominated by lactic acid bacteria, indicating the importance of the production of lactic acid as a community function. the 5th community type didn't contain an abundance of LAB and this accounted for 25% of women
group 4 is the diverse community lacking in LAB - this is more common in black and hispanic women than white or asian women
the prevailing view that species of lactobacillus are both necessary and sufficient for maintiaining health may well be overly simplistic because functionally equivalent species may in fact substitute for species of lactobacillus
found an unexpected prevalence of prevotella species which positively affects the growth of gardnerella vaginalis and peptostreptococcus anaerobius (linked to bacterial vaginosis) by providing these bacteria with key nutrients
maternal provisioning of the microbiome in humans
for a long time it was believed that humans ae sterile immediately before birth
challenged in recent years, and some studies purport to show maternal provisioning of microbes from the mother
enterococcus fecalis, staphylococcus epidermidis and e coli having been isolated from the meconium of healthy neonates
some evidence that the placenta is not colonised by microorganisms in healthy preganancies
analysed placenta samples both shotgun metagenomics and 16S rRNA gene amplicon sequencing, to account for technique-specific potential biasess
used negative and positive controls produced by spiking samples with a known amount of the bacterium salmonella bongori, to calibrate the abundance of other microbes that might be in the samples
the results clearly showed the placenta does not harbour microbes during healthy pregnancy, and contamination issues were a convincing explanation for the presence of any detected bacteria
c section and the acquisition of the early microbiome
the neonate immune system is immature and this helps the rapid establishment of a microbiome
the microbiota of babies delivered vaginally are dominated by lactobacillus, prevotella and atopobium whereas babies delivered by c section have a microbiota that more closely resembles that of the skin community (not necessarily from the mother) with staphylococci being a dominant early memebr
although infects delivery day c section exhibit a delayed acquisition of the members which dominate the adult microbiome, these microbiomes do eventually catch up that of their vaginally delivered counterparts
some evidence that infants delivered by c section are more likely to suffer from allergies, asthma inflammatory bowel disease and diabetes later in life. maternally provisioned vaginal or feral microbes may help illicit immune maturation
even possible that changes in the vaginal microbiome during pregnancy (increase of certain lactobacillus species) function to establish a rapid gut microbiome in the neonate
preterm infants lack tow of the main "good" bacterial genera in healthy term infants; bifidobacterium and lactobacillus, instead displaying a dominance of the proteobacteria
microbiota diversifies over the first few weeks of life from 100 species at birth to form a complex anaerobe dominated microbial community at weaning
studies comparing infants feral microbiota with that of the mother at one and 11 months after birth suggests that early colonisers are readily replaced by bacteria from the external envirpnemnte
each dietary juncture as the infant progresses towards adulthood is paralleled by shifts in th microbiota and a predominance of genes specialised towards microbial digestion of that diet
sources of microbial transmission in humans from mother to child
mouth
amniotic fluid bacteria with an oral origin include fusobacterium nucleate, streptococcus spp, bergeyella spp, porphyromonas gingivalis, rothia dentocariosa and fifactor alocis
oral bacteria are likely transmitted to the uterus Bia the blood stream, especially if gingiva inflammation is present
internal breast
aseptically0colected breast milk contains 100-600 OTUs. abundant genera include streptococcus, staphylococcus, serrate, corynebacteria, lactococcus, weisella, aleconostoc
an entero-mammary pathway brings gut bacteria to the mammary gland via lymph and blood circulation. external sources of milk microbes include the maternal skin and infant oral cavity
breast milk contains microbes, metabolites, IgA and immune cells as well as cytokine. these work together to shape the microbiota and the response of the host to these microbes
external breast
the sebaceous skin of the breast is an external source of microbes for breast milk but may also provide skin bacteria not common in milk to the suckling infant
uterus
contrary to sterile womb paradigm, bacteria are found in umbilical cord blood, amniotic fluid, focal membranes and meconium of healthy term infants
meconium microbiomes are dominated by enterobacteriaceae and lactic acid bacteria
microbes likely fain access to the womb through ascension from the vagina and.or through the blood stream for bacteria of intestinal or oral orgiign
vagina
vaginal microbial communities vary significantly among women of different ethnicities and count influence which microbes are transferred to an infant
the vaginal microbiota becomes less diverse during pregnancy while certain lactobacillus species become enriched
the initial microbiota of vaginally born infants resembles that of their mothers vagina, while that of c section infants is dominated by skin microbes not related to those of theyr mother