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Education & Practice Online First, published on February 28, 2017 as 10.1136/archdischild-2016-311643
RESEARCH IN PRACTICE

What is the microbiome?

Protima Amon, Ian Sanderson

Centre for Immunobiology, INTRODUCTION well as an influence on human behaviour,

Blizard Institute, London, UK There has been an explosion in our making it an essential organ of the body
Correspondence to understanding of the human microbiome without which we would not function
Dr Protima Amon, Centre for (the genome of all our microbes) in the correctly (figure 1).
Immunobiology, Blizard Institute, recent years. Advances in genome
4 Newark Street, London E1
2AT, UK; p.amon@qmul.ac.uk
sequencing technologies and metage- MICROBIOME COMPOSITION
nomic analysis (genetic study of genomes Unlike the host genome, which is rela-
Received 19 September 2016 taken directly from environmental tively constant, the microbiome is
Revised 23 January 2017 samples) have enabled scientists to study
Accepted 24 January 2017 dynamic and changes with early develop-
these microbes and their function and to ment, environmental factors such as diet
research microbiome–host interactions and use of antibiotics and especially in
both in health and disease. The human response to disease.4 The most dramatic
microbiome has an estimated 100 trillion changes in composition occur in infancy
microbes, the bulk of which live in our and early childhood.5 The intestinal
gut. This summary gives an overview microbiome of an infant is affected by
about what is known about the micro- gestational age (full term or premature),
biota (microbial community) in paediatric mode of delivery (vaginal birth or caesar-
practice. This short article is written for ean section), type of feed (breast milk or
the practising paediatrician. For a scien- formula feeds), maternal nutritional
tific overview, the reader is referred to status (overweight or undernourished)
reviews.1 2 An understanding of this and use of antibiotics.6 The complexity
complex ecological community is import- and plasticity of the infant microbiota
ant as it affects our patients, and manipu- during this early-life development is
lation of the gut microbiome has the believed to be important in maintaining
potential to be used in the treatment of homeostasis with the host’s immune
childhood diseases in the future. system and has an impact on health later
in life.7
THE HUMAN MICROBIOME: AN A healthy human gut can house at least
ORGAN IN ITS OWN RIGHT 1000 different species of bacteria, com-
The human microbiome is composed of prising of two major phyla, namely
communities of bacteria (and viruses and Bacteroidetes and Firmicutes. Elucidating
fungi) that have a greater complexity the microbiome composition in healthy
than the human genome itself. individuals is important to understanding
Large-scale metagenomic projects (com- what consequences changes in micro-
munity and environmental genomics), biome composition may have to human
such as the European Metagenomics of health and disease susceptibilities.
the Human Intestinal Tract and the Other microbes also live in the gut
Human Microbiome Project, have including viruses, fungi and archaea.
reported 3.3 million unique protein- However, research on them has been
encoding genes as compared with the small compared with that on bacteria.
entire human genome, which has around
23 000 genes. These studies have THE HUMAN MICROBIOME AND
described the beneficial functions of the DISEASE
normal gut microbiota on health down to The relationship between changes in
the genetic level.3 The human micro- microbiome composition and disease
To cite: Amon P, biome has extensive functions such as pathogenesis is uncertain. The challenge
Sanderson I. Arch Dis Child development of immunity, defence is to identify whether microbial imbal-
Educ Pract Ed Published
Online First: [ please include
against pathogens, host nutrition includ- ance is related to disease, sometimes
Day Month Year] ing production of short-chain fatty acids termed ‘dysbiosis’, and to be able to dis-
doi:10.1136/archdischild- important in host energy metabolism, tinguish between cause and effect. The
2016-311643 synthesis of vitamins and fat storage as following section highlights some

Amon P, Sanderson I. Arch Dis Child Educ Pract Ed 2017;0:1–4. doi:10.1136/archdischild-2016-311643 1

Copyright Article author (or their employer) 2017. Produced by BMJ Publishing Group Ltd under licence.
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Research in practice

Figure 1 The human microbiome plays an important role in control of vital homeostatic mechanisms in the body. These include
enhanced metabolism, resistance to infection and inflammation, prevention against autoimmunity as well as an effect on the gut–
brain axis. SCFA, short-chain fatty acid.

conditions seen in paediatrics that have been asso- is thought to play a crucial role. Studies in both
ciated with changes in the gut microbiota (table 1).8– humans and animal models have described changes in
16
the gut microbiota including a reduction in bacterial
Inflammatory bowel disease (IBD)—This is one of diversity and increased abundances of Proteobacteria
the most extensively studied human conditions asso- in preterm infants with NEC compared with healthy
ciated with the gut microbiota. The composition of preterm infants.20 However, the results have been
the gut microbiota differs between healthy individuals inconsistent across studies, and to date, no single
and patients with IBD both in terms of species rich- causative set of microorganisms has been identified.
ness (ie, numbers of bacterial species) and species Atopic diseases—Conditions such as eczema, asthma
abundances (ie, number of individuals per species). As and food allergies are increasing in incidence. This is
bacteria are identified by sequencing, rather than by often linked to the hygiene hypothesis. It is thought
functional characteristics in the culture laboratory, the that the lack of early-life exposure to microbial anti-
individual bacterial species or genus (depending on gens in hygienic developed countries alters the micro-
the classification of sequence data) are commonly biota composition of the infant gut, which disrupts
referred to as operational taxonomic units in micro- immune development causing allergic disease.21 For
biota research. example, species like Bacteroides fragilis reportedly
Studies have reported patients with IBD to have induces immunological tolerance through immune
decreased bacterial diversity, and reduced abundances receptor signalling pathways.22 Also the infant gut
of Firmicutes and Bacteroidetes and an increased microbiota is affected by environmental factors
abundance of Proteobacteria compared with healthy including pets, residing in rural homes and siblings
individuals.17 Latest research suggests that IBD patho- shown to have protective effects against asthma and
genesis is due to the interaction of environmental allergies.23 The concept that altered microbiome
factors (eg, smoking, diet and stress) and the host’s composition influences childhood allergic disease sus-
genetic susceptibility, which is influenced by com- ceptibility is further supported by data from epi-
mensal microbiota, which activates either pathogenic demiological studies that report higher prevalence of
or protective immune responses.18 Evidence from atopic diseases in infants delivered by caesarean sec-
mouse models provides further support for the role of tions, formula fed infants and those exposed to
gut microbiota in pathogenesis of IBD.19 antibiotics.24
Necrotising enterocolitis (NEC)—The pathogenesis Type 1 diabetes—The gut microbiota is involved in
of NEC is multifactorial although the gut microbiota regulation of the metabolic–immune axis.8 Research

2 Amon P, Sanderson I. Arch Dis Child Educ Pract Ed 2017;0:1–4. doi:10.1136/archdischild-2016-311643

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Research in practice

Table 1 Alterations in gut microbiota exert an influence on organ systems in the body leading to disease
Organ Examples of diseases linked with altered microbiota Microbiota-mediated changes References
9, 25
Brain Autism spectrum disorder Abundance of bacterial toxins
Disrupted fermentation
11, 12, 21, 23, 24
Lung Asthma Reduced immunological tolerance
Cystic fibrosis Altered gene expression
13
Heart Cardiovascular disease Production of proinflammatory metabolites
8
Pancreas Type 1 and type 2 diabetes Reduced insulin sensitivity
10
Liver Non-alcoholic fatty liver disease Altered bile acid metabolism
8, 14, 15
Adipose tissue Metabolic syndrome Reduced intestinal gluconeogenesis
Obesity Insulin resistance
17–20, 22
Gastrointestinal tract Inflammatory bowel syndrome Dysregulated immune response
Irritable bowel syndrome Altered mucosal barrier
Gut infections
16
Skin Acne Increased pathogenic strains
Eczema Dysregulated immune response
Allergic diseases

studies speculating the specific causative microbial Contributors PA wrote the manuscript and IS reviewed and
composition and function have not been consistent. provided critical comments.
However, Bifidobacteria is believed to be protective, Competing interests None declared.
while Proteobacteria is a reported risk factor. Patient consent Obtained.
Similarly, changes in gut microbiota caused by lifestyle Provenance and peer review Commissioned; externally peer
(eg, mode of delivery and diet) are known risk factors reviewed.
for the development of type 1 diabetes, like birth by Open Access This is an Open Access article distributed in
accordance with the terms of the Creative Commons
caesarean section reportedly increases the risk of Attribution (CC BY 4.0) license, which permits others to
developing type 1 diabetes by 20%.7 distribute, remix, adapt and build upon this work, for
Autistic spectrum disorder (ASD)—The gut micro- commercial use, provided the original work is properly cited.
See: http://creativecommons.org/licenses/by/4.0/
biota can influence human behaviour by modulating
the gut–brain axis via endocrine (cortisol), immune
(cytokines) and neural (vagus and enteric nervous
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What is the microbiome?

Protima Amon and Ian Sanderson

Arch Dis Child Educ Pract Ed published online February 28, 2017

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