Human microbiome extra reading Flashcards
The Human Intestinal Microbiome
in Health and Disease
The new england journal of medicine
Biomarker sequencing: The process of cataloguing microbes in a mixed-species community through
analysis of sequence variation in a single ubiquitous gene.
Holobiont: The totality of organisms in a given ecosystem (e.g., the shared human and microbial
ecosystem); also called a superorganism.
Metabolome: The complete set of small-molecule chemicals found in a biologic sample.
Metagenome: All the genetic material present in an environmental sample, consisting of the genomes of many individual organisms.
Methanogenic archaea: Methane-producing microbes of the ancient Archaea kingdom.
Microbiome: The collection of all genomes of microbes in an ecosystem.
Microbiota: The microbes that collectively inhabit a given ecosystem.
Pathobionts: Typically benign endogenous microbes with the capacity, under altered ecosystem
conditions, to elicit pathogenesis.
Prebiotics: Nutritional substrates that promote the growth of microbes that confer health benefits
in the host.
Probiotics: Live microbes that confer health benefits when administered in adequate amounts in
the host.
Synbiotics: Formulations consisting of a combination of prebiotics and probiotics.
Functions of the microbiome
More than a billion years of mammalian–microbial coevolution has led to interdependency.
As a result, the intestinal microbiota play a critical role in the maturation and continued education of the host immune response:
Protection against pathogen overgrowth
Influence host-cell proliferation
Regulate intestinal endocrine functions
Neurologic signaling
Bone density
Provide a source of energy biogenesis (5 to 10% of daily host energy requirements)
Biosynthesize vitamins
Neurotransmitters
and multiple other compounds with as yet unknown targets
Metabolize bile salts
React to or modify
specific drugs
Eliminate exogenous toxins
Studies of the microbiome
the focus of research into a broad range of chronic diseases, including: cancer and diseases with inflammatory metabolic cardiovascular autoimmune neurologic, and psychiatric components.
Gut Microbiota across the Ages
The in utero environment has, until relatively
recently, been considered sterile. However, DNA based microbiota studies have detected bacterial species in the placentas of healthy mothers, in amniotic fluid of preterm infants, and in meconium. At parturition, the mode of delivery influences postnatal microbial exposure.
The gut microbiota of vaginally delivered neonates is taxonomically similar to the maternal gut and vaginal microbiota
This study also showed that the composition of the gut microbiota in infants changes to resemble adult microbiota in association with the cessation of breast-feeding
Childhood:
The rapid rate of expansion in bacterial diversity that is observed in infancy slows in early childhood (between 1 and 5 years of age)
In preadolescents, as compared with adults, the gut microbiota are enriched in anaerovorax, bifidobacterium, faecalibacterium, and Lachnospiraceae and for pathways involved in vitamin B12 and folate biosynthesis; folate biosynthesis is also characteristically increased in babies as compared with adults
Adulthood: Healthy adult gut microbiota are dominated by Bacteroidetes and Firmicutes but also include smaller proportions of Actinobacteria, Proteobacteria, and Verrucomicrobia, as well as methanogenic archaea (primarily Methanobrevibacter smithii), Eucarya (predominantly yeasts), and multiple phages The microbial collection in each person is unique. Despite this taxonomic interindividual variation, the functional capacity of the adult gut microbiota is relatively consistent across healthy persons, with pathways involved in: Metabolism Fermentation Methanogenesis Oxidative phosphorylation Lipopolysaccharide biosynthesis
Old age:
In the elderly, the gut microbiota become compositionally unstable and less diverse, events that are associated with coexisting conditions and age-related declines in immunocompetence
Influences on the Gut Microbiota
Endogenous (internal) and exogenous (external) factors influence the gut microbiota:
Mode of delivery
Host genetic features
Host immune response
Diet (including dietary supplements, breast-feeding, and formula-feeding)
Xenobiotics (a chemical substance found within an organism that is not naturally produced, including antibiotics)
Other drugs
Infections
Diurnal rhythm
Environmental microbial exposures
Some of these are risk factors for childhood diseases such as obesity and allergy
Recently, three compositionally, functionally, and metabolically distinct gut microbiota states were described in babies who were approximately 1 month of age; one of these conferred a significantly higher relative risk of allergy in 2-year-old children and of asthma in 4-year-old children.
In ex vivo assays, the associated products of the high-risk microbiota state induced an increase in CD4+ cells that produce interleukin-4 , increased interleukin-4 production, and reduced the number of CD4+CD25+FOXP3+ cells, indicating that perturbation of early-life gut microbiota may contribute to subclinical inflammation that precedes childhood disease development
Diet and Other Environmental Influences
Meat consumption selectively enriching for bile metabolizing microbiota, the expansion of which
is associated with inflammatory bowel disease, and vegetable consumption increasing plant polysaccharide-fermenting organisms.
It has also been reported that persons have very different metabolic responses to identical meals
Emerging data also indicate that the microbiota is distinct in house dust from residences associated with protection against, or development of childhood
allergic disease
Oral supplementation or nasal exposure of mice to protective house dust prevents airway sensitization,
indicating that exposure to environmental microbes modulates mucosal immunity
Other influences on the gut microbiota include pathogenic infection. For example, Vibrio cholerae initially dominates fecal bacterial communities during a
cholera infection, and clinical recovery is associated with a restoration of the preinfection composition of the gut microbiota resembling that observed in infancy
Drug induced viral suppression of HIV replication is successful, the gut microbiota of patients with HIV infection frequently remain perturbed, a feature related
to the degree of peripheral immune activation
Dysbiosis of Gut Microbiota
Association studies in humans and rodents have shown disease-related dysbioses across a wide spectrum of common chronic disorders, including atherosclerosis, metabolic disorders, asthma, and autism spectrum disorder
Many clinical studies have used targeted sequencing of
16S ribosomal RNA (rRNA), which although economical, is limited to assessment of bacterial taxonomic composition.
However, PICRUSt (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States), an algorithm that uses 16S rRNA sequence data to predict conserved bacterial functional capacity, permits
in silico (via computer) bacterial metagenomic analyses. Studies have applied high-throughput methods of untargeted DNA sequencing in conjunction with
the newly expanded human microbial gene catalogues, draft genomes, and new genome assembly, permitting microbial species-level and strain-level resolution and detailed functional annotations of microbial communities
Studies have addressed human obesity, kwashiorkor, childhood asthma, massive weight loss after bariatric surgery, and the insulin-resistant state of third-trimester pregnancy.
In addition, a study combining analyses of human host insulin sensitivity, fasting serum metabolome, and the gut microbiome with findings from experiments in mice suggests that specific bacteria may cause insulin resistance.
Also, transplantation of fecal microbiota from healthy lean human donors to obese patients with insulin resistance is associated with improvement in whole-body insulin sensitivity in the recipients, further supporting the notion that microbiota-associated
phenotypes may be transferred and reproduced,
at least to some extent, in a genetically susceptible recipient
Problems with microbiome study
The study of the gut microbiome in human health and disease remains fraught with challenges.
These include:
Major intraindividual variability of the microbiome
with changes in lifestyle, reproducibility issues, and statistically underpowered case–control studies
in addition to studies in which the cases and controls are phenotypically, etiologically, and microbiologically heterogeneous (two or more things are unlike in substance or nature)
lack of stratification based on drug treatment, which potentially confounds analytical outcomes, and a lack of statistically powered longitudinal and interventional
studies involving study participants with well defined diseases or preclinical at-risk conditions
Despite evidence linking dysbiosis of the gut microbiome with disease manifestations at sites distant from the gut, most studies have not explored mechanisms outside the affected site
nor have they considered the effect of the microbiome and its varied products on the multitude of molecular pathways potentially involved.
Stool samples are often used as proxies for the microbial content of the entire gastrointestinal tract, which covers more than 30 luminal intestinal square meters and contains distinct macroecosystems and microecosystems.
Moreover, since bacterial genome databases are incomplete, the majority of genes in human gut microbiomes cannot be functionally assigned, a problem that is exacerbated by our lack of knowledge of both the dynamic transcriptional and translational activities of the gut microbiome and the biologic effect of the enormous numbers of polymorphisms and other
structural variations of the microbiome.
Finally, most studies have focused primarily on bacterial
species rather than on the functional interplay among bacteria, archaea, viruses, fungi, and eukaryotes throughout the human gastrointestinal tract
‘Common ground’ hypothesis
This hypothesis posits that:
- Various endogenous or exogenous factors, or combinations of such factors, trigger an increase in gut permeability (“leaky mucosa”) or mucosal inflammation either directly or through selective pressure on the gut microbiota;
- In persons who are genetically susceptible to one
or more chronic disorders, the subclinical intestinal abnormalities favor the expansion of opportunistic microbes and the transition to pathobionts - Microbial gene products from the dysbiotic pathobiont gut communities promote local or systemic morphologic and functional changes that are pathogenic
- That once disease-associated gut microbiota have
been expressed in a genetically susceptible person, they can be transferred from that person to a genetically sensitive recipient, acting as a continual and contributing pathogenic mechanism
Therapeutic and Preventive Opportunities
Infection with Clostridium difficile
Fecal microbial transplantation for severe cases
of recurrent diarrhea caused by antibiotic-resistant C. difficile infection is efficacious in approximately 90% of affected patients. This finding remains the prime proof of principle that healthy gut microbiota can reproducibly correct a severe and specific microbial dysbiosis and that transplantation of healthy microbiota is therefore medically actionable
IBD
For chronic inflammatory bowel diseases, clinical remission is less predictable, and success rates are more modest.83 Because many persons dislike aspects of fecal microbial transplantation and, more important, because transplantation carries the potential risk of transferring to recipients infections and other phenotypes that are clinically silent in donors, several
preclinical and clinical initiatives are under
way
Atherosclerosis
Studies have shown that gut microbiota metabolism of dietary phosphatidylcholine and l-carnitine produces trimethylamine, which subsequently undergoes flavin monooxygenase 3–dependent oxidation to trimethylamine-N-oxide (TMAO); elevated circulating levels of TMAO appear to be a strong risk factor for atherosclerosis in humans and animals.
A study of a mouse model showed how oral application of a structural analogue of choline, 3,3-dimethyl-1-butanol, inhibited commensal microbial trimethylamine production, lowered plasma TMAO levels, and prevented atherosclerosis without apparent side effects, despite a pro-atherosclerosis diet
Antibiotics Bacteriocins represent another class of products of the mammalian gut microbiota. These high-potency peptide toxins may offer leads for the development of species-specific or strain specific alternatives to current antibiotics
Autism
the maternal immune activation (MIA) model. The offspring of MIA mice exhibit autistic-like behavior, gut microbiota dysbiosis, increased gut mucosa permeability, and an altered serum metabolome, with an increase in 4-ethylphenylsulfate
Injection of this neurotoxin into the blood of healthy mice resulted in an anxiety phenotype. Feeding MIA mice a strain of Bacteroides fragilis ameliorated the intestinal dysbiosis, restored the integrity of the mucosal barrier, and diminished behavioral abnormalities in conjunction with significant decreases in circulating 4EPS levels.
Allergy
Similar studies have been performed in mouse models of allergic airway disease in which oral supplementation
with Lactobacillus johnsonii, a human vaginal commensal species, provides airway protection against
both allergen challenge and respiratory viral infection.
Cancer
Of specific interest is the capacity of some commensal bacteria to modulate the tumor microenvironment and anticancer therapies
A recent study comparing melanoma growth in mice with distinct gut commensals support the hypothesis that certain microbes enhance the efficacy of cancer immunotherapy.
Oral administration of a mixture of bifidobacterium species modulates the activation of dendritic cells, which in turn helps improve the effector function of tumor-specific CD8+ T cells.
Bifidobacterium supplementation improved tumor
control to the same degree as anti–PD-L1 (programmed cell death ligand 1) therapy (checkpoint blockade) in an animal model, and combination treatment (bifidobacterium supplementation and anti–PD-L1 therapy) almost completely eliminated tumor expansion.
Studies in both humans and mice have shown that the antitumor effect of treatment with antibodies against cytotoxic T-lymphocyte–associated antigen 4 (CTLA-4)
is potentiated by specific members of the gut
microbiota.
T-cell responses specific for B. thetaiotaomicron or B. fragilis were associated with the efficacy of CTLA-4 blockade, and the introduction of B. fragilis to tumorigenic, germ-free mice, which do not have a response to CTLA-4 treatment, brought about a response.
The discovery of a tumor-inhibiting molecule produced by a probiotic strain was recently made. L. casei strain
ATCC 334 produces ferrichrome, which has been
shown to inhibit progression of colon cancer by means of apoptosis mediated through the c-Jun N-terminal kinase pathway.
Inflammatory and Metabolic Diseases
A mixture of 17 human clostridium strains has been shown to diminish the severity of experimentally induced allergic colitis in rodents through mechanisms that promote the expansion and activity of Treg cells
Lactococcus lactis expressing interleukin-10, an
antiinflammatory cytokine, has been shown to be safe in a phase 1 clinical trial and was effective in reducing inflammation in mouse models of colitis and allergic airway inflammation
Within the area of metabolism, studies suggest that proteins secreted by E coli, including ClpB, a chaperone protein and a mimic of alphamelanocyte–stimulating hormone, affect food intake and meal patterns in rodents, with the magnitude of the effect depending on the bacterial growth phase.
E. coli proteins stimulated intestinal hormones, glucagon-like peptide 1 (a potent antihyperglycemic hormone), and peptide YY (produced in the ileum in response to feeding) and activated anorexigenic pathways in the brain, inducing those that mediate satiety.
In a preclinical setting, an E. coli strain was genetically manipulated to biosynthesize precursors of the anorexigenic N-acylethanolamides, which are produced
in the ileum in response to feeding and serve to
reduce food intake and, thus, obesity
In studies of rats with diabetes, commensals engineered to synthesize and release glucagon-like peptide 1 have been shown to stimulate epithelial secretion of insulin, thereby improving carbohydrate metabolism.
Type 1 Diabetes
A study gave a prebiotic supplement (administered between 0 and 27 days after birth) was associated with a 60% reduction in the risk of pancreatic islet autoimmunity before school age, as compared with either no supplementation or intervention after 27 days, with the association accounted for by high-risk children
with the HLA-DR3/4 genotype. This finding raises the question of whether the introduction of more targeted formulations in neonates who are at increased risk for autoimmunity would prevent the subsequent development of autoimmune disorders.
The findings suggest that microbial-based therapeutics or preventives may have an advantage over interventions with synthetic drugs. They may be less likely to have severe side effects, given the coevolution of human-derived microbial strains and humans
