Rec Reading for Lec 3 Flashcards
The role of the microbiome in human health and disease
Vincent Young BMJ
The microbiome the produces important resources, bioconversion of nutrients, and protection against pathogenic microbes. Thus disease can result from a loss of beneficial functions or the introduction of maladaptive functions by invading microbes
One important area is the ability of the microbiota of the intestinal tract to ferment resistant starch (polysaccharides that cannot be digested by the host) to produce a variety of compounds, most notably short chain fatty acids, which can have a variety of effects on the host.
For example, the short chain fatty acid butyrate is the preferred energy source for colonic enterocytes and has a variety of effects on host physiology, ranging from anti-inflammatory effects to antitumor activity
One example of host-microbe co-metabolism is the conversion of bile salts and bile acids in the gut.
These compounds, synthesized in the host’s liver and secreted as conjugated bile salts, can undergo microbially mediated conversions within the intestine to release unconjugated bile acids and generate secondary bile acids.
Although these compounds have distinct activities from the parent ones, the host has evolved the ability to recognize and respond to these microbially generated compounds in a manner similar to the response to bacterially generated short chain fatty acids.
Farnesoid X receptors (FXRs) are nuclear hormone receptors that respond to bile acids. Signaling through FXRs and other bile acid receptors can have a variety of effects on the host. Because bile acids are the end products of cholesterol catabolism, changes to bile acid metabolism can have effects on cholesterol and lipid metabolism.
Changes in the gut microbiota are associated with altered lipid metabolism and various FXR agonists are being developed as potential treatments for various meta- bolic disorders, ranging from obesity and insulin resist- ance to liver fibrosis and non-alcoholic steatohepatitis
The role of the microbiome in human health and disease
Vincent Young BMJ
Techniques for studying the microbiome
One of the most common techniques for performing a census of microbes involves the retrieval of sequence data of the gene that encodes the RNA component of the small ribo- somal subunit (16S rRNA). This sequence dependent method does not depend on microbial cultivation. DNA is extracted from a sample of the microbial community of interest and polymerase chain reaction (PCR) primers targeting broadly conserved regions of the 16S gene are used to amplify most of the microbial species present. These PCR amplicons are then subjected to high throughput DNA sequence analysis Analysis of 16S data ultimately involves grouping the sequences obtained into discrete bins that give rise to a taxonomy 1) All of the DNA sequences in a given analysis are compared with each other and grouped into operational taxonomic units (OTUs) 2) Each sequence of 16S amplicons individually and com- pares it to a set database of sequences and thus classifies each sequence in the experiment to a previously defined bin With regard to human health, investigators use 16S analysis to compare people with and without a given disease in a cross sectional manner. In addition, longi- tudinal analysis can be conducted to monitor the effect of treatments or the development of disease on the struc- ture of the microbiota. However, although this type of analysis is powerful and provides important observations about the potential role of microbes in health, it does not directly assess the function of the microbiota The 16S gene gives insight into the phylogenetic characterization of a given bacterium in a community, but it does not provide information on the functions encoded by the rest of the genome Metagenomic sequence analysis has been developed to assess the functional potential of an entire microbial community - nstead of using PCR to amplify this particular phylogenetic marker, the DNA sequence of the entire community is sequenced directly using high throughput techniques. The relative abundance of specific metabolic pathways that are exhibited by the community can help predict the functional capacity of that community Measuring in situ microbial function - Using sequence based techniques, metatranscriptomic analysis assays the proportion of a microbial metagenome that is being expressed at a specific point in time under certain conditions. This technique assays the RNA transcripts present in a microbiome by performing sequence analysis of all of the expressed genes through reverse transcriptase mediated RNA sequencing Two other techniques are often used to determine directly the effect of transcriptional activity on the metabolic environment of the microbiome. These final two techniques, proteomic and metabolomic analysis, use advanced mass spectros- copy to measure the relative abundance of proteins and metabolites (including peptides, oligosaccharides, and lipids) in a given microbiome
The role of the microbiome in human health and disease Vincent Young BMJ Disease associations with the microbiome
C difficile infection has been taught in medical school as an example of a disease where disruption of the normal microbiota plays a key role in the pathogenesis microbial functions encoded by the indigenous microbiota that serve to mediate colonization resistance against C difficile. One area is the role that the intestinal microbiota play in bile salt and bile acid metabolism. When conjugated bile salts are secreted by the liver into the gastrointestinal tract microbes that can perform de-conjugation and conversion (for example, dehydroxylation) reactions convert these compounds into unconjugated primary and secondary bile acids. Some of these molecular species promote the germination of C difficile spores whereas others inhibit the growth of the vegetative form of the organism IBDs In the IBDs Crohn’s disease and ulcerative colitis no classic pathogen has been definitively identified. In this case, the intestinal microbiota itself is thought to be pathogenic and in predisposed hosts contributes to the development of the dysregulated inflammatory response that characterizes these diseases. Multiple studies show that the intestinal microbiota of patients with IBD is distinct from that of people without IBD Studies of the genetic susceptibility to the development of IBD highlight the importance of host immunity and the pathogenesis of this disease. Of particular relevance is the fact that genetic variations in the host machinery that interact with microbes are associated with an increased risk of developing IBD. Thus, IBD truly is a microbiome related disease because both the host and microbe, and thus the environment created through their interaction, are altered in this condition Obesity and metabolic syndrome It is clear that the microbiota can influence the handling of nutrients by the intestinal tract. Microbially produced products such as short chain fatty acids and bile acids can influence the expression of important metabolic regulatory peptides such as glucagon-like peptide 1 and peptide YY Studies have shown that manipulation of the host diet has effects on the intestinal microbiota, setting up a complex system whereby intrinsic and extrinsic associa- tions in the microbiome can alter host metabolism. An interesting line of research that has received much attention is how unintentional alteration of the microbiota— for example, through antibiotic administration—can disrupt the normal balance and skew towards development of the metabolic syndrome and obesity Recent work has looked at the effects of microbial metab- olism on other organ systems. A key example studied the role of the metabolism of trimethylamine N-oxide (TMAO), a metabolite that is used to predict the risk of developing cardiovascular disease. Dietary choline was shown to be metabolized by the intestinal microbiota to generate TMAO and modulation of the microbiota to increase dietary choline blocked enhanced atherosclerosis. This work provides a potential mechanism by which the indig- enous microbiota can explain the well established link between certain dietary habits and the development of a given health condition, such as cardiovascular disease Lung Disease It has long been known that many patients with cystic fibrosis become chronically colonized with pathogenic organisms, but more recently the lungs of these patients have been found to contain a much more diverse community than had previously been recognized bacteria found in the lungs of these patients may be adapted to degrade the excess mucin seen in cystic fibrosis and this may support the growth of the typical pathogens seen in this environment Important work is being done on the role of microbial communities in the pathogenesis of lung diseases such as asthma and chronic obstructive pulmonary disease (COPD). Many of the early studies show association rather than causation, but more recent work is examining how the lung microbiota may drive the inflammatory responses central to the pathogenesis of COPD Polymicrobial interactions in acute and chronic rhinosinusitis have been investigated. Specifc microbes have been found to be enriched in sinusitis. In one study humans with sinusitis had an increase in the abundance of Corynebacterium tuberculostearicum, which had not been previously recognized as a potential pathogen. Installation of this organism into a mouse model of sinusitis demonstrated its pathogenic potential. Further examination of the indigenous microbiota of the upper respiratory tract in patients with and without sinus disease suggested that other members of the indigenous sinus community mediate resistance to colonization by this organism In a manner analogous to the interaction between pathogens and the microbiota in the intestinal tract, the status of the upper respiratory tract microbiota may be associated with susceptibility to both viral and bacterial upper respiratory tract infections. Additionally, acute upper respiratory tract infection with rhinovirus can alter the microbiota, and it has been suggested that this can lead to increased susceptibility to infections elsewhere in the respiratory tract, such as otitis media and pneumonia
The role of the microbiome in human health and disease Vincent Young BMJ Emerging treatments: the microbiome as a therapeutic target
Antibiotics Although collateral damage from therapeutic antibiotics on the indigenous gut microbiota plays a key role in the pathogenesis of C difcile infection, antibiotic mediated alteration of the microbiota may serve to alter a disease associated microbial community to restore a healthy state One obvious disadvantage of this approach is that it is generally empiric in nature. As yet, we cannot predict exactly how a particular course of antibiotics will affect a given microbial community C.diff More recent antibiotics developed for the treatment of C diffcile infection are designed to be more narrowly restricted to the pathogen in the hope of limiting collateral damage to the indigenous microbiota, which is associated with recurrent disease. The use of fidaxomicin, which has less microbiota disrupting potential, is also associated with lower rates of recurrent disease while maintaining good e cacy against the pathogen. This strategy is restricted to treating C diffcile infection, but the use of broad spec- trum antibiotics should be limited when treating a known bacterial pathogen to spare the microbiota when treat- ing any infection. Therefore, appropriate antibiotic stewardship helps limit the development or selection of antibiotic resistant organisms and can prevent excessive damage to the indigenous microbiota Bacteriophage Live Microbial Therapies
Summary table
Prolonged antibiotic treatment induces a diabetogenic intestinal microbiome that accelerates diabetes in NOD mice
Summary: Accumulating evidence supports that the intestinal microbiome is involved in Type 1 diabetes (T1D) pathogenesis through the gut-pancreas nexus. Our aim was to determine whether the intestinal microbiota in the non-obese diabetic (NOD) mouse model played a role in T1D through the gut. To examine the effect of the intestinal microbiota on T1D onset, we manipulated gut microbes by: (1) the fecal transplantation between non-obese diabetic (NOD) and resistant (NOR) mice and (2) the oral antibiotic and probiotic treatment of NOD mice. We monitored diabetes onset, quantified CD4+T cells in the Peyer’s patches, profiled the microbiome and measured fecal short-chain fatty acids (SCFA). The gut microbiota from NOD mice harbored more pathobionts and fewer beneficial microbes in comparison with NOR mice. Fecal transplantation of NOD microbes induced insulitis in NOR hosts suggesting that the NOD microbiome is diabetogenic. Moreover, antibiotic exposure accelerated diabetes onset in NOD mice accompanied by increased T-helper type 1 (Th1) and reduced Th17 cells in the intestinal lymphoid tissues. The diabetogenic microbiome was characterized by a metagenome altered in several metabolic gene clusters. Furthermore, diabetes susceptibility correlated with reduced fecal SCFAs. In an attempt to correct the diabetogenic microbiome, we administered VLS#3 probiotics to NOD mice but found that VSL#3 colonized the intestine poorly and did not delay diabetes. We conclude that NOD mice harbor gut microbes that induce diabetes and that their diabetogenic microbiome can be amplified early in life through antibiotic exposure. Protective microbes like VSL#3 are insufficient to overcome the effects of a diabetogenic microbiome
