Sex‐specific associations between AD genotype and the microbiome of human amyloid beta knock‐in (hAβ‐KI) mice

IntroductionEmerging evidence links changes in the gut microbiome to late-onset Alzheimer's disease (LOAD), necessitating examination of AD mouse models with consideration of the microbiome.MethodsWe used shotgun metagenomics and untargeted metabolomics to study the human amyloid beta knock-in (hAβ-KI) murine model for LOAD compared to both wild-type (WT) mice and a model for early-onset AD (3xTg-AD).ResultsEighteen-month female (but not male) hAβ-KI microbiomes were distinct from WT microbiomes, with AD genotype accounting for 18% of the variance by permutational multivariate analysis of variance (PERMANOVA). Metabolomic diversity differences were observed in females, however no individual metabolites were differentially abundant. hAβ-KI mice microbiomes were distinguishable from 3xTg-AD animals (81% accuracy by random forest modeling), with separation primarily driven by Romboutsia ilealis and Turicibacter species. Microbiomes were highly cage specific, with cage assignment accounting for more than 40% of the PERMANOVA variance between the groups.DiscussionThese findings highlight a sex-dependent variation in the microbiomes of hAβ-KI mice and underscore the importance of considering the microbiome when designing studies that use murine models for AD.HighlightsMicrobial diversity and the abundance of several species differed in human amyloid beta knock-in (hAβ-KI) females but not males. Correlations to Alzheimer's disease (AD) genotype were stronger for the microbiome than the metabolome. Microbiomes from hAβ-KI mice were distinct from 3xTg-AD mice. Cage effects accounted for most of the variance in the microbiome and metabolome

Investigating the interplay between diet, the human gut microbiota, and cancer

As the world continues to industrialize, there has been a decreased incidence of infectious diseases and an increased incidence in non-communicable chronic diseases, such as obesity and cancer. One potential causal factor is the human microbiome, which refers to the collection of commensal bacteria, fungi, viruses, archaea, and other microorganisms that inhabit our bodies. The human microbiome has a collective genome which outnumbers human genes by 150-to-1, and it produces an expansive repertoire of metabolites which affect health. As such, the gut microbiome has major implications in digestion, educating the host immune system, preventing the colonization of pathogenic bacteria by occupying intestinal niches, and more.Several components of the industrialized lifestyle have been known to alter the gut microbiome, leading to negative health consequences. The result is a microbiome that promotes inflammation and is associated with non-communicable chronic diseases. As these diseases become more prevalent in industrialized countries, there is an urgency to understand the role of the microbiota in human health. To investigate this issue, my research seeks to answer the following three questions: (1) What is the role of the industrialized gut microbiome in the development of colorectal cancer? (2) How does diet affect the gut microbiome and inflammation in people with myeloproliferative neoplasms? (3) How is dietary fiber utilized by the gut microbiota of US and Moroccan individuals in vitro?To answer the first question, samples were collected at the UCI Medical Center from 140 subjects during and after colonoscopy to characterize the microbiome associated with colorectal polyps. I used a combination of amplicon and shotgun metagenomic sequencing approaches to understand the effect of sampling method on microbial composition, and to describe the microbiome associated with healthy tissue and two types of colorectal polyps. I discovered that sampling method significantly explained 10-15% of the variation observed in microbiome composition. Additionally, using samples obtained from the colon mucosa, I was able to find associations with microbiome composition and colorectal polyps derived from the serrated pathway of colorectal carcinogenesis, such as a depletion in the lignan-degrading microbe, Eggerthella lenta. Lastly, I was able to use the microbiome to inform machine learning classifiers to accurately distinguish between healthy and polyp-bearing samples (Area under curve = 0.87-0.99).To address the second question, we collaborated with Dr. Angela G. Fleischman, who conducted a dietary intervention in subjects afflicted with myeloproliferative neoplasms, a class of blood cancer. In this 15-week clinical trial, 28 individuals were assigned to receive dietary counseling following either a Mediterranean style eating pattern or one following U.S. guidelines. Blood and fecal samples were collected to examine inflammation and the gut microbiome, respectively. Using shotgun metagenomic sequencing, I discovered no significant alterations in gut microbiome diversity and composition due to a Mediterranean diet. I did find a significant association between the gut microbiome and myeloproliferative neoplasm subtype, explaining approximately 6% of the variance in microbiome composition. Lastly, I found several significant correlations between microbial species, function, and cytokine concentrations.My first two chapters suggested a link between the microbiome and dietary fiber, thus, in my final chapter I explored the effect of dietary fiber on microbial growth in vitro. In these experiments, I took the feces of 15 healthy individuals from the US and 15 Moroccans and cultured them anaerobically for 24 hours in the absence and presence of inulin, pectin, or psyllium husk. I found significant cohort effects on the microbiome, with US samples becoming dominated with Bifidobacterium and Moroccan samples becoming dominated with Clostridia. Furthermore, I demonstrate that pectin and psyllium husk perform differential enrichment of microbes and their associated carbohydrate-active enzymes

Distinct colon mucosa microbiomes associated with Tubular Adenomas and Serrated Polyps

Background: Colorectal cancer is the second most deadly and third most common cancer in the world. Its development is heterogenous, with multiple mechanisms of carcinogenesis. Two distinct mechanisms include the adenoma-carcinoma sequence and the serrated pathway. The gut microbiome has been identified as a key player in the adenoma-carcinoma sequence, but its role in serrated carcinogenesis is less clear. In this study, we characterized the gut microbiome of 140 polyp-free and polyp-bearing individuals using colon mucosa and fecal samples to determine if microbiome composition was associated with each of the two key pathways. Methods: Characterization of the gut microbiome was performed using a combination of amplicon and shotgun sequencing. Microbial taxonomy was assigned, and we compared the diversity and composition of different sampling methods within the same individual. Additionally, we also compared the microbial diversity and composition of mucosal samples from polyp-free, tubular adenoma, and serrated polyp-bearing individuals. Shotgun samples were also cross-assembled into contiguous sequences to examine the functional potential of microbial metagenomes. Results: We discovered significant differences between the microbiomes of colon mucosa and fecal samples, with sample type explaining 14% of the variation observed in the microbiome. Multiple mucosal samples were collected from each individual to investigate whether the gut microbiome differed between polyp and healthy intestinal tissue, but no differences were found. Colon mucosa sampling revealed that the microbiomes of individuals with tubular adenomas and serrated polyps were significantly different from each other and polyp-free individuals, explaining 2-10% of the variance in the microbiome. Further analysis revealed differential abundances of 6 microbes and 1,143 microbial genes across tubular adenoma, serrated polyp, and polyp-free cases

Microbiome distinctions between the CRC carcinogenic pathways

Colorectal cancer (CRC) is the third most commonly diagnosed cancer, the third leading cause of cancer-related deaths, and has been on the rise among young adults in the United States. Research has established that the colonic microbiome is different in patients with CRC compared to healthy controls, but few studies have investigated if and how the microbiome may relate to CRC progression through the serrated pathway versus the adenoma-carcinoma sequence. Our view is that progress in CRC microbiome research requires consideration of how the microbiome may contribute to CRC carcinogenesis through the distinct pathways that lead to CRC, which could enable the creation of novel and tailored prevention, screening, and therapeutic interventions. We first highlight the limitations in existing CRC microbiome research and offer corresponding solutions for investigating the microbiome’s role in the adenoma-carcinoma sequence and serrated pathway. We then summarize the findings in the select human studies that included data points related to the two major carcinogenic pathways. These studies investigate the microbiome in CRC carcinogenesis and 1) utilize mucosal samples and 2) compare polyps or tumors by histopathologic type, molecular/genetic type, or location in the colon. Key findings from these studies include: 1) Fusobacterium is associated with right-sided, more advanced, and serrated lesions; 2) the colons of people with CRC have bacteria typically associated with normal oral flora; and 3) colons from people with CRC have more biofilms, and these biofilms are predominantly located in the proximal colon (single study)

Microbiome distinctions between the CRC carcinogenic pathways.

Colorectal cancer (CRC) is the third most commonly diagnosed cancer, the third leading cause of cancer-related deaths, and has been on the rise among young adults in the United States. Research has established that the colonic microbiome is different in patients with CRC compared to healthy controls, but few studies have investigated if and how the microbiome may relate to CRC progression through the serrated pathway versus the adenoma-carcinoma sequence.Our view is that progress in CRC microbiome research requires consideration of how the microbiome may contribute to CRC carcinogenesis through the distinct pathways that lead to CRC, which could enable the creation of novel and tailored prevention, screening, and therapeutic interventions. We first highlight the limitations in existing CRC microbiome research and offer corresponding solutions for investigating the microbiome's role in the adenoma-carcinoma sequence and serrated pathway. We then summarize the findings in the select human studies that included data points related to the two major carcinogenic pathways. These studies investigate the microbiome in CRC carcinogenesis and 1) utilize mucosal samples and 2) compare polyps or tumors by histopathologic type, molecular/genetic type, or location in the colon.Key findings from these studies include: 1) Fusobacterium is associated with right-sided, more advanced, and serrated lesions; 2) the colons of people with CRC have bacteria typically associated with normal oral flora; and 3) colons from people with CRC have more biofilms, and these biofilms are predominantly located in the proximal colon (single study)

Distinct colon mucosa microbiomes associated with tubular adenomas and serrated polyps.

Colorectal cancer is the second most deadly and third most common cancer in the world. Its development is heterogenous, with multiple mechanisms of carcinogenesis. Two distinct mechanisms include the adenoma-carcinoma sequence and the serrated pathway. The gut microbiome has been identified as a key player in the adenoma-carcinoma sequence, but its role in serrated carcinogenesis is less clear. In this study, we characterized the gut microbiome of 140 polyp-free and polyp-bearing individuals using colon mucosa and fecal samples to determine if microbiome composition was associated with each of the two key pathways. We discovered significant differences between the microbiomes of colon mucosa and fecal samples, with sample type explaining 10-15% of the variation observed in the microbiome. Multiple mucosal brushings were collected from each individual to investigate whether the gut microbiome differed between polyp and healthy intestinal tissue, but no differences were found. Mucosal aspirate sampling revealed that the microbiomes of individuals with tubular adenomas and serrated polyps were significantly different from each other and polyp-free individuals, explaining 1-4% of the variance in the microbiome. Microbiome composition also enabled the accurate prediction of subject polyp types using Random Forest, which produced an area under curve values of 0.87-0.99. By directly sampling the colon mucosa and distinguishing between the different developmental pathways of colorectal cancer, our study helps characterize potential mechanistic targets for serrated carcinogenesis. This research also provides insight into multiple microbiome sampling strategies by assessing each method's practicality and effect on microbial community composition

Fecal Microbial Community Composition in Myeloproliferative Neoplasm Patients Is Associated with an Inflammatory State.

The capacity of the human microbiome to modulate inflammation in the context of cancer is becoming increasingly clear. Myeloproliferative neoplasms (MPNs) are chronic hematologic malignancies in which inflammation plays a key role in disease initiation, progression, and symptomatology. To better understand the composition of the gut microbiome in patients with MPN, triplicate fecal samples were collected from 25 MPN patients and 25 non-MPN controls. Although most of the variance between the microbial community compositions could be attributed to the individual (permutational analysis of variance [PERMANOVA], R2 = 0.92, P = 0.001), 1.7% of the variance could be attributed to disease status (MPN versus non-MPN). When a more detailed analysis was performed, significantly fewer reads mapping to a species of Phascolarctobacterium, a microbe previously associated with reduced inflammation, were found in MPNs. Further, our data revealed an association between Parabacteroides and tumor necrosis factor alpha (TNF-α), an inflammatory cytokine elevated in MPNs. Taken together, our results indicate a significant difference in the microbiome of MPN patients compared to non-MPN controls, and we identify specific species which may have a role in the chronic inflammation central to this disease. IMPORTANCE MPNs are chronic blood cancers in which inflammation plays a key role in disease initiation, progression, and symptomatology. The gut microbiome modulates normal blood development and inflammation and may also impact the development and manifestation of blood cancers. Therefore, the microbiome may be an important modulator of inflammation in MPN and could potentially be leveraged therapeutically in this disease. However, the relationship between the gut microbiome and MPNs has not been defined. Therefore, we performed an evaluation of the MPN microbiome, comparing the microbiomes of MPN patients with healthy donors and between MPN patients with various states of disease