Gut Microbiome Profiles Research Articles

Metabolomic and gut microbiome profiles across the spectrum of community-based COVID and non-COVID disease

Whilst most individuals with SARS-CoV-2 infection have relatively mild disease, managed in the community, it was noted early in the pandemic that individuals with cardiovascular risk factors were more likely to experience severe acute disease, requiring hospitalisation. As the pandemic has progressed, increasing concern has also developed over long symptom duration in many individuals after SARS-CoV-2 infection, including among the majority who are managed acutely in the community. Risk factors for long symptom duration, including biological variables, are still poorly defined. Here, we examine post-illness metabolomic profiles, using nuclear magnetic resonance (Nightingale Health Oyj), and gut-microbiome profiles, using shotgun metagenomic sequencing (Illumina Inc), in 2561 community-dwelling participants with SARS-CoV-2. Illness duration ranged from asymptomatic (n = 307) to Post-COVID Syndrome (n = 180), and included participants with prolonged non-COVID-19 illnesses (n = 287). We also assess a pre-established metabolomic biomarker score, previously associated with hospitalisation for both acute pneumonia and severe acute COVID-19 illness, for its association with illness duration. We found an atherogenic-dyslipidaemic metabolic profile, including biomarkers such as fatty acids and cholesterol, was associated with longer duration of illness, both in individuals with and without SARS-CoV-2 infection. Greater values of a pre-existing metabolomic biomarker score also associated with longer duration of illness, regardless of SARS-CoV-2 infection. We found no association between illness duration and gut microbiome profiles in convalescence. This highlights the potential role of cardiometabolic dysfunction in relation to the experience of long duration symptoms after symptoms of acute infection, both COVID-19 as well as other illnesses.

Changes in the Human Gut Microbiome Caused by the Short-Term Impact of Lactic Acid Bacteria Consumption in Healthy People.

The gut microbiome is one of the main factors affecting human health. It has been proven that probiotics can regulate the metabolism in the host body. A large number of people use probiotics not as medicines, but as a prophylactic supplement. The aim of our study was to evaluate the effect of lactic acid bacteria on the gut microbiome of healthy people using the V3 region of the 16S rRNA gene. Our study showed changes in the generic composition in the gut of healthy people when taking the supplement. There was an increase in the members responsible for the production of short-chain fatty acids in the gut of the host (Blautia, Fusicatenibacter, Eubacterium hallii group, Ruminococcus), as well as bacteria that improve intestinal homeostasis (Dorea and Barnesiella). There was also a decrease in the abundance of bacteria in the genera Catenibacterium, Hungatella, Escherichia-Shigella, and Pseudomonas, associated with an unhealthy profile of the human gut microbiome. An increase in members of the phylum Actinobacteriota was also observed, which has a positive effect on the host organism. Our results indicate that short-term prophylactic use of lactic acid bacteria-based supplements can be effective, as it contributes to a beneficial effect on the gut microbiome of healthy people.

O-030 Gut microbiome in endometriosis: a cohort study on 1000 individuals

Abstract Study question Do gut microbial composition and functionality differ between women with and without endometriosis? Summary answer Gut microbiome diversity and composition (species and microbial pathways) were not significantly different between women with and without endometriosis. What is known already Endometriosis, defined as the presence of endometrial-like tissue outside of the uterus, is one of the most common female reproductive disorders. Although different theories of the possible causes of endometriosis have been proposed, its pathogenesis is not clear. Novel studies indicate that the gut microbiome may be involved in the etiology of endometriosis, nevertheless, the connection between microbes, its dysbiosis and the development of endometriosis remains unexplored. This study aims to analyze and compare the gut microbiome profile in women with and without endometriosis in a large cohort to identify microbial targets potentially involved in the development of the disease. Study design, size, duration This case-control study included a subsample of 1000 women (age = 45.61±10.36 years; BMI = 25.67±5.59) of the Estonian Microbiome (EstMB) cohort, a volunteer-based sub-cohort of the Estonian Biobank created in 2017. 136 women with endometriosis and 864 control women who have not been diagnosed with endometriosis or any of its most prevalent comorbidities (systemic lupus erythematosus, rheumatoid arthritis, autoimmune thyroiditis, celiac disease, multiple sclerosis and irritable bowel syndrome) were included in this study. Participants/materials, setting, methods Microbial DNA from fecal samples was extracted and sequenced by paired-end metagenomic shotgun sequencing (Illumina Novaseq 6000 platform). Microbial functional pathways were annotated using the Kyoto Encyclopedia of Genes and Genomes (KEGG) database (https://www.genome.jp/kegg/). Partitioning around medoids (PAM) algorithm was performed to cluster the microbial profile of the Estonian population. The alpha- and beta-diversity and differential abundance analyses were performed to assess the gut microbiome (species and KEGG orthologies [KO]) in both groups. Main results and the role of chance After metagenomics analysis, 17180 microbes and 7869 KO were detected. Those bacteria and KO with a relative abundance > 1 % were used for the diversity and differential abundance analyses, resulting in 2442 species and 1974 KO. PAM clustering analysis stratified the study population into two enterotypes: one characterized by a high abundance of Prevotella copri and the second presented a high abundance of Bacteroides genus (PERMANOVA, p = 0.001). However, the enterotypes were not associated with the presence/absence of endometriosis. Microbial alpha-diversity (observed richness and Shannon’s index) was not significantly different between women with and without endometriosis (all p-value > 0.05). Beta-diversity analyses on the microbial and functional profile (species and KO profile) indicated no significant dissimilarity between groups (PERMANOVA, all p > 0.05). No differential species nor KO were detected after multiple testing adjustment (all FDR p > 0.05). Limitations, reasons for caution This case-control study did not identify a distinct gut microbial profile in women with endometriosis. A deeper analysis considering potential confounders (specifically hormonal treatment in patients) is needed to further confirm our results. Wider implications of the findings Endometriosis is a widespread disorder affecting ∼10% of reproductive-age women. To the best of our knowledge, this is the biggest metagenome study performed in women with endometriosis. Our findings do not find enough evidence to support the existence of a gut microbiome-dependent mechanism implicated in the pathogenesis of endometriosis. Trial registration number Not applicable

16S rRNA gene sequencing reveals the correlation between the gut microbiota and the susceptibility to pathological scars.

The gut microbiome profile in patients with pathological scars remains rarely known, especially those patients who are susceptible to pathological scars. Previous studies demonstrated that gut microbial dysbiosis can promote the development of a series of diseases via the interaction between gut microbiota and host. The current study aimed to explore the gut microbiota of patients who are prone to suffer from pathological scars. 35 patients with pathological scars (PS group) and 40 patients with normal scars (NS group) were recruited for collection of fecal samples to sequence the 16S ribosomal RNA (16S rRNA) V3-V4 region of gut microbiota. Alpha diversity of gut microbiota showed a significant difference between NS group and PS group, and beta diversity indicated that the composition of gut microbiota in NS and PS participants was different, which implied that dysbiosis exhibits in patients who are susceptible to pathological scars. Based on phylum, genus, species levels, we demonstrated that the changing in some gut microbiota (Firmicutes; Bacteroides; Escherichia coli, etc.) may contribute to the occurrence or development of pathological scars. Moreover, the interaction network of gut microbiota in NS and PS group clearly revealed the different interaction model of each group. Our study has preliminary confirmed that dysbiosis exhibits in patients who are susceptible to pathological scars, and provide a new insight regarding the role of the gut microbiome in PS development and progression.

185-OR: Machine-Learning Approach Reveals Microbiome, Metabolome, Lipidome, and Their Interaction in Type 1 Diabetes Mellitus

Background: An increasing amount of research shows that the gut microbiota and metabolites play a role in type 1 diabetes mellitus (T1D). We aimed to use machine learning to explore gut microbiota, serum metabolites, and lipids signatures in T1D individuals. Methods: We evaluated 137 individuals in a cross-sectional cohort that included 38 T1D patients, 38 healthy controls, and 61 T1D patients for validation. After clinical examination and biospecimen collection, we characterized the gut microbiome profile with 16S rRNA gene amplicon sequencing and analyzed serum metabolites and lipids with liquid chromatography-mass spectrometry. All molecular data were analyzed using a combination of univariate, multivariate, and machine-learning approaches (Logistic Regression, Support Vector Machine, Gaussian Naive Bayes, and Random Forest). Results: Machine-learning approaches using microbiota composition did not accurately predict T1D status (model accuracy=0.7555), while the accuracy of model using metabolite composition was 0.9333. Based on bacterial species-level composition, Ruminococcus torques, Anaerostipes, Veillonella, Erysipelotrichaceae UCG-003, Blautia, and Coprococcus were coincident microbes which all increased in T1D. Increased 3-hydroxybutyric acid and 9-oxo-ode (AUC=0.70 and 0.67) were meaningful coincident metabolites in T1D. PC(36:4e)(rep) was the most significant lipid (coefficient index=3.11e-9, increased in T1D). We confirmed the biological relevance of the microbiome, metabolome, and lipidome features in the validation group. Ruminococcus torques was positively associated with 3-hydroxybutyric acid (p<0.01). Conclusions: By using machine-learning algorithms and multi-omics, we demonstrated that T1D patients are associated with altered microbiota, metabolites, and lipidomic signatures or functions. Machine-learning approaches have potential clinical applications in T1D diagnostics and treatment. Disclosure H.Tan: None. J.Yan: None. S.Luo: None. J.Weng: None. X.Zheng: None. Y.Shi: None. T.Yue: None. D.Zheng: None. C.Wang: None. Z.Liu: None. D.Yang: None. Y.Ding: None. W.Xu: None. Funding National Natural Science Foundation of China (82100822); Anhui Provincial Natural Science Foundation (2008085MH248, 2008085MH278); Guangdong Basic and Applied Basic Research Foundation (2019A1515010979); National Key R&D Program (2017YFC1309600)

Anti-Inflammatory Effect of Clostridium Butyricum-Derived Extracellular Vesicles in Ulcerative Colitis: Impact on Host microRNAs Expressions and Gut Microbiome Profiles.

Probiotics extracellular vesicles (EVs) have shown potential as EV-based nanomaterials therapy for the treatment of inflammatory bowel disease (IBD). Although probiotic Clostridium butyricum has been reported to be protective in various models of intestinal inflammation, the therapeutic effects of Clostridium butyricum-derived extracellular vesicles (CbEVs) in IBD remain to be demonstrated. In this study, we combined multi-omics sequencing with an in vitro model of lipopolysaccharide-induced RAW264.7 cells and an in vivo mouse model of dextran sodium sulfate-induced colitis to explore the regulatory impact and mechanism of CbEVs in ulcerative colitis. Through small RNA sequencing, we found that microRNA is involved in the alleviation of colonic inflammation under CbEVs treatment. Mechanistically, CbEVs restored miR-199a-3p expression, interacting with map3k4, and thereby suppressed proinflammatory MAPK and NF-κB signaling. Additionally, metagenomic sequencing demonstrated that CbEVs alleviated bacterial dysbiosis in colitis mice and significantly reduced the abundance of the bacterial pathogens Escherichia coli and Shigella flexneri. Furthermore, CbEVs regulated the microbial tryptophan metabolites, which further improved intestinal barrier integrity and inhibited the inflammatory response in colitis mice. Clostridium butyricum-derived extracellular vesicles could be a novel agent for the treatment of colitis and miR-199a-3p could be a potential target for IBD treatment. This article is protected by copyright. All rights reserved.

Integrative multiomics analysis of infant gut microbiome and serum metabolome reveals key molecular biomarkers of early onset childhood obesity

Evidence supports a complex interplay of gut microbiome and host metabolism as regulators of obesity. The metabolic phenotype and microbial metabolism of host diet may also contribute to greater obesity risk in children early in life. This study aimed to identify features that discriminated overweight/obese from normal weight infants by integrating gut microbiome and serum metabolome profiles. This prospective analysis included 50 South Asian children living in Canada, selected from the SouTh Asian biRth cohorT (START). Serum metabolites were measured by multisegment injection-capillary electrophoresis-mass spectrometry and the relative abundance of bacterial 16S rRNA gene amplicon sequence variant was evaluated at 1 year. Cumulative body mass index (BMIAUC) and skinfold thickness (SSFAUC) scores were calculated from birth to 3 years as the total area under the growth curve (AUC). BMIAUC and/or SSFAUC >85th percentile was used to define overweight/obesity. Data Integration Analysis for Biomarker discovery using Latent cOmponent (DIABLO) was used to identify discriminant features associated with childhood overweight/obesity. The associations between identified features and anthropometric measures were examined using logistic regression. Circulating metabolites including glutamic acid, acetylcarnitine, carnitine, and threonine were positively, whereas γ-aminobutyric acid (GABA), symmetric dimethylarginine (SDMA), and asymmetric dimethylarginine (ADMA) were negatively associated with childhood overweight/obesity. The abundance of the Pseudobutyrivibrio and Lactobacillus genera were positively, and Clostridium sensu stricto 1 and Akkermansia were negatively associated with childhood overweight/obesity. Integrative analysis revealed that Akkermansia was positively whereas Lactobacillus was inversely correlated with GABA and SDMA, and Pseudobutyrivibrio was inversely correlated with GABA. This study provides insights into metabolic and microbial signatures which may regulate satiety, energy metabolism, inflammatory processes, and/or gut barrier function, and therefore, obesity trajectories in childhood. Understanding the functional capacity of these molecular features and potentially modifiable risk factors such as dietary exposures early in life may offer a novel approach for preventing childhood obesity.

A novel gut microbiome–immune axis influencing pathology in HCMV infected infants with neonatal cholestasis

The interplay of active HCMV infection with gut dysbiosis in the immunopathology of cholestasis in neonates and infants remains unexplored. In this study, we evaluated gut microbiome profiles and immune dysfunction in a cohort of HCMV infected cholestatic infants (IgM positive, N = 21; IgM negative, N = 25) compared to healthy infants, N = 10. HCMV infected IgM positive individuals exhibited increased clinical severity in terms of liver dysfunction, altered CD4+: CD8+ ratio, and elevated Granzyme B levels in cellular immune subsets. Gut microbiome analysis revealed distinct and differential diversity and composition within infected groups aligned with clinical severity reflected through the increased abundance of Gammaproteobacteria, reduced Bifidobacteria, and a unique signature mapping to the HCMV infected IgM negative group. Correlation analyses revealed associations between Bifidobacterium breve, Gammaproteobacteria, Firmicutes, Clostridia, Finegoldia magna, Veillonella dispar, and Granzyme B expressing immune cell subsets. Our study describes a novel gut microbiome–immune axis that may influence disease severity in cholestatic infants with active HCMV infection.

Phage-inclusive profiling of human gut microbiomes with Phanta.

Due to technical limitations, most gut microbiome studies have focused on prokaryotes, overlooking viruses. Phanta, a virome-inclusive gut microbiome profiling tool, overcomes the limitations of assembly-based viral profiling methods by using customized k-mer-based classification tools and incorporating recently published catalogs of gut viral genomes. Phanta's optimizations consider the small genome size of viruses, sequence homology with prokaryotes and interactions with other gut microbes. Extensive testing of Phanta on simulated data demonstrates that it quickly and accurately quantifies prokaryotes and viruses. When applied to 245 fecal metagenomes from healthy adults, Phanta identifies ~200 viral species per sample, ~5× more than standard assembly-based methods. We observe a ~2:1 ratio between DNA viruses and bacteria, with higher interindividual variability of the gut virome compared to the gut bacteriome. In another cohort, we observe that Phanta performs equally well on bulk versus virus-enriched metagenomes, making it possible to study prokaryotes and viruses in a single experiment, with a single analysis.

Crop, Host, and Gut Microbiome Variation Influence Precision Nutrition: An Example of Blueberries.

Epidemiological studies have shown associations between polyphenol-rich fruit intake and bone health, and preclinical studies have shown that blueberries improve bone health. To determine the genotype and dose of blueberries that are effective in ameliorating age-related bone loss, a multi-institutional team of investigators performed in vitro, preclinical, and clinical studies on blueberry varieties that differed in flavonoid profiles. Principal component analysis was used to select blueberry genotypes that varied in anthocyanin profiles. Total phenolic content did not predict the bioavailability of polyphenolic compounds in rats. A range in bioavailability was observed in individual polyphenolic compounds across genotypes. Both alpha and beta diversity analyses indicated that gut microbiome profiles varied with blueberry dose in rats. Additionally, the identification of specific taxa, such as Prevotellaceae_UCG-001 and Coriobacteriales, increasing after blueberry consumption adds to the mounting evidence of their role in polyphenol metabolism. All of the sources of variation can inform blueberry breeding practices to influence precision nutrition.

Alterations of the gut microbiome and metabolic profile in CVB3-induced mice acute viral myocarditis

BackgroundAcute viral myocarditis (AVMC) is an inflammatory disease of the myocardium. Evidence indicates that dysbiosis of gut microbiome and related metabolites intimately associated with cardiovascular diseases through the gut-heart axis.MethodsWe built mouse models of AVMC, then applied 16 S rDNA gene sequencing and UPLC-MS/MS metabolomics to explore variations of gut microbiome and disturbances of cardiac metabolic profiles.ResultsCompared with Control group, analysis of gut microbiota showed lower diversity in AVMC, decreased relative abundance of genera mainly belonging to the phyla Bacteroidetes, and increased of phyla Proteobacteria. Metabolomics analysis showed disturbances of cardiac metabolomics, including 62 increased and 84 decreased metabolites, and mainly assigned to lipid, amino acid, carbohydrate and nucleotide metabolism. The steroid hormone biosynthesis, cortisol synthesis and secretion pathway were particularly enriched in AVMC. Among them, such as estrone 3-sulfate, desoxycortone positively correlated with disturbed gut microbiome.ConclusionIn summary, both the structure of the gut microbiome community and the cardiac metabolome were significantly changed in AVMC. Our findings suggest that gut microbiome may participate in the development of AVMC, the mechanism may be related to its role in dysregulated metabolites such as steroid hormone biosynthesis.

Gut Microbiome and Metabonomic Profile Predict Early Remission to Anti-Integrin Therapy in Patients with Moderate to Severe Ulcerative Colitis.

Patients with ulcerative colitis (UC) have low response rates to anti-integrin medications, necessitating the identification of noninvasive biomarkers for predicting remission to anti-integrin therapy. In this study, patients with moderate to severe UC commencing anti-integrin therapy (n = 29), inactive to mild UC patients (n = 13), and healthy controls (n = 11) were selected. Besides clinical evaluation, fecal samples were collected at baseline and week 14 from moderate to severe UC patients. The clinical remission was defined based on the Mayo score. Fecal samples were assessed with 16S rRNA gene sequencing, liquid chromatography-tandem mass spectrometry, and gas chromatography-mass spectrometry (GC-MS). We identified that Verrucomicrobiota was significantly more abundant in the remission group (P < 0.001) than that of nonremission group at phylum level for patients commencing vedolizumab. GC-MS analysis revealed that the concentrations of butyric acid (P = 0.024) and isobutyric acid (P = 0.042) were significantly higher in the remission group compared to the nonremission group at baseline. Finally, the combination of Verrucomicrobiota, butyric acid, and isobutyric acid improved the diagnosis of early remission to anti-integrin therapy (area under the concentration-time curve = 0.961). We identified significantly higher phylum level diversity of Verrucomicrobiota in remission than the nonremission groups at baseline. Notably, the combination of gut microbiome and metabonomic profiles improved the diagnosis of early remission to anti-integrin therapy. IMPORTANCE It is reported that patients with ulcerative colitis (UC) have low response rates to anti-integrin medications in the latest VARSITY study. Therefore, our primary goals were to discover differences in the gut microbiome and metabonomics patterns between early remission and nonremission patients and to explore the diagnostic value in predicting clinical remission to anti-integrin therapy accurately. In this study, we found that Verrucomicrobiota was significantly more abundant in the remission group (P < 0.001) than that of nonremission group at phylum level for patients commencing vedolizumab. Gas chromatography-mass spectrometry analysis revealed that the concentrations of butyric acid (P = 0.024) and isobutyric acid (P = 0.042) were significantly higher in the remission group compared with the nonremission group at baseline. Notably, the combination of Verrucomicrobiota, butyric acid, and isobutyric acid improved the diagnosis of early remission to anti-integrin therapy (area under the concentration-time curve = 0.961).

Mongolian medicine formulae Ruda-6 alleviates indomethacin-induced gastric ulcer by regulating gut microbiome and serum metabolomics in rats

Ethnopharmacological relevanceRuda-6 (RD-6), a typical traditional Mongolian medicine formulae consisting of 6 herbs, has been traditionally used in treating gastric disorders. Even though it has been shown to protect against gastric ulcers (GU) in animal models, the gut microbiome and serum metabololite-related mechanisms that prevent GU are not well understood. Aim of the studyThis study was conducted to evaluate the gastroprotective mechanism of RD-6 associated with the alteration of the gut microbiome and serum metabolic profiles in GU rats. Materials and methodsRD-6 (0.27, 1.35 and 2.7 g/kg) or ranitidine (40 mg/kg) were orally administered in rats for three weeks before the induction of gastric ulcer using indomethacin (30 mg/kg, single oral dose). The gastric ulcer index, ulcer area, H&E staining, and the levels of TNF-α, iNOS, MPO and MDA were quantified to evaluate the ulcer inhibitory effects of RD-6. Then, 16S rRNA gene sequencing combined with LC-MS metabolic profiling was performed to investigate the effect of RD-6 on the gut microbiota and serum metabolites in rats. Moreover, a spearman analysis was used to calculate the correlation coefficient between the different microbiota and the metabolites. ResultsRD-6 inhibited the gastric lesion damage caused by indomethacin in rats, decreased the ulcer index by 50.29% (p < 0.05), reduced the levels of TNF-α, iNOS, MDA and MPO in gastric tissue. Additionally, RD-6 reshaped the diversity and microbial composition, and reversed the reduced bacteria including [Eubacterium]_xylanophilum group, Sellimonas, Desulfovibrio, and UCG-009, and the increased bacteria Aquamicrobium caused by indomethacin induction. Furthermore, RD-6 regulated the levels of metabolites including amino acids and organic acids, and these affected metabolites were involved in taurine and hypotaurine metabolism and tryptophan metabolism. Spearman analysis revealed that the perturbed gut microbiota were closely related to the changes in differential serum metabolites. ConclusionIn view of the 16S rRNA gene sequencing and LC-MS metabolic results, the present study suggests the mechanism of RD-6 ameliorating GU via modulating intestinal microbiota and their metabolites.

Obesity, Gut Microbiota, and Metabolome: From Pathophysiology to Nutritional Interventions.

Obesity is a disorder identified by an inappropriate increase in weight in relation to height and is considered by many international health institutions to be a major pandemic of the 21st century. The gut microbial ecosystem impacts obesity in multiple ways that yield downstream metabolic consequences, such as affecting systemic inflammation, immune response, and energy harvest, but also the gut-host interface. Metabolomics, a systematized study of low-molecular-weight molecules that take part in metabolic pathways, represents a serviceable method for elucidation of the crosstalk between hosts' metabolism and gut microbiota. In the present review, we confer about clinical and preclinical studies exploring the association of obesity and related metabolic disorders with various gut microbiome profiles, and the effects of several dietary interventions on gut microbiome composition and the metabolome. It is well established that various nutritional interventions may serve as an efficient therapeutic approach to support weight loss in obese individuals, yet no agreement exists in regard to the most effective dietary protocol, both in the short and long term. However, metabolite profiling and the gut microbiota composition might represent an opportunity to methodically establish predictors for obesity control that are relatively simple to measure in comparison to traditional approaches, and it may also present a tool to determine the optimal nutritional intervention to ameliorate obesity in an individual. Nevertheless, a lack of adequately powered randomized trials impedes the application of observations to clinical practice.

Comparison of gut microbiome profile in patients with schizophrenia and healthy controls - A plausible non-invasive biomarker?

The human gut microbiome regulates brain function through the microbiome-gut-brain axis and is implicated in several neuropsychiatric disorders. However, the relationship between the gut microbiome and the pathogenesis of schizophrenia (SCZ) is poorly defined, and very few studies have examined the effect of antipsychotic treatment response. We aim to study the differences in the gut microbiota among drug-naïve (DN SCZ) and risperidone-treated SCZ patients (RISP SCZ), compared to healthy controls (HCs). We recruited a total of 60 participants, from the clinical services of a large neuropsychiatric hospital, which included DN SCZ, RISP SCZ and HCs (n = 20 each). Fecal samples were analyzed using 16s rRNA sequencing in this cross-sectional study. No significant differences were found in taxa richness (alpha diversity) but microbial composition differed between SCZ patients (both DN and RISP) and HCs (PERMANOVA, p = 0.02). Linear Discriminant Analysis Effect Size (LEfSe) and Random Forest model identified the top six genera, which significantly differed in abundance between the study groups. A specific genus-level microbial panel of Ruminococcus, UCG005, Clostridium_sensu_stricto_1 and Bifidobacterium could discriminate SCZ patients from HCs with an area under the curve (AUC) of 0.79, HCs vs DN SCZ (AUC: 0.68), HCs vs RISP SCZ (AUC: 0.93) and DN SCZ vs RISP SCZ (AUC: 0.87). Our study identified distinct microbial signatures that could aid in the differentiation of DN SCZ, RISP SCZ, and HCs. Our findings contribute to a better understanding of the role of the gut microbiome in SCZ pathophysiology and suggest potential targeted interventions.

MetaPhlAn 4 profiling of unknown species-level genome bins improves the characterization of diet-associated microbiome changes in mice

Mouse models are key tools for investigating host-microbiome interactions. However, shotgun metagenomics can only profile a limited fraction of the mouse gut microbiome. Here, we employ a metagenomic profiling method, MetaPhlAn 4, which exploits a large catalog of metagenome-assembled genomes (including 22,718 metagenome-assembled genomes from mice) to improve the profiling of the mouse gut microbiome. We combine 622 samples from eight public datasets and an additional cohort of 97 mouse microbiomes, and we assess the potential of MetaPhlAn 4 to better identify diet-related changes in the host microbiome using a meta-analysis approach. We find multiple, strong, and reproducible diet-related microbial biomarkers, largely increasing those identifiable by other available methods relying only on reference information. The strongest drivers of the diet-induced changes are uncharacterized and previously undetected taxa, confirming the importance of adopting metagenomic methods integrating metagenomic assemblies for comprehensive profiling.

The “microbiome-gut-brain axis” in Alzheimer's disease and its role in neurocognitive decline

Alzheimer’s disease (AD) is a progressive neurocognitive disease characterized by amyloid beta plaques and neurofibrillary tangles in the brain along with inflammation both in the brain and systemically. This has led to the theory of microbial communities or infections as being causative in the development of neuroinflammation as well as immunosenescence and inflamm-aging seen in AD. Our own research has demonstrated a decreased abundance of anti-inflammatory taxa and an increased abundance of pro-inflammatory taxa in the gut microbiome of AD patients. However, it is unclear how the AD microbiome exerts effects on the central nervous system. To address this gap in knowledge we have performed gut microbiome profiling, analysis of immune cell populations in serum, blood cytokine profiling, and cognitive assessments of AD older adults at 90-day intervals. In our early data collected from this ongoing study we have observed changes in B-cell populations with an increased abundance of class-switched B-cells in older adults with greater levels of cognitive impairment. We have further demonstrated that colonization of mice with the microbiome of AD older adults promotes B-cell class-switching when compared with cognitively impaired older adults without AD. Additionally, we have discovered a loss of phytoestrogen-metabolizing bacteria such as Adlercreutzia equolifaciens among AD older adults with rapidly progressing dementia. Phytoestrogens have been previously identified in protecting the intestinal epithelium from oxidative stress and epithelial permeability. Our preliminary studies have suggested that that the phytoestrogen (s)-equol, produced by A. equolifaciens, confers resistance to epithelial damage in the setting of bacterial lipopolysaccharide. Thus, we hypothesize that Adlercreutzia equolifaciens and similar phytoestrogen-metabolizing bacteria maintain epithelial homeostasis in the setting of inflammation while a gain of pro-inflammatory taxa in AD leads to intestinal barrier disruption, increased antigen presentation, immune cell dysregulation, and ultimately cognitive decline. This continuing work aims to further establish the connection between AD related neurocognitive decline, the microbiome, and immune system. This research was funded by grant numbers R01DK125407, R01AG067483, and 5T32A1007349-31 from the National Institutes of Health This is the full abstract presented at the American Physiology Summit 2023 meeting and is only available in HTML format. There are no additional versions or additional content available for this abstract. Physiology was not involved in the peer review process.

Differences in Gut Microbiome Profile between Healthy Children and Children with Inflammatory Bowel Disease and/or Autoimmune Liver Disease: A Case-Control Study.

The role of gastrointestinal microbiome in health and disease is increasingly appreciated. A significant amount of evidence clearly points to a dysbiosis manifest in inflammatory bowel disease (IBD) when compared to healthy controls. Less understood is the microbiome profile in autoimmune liver disease (AILD). Both adult and paediatric data indicate a distinct microbial signature in patients with IBD and co-existent primary sclerosing cholangitis (PSC), which is unique and different compared to the microbial signature that exists in patients with IBD alone. However, there is limited information on the microbiome make-up of patients with parenchymal liver disease, with or without IBD. The present study sought to compare the microbiome of children with IBD, to those with IBD-AILD, those with AILD alone and those of healthy controls. Results from this work indicate that children with AILD have a microbiome profile that mirrors healthy controls. Those with IBD-AILD and IBD have similar microbiome profiles which are distinct from AILD alone and healthy controls. This suggests that the dysbiosis in these groups is primarily due to IBD rather than AILD.

Abstract 4854: PKM2 Modulates hepatic macrophage regulation of NASH, ferroptosis and HCC through TGF-β signaling

Abstract Background: Non-alcoholic steatohepatitis (NASH) and cirrhosis are major risk factors for hepatocellular carcinoma (HCC), which affects men 2-4 times more than women. In tumors Pyruvate kinase M2 (PKM2), induces aerobic glycolysis (Warburg effect) and proinflammatory and non-apoptotic cell death, ferroptosis. Raised levels of hepatic macrophage PKM2 expression are associated with poor prognosis HCC. We previously found that liver specific TGF-β/SMAD4 knockout mice develop iron deposition and hemochromatosis due to a dramatic loss of hepcidin. Moreover, Smad4+/−Sptbn1+/− mice develop gastrointestinal cancers but only in the presence of an altered microbiome. Recently, we found that liver-specific knockout of a TGF-β/SMAD3/4 adaptor protein, βII-spectrin (LSKO) blocks diet-induced NASH and HCC in mice, as well as in siRNA treated human NASH microfluidic cultures (Sci Transl Med. 2021;13(624): eabk2267). We hypothesized that βII-spectrin modulates PKM2 expression in NASH fatty liver, promoting proinflammatory cytokine release, inflammation and tumorigenesis. In addition, microbiome changes could alter hepcidin function and modulate ferroptosis. Our goal is to understand the molecular mechanism underlying PKM2 driven NASH and HCC. Methods: For our NASH mouse model, we fed SPTBN1Flox (control) and liver-specific βII-spectrin knockout (SPTBN1LSKO) mice a Western diet (WD). Body weight, total cholesterol, and triglyceride concentrations in serum were monitored, and PKM2 expression levels in the liver tissues was analyzed. SPTBN1Flox and SPTBN1LSKO mice were treated with both WD and Diethylnitrosamine (DEN) for HCC, and gut microbiome profiles were performed in these mice. To evaluate PKM2 expression in the NASH-associated HCC mouse model, immunohistochemical labeling was performed on liver tissues of these mice with PKM2-specific antibody. Inflammation, lipidosis and fibrosis were determined with H&amp;E, Oil Red O and Sirius Red staining. Results: We found upregulation of PKM2 expression in NASH and HCC Kupffer cells (WD SPTBN1Flox mice). In contrast, PKM2 expression was markedly reduced in the liver in WD SPTBN1LSKO that blocked NASH and HCC. Interestingly, microbiome profiles were altered and TGF-β/SMAD3-regulated fibrosis as well as expression of inflammatory genes were significantly reduced in LSKO mice, compared to the NASH mice. Conclusions: Our findings suggest that the knockdown of the Smad3/4 adaptor βII-spectrin decreases PKM2 expression in Kupffer cells, thereby suppressing pro-inflammatory cytokine production, blocking NASH-associated HCC. Hepatic macrophages such as Kupffer cells and monocyte-derived macrophages could therefore play a critical role in the ferroptosis-mediated protumor immune microenvironment. In addition, our work provides new insight into potential mechanism for two disorders that affect males more than females, hemochromatosis and HCC. Citation Format: Kazufumi Ohshiro, Krishanu Bhowmick, Xiaochun Yang, Addison Klebanov, Sahara John, Dillon Voss, Adrian Krainer, Lopa Mishra. PKM2 Modulates hepatic macrophage regulation of NASH, ferroptosis and HCC through TGF-β signaling. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 4854.

Abstract 5901: Microbiome and genomic profiling in rectal adenocarcinoma

Abstract Introduction: Recent studies have identified bacteria associated with colorectal cancer (CRC), with some data supporting causality in preclinical CRC models. We examined the gut microbiome composition and tumor genomic profiles in a diverse cohort of rectal cancer patients. Methods: Twenty-two patients with newly-diagnosed, Stage II-IV rectal cancer without pathogenic germline mutations (mismatch repair genes, MUTYH) were included in the study. Gut microbiome profiling was performed on genomic DNA extracted from collected fecal samples (16S rRNA sequencing, V4 region). Tumor specimens were tested for somatic and germline mutations using the Tempus xT 648-gene panel and whole transcriptome RNA sequencing, providing information on tumor mutation burden (TMB), pathogenic KRAS mutation status and consensus molecular subtype (CMS). We then assessed differential abundance of microbial taxa (using ANCOM-BC) between the following groups: high vs low TMB (dichotomized at median, 3.7 mut/MB), presence versus absence of pathogenic KRAS mutation, and CMS subtype. Results: The median age of study subjects was 49 years (range 37-78). Racial/ethnic breakdown was as follows: 2 non-Hispanic Asian, 4 non-Hispanic Black, 5 non-Hispanic White, and 11 White Hispanic. Twelve tumors carried a pathogenic KRAS variant and the median TMB was 3.7 m/MB (range 0.5-8.9 m/MB). Among 20 tumors that underwent whole transcriptome RNA sequencing, 1 was categorized as CMS1, 8 CMS2, 3 CMS3, 7 CMS4, and 2 CMS undetermined. There were no statistically significant differences in gut bacteria taxa abundance by KRAS mutation status or among CMS subtypes. The group with greater than median TMB, however, had statistically significant enrichment of Pepostreptococcus stomatis (18.4 fold increase, p=0.039 after Benjamini-Hotchberg adjustment with FDR = 0.05). Conclusions: In this pilot study, we found that CRC patients with higher TMB had an enrichment of Peptostreptococcus stomatis, a bacteria associated with colonic dysplasia in mouse models and enriched in CRC patients as compared to healthy controls. (PMID 28823860, 35292756) Higher TMB is a predictive biomarker for response to immunotherapy across cancer types including CRC. Since the gut microbiome is potentially modifiable, further research is needed to better elucidate the connection between microbiome and CRC carcinogenesis including specific mutation profiles, which could pave the way for microbiome-related risk reduction or therapeutic strategies in CRC. Citation Format: David Hein, Laura Coughlin, Nicole Poulides, Andrew Koh, Nina Sanford. Microbiome and genomic profiling in rectal adenocarcinoma. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 5901.