Eggerthella Lenta Research Articles

Identification of age-associated microbial changes via long-read 16S sequencing

BackgroundAge-related gut microbial changes have been widely investigated over the past decade. Most of the previous age-related microbiome studies were conducted on the Western population, and the short-read sequencing (e.g., 16S V4 or V3-V4 region) was the most common microbiota profiling method. We evaluated the gut compositional differences using the long-read sequencing approach (i.e., PacBio sequencing targeting the full-length V1-V9 regions) to enable a deeper taxonomic resolution and better characterize the gut microbiome of Singaporeans from different age groups.ResultsA total of 83 research participants were included in this study. Although no significant differences were detected in alpha and beta diversity, our study demonstrated several bacterial taxa with abundances that were significantly different across age groups. With young individuals as the reference group, Eggerthella lenta and Bacteroides uniformis were found to be significantly altered in the middle-aged group, while Catenibacterium mitsuokai and Bacteroides plebeius were significantly altered in the elderly group. These age-related differences in the gut microbiome were associated with aberrations in several predicted functional pathways, including dysregulations of pathways related to lipopolysaccharide and tricarboxylic acid cycle in older adults.ConclusionsThe utilization of long-read sequencing facilitated the identification of species- and strain-level differences across age groups, which was challenging with the partial 16S rRNA sequencing approach. Nevertheless, replication studies are warranted to confirm our findings, and if confirmed, further in vitro and in vivo studies are crucial to better understand the impact of the altered levels of age-related bacterial taxa. Additionally, the modest performance of strain-level taxonomic classification using 16S-ITS-23S gene sequences, likely due to the limited depth of currently available alignment databases, highlights the need for optimization and refinement in curating these databases for the long-read sequencing approach.

Diversity in gut microbiota among colorectal cancer patients: findings from a case–control study conducted at a Tunisian University Hospital

PurposeGlobally, colorectal cancer (CRC) is among the most prevalent cancers. One distinctive feature of colorectal cancer is its close relationship to the gut microbiota, which is a crucial component of the tumor microenvironment. Over the last ten years, research has demonstrated that colorectal cancer is accompanied with dysbiosis of gut bacteria, fungi, viruses, and Archaea, and that these alterations may be causal. Objectives: This study aimed to evaluate the disruption of the microorganism composition in the intestine, especially bacteria and to determine their relationship with colorectal cancer.MethodsAn evaluation system for determining colorectal cancer (CRC) risk and prognosis can be established more easily with the help of accurate gut microbiota profiling. Stool samples from 14 CRC patients and 13 controls were collected and the flora relative abundance was measured using targeted quantitative PCR (qPCR) assays to evaluate diagnostic potential of selected biomarkers: Streptococcus gallolyticus and Enterococcus faecalis. Culture and MALDI-TOF mass spectrometry were coupled to identify the gut microbiota in both colorectal cancer and control groups.ResultsCompared with controls, the gut microbiota of CRC patients showed an increase in the abundance of Enterococcus, Fusobacterium and Streptococcus. At the species level, the CRC enriched bacterium including Escherichia coli, Enterococcus faecalis, Fusobacterium nucleatum, Streptococcus gallolyticus, Flavoni fractorplautii and Eggerthella lenta acted as promising biomarkers for early detection of CRC.ConclusionThis study highlights the potential of gut microbiota biomarkers as a promising non-invasive tool for the accurate detection and distinction of individuals with CRC.

Identification of volatile metabolites produced from levodopa metabolism by different bacteria strains of the gut microbiome

Interspecies pathways in the gut microbiome have been shown to metabolize levodopa, the primary treatment for Parkinson’s disease, and reduce its bioavailability. While the enzymatic reactions have been identified, the ability to establish the resulting macromolecules as biomarkers of microbial metabolism remains technically challenging. In this study, we leveraged an untargeted mass spectrometry-based approach to investigate volatile organic compounds (VOCs) produced during levodopa metabolism by Enterococcus faecalis, Clostridium sporogenes, and Eggerthella lenta. We cultured these organisms with and without their respective bioactive metabolites and detected levodopa-induced shifts in VOC profiles. We then utilized bioinformatics to identify significant differences in 2,6-dimethylpyrazine, 4,6-dimethylpyrimidine, and 4,5-dimethylpyrimidine associated with its biotransformation. Supplementing cultures with inhibitors of levodopa-metabolizing enzymes revealed specific modulation of levodopa-associated diazines, verifying their relationship to its metabolism. Furthermore, functional group analysis depicts strain-specific VOC profiles that reflect interspecies differences in metabolic activity that can be leveraged to assess microbiome functionality in individual patients. Collectively, this work identifies previously uncharacterized metabolites of microbe-mediated levodopa metabolism to determine potential indicators of this activity and further elucidate the metabolic capabilities of different gut bacteria.

Discovery of disease-adapted bacterial lineages in inflammatory bowel diseases

Gut bacteria are implicated in inflammatory bowel disease (IBD), but the strains driving these associations are unknown. Large-scale studies of microbiome evolution could reveal the imprint of disease on gut bacteria, thus pinpointing the strains and genes that may underlie inflammation. Here, we use stool metagenomes of thousands of IBD patients and healthy controls to reconstruct 140,000 strain genotypes, revealing hundreds of lineages enriched in IBD. We demonstrate that these strains are ancient, taxonomically diverse, and ubiquitous in humans. Moreover, disease-associated strains outcompete their healthy counterparts during inflammation, implying long-term adaptation to disease. Strain genetic differences map onto known axes of inflammation, including oxidative stress, nutrient biosynthesis, and immune evasion. Lastly, the loss of health-associated strains of Eggerthella lenta was predictive of fecal calprotectin, a biomarker of disease severity. Our work identifies reservoirs of strain diversity that may impact inflammatory disease and can be extended to other microbiome-associated diseases.

Novel screening approach for cancer cachexia using metagenomic gut microbiome profiling in patients with advanced non-small cell lung cancer.

12090 Background: Cancer cachexia (CC) is a multifactorial syndrome involving immune-metabolic crosstalk across multiple organs and has been associated with a negative clinical impact in patients with non-small cell lung cancer (NSCLC) amenable to immune checkpoint inhibitors (ICIs). In parallel, the gut microbiome (GM) has emerged as a key contributor to ICI response. In this study, we aimed to evaluate the association between CC and GM composition and its metabolic potentials. Methods: We collected fecal samples from 139 patients with advanced NSCLC treated with ICI. In addition to 16S rRNA sequencing for all patients, shotgun metagenomic microbiome profiling was performed for 69 patients to estimate the species-level composition and functional capacity of the GM. Cancer cachexia was diagnosed according to the international consensus based on the body weight changes over the previous six months. Survival time was calculated using the Kaplan-Meier method. GM diversity indices, differential abundance, and functional profiles based on the MetaCyc database were compared between the patients with and without CC. Results: Median progression-free survival (PFS) and overall survival (OS) were significantly shorter in the cachexia group compared to the non-cachexia group [4.5 vs. 11.5 months (p < 0.001) and 10.8 vs. 44.9 months (p < 0.01), respectively]. Both GM profiling techniques revealed a significant difference in beta diversity between both groups (p < 0.01). In addition, metagenomic analyses revealed the distinct characteristics of GM at the species level between the groups. The CC group showed an overrepresentation of the commensal bacteria, such as Escherichia coli, Ruthenibacterium lactatiformans, Hungatella hathewayi,and Eggerthella lenta, whereas the non-CC group showed an enrichment of Parabacteroides distasonis, Eubacterium rectale,and Roseburia inulinivorans. Moreover, functional analysis revealed the significantly different metabolic potentials of GM in the CC group. The CC group showed an enrichment of pathways, such as D-arabinose degradation II, L-lysine degradation, and octan oxidation. Finally, the clustering of patients based on significant metabolic pathways or gene reactions provided a high predictive ability to discriminate between patients with and without CC. Conclusions: The shotgun metagenomic approach allowed for the characterization of the altered gut microbes and their metabolic potentials in patients with CC. Stratification based on the GM profiles may be useful as a novel screening method for CC, which is progressive and may involve more multistage pathology than identified by the conventional approach.

Comparative evaluation of antimicrobial activity of spinel structured transition metal ferrites supported on reduced graphene oxide against pathogenic strains of bacteria and fungi.

One of the global challenges for living things is to provide pollution and harmful microbes-free environment. In this study, magnetically retrievable spinel-structured manganese zinc ferrite (Mn0.5Zn0.5Fe2O4) (MZF) was synthesized by a facile solvothermal method. Further, the MZF with different weight percentages (10 wt%, 50 wt%, and 80 wt%) were supported on reduced graphene oxide (rGO). The phase purity and morphology of MZF and MZF/rGO nanocomposite were confirmed by x-ray diffraction technique and scanning electron microscopy, respectively. The Fourier transform infrared spectroscopy, Raman, UV-visible spectroscopy, and thermogravimetric analyses of the as-synthesized nanocomposites were examined for the detection of various chemical groups, band gap, and thermal properties, respectively. The MZF/rGO nanocomposite exhibited significant antibacterial and antifungal activity againstEggerthella lenta, Enterococcus faecalis, Klebsiella pneumonia, Pseudomonas aeruginosa,andCandida albicanscompared to bare MZF and rGO. The high surface area of rGO plays a crucible role in antimicrobial analysis. Additionally, the antibacterial and antifungal activity is compared by synthesizing various metal ferrites such as MnFe2O4, ZnFe2O4, and Fe3O4. The 50 wt% MZF/rGO nanocomposite exhibits significantly high antibacterial activity. However, 10 wt% MZF/rGO nanocomposite shows good antifungal activity than Fe3O4, MnFe2O4, ZnFe2O4, MnZnFe2O4, 50 wt%, and 80 wt% MZF/rGO nanocomposites. These findings suggest that the prepared ferrite nanocomposites hold promise for microbial inhibition.

Gut bacteria convert glucocorticoids into progestins in the presence of hydrogen gas

Recent studies suggest that human-associated bacteria interact with host-produced steroids, but the mechanisms and physiological impact of such interactions remain unclear. Here, we show that the human gut bacteria Gordonibacter pamelaeae and Eggerthella lenta convert abundant biliary corticoids into progestins through 21-dehydroxylation, thereby transforming a class of immuno- and metabo-regulatory steroids into a class of sex hormones and neurosteroids. Using comparative genomics, homologous expression, and heterologous expression, we identify a bacterial gene cluster that performs 21-dehydroxylation. We also uncover an unexpected role for hydrogen gas production by gut commensals in promoting 21-dehydroxylation, suggesting that hydrogen modulates secondary metabolism in the gut. Levels of certain bacterial progestins, including allopregnanolone, better known as brexanolone, an FDA-approved drug for postpartum depression, are substantially increased in feces from pregnant humans. Thus, bacterial conversion of corticoids into progestins may affect host physiology, particularly in the context of pregnancy and women's health.

#983 Identification of gut microbiome signatures associated with albuminuria in diabetes mellitus

Abstract Background and Aims Diabetes is a growing global problem with serious complications, including kidney impairment and cardiovascular morbidity and mortality. Monitoring albuminuria, which is associated with these complications, is crucial in optimal diabetes management. Recent research suggests a link between the gut microbiome, plasma metabolites and albuminuria development in diabetes patients, highlighting the need for further investigation using deep metagenomic sequencing. Method We investigated the relationship between 1002 gut microbial species, 1308 metabolites and albuminuria in 752 participants with diabetes from the Swedish CArdioPulmonary BioImage Study. To determine the relative abundance of species, we employed deep shotgun metagenomic sequencing of fecal samples. Plasma metabolites were analyzed using mass spectrometry-based methods. Results Shannon diversity index was inversely associated with albuminuria after adjusting for confounding factors (Fig. 1). Our multivariable-adjusted models revealed seven metagenomic species that were associated with albuminuria (Fig. 2). Furthermore, employing a global metabolomics approach, we identified phenyl sulfate, among 98 annotated metabolites (Fig. 3), as linked to the species Clostridium sp. AT4 and Eggerthella lenta. Notably, phenyl sulfate is involved in tyrosine metabolism, and we also observed an association between the gut metabolic module of Tyrosine degradation II and albuminuria. Conclusion In the present study, we identified seven gut microbial species linked to albuminuria and established a connection between these species and phenyl sulfate, which previously has been associated with podocyte damage and the development of albuminuria. These findings provided additional evidence of the impact of microbial species and contribute to our understanding of the complex relationship between the gut microbiome, plasma metabolites, and albuminuria in patients with diabetes.

Cognitive Function, Diet, and Gender are Associated with Unique Microbiome Signatures in Cancer Survivors

Despite the development of new and highly effective cancer therapies, emerging evidence suggests that these treatments are associated with long-term side effects, which may contribute to cognitive impairment (CI) or dementia in cancer survivors. Many of these side effects are linked to gut health and a perturbed gut microbiome. However, the role of the gut microbiota in cancer treatment-related side effects, especially in older adults, remains largely unknown. Furthermore, it remains elusive how other factors, such as diet and gender, may impact gut microbiota. We hypothesize that cancer survivors have a distinct microbiome signature compared to non-cancer controls and that CI, diet, and gender are associated with unique microbiomes in survivors. Here, we analyzed the gut microbiome (using whole genome sequencing) and cognitive function (using the Montreal Cognitive Assessment [MoCA]) of 150 older adults (≥ 60 years) from the MiaGB (Microbiome in aging Gut and Brain) consortium. We first assessed microbiome signatures of cancer survivors in our cohort compared to non-cancer controls. We show that the gut of cancer survivors is significantly enriched with Escherichia, Eggerthella lenta, and Lachnospiraceae bacterium OF09 33XD. Next, participants were further stratified based on MoCA score, diet (yogurt/probiotic consumption), and gender and we assessed their microbiota. E. lenta and L. bacterium OF09 33XD remained enriched in cancer survivors when separating based on all three of these factors. We also found that cognitive function, yogurt/probiotic use, and gender were linked with unique microbiome signatures in cancer survivors. Interestingly, the abundances of two well-studied probiotics, Streptococcus thermophilus and Lactobacillus rhamnosus, were significantly low in cancer survivors with CI. Additionally, increased S. thermophilus abundance was positively correlated with MoCA score (Spearman p = 0.054, r = 0.159). Our results indicate that older adult cancer survivors harbor a unique gut microbiome, which could also be impacted by cognitive function, yogurt/probiotic consumption, and gender. Elucidating how these factors modulate the microbiome, independently and together, will aid in the development of novel and precision microbiome-based therapies to combat cancer treatment-related side effects in survivors. We would like to thank the Ed and Ethel Moore Alzheimer’s Disease Research Program of the Florida Department of Health (22A17), the National Institutes of Health, National Institute of Aging (R56AG069676, R56AG064075, RF1AG071762, R21AG072379, U01AG076928), and the Department of Defense (W81XWH-18-PRARP AZ180098) for funding support. This is the full abstract presented at the American Physiology Summit 2024 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.

Fecal microbiota is associated with extraintestinal manifestations in inflammatory bowel disease

Introduction A large proportion of patients with inflammatory bowel disease (IBD) experience IBD-related inflammatory conditions outside of the gastrointestinal tract, termed extraintestinal manifestations (EIMs) which further decreases quality of life and, in extreme cases, can be life threatening. The pathogenesis of EIMs remains unknown, and although gut microbiota alterations are a well-known characteristic of patients with IBD, its relationship with EIMs remains sparsely investigated. This study aimed to compare the gut microbiota of patients with IBD with and without EIMs. Methods A total of 131 Danish patients with IBD were included in the study, of whom 86 had a history of EIMs (IBD-EIM) and 45 did not (IBD-C). Stool samples underwent 16S rRNA sequencing. Amplicon sequence variants (ASVs) were mapped to the Silva database. Diversity indices and distance matrices were compared between IBD-EIM and IBD-C. Differentially abundant ASVs were identified using a custom multiple model statistical analysis approach, and modules of co-associated bacteria were identified using sparse correlations for compositional data (SparCC) and related to patient EIM status. Results Patients with IBD and EIMs exhibited increased disease activity, body mass index, increased fecal calprotectin levels and circulating monocytes and neutrophils. Microbiologically, IBD-EIM exhibited lower fecal microbial diversity than IBD-C (Mann–Whitney’s test, p = .01) and distinct fecal microbiota composition (permutational multivariate analysis of variance; weighted UniFrac, R 2 = 0.018, p = .01). A total of 26 ASVs exhibited differential relative abundances between IBD-EIM and IBD-C, including decreased Agathobacter and Blautia and increased Eggerthella lenta in the IBD-EIM group. SparCC analysis identified 27 bacterial co-association modules, three of which were negatively related to EIM (logistic regression, p < .05) and included important health-associated bacteria, such as Agathobacter and Faecalibacterium. Conclusions The fecal microbiota in IBD patients with EIMs is distinct from that in IBD patients without EIM and could be important for EIM pathogenesis.

Microbial Features Linked to Medication Strategies in Cardiometabolic Disease Management.

Human gut microbiota are recognized as critical players in both metabolic disease and drug metabolism. However, medication-microbiota interactions in cardiometabolic diseases are not well understood. To gain a comprehensive understanding of how medication intake impacts the gut microbiota, we investigated the association of microbial structure with the use of single or multiple medications in a cohort of 134 middle-aged adults diagnosed with cardiometabolic disease, recruited from Alberta's Tomorrow Project. Predominant cardiometabolic prescription medication classes (12 total) were included in our analysis. Multivariate Association with Linear Model (MaAsLin2) was employed and results were corrected for age, BMI, sex, and diet to evaluate the relationship between microbial features and single- or multimedication use. Highly individualized microbiota profiles were observed across participants, and increasing medication use was negatively correlated with α-diversity. A total of 46 associations were identified between microbial composition and single medications, exemplified by the depletion of Akkermansia muciniphila by β-blockers and statins, and the enrichment of Escherichia/Shigella and depletion of Bacteroides xylanisolvens by metformin. Metagenomics prediction further indicated alterations in microbial functions associated with single medications such as the depletion of enzymes involved in energy metabolism encoded by Eggerthella lenta due to β-blocker use. Specific dual medication combinations also had profound impacts, including the depletion of Romboutsia and Butyriciocccus by statin plus metformin. Together, these results show reductions in bacterial diversity as well as species and microbial functional potential associated with both single- and multimedication use in cardiometabolic disease.

A case of bacteremia caused by Dialister micraerophilus with Enterocloster clostridioformis and Eggerthella lenta in a patient with pyometra

BackgroundInfection by Dialister micraerophilus, an obligate anaerobic gram-negative bacillus, has rarely been described, and its clinical characteristics remain unclear.Case presentationWe report a case of bacteremia caused by D. micraerophilus, Enterocloster clostridioformis, and Eggerthella lenta in a 47-year-old woman, associated with pyometra. D. micraerophilus was identified using 16S rRNA gene sequencing and matrix-assisted laser desorption ionization time-of-flight mass spectrometry. D. micraerophilus was detected by polymerase chain reaction using D. micraerophilus-specific primers and E. clostridioformis and E. lenta was isolated from the drainage pus sample obtained from the pyometra uterus. The patient achieved a cure after abscess drainage and 2-week antibiotic treatment.ConclusionsTo the best of our knowledge, this is the first report of D. micraerophilus bacteremia. D. micraerophilus may be associated with gynecological infections. Clinicians should consider both oral and gynecological sites when searching to identify the focus of D. micraerophilus infection.

The human intestinal bacterium Eggerthella lenta influences gut metabolomes in gnotobiotic mice.

The intestinal microbiota and its metabolites are known to influence host metabolic health. However, little is known about the role of specific microbes. In this work, we used the minimal consortium Oligo-Mouse-Microbiota (OMM12) to study the function of Coriobacteriia under defined conditions in gnotobiotic mice. OMM12 mice with or without the addition of the dominant gut bacterium Eggerthella lenta (E. lenta) were fed with diets varying in fat content and primary bile acids. E. lenta stably colonised the mouse caecum at high relative abundances (median: 27.5%). This was accompanied by decreased occurrence of Akkermansia muciniphila and Enterococcus faecalis, but results did not reach statistical significance in all groups depending on diet and inter-individual differences. Changes in host parameters (anthropometry, blood glucose, and cholesterol) and liver proteomes were primarily due to diet. In contrast, metabolomes in colon content differed significantly between the colonisation groups. The presence of E. lenta was associated with elevated levels of latifolicinin C acid and decreased creatine, sarcosine, N,N-dimethylarginine, and N-Acetyl-DL-methionine. In conclusion, E. lenta altered specific metabolites in the colon but did not have significant effects on the mice or liver proteomes under the conditions tested due to marked inter-individual differences.

Dietary- and host-derived metabolites are used by diverse gut bacteria for anaerobic respiration.

Respiratory reductases enable microorganisms to use molecules present in anaerobic ecosystems as energy-generating respiratory electron acceptors. Here we identify three taxonomically distinct families of human gut bacteria (Burkholderiaceae, Eggerthellaceae and Erysipelotrichaceae) that encode large arsenals of tens to hundreds of respiratory-like reductases per genome. Screening species from each family (Sutterella wadsworthensis, Eggerthella lenta and Holdemania filiformis), we discover 22 metabolites used as respiratory electron acceptors in a species-specific manner. Identified reactions transform multiple classes of dietary- and host-derived metabolites, including bioactive molecules resveratrol and itaconate. Products of identified respiratory metabolisms highlight poorly characterized compounds, such as the itaconate-derived 2-methylsuccinate. Reductase substrate profiling defines enzyme-substrate pairs and reveals a complex picture of reductase evolution, providing evidence that reductases with specificities for related cinnamate substrates independently emerged at least four times. These studies thus establish an exceptionally versatile form of anaerobic respiration that directly links microbial energy metabolism to the gut metabolome.

UNIQUE MICROBIOME SIGNATURES RELATED TO CANCER SURVIVORSHIP AND COGNITIVE DECLINE IN OLDER ADULTS

Abstract Significant scientific advancements have resulted in new and effective therapies for patients with cancer. Although this leads to an increased cancer survivor population, there are several long-term side effects of cancer treatments, including a high risk of developing dementia. Emerging evidence shows that the gut microbiota significantly contributes to brain health and dementia pathology; however, its role in cancer treatment-related side effects, specifically in older adults, is not well known. Here, we used 110 participants from our MiaGB (Microbiome in aging Gut and Brain) consortium aged 60 years and older and analyzed their gut microbiome (using whole genome sequencing) with cognitive function (using Montreal Cognitive Assessment (MoCA) and MiniCog). We observed an 8% increase in cognitive impairment (CI) in cancer survivors compared to non-cancer participants (46% vs 38%, respectively). When only comparing cognitively healthy versus CI, the abundance of Escherichia coli was significantly higher in the CI group, while Streptococcus thermophilus was higher in the cognitively healthy group. Additionally, the abundances of Dorea sp. CAG 317, Ruminococcus gnavus, Roseburia faecis, and Eggerthella lenta were significantly increased in the gut of cancer survivors compared to non-cancer participants. Specifically, the abundance of Dorea sp. CAG 317 was increased in cancer survivors with CI. These findings suggest that unique microbiome signatures induced by cancer treatments may impair cognitive function. Furthermore, understanding the associations between the microbiota and cognitive function in cancer survivors will aid the development of therapeutics to combat cancer treatment-related side effects, which are a growing public health concern.

Identification of inulin-responsive bacteria in the gut microbiota via multi-modal activity-based sorting

Prebiotics are defined as non-digestible dietary components that promote the growth of beneficial gut microorganisms. In many cases, however, this capability is not systematically evaluated. Here, we develop a methodology for determining prebiotic-responsive bacteria using the popular dietary supplement inulin. We first identify microbes with a capacity to bind inulin using mesoporous silica nanoparticles functionalized with inulin. 16S rRNA gene amplicon sequencing of sorted cells revealed that the ability to bind inulin was widespread in the microbiota. We further evaluate which taxa are metabolically stimulated by inulin and find that diverse taxa from the phyla Firmicutes and Actinobacteria respond to inulin, and several isolates of these taxa can degrade inulin. Incubation with another prebiotic, xylooligosaccharides (XOS), in contrast, shows a more robust bifidogenic effect. Interestingly, the Coriobacteriia Eggerthella lenta and Gordonibacter urolithinfaciens are indirectly stimulated by the inulin degradation process, expanding our knowledge of inulin-responsive bacteria.

Abstract B034: Characterization of a dual steroid 3β-,17β-oxidoreductase in the gut bacterium Eggerthella lenta

Abstract As of 2023 there are over 200,000 new cases and over 30,000 deaths caused by prostate cancer with African-American (AA) men having a higher incidence then other ethnicities according to the American Cancer Society. Although numerous therapeutic methods are used to treat prostate cancer such as hormone therapy, radiation therapy, chemotherapy, and chemical castration, prostate cancer often becomes metastatic resulting in death with the five year survival rate for AA men presenting with castration resistant prostate cancer (CRPC) being ~ 32%. Androgen production is known to be the main driver of CRPC progression. Researchers are baffled as to why this progression is taking place after patients have received a combination of these therapeutic methods to stop androgen production and metabolism. Eggerthella lenta has a long history as an important bile acid and steroid metabolizing gut microbial species. We and others have previously published on the extensive oxidation and epimerization of bile acid hydoxyl groups. Previous work demonstrated that E. lenta may be involved in the conversion of 17-keto steroids to testosterone. By cloning, expressing, and purifying genes predicted to encode pyridine nucleotide-dependent oxidoreductases from E. lenta DSM 2243, we identified a recombinant enzyme with dual 3beta, 17beta-hydroxysteroid dehydrogenase activity. We performed kinetic analysis on both 5alpha-reduced bile acids ("allo"-bile acids) and 5alpha-reduced steroids. There is a paucity of work at present on gut bacteria that metabolize the 17beta-hydroxy group on steroids, so this observation demonstrates that a unique enzyme in the gut microbiome can alter host steroids. These findings are consistent with the possibility that gut or urinary tract bacteria may contribute to CRPC. Citation Format: Briawna J. Binion, Rex Gaskins, Jason Ridlon. Characterization of a dual steroid 3β-,17β-oxidoreductase in the gut bacterium Eggerthella lenta [abstract]. In: Proceedings of the 16th AACR Conference on the Science of Cancer Health Disparities in Racial/Ethnic Minorities and the Medically Underserved; 2023 Sep 29-Oct 2;Orlando, FL. Philadelphia (PA): AACR; Cancer Epidemiol Biomarkers Prev 2023;32(12 Suppl):Abstract nr B034.

Exploring the role of gut microbiota in advancing personalized medicine

Ongoing extensive research in the field of gut microbiota (GM) has highlighted the crucial role of gut-dwelling microbes in human health. These microbes possess 100 times more genes than the human genome and offer significant biochemical advantages to the host in nutrient and drug absorption, metabolism, and excretion. It is increasingly clear that GM modulates the efficacy and toxicity of drugs, especially those taken orally. In addition, intra-individual variability of GM has been shown to contribute to drug response biases for certain therapeutics. For instance, the efficacy of cyclophosphamide depends on the presence of Enterococcus hirae and Barnesiella intestinihominis in the host intestine. Conversely, the presence of inappropriate or unwanted gut bacteria can inactivate a drug. For example, dehydroxylase of Enterococcus faecalis and Eggerthella lenta A2 can metabolize L-dopa before it converts into the active form (dopamine) and crosses the blood–brain barrier to treat Parkinson’s disease patients. Moreover, GM is emerging as a new player in personalized medicine, and various methods are being developed to treat diseases by remodeling patients’ GM composition, such as prebiotic and probiotic interventions, microbiota transplants, and the introduction of synthetic GM. This review aims to highlight how the host’s GM can improve drug efficacy and discuss how an unwanted bug can cause the inactivation of medicine.

Methanomethylophilus alvi gen. nov., sp. nov., a Novel Hydrogenotrophic Methyl-Reducing Methanogenic Archaea of the Order Methanomassiliicoccales Isolated from the Human Gut and Proposal of the Novel Family Methanomethylophilaceae fam. nov.

The methanogenic strain Mx-05T was isolated from the human fecal microbiome. A phylogenetic analysis based on the 16S rRNA gene and protein marker genes indicated that the strain is affiliated with the order Methanomassiliicoccales. It shares 86.9% 16S rRNA gene sequence identity with Methanomassiliicoccus luminyensis, the only member of this order previously isolated. The cells of Mx-05T were non-motile cocci, with a diameter range of 0.4-0.7 μm. They grew anaerobically and reduced methanol, monomethylamine, dimethylamine, and trimethylamine into methane, using H2 as an electron donor. H2/CO2, formate, ethanol, and acetate were not used as energy sources. The growth of Mx-05T required an unknown medium factor(s) provided by Eggerthella lenta and present in rumen fluid. Mx-05T grew between 30 °C and 40 °C (optimum 37 °C), over a pH range of 6.9-8.3 (optimum pH 7.5), and between 0.02 and 0.34 mol.L-1 NaCl (optimum 0.12 mol.L-1 NaCl). The genome is 1.67 Mbp with a G+C content of 55.5 mol%. Genome sequence annotation confirmed the absence of the methyl branch of the H4MPT Wood-Ljungdahl pathway, as described for other Methanomassiliicoccales members. Based on an average nucleotide identity analysis, we propose strain Mx-05T as being a novel representative of the order Methanomassiliicoccales, within the novel family Methanomethylophilaceae, for which the name Methanomethylophilus alvi gen. nov, sp. nov. is proposed. The type strain is Mx-05T (JCM 31474T).

Simvastatin induces human gut bacterial cell surface genes.

Drugs intended to target mammalian cells can have broad off-target effects on the human gut microbiota with potential downstream consequences for drug efficacy and side effect profiles. Yet, despite a rich literature on antibiotic resistance, we still know very little about the mechanisms through which commensal bacteria evade non-antibiotic drugs. Here, we focus on statins, one of the most prescribed drug types in the world and an essential tool in the prevention and treatment of high circulating cholesterol levels. Prior work in humans, mice, and cell culture support an off-target effect of statins on human gut bacteria; however, the genetic determinants of statin sensitivity remain unknown. We confirmed that simvastatin inhibits the growth of diverse human gut bacterial strains grown in communities and in pure cultures. Drug sensitivity varied between phyla and was dose-dependent. We selected two representative simvastatin-sensitive species for more in-depth analysis: Eggerthella lenta (phylum: Actinobacteriota) and Bacteroides thetaiotaomicron (phylum: Bacteroidota). Transcriptomics revealed that both bacterial species upregulate genes in response to simvastatin that alter the cell membrane, including fatty acid biogenesis (E. lenta) and drug efflux systems (B. thetaiotaomicron). Transposon mutagenesis identified a key efflux system in B. thetaiotaomicron that enables growth in the presence of statins. Taken together, these results emphasize the importance of the bacterial cell membrane in countering the off-target effects of host-targeted drugs. Continued mechanistic dissection of the various mechanisms through which the human gut microbiota evades drugs will be essential to understand and predict the effects of drug administration in human cohorts and the potential downstream consequences for health and disease.