Changes In Microbiome Composition Research Articles

Take a Walk to the Wild Side of Caenorhabditis elegans-Pathogen Interactions.

Microbiomes form intimate functional associations with their hosts. Much has been learned from correlating changes in microbiome composition to host organismal functions. However, in-depth functional studies require the manipulation of microbiome composition coupled with the precise interrogation of organismal physiology-features available in few host study systems. Caenorhabditis elegans has proven to be an excellent genetic model organism to study innate immunity and, more recently, microbiome interactions. The study of C. elegans-pathogen interactions has provided in depth understanding of innate immune pathways, many of which are conserved in other animals. However, many bacteria were chosen for these studies because of their convenience in the lab setting or their implication in human health rather than their native interactions with C. elegans In their natural environment, C. elegans feed on a variety of bacteria found in rotting organic matter, such as rotting fruits, flowers, and stems. Recent work has begun to characterize the native microbiome and has identified a common set of bacteria found in the microbiome of C. elegans While some of these bacteria are beneficial to C. elegans health, others are detrimental, leading to a complex, multifaceted understanding of bacterium-nematode interactions. Current research on nematode-bacterium interactions is focused on these native microbiome components, both their interactions with each other and with C. elegans We will summarize our knowledge of bacterial pathogen-host interactions in C. elegans, as well as recent work on the native microbiome, and explore the incorporation of these bacterium-nematode interactions into studies of innate immunity and pathogenesis.

Acute cyanotoxin poisoning reveals a marginal effect on mouse gut microbiome composition but indicates metabolic shifts related to liver and gut inflammation

Freshwater harmful algal blooms (HABs) are a major environmental health problem worldwide. HABs are caused by a predominance of cyanobacteria, some of which produce potent toxins. The most ubiquitous cyanotoxin is microcystin (MC) and the congener MC-LR is the most studied due to its toxicity. Short-term exposure to toxins can cause gut microbiome disturbances, but this has not been well described with MC-LR exposure. This study investigated the gut microbial communities of mice from a prior study, which identified significant liver toxicity from ingestion of MC-LR daily for 8 days. CD-1 mice were divided into three dosage groups: control, low exposure (sub-lethal MC-LR concentration), and high exposure (near-lethal MC-LR concentration). Fecal samples were analyzed using 16S rRNA sequencing. Results revealed that at population level, there were no significant shifts in bacterial diversity or the microbial community structure over the exposure period. However, there were significant differences between male and female mice. Predictive functional gene analysis indicated that several metabolic pathways were significantly different in the high dose group before exposure and following 7 doses of MC-LR, as well as between the control and high dose groups on Day 8. Significant differentially abundant taxa were also identified contributing to these pathways. Several pathways, including superpathway of N-acetylneuraminate degradation, were related to liver and gut inflammation. The outcome of this study suggests a need for in-depth investigation of metabolic activity and other functions in the gut in future studies, as well as potential consideration of the role of sex in MC-LR toxicity.

Explainable AI reveals changes in skin microbiome composition linked to phenotypic differences

Alterations in the human microbiome have been observed in a variety of conditions such as asthma, gingivitis, dermatitis and cancer, and much remains to be learned about the links between the microbiome and human health. The fusion of artificial intelligence with rich microbiome datasets can offer an improved understanding of the microbiome’s role in human health. To gain actionable insights it is essential to consider both the predictive power and the transparency of the models by providing explanations for the predictions. We combine the collection of leg skin microbiome samples from two healthy cohorts of women with the application of an explainable artificial intelligence (EAI) approach that provides accurate predictions of phenotypes with explanations. The explanations are expressed in terms of variations in the relative abundance of key microbes that drive the predictions. We predict skin hydration, subject's age, pre/post-menopausal status and smoking status from the leg skin microbiome. The changes in microbial composition linked to skin hydration can accelerate the development of personalized treatments for healthy skin, while those associated with age may offer insights into the skin aging process. The leg microbiome signatures associated with smoking and menopausal status are consistent with previous findings from oral/respiratory tract microbiomes and vaginal/gut microbiomes respectively. This suggests that easily accessible microbiome samples could be used to investigate health-related phenotypes, offering potential for non-invasive diagnosis and condition monitoring. Our EAI approach sets the stage for new work focused on understanding the complex relationships between microbial communities and phenotypes. Our approach can be applied to predict any condition from microbiome samples and has the potential to accelerate the development of microbiome-based personalized therapeutics and non-invasive diagnostics.

How Diet-Induced Changes in the “Gut-Liver” Axis Affect Chronic Liver Disease Outcome?

Hepatocellular carcinoma (HCC) occurs in patients with chronic liver damage, inflammation and cirrhosis. The facilitators involved in increasing the HCC risk in the damaged liver are yet to be discovered. Diet and lifestyle have a profound effect on the liver inflammation and HCC. The term “gut liver axis” describes the bidirectional relationship between the liver and the gut, which are both anatomically and functionally related. Chronic liver damage is characterised by increased intestinal permeability that allows the translocation of various components and metabolites from the gut microbiota to the liver, resulting in liver inflammation and fibrosis. In this review, we discuss how diet-induced changes in gut microbiome composition, such as lipopolysaccharide and lipoteichoic acid, and its metabolites, such as bile acids, play a role in the pathogenesis of liver fibrosis and HCC.

Gut Microbiome Profiles and Associated Metabolic Pathways in HIV-Infected Treatment-Naïve Patients.

The normal composition of the intestinal microbiota is a key factor for maintaining healthy homeostasis, and accordingly, dysbiosis is well known to be present in HIV-1 patients. This article investigates the gut microbiota profile of antiretroviral therapy-naive HIV-1 patients and healthy donors living in Latin America in a cohort of 13 HIV positive patients (six elite controllers, EC, and seven non-controllers, NC) and nine healthy donors (HD). Microbiota compositions in stool samples were determined by sequencing the V3-V4 region of the bacterial 16S rRNA, and functional prediction was inferred using PICRUSt. Several taxa were enriched in EC compared to NC or HD groups, including Acidaminococcus, Clostridium methylpentosum, Barnesiella, Eubacterium coprostanoligenes, and Lachnospiraceae UCG-004. In addition, our data indicate that the route of infection is an important factor associated with changes in gut microbiome composition, and we extend these results by identifying several metabolic pathways associated with each route of infection. Importantly, we observed several bacterial taxa that might be associated with different viral subtypes, such as Succinivibrio, which were more abundant in patients infected by HIV subtype B, and Streptococcus enrichment in patients infected by subtype C. In conclusion, our data brings a significant contribution to the understanding of dysbiosis-associated changes in HIV infection and describes, for the first time, differences in microbiota composition according to HIV subtypes. These results warrant further confirmation in a larger cohort of patients.

Examining the Role of Microbiota in Emotional Behavior: Antibiotic Treatment Exacerbates Anxiety in High Anxiety-Prone Male Rats

Intestinal microbiota are essential for healthy gastrointestinal function and also broadly influence brain function and behavior, in part, through changes in immune function. Gastrointestinal disorders are highly comorbid with psychiatric disorders, although biological mechanisms linking these disorders are poorly understood. The present study utilized rats bred for distinct emotional behavior phenotypes to examine relationships between emotionality, the microbiome, and immune markers. Prior work showed that Low Novelty Responder (LR) rats exhibit high levels of anxiety- and depression-related behaviors as well as myriad neurobiological differences compared to High Novelty Responders (HRs). Here, we hypothesized that the divergent HR/LR phenotypes are accompanied by changes in fecal microbiome composition. We used next-generation sequencing to assess the HR/LR microbiomes and then treated adult HR/LR males with an antibiotic cocktail to test whether it altered behavior. Given known connections between the microbiome and immune system, we also analyzed circulating cytokines and metabolic factors to determine relationships between peripheral immune markers, gut microbiome components, and behavioral measures. There were no baseline HR/LR microbiome differences, and antibiotic treatment disrupted the microbiome in both HR and LR rats. Antibiotic treatment exacerbated aspects of HR/LR behavior, increasing LRs’ already high levels of anxiety-like behavior while reducing passive stress coping in both strains. Our results highlight the importance of an individual’s phenotype to their response to antibiotics, contributing to the understanding of the complex interplay between gut microbes, immune function, and an individual’s emotional phenotype.

The pleiotropic effects of prebiotic galacto-oligosaccharides on the aging gut

BackgroundPrebiotic galacto-oligosaccharides (GOS) have an extensively demonstrated beneficial impact on intestinal health. In this study, we determined the impact of GOS diets on hallmarks of gut aging: microbiome dysbiosis, inflammation, and intestinal barrier defects (“leaky gut”). We also evaluated if short-term GOS feeding influenced how the aging gut responded to antibiotic challenges in a mouse model of Clostridioides difficile infection. Finally, we assessed if colonic organoids could reproduce the GOS responder—non-responder phenotypes observed in vivo.ResultsOld animals had a distinct microbiome characterized by increased ratios of non-saccharolytic versus saccharolytic bacteria and, correspondingly, a lower abundance of β-galactosidases compared to young animals. GOS reduced the overall diversity, increased the abundance of specific saccharolytic bacteria (species of Bacteroides and Lactobacillus), increased the abundance of β-galactosidases in young and old animals, and increased the non-saccharolytic organisms; however, a robust, homogeneous bifidogenic effect was not observed. GOS reduced age-associated increased intestinal permeability and increased MUC2 expression and mucus thickness in old mice. Clyndamicin reduced the abundance Bifidobacterium while increasing Akkermansia, Clostridium, Coprococcus, Bacillus, Bacteroides, and Ruminococcus in old mice. The antibiotics were more impactful than GOS on modulating serum markers of inflammation. Higher serum levels of IL-17 and IL-6 were observed in control and GOS diets in the antibiotic groups, and within those groups, levels of IL-6 were higher in the GOS groups, regardless of age, and higher in the old compared to young animals in the control diet groups. RTqPCR revealed significantly increased gene expression of TNFα in distal colon tissue of old mice, which was decreased by the GOS diet. Colon transcriptomics analysis of mice fed GOS showed increased expression of genes involved in small-molecule metabolic processes and specifically the respirasome in old animals, which could indicate an increased oxidative metabolism and energetic efficiency. In young mice, GOS induced the expression of binding-related genes. The galectin gene Lgals1, a β-galactosyl-binding lectin that bridges molecules by their sugar moieties and is an important modulator of the immune response, and the PI3K-Akt and ECM-receptor interaction pathways were also induced in young mice. Stools from mice exhibiting variable bifidogenic response to GOS injected into colon organoids in the presence of prebiotics reproduced the response and non-response phenotypes observed in vivo suggesting that the composition and functionality of the microbiota are the main contributors to the phenotype.ConclusionsDietary GOS modulated homeostasis of the aging gut by promoting changes in microbiome composition and host gene expression, which was translated into decreased intestinal permeability and increased mucus production. Age was a determining factor on how prebiotics impacted the microbiome and expression of intestinal epithelial cells, especially apparent from the induction of galectin-1 in young but not old mice.7Hn5CXANwfeha3RgfUXqAuVideo abstract

Fecal IgA, Antigen Absorption, and Gut Microbiome Composition Are Associated With Food Antigen Sensitization in Genetically Susceptible Mice.

Food allergy is a potentially fatal disease affecting 8% of children and has become increasingly common in the past two decades. Despite the prevalence and severe nature of the disease, the mechanisms underlying sensitization remain to be further elucidated. The Collaborative Cross is a genetically diverse panel of inbred mice that were specifically developed to study the influence of genetics on complex diseases. Using this panel of mouse strains, we previously demonstrated CC027/GeniUnc mice, but not C3H/HeJ mice, develop peanut allergy after oral exposure to peanut in the absence of a Th2-skewing adjuvant. Here, we investigated factors associated with sensitization in CC027/GeniUnc mice following oral exposure to peanut, walnut, milk, or egg. CC027/GeniUnc mice mounted antigen-specific IgE responses to peanut, walnut and egg, but not milk, while C3H/HeJ mice were not sensitized to any antigen. Naïve CC027/GeniUnc mice had markedly lower total fecal IgA compared to C3H/HeJ, which was accompanied by stark differences in gut microbiome composition. Sensitized CC027/GeniUnc mice had significantly fewer CD3+ T cells but higher numbers of CXCR5+ B cells and T follicular helper cells in the mesenteric lymph nodes compared to C3H/HeJ mice, which is consistent with their relative immunoglobulin production. After oral challenge to the corresponding food, peanut- and walnut-sensitized CC027/GeniUnc mice experienced anaphylaxis, whereas mice exposed to milk and egg did not. Ara h 2 was detected in serum collected post-challenge from peanut-sensitized mice, indicating increased absorption of this allergen, while Bos d 5 and Gal d 2 were not detected in mice exposed to milk and egg, respectively. Machine learning on the change in gut microbiome composition as a result of food protein exposure identified a unique signature in CC027/GeniUnc mice that experienced anaphylaxis, including the depletion of Akkermansia. Overall, these results demonstrate several factors associated with enteral sensitization in CC027/GeniUnc mice, including diminished total fecal IgA, increased allergen absorption and altered gut microbiome composition. Furthermore, peanuts and tree nuts may have inherent properties distinct from milk and eggs that contribute to allergy.

Effect of green-Mediterranean diet on intrahepatic fat: the DIRECT PLUS randomised controlled trial

ObjectiveTo examine the effectiveness of green-Mediterranean (MED) diet, further restricted in red/processed meat, and enriched with green plants and polyphenols on non-alcoholic fatty liver disease (NAFLD), reflected by intrahepatic fat...

The clinical and microbiological utility of inhaled aztreonam lysine for the treatment of acute pulmonary exacerbations of cystic fibrosis: An open-label randomised crossover study (AZTEC-CF)

BackgroundThe objective of this study was to explore the clinical and microbiological outcomes associated with substituting inhaled aztreonam lysine for an intravenous antibiotic in the treatment of acute pulmonary exacerbations of CF. MethodsAn open-label randomised crossover pilot trial was conducted at a UK CF centre among 16 adults with CF and P. aeruginosa infection. Median [IQR] age was 29.5 [24.5-32.5], mean ± SD forced expiratory volume in 1 second (FEV1) was 52.4 ± 14.7 % predicted. Over the course of two exacerbations, participants were randomised to sequentially receive 14 days of inhaled aztreonam lysine plus IV colistimethate (AZLI+IV), or dual IV antibiotics (IV+IV). Primary outcome was absolute change in % predicted FEV1. Other outcomes evaluated changes in quality of life, bacterial load and the lung microbiota. ResultsThe difference between mean change in lung function at day 14 between AZLI+IV and IV+IV was +4.6% (95% CI 2.1-7.2, p=0.002). The minimum clinically important difference of the Cystic Fibrosis Revised Questionnaire (CFQ-R) was achieved more frequently with AZLI+IV (10/12, 83.3%) than IV+IV (7/16, 43.8%), p=0.05. No differences were observed for modulation of serum white cell count, C-reactive protein or sputum bacterial load. Microbiome compositional changes were observed with IV+IV (Bray-Curtis r2=0.14, p=0.02), but not AZLI+IV (r2=0.03, p=0.64). ConclusionIn adults with CF and P. aeruginosa infection experiencing an acute pulmonary exacerbation, AZLI+IV improved lung function and quality of life compared to the current standard treatment. These findings support the need for larger definitive trials of inhaled antibiotics in the acute setting. Clinical trial registrationEudraCT 2016-002832-34ClinicalTrials.org NCT02894684

Alcoholic fatty liver disease inhibited the co-expression of Fmo5 and PPAR\u03b1 to activate the NF-\u03baB signaling pathway, thereby reducing liver injury via inducing gut microbiota disturbance

BackgroundAlcohol-induced intestinal dysbiosis disrupts and inflammatory responses are essential in the development of alcoholic fatty liver disease (AFLD). Here, we investigated the effects of Fmo5 on changes in enteric microbiome composition in a model of AFLD and dissected the pathogenic role of Fmo5 in AFLD-induced liver pathology.MethodsThe expression profile data of GSE8006 and GSE40334 datasets were downloaded from the GEO database. The WGCNA approach allowed us to investigate the AFLD-correlated module. DEGs were used to perform KEGG pathway enrichment analyses. Four PPI networks were constructed using the STRING database and visualized using Cytoscape software. The Cytohubba plug-in was used to identify the hub genes. Western blot and immunohistochemistry assays were used to detect protein expression. ELISA assay was used to detect the levels of serum inflammatory cytokines. Lipid droplets in the cytoplasm were observed using Oil Red O staining. Apoptosis was detected using a TUNEL assay and flow cytometry analysis. ROS levels were detected using flow cytometry analysis. Nuclear translocation of NF-κB p65 was observed using immunofluorescence staining. Co-immunoprecipitation was used to detect the co-expression of PPARα and Fmo5 in L02 cells. 16S rDNA sequencing defined the bacterial communities in mice with AFLD.ResultsFmo5 is a key DEG and is closely associated with the gut microbiota and PPAR signaling pathway. Gut microbiome function in AFLD was significantly related to the PPAR signaling pathway. AFLD induced shifts in various bacterial phyla in the cecum, including a reduction in Bacteroidetes and increased Firmicutes. Fmo5 and PPARα co-expression in cell and animal models with AFLD, which decreased significantly. Silencing of Fmo5 and PPARα aggravated the functions of AFLD inducing apoptosis and inflammatory response, promoting liver injury, and activating the NF-κB signaling pathway in vivo and in vitro. The NF-κB inhibitor abolished the functions of silencing of Fmo5 and PPARα promoting AFLD-induced apoptosis, inflammatory response, and liver injury.ConclusionOur data indicated that the co-expression of Fmo5 and PPARα was involved in AFLD-related gut microbiota composition and alleviated AFLD-induced liver injury, apoptosis, and inflammatory response by inhibiting the nuclear translocation of NF-κB p65 to inhibit the NF-κB signaling pathway.

Dynamic Changes in Microbiome Composition and Genomic Functional Potentials in Bovine Mastitis

We provide a mini review on the previously published study entitled “Microbiome Dynamics of Bovine Mastitis Progression and Genomic Determinants”, where we reported the possible dynamic changes in microbiome compositions favored by their genomic functional potentials in different pathophysiological states of bovine mastitis. Using the cutting-edge whole metagenome sequencing (WMS) approach, we reported distinct variation in microbiome composition and abundances across the clinical mastitis (CM), recurrent clinical mastitis (RCM), subclinical mastitis (SCM) and healthy (H) milk metagenomes (CM>H>RCM>SCM). Bacteria were the predominating microbial domain (>99.0% relative abundance) followed by archaea and viruses. Dynamic changes in bacteriome composition across the four metagenomes were numerically dominated by 67.19% inclusion of previously unreported opportunistic strains in mastitis metagenomes. This study also reported the unique and shared distribution of microbiomes across these metagenomes. In addition to microbiome composition and diversity, the study reported the association of several virulence factors-associated genes (VFGs), and antibiotic resistant genes (AGRs) in CM, RCM, SCM, and H-microbiomes. Functional annotation detected several metabolic pathways related to different episodes of mastitis. Therefore, the published data revealed that changes in microbiome composition in different types of mastitis, concurrent assessment of VFGS, ARGs, and genomic functional potentials can contribute to develop microbiome-based diagnostics, and therapeutics for mastitis, and carries significant implications on curtailing the economic fallout from this disease

Low production of 12α-hydroxylated bile acids prevents hepatic steatosis in Cyp2c70−/− mice by reducing fat absorption

Bile acids (BAs) play important roles in lipid homeostasis, and BA signaling pathways serve as therapeutic targets for nonalcoholic fatty liver disease (NAFLD). Recently, we generated cytochrome P450, family 2, subfamily C, polypeptide 70 (Cyp2c70−/−) mice with a human-like BA composition lacking mouse-/rat-specific muricholic acids to accelerate translation from mice to humans. We employed this model to assess the consequences of a human-like BA pool on diet-induced obesity and NAFLD development. Male and female Cyp2c70−/− mice and WT littermates were challenged with a 12-week high-fat Western-type diet (WTD) supplemented with 0.25% cholesterol. Cyp2c70 deficiency induced a hydrophobic BA pool with high abundances of chenodeoxycholic acid, particularly in females, because of sex-dependent suppression of sterol 12α-hydroxylase (Cyp8b1). Plasma transaminases were elevated, and hepatic fibrosis was present in Cyp2c70−/− mice, especially in females. Surprisingly, female Cyp2c70−/− mice were resistant to WTD-induced obesity and hepatic steatosis, whereas male Cyp2c70−/− mice showed similar adiposity and moderately reduced steatosis compared with WT controls. Both intestinal cholesterol and FA absorption were reduced in Cyp2c70−/− mice, the latter more strongly in females, despite unaffected biliary BA secretion rates. Intriguingly, the biliary ratio 12α-/non-12α-hydroxylated BAs significantly correlated with FA absorption and hepatic triglyceride content as well as with specific changes in gut microbiome composition. The hydrophobic human-like BA pool in Cyp2c70−/− mice prevents WTD-induced obesity in female mice and NAFLD development in both genders, primarily because of impaired intestinal fat absorption. Our data point to a key role for 12α-hydroxylated BAs in control of intestinal fat absorption and modulation of gut microbiome composition.

Microbiota associated with echinoid eggs and the implications for maternal provisioning

Mothers impact the survival and performance of their offspring through the resources they provision, and the degree of maternal investment in an individual offspring can be broadly estimated by egg size for organisms that lack parental care. Animals may also actively maintain symbiotic partnerships with microorganisms through the germ line, but whether microbes are a fundamental component of maternal provisioning is an untested hypothesis in evolutionary symbiosis. We present a preliminary test of this by comparing the egg-associated microbiota of 10 sea urchin species with ecological factors known to influence egg size. We found that the microbiota associated with sea urchin eggs had a phylogenetic signal in both composition and richness, which varied between years but not between individuals or within a clutch. Moreover, we found a negative correlation between microbiome richness and taxonomic dominance, and that community diversity covaried with egg size and energetic content but not with pelagic larval duration or latitude. These data suggest that there are multiple parallels between the ecological factors that govern changes in egg size and microbiome composition and diversity, implying that microbial symbionts may be another constituent potentially provided by the mother.

Effects of fecal microbiota transplant on DNA methylation in subjects with metabolic syndrome

ABSTRACT Accumulating evidence shows that microbes with their theater of activity residing within the human intestinal tract (i.e., the gut microbiome) influence host metabolism. Some of the strongest results come from recent fecal microbial transplant (FMT) studies that relate changes in intestinal microbiota to various markers of metabolism as well as the pathophysiology of insulin resistance. Despite these developments, there is still a limited understanding of the multitude of effects associated with FMT on the general physiology of the host, beyond changes in gut microbiome composition. We examined the effect of either allogenic (lean donor) or autologous FMTs on the gut microbiome, plasma metabolome, and epigenomic (DNA methylation) reprogramming in peripheral blood mononuclear cells in individuals with metabolic syndrome measured at baseline (pre-FMT) and after 6 weeks (post-FMT). Insulin sensitivity was determined with a stable isotope-based 2 step hyperinsulinemic clamp and multivariate machine learning methodology was used to uncover discriminative microbes, metabolites, and DNA methylation loci. A larger gut microbiota shift was associated with an allogenic than with autologous FMT. Furthemore, the data results of the the allogenic FMT group data indicates that the introduction of new species can potentially modulate the plasma metabolome and (as a result) the epigenome. Most notably, the introduction of Prevotella ASVs directly correlated with methylation of AFAP1, a gene involved in mitochondrial function, insulin sensitivity, and peripheral insulin resistance (Rd, rate of glucose disappearance). FMT was found to have notable effects on the gut microbiome but also on the host plasma metabolome and the epigenome of immune cells providing new avenues of inquiry in the context of metabolic syndrome treatment for the manipulation of host physiology to achieve improved insulin sensitivity.

30. Antimicrobial Resistance Genes Are Reduced Following Administration of Investigational Microbiota-based Therapeutic RBX7455 to Individuals with Recurrent clostrioides Difficile Infection

BackgroundAntimicrobial resistance (AMR) is a challenge in individuals at risk for recurrent Clostrioides difficile infection (rCDI). Recognizing that AMR bacteria colonize the intestinal microbiota, therapeutic approaches that decolonize the gut of AMR bacteria would be valuable. Herein, we assessed the microbial resistome before and after treatment with RBX7455—a room temperature-stable, orally-administered investigational microbiota-based therapeutic—in a Phase 1 trial for reducing CDI recurrence.MethodsThis investigator-sponsored trial enrolled 30 rCDI patients in 3 open-label treatment groups (n=10 per group): 1) Four RBX7455 capsules BID for 4 days, 2) Four RBX7455 capsules BID for 2 days, 3) Two RBX7455 capsules BID for 2 days. RBX7455 administration began 48 hours after finishing CDI antibiotics. Participants were asked to submit stool samples at baseline, 1, 7, 28 and 56 days after treatment. These were extracted and sequenced using a shallow shotgun method. Relative taxonomic abundances at the class level and the presence of AMR genes were determined for 148 participant samples and 11 product samples using 90% K-mer sequence coverage based on the MEGARes database.ResultsNinety percent of participants met the primary endpoint of no CDI recurrence through 8 weeks after treatment, and participant microbiome compositions became more similar to RBX7455 after treatment. The total AMR counts per participant decreased from before to after treatment (p< .05, mixed effects model), with the pattern of AMRs identified (resistome) becoming more like the RBX7455 resistome (Figure 1). Most notably, AMRs associated with multi-drug, fluoroquinolone, and betalactam resistance decreased from before to after treatment. There was no significant difference among the groups with respect to clinical response or changes in microbiome composition and AMR content.Figure 1 Average total and per-class AMR gene counts in participant samples before and after RBX7455 treatment. ConclusionIn a Phase 1 trial of RBX7455 for rCDI, AMR gene content decreased after treatment. This underscores the potential of microbiota-based therapies for decolonizing AMR bacteria from the gut microbiota. Continued clinical evaluation of RBX7455 is underway.Disclosures Dana Walsh, PhD, Rebiotix Inc. (Employee) Carlos Gonzalez, MS, BioRankings, LLC (Employee) Bill Shannon, PhD MBA, BioRankings, LLC (Employee) Ken Blount, PhD, Rebiotix Inc. (Employee)

29. Rapid Restoration of Bile Acid Compositions After Treatment with Investigational Microbiota-based Therapeutic RBX2660 for Recurrent clostrioides Difficile Infection

BackgroundRecurrent Clostrioides difficile infection (rCDI) is a public health threat associated with intestinal microbiome disruption (dysbiosis), which is postulated to increase CDI recurrence risk via disruption of bile acid(BA)-mediated resistance to C. difficile colonization. RBX2660 is an investigational microbiota-based therapeutic in clinical development for reducing rCDI recurrence. Herein, we assessed BA composition among participants in a Phase 2 trial of RBX2660 for rCDI.MethodsIn a double-blinded trial (PUNCH CD2), rCDI participants were randomized to receive RBX2660 or placebo. Primary efficacy was defined as absence of CDI recurrence at 8 weeks after the last study treatment. Participants were asked to provide stool samples before (baseline) and up to 24 months after treatment. A liquid chromatography tandem mass spectrometry method was developed to extract and quantify 36 BAs from a total of 167 participant stool samples from 47 participants. Participant-matched samples at baseline and 1, 4, and 8 weeks were compared with a linear mixed effects model.ResultsPrimary BAs predominated at baseline but were significantly reduced (p< .02) as early as 1 week after treatment and remained so to 24 months. Concurrently, secondary BAs, most notably deoxycholic acid (DCA) and lithocholic acid (LCA), were significantly increased (p< .01) after treatment and remained so throughout. Moreover, increases in DCA and LCA were associated with treatment response (p=.05 and p< .01, respectively), recognizing the limited sample size of treatment failures. Observed BA changes coincided with changes in taxonomic compositions—a shift from Gammaproteobacteria and Bacilli predominance before treatment to Clostridia and Bacteroidia predominance after treatment.Figure 1: BA restoration of successfully-treated participants ConclusionIn a trial of RBX2660 for rCDI, participant BA compositions significantly changed from before to after treatment, remained so for at least two years, and correlated with treatment outcome. The resulting predominance of secondary BAs coincided with microbiome compositional changes. Because secondary BA are thought to repress C. difficile colonization, these changes may partly explain how RBX2660 reduced CDI recurrence. Continued evaluation of RBX2660 for rCDI is underway.Disclosures Romeo Papazyan, PhD, Ferring Pharmaceuticals (Employee) Dana Walsh, PhD, Rebiotix Inc. (Employee) Steve Qi, PhD, Ferring Pharmaceuticals (Employee) Ken Blount, PhD, Rebiotix Inc. (Employee) Karthik Srinivasan, PhD, Ferring Pharmaceuticals (Employee) Bryan Fuchs, PhD, Ferring Pharmaceuticals (Employee)

Gut microbiome mediates host genomic effects on phenotypes: a case study with fat deposition in pigs

A large number of studies have highlighted the importance of gut microbiome composition in shaping fat deposition in mammals. Several studies have also highlighted how host genome controls the abundance of certain species that make up the gut microbiota. We propose a systematic approach to infer how the host genome can control the gut microbiome, which in turn contributes to the host phenotype determination. We implemented a mediation test that can be applied to measured and latent dependent variables to describe fat deposition in swine (Sus scrofa). In this study, we identify several host genomic features having a microbiome-mediated effects on fat deposition. This demonstrates how the host genome can affect the phenotypic trait by inducing a change in gut microbiome composition that leads to a change in the phenotype. Host genomic variants identified through our analysis are different than the ones detected in a traditional genome-wide association study. In addition, the use of latent dependent variables allows for the discovery of additional host genomic features that do not show a significant effect on the measured variables. Microbiome-mediated host genomic effects can help understand the genetic determination of fat deposition. Since their contribution to the overall genetic variance is usually not included in association studies, they can contribute to filling the missing heritability gap and provide further insights into the host genome – gut microbiome interplay. Further studies should focus on the portability of these effects to other populations as well as their preservation when pro-/pre-/anti-biotics are used (i.e. remediation).

Does the Microbiome Affect the Outcome of Renal Transplantation?

The role of the human microbiome in health and disease is becoming increasingly apparent. Emerging evidence suggests that the microbiome is affected by solid organ transplantation. Kidney transplantation is the gold standard treatment for End-Stage Renal Disease (ESRD), the advanced stage of Chronic Kidney Disease (CKD). The question of how ESRD and transplantation affect the microbiome and vice versa includes how the microbiome is affected by increased concentrations of toxins such as urea and creatinine (which are elevated in ESRD), whether restoration of renal function following transplantation alters the composition of the microbiome, and the impact of lifelong administration of immunosuppressive drugs on the microbiome. Changes in microbiome composition and activity have been reported in ESRD and in therapeutic immunosuppression, but the effect on the outcome of transplantation is not well-understood. Here, we consider the current evidence that changes in kidney function and immunosuppression following transplantation influence the oral, gut, and urinary microbiomes in kidney transplant patients. The potential for changes in these microbiomes to lead to disease, systemic inflammation, or rejection of the organ itself is discussed, along with the possibility that restoration of kidney function might re-establish orthobiosis.

Temporal Variation of the Facial Skin Microbiome: A 2-Year Longitudinal Study in Healthy Adults.

The human skin microbiome is highly personalized, depending on, for example, body site, age, gender, and lifestyle factors. The temporal stability of an individual's skin microbiome-its resiliency and robustness over months and years-is also a personalized feature of the microbiome. The authors measured the temporal stability of the facial skin microbiome in a large cohort of subjects. In addition to measuring microbiome dynamics, they tracked facial skin condition using noninvasive, objective imaging and biophysical measures to identify significant facial features associated with temporal changes in microbiome diversity and composition. The authors used 16S ribosomal RNA amplicon sequencing to track cheek and forehead skin microbiome diversity and composition annually over a 2-year period (2017-2019) in 115 healthy adult men and women. Skin metadata included facial features, such as wrinkles, hyperpigmentation, porphyrins, and skin color tone, as well as biophysical parameters for stratum corneum barrier function, pH, hydration, and elasticity. Across the subject population, the facial skin microbiome composition and diversity were relatively stable, showing minor variation over the 2-year period. However, for some subjects, composition, diversity, and relative abundance of specific organisms showed substantial changes from one year to the next, and these changes were associated with changes in stratum corneum barrier function and follicular porphyrins. For healthy people, facial skin microbiome diversity and composition are relatively stable from year to year. Tracking the temporal changes in the microbiome along with skin phenotypic changes allows for a deeper understanding of the skin microbiome's role in health and disease. These results should be helpful in the design of longer-term intervention trials with microbiome-based skin care treatments.