Eric Pamer

Recent advances in sequencing techniques unveiled the vast potential of ribosomally synthesized and post-translationally modified peptides (RiPPs) encoded in microbiomes. Class I lantibiotics such as nisin A, widely used as a food preservative, have been investigated for their efficacy in killing pathogens. However, the impact of nisin and nisin-like class I lantibiotics on commensal bacteria residing in the human gut remains unclear. Here, we report six gut-derived class I lantibiotics that are close homologues of nisin, four of which are novel. We applied an improved lantibiotic expression platform to produce and purify these lantibiotics for antimicrobial assays. We determined their minimal inhibitory concentration (MIC) against both Gram-positive human pathogens and gut commensals and profiled the lantibiotic resistance genes in these pathogens and commensals. Structure–activity relationship (SAR) studies …

Metabolites produced by the intestinal microbiome modulate mucosal immune defenses and optimize epithelial barrier function. Intestinal dysbiosis, including loss of intestinal microbiome diversity and expansion of antibiotic-resistant pathobionts, is accompanied by changes in fecal metabolite concentrations and increased incidence of systemic infection. Laboratory tests that quantify intestinal dysbiosis, however, have yet to be incorporated into clinical practice. We quantified fecal metabolites in 107 patients undergoing liver transplantation (LT) and correlated these with fecal microbiome compositions, pathobiont expansion, and postoperative infections. Consistent with experimental studies implicating microbiome-derived metabolites with host-mediated antimicrobial defenses, reduced fecal concentrations of short- and branched-chain fatty acids, secondary bile acids, and tryptophan metabolites correlate with …

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 …

The present disclosure relates to compositions and methods for the diagnosis and treatment or prevention of cancers that exhibit elevated expression of the glutamate/cysteine transporter SLC7A11, reduced expression of the fatty acid transporter SLC25A45 and/or reduced expression of FAM3 metabolism regulating signaling molecule B (FAM3B). In particular, the instant disclosure provides for identification of a cancer as possessing elevated SLC7A11 expression, reduced expression of SLC25A45 and/or reduced expression of FAM3B, and selecting and/or administering a glutaminase inhibitor as a therapeutic agent for such a cancer and/or subject having or at risk of developing such a cancer. Methods and compositions for therapies that combine such selection of cancers/subjects for glutaminase inhibitor therapy with other cancer therapies and/or chemotherapeutic agents are also provided.

Carbapenem-resistant Klebsiella pneumoniae (CR-Kp) is a significant threat to public health worldwide. The primary reservoir for CR-Kp is the intestinal tract. There, the bacterium is usually present at low density but can bloom following antibiotic treatment, mostly in hospital settings. The impact of disturbances in the intestinal environment on the fitness, survival, expansion, and drug susceptibility of this pathogen is not well-understood, yet it may be relevant to devise strategies to tackle CR-Kp colonization and infection. Here, we adopted an in vivo model to examine the transcriptional adaptation of a CR-Kp clinical isolate to immune activation in the intestine. We report that as early as 6 hours following host treatment with anti-CD3 antibody, CR-Kp underwent rapid transcriptional changes including downregulation of genes involved in sugar utilization and amino acid biosynthesis and upregulation of genes …

Species of the Bacteroidales order are among the most abundant and stable bacterial members of the human gut microbiome with diverse impacts on human health. While Bacteroidales strains and species are genomically and functionally diverse, order-wide comparative analyses are lacking. We cultured and sequenced the genomes of 408 Bacteroidales isolates from healthy human donors representing nine genera and 35 species and performed comparative genomic, gene-specific, mobile gene, and metabolomic analyses. Families, genera, and species could be grouped based on many distinctive features. However, we also show extensive DNA transfer between diverse families, allowing for shared traits and strain evolution. Inter- and intra-specific diversity is also apparent in the metabolomic profiling studies. This highly characterized and diverse Bacteroidales culture collection with strain-resolved genomic and metabolomic analyses can serve as a resource to facilitate informed selection of strains for microbiome reconstitution.

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Clostridioides difficile produces toxins that damage the colonic epithelium, causing colitis. Variation in disease severity is poorly understood and has been attributed to host factors and virulence differences between C. difficile strains. We test 23 epidemic ST1 C. difficile clinical isolates for their virulence in mice. All isolates encode a complete Tcd pathogenicity locus and achieve similar colonization densities. However, disease severity varies from lethal to avirulent infections. Genomic analysis of avirulent isolates reveals a 69-bp deletion in the cdtR gene, which encodes a response regulator for binary toxin expression. Deleting the 69-bp sequence in virulent R20291 strain renders it avirulent in mice with reduced toxin gene transcription. Our study demonstrates that a natural deletion within cdtR attenuates virulence in the epidemic ST1 C. difficile isolates without reducing colonization and persistence. Distinguishing …

The intestinal microbiota is composed of hundreds of distinct microbial species that interact with each other and their mammalian host. Antibiotic exposure dramatically impacts microbiota compositions and leads to acquisition of antibiotic-resistance genes. Lantibiotics are ribosomally synthesized and post-translationally modified peptides produced by some bacterial strains to inhibit the growth of competing bacteria. Nisin A is a lantibiotic produced by Lactococcus lactis that is commonly added to food products to reduce contamination with Gram-positive pathogens. Little is known, however, about lantibiotic-resistance of commensal bacteria inhabiting the human intestine. Herein, we demonstrate that Nisin A administration to mice alters fecal microbiome compositions and the concentration of taurine-conjugated primary bile acids. Lantibiotic Resistance System genes (LRS) are encoded by lantibiotic-producing …

BackgroundLiver transplantation (LT) is associated with postoperative infections caused by antibiotic-resistant bacterial pathogens that reside in the intestine. An intact intestinal microbiome suppresses expansion of enteric pathogens, however patients with severe liver disease often have reduced microbiome diversity and increased density of antibiotic-resistant Enterococcus and Enterobacterales species. (–) Experimental models have demonstrated that metabolites produced by the intestinal microbiome, including short chain fatty acids (SCFAs), secondary bile acids and indole compounds, enhance host epithelial and immune defenses against enteric pathogens.(–) Microbiome derived metabolites likely contribute to resistance against infectious diseases in LT patients, however, this remains uninvestigated.MethodsWe prospectively enrolled 107 liver transplant candidates and determined peri-transplant fecal microbiome compositions including relative and absolute fecal metabolite concentrations.ResultsFecal microbiomes in LT recipients ranged from highly diverse to complete loss of diversity resulting in expansion of Enterococcus and/or Enterobacterales species that were associated with postoperative infection. Gas chromatographic (GC-) and liquid chromatographic (LC-) Mass spectrometric analyses revealed decreased concentrations of SCFAs, secondary bile acids, and indole compounds in fecal samples with low microbiome diversity and associated expansion of Enterococcus and Enterobacterales populations.ConclusionFecal metabolite abundances accurately predicted LT patients with reduced microbial diversity and those who …

Rationale Risk factors associated with reduced long-term survival in ICU patients include increased age, illness severity, comorbidities, and mechanical ventilation. Previous works have studied COVID-19 patient outcomes independently in the short-term, but few have compared long-term outcomes between ICU survivors with and without COVID-19. Methods This prospective observational study was conducted at a single academic center in Chicago, IL. Consecutive patients who survived to hospital discharge from the medical ICU with and without COVID-19 infection from April 2020 thru June 2021 were eligible for enrollment. Exclusion criteria included severe dementia, bedbound, or nonverbal at baseline. Patients were followed for one-year and survival data were collected from medical records and phone interviews. To evaluate the effect of COVID-19 on one-year survival after critical illness, we used the …

Background Emerging evidence is revealing the impact of the gut microbiome on hematopoietic and solid organ transplantation. Prior studies postulate that this influence is mediated by bioactive metabolites produced by gut-dwelling commensal bacteria. However, gut microbial metabolite production has not previously been measured among heart transplant (HT) recipients. Methods In order to investigate the potential influence of the gut microbiome and its metabolites on HT, we analyzed the composition and metabolite production of the fecal microbiome among 48 HT recipients at the time of HT. Results Compared to 20 healthy donors, HT recipients have significantly reduced alpha, i.e. within-sample, microbiota diversity, with significantly lower abundances of key anaerobic commensal bacteria and higher abundances of potentially pathogenic taxa that have been correlated with adverse outcomes in other forms of transplantation. HT recipients have a wide range of microbiota-derived fecal metabolite concentrations, with significantly reduced levels of immune modulatory metabolites such as short chain fatty acids and secondary bile acids compared to healthy donors. These differences were likely due to disease severity and prior antibiotic exposures but were not explained by other demographic or clinical factors. Conclusions Key potentially immune modulatory gut microbial metabolites are quantifiable and significantly reduced among HT recipients compared to healthy donors. Further study is needed to understand whether this wide range of gut microbial dysbiosis and metabolite alterations impact clinical outcomes and if they can be used …

The human gut microbiome contains many bacterial strains of the same species (‘strain-level variants’). Describing strains in a biologically meaningful way rather than purely taxonomically is an important goal but challenging due to the genetic complexity of strain-level variation. Here, we measured patterns of co-evolution across> 7,000 strains spanning the bacterial tree-of-life. Using these patterns as a prior for studying hundreds of gut commensal strains that we isolated, sequenced, and metabolically profiled revealed widespread structure beneath the phylogenetic level of species. Defining strains by their co-evolutionary signatures enabled predicting their metabolic phenotypes and engineering consortia from strain genome content alone. Our findings demonstrate a biologically relevant organization to strain-level variation and motivate a new schema for describing bacterial strains based on their evolutionary …

Progression of chronic liver diseases is precipitated by hepatocyte loss, inflammation and fibrosis. This process results in the loss of critical hepatic functions, increasing morbidity and the risk of infection. Medical interventions that treat complications of hepatic failure, including antibiotic administration for systemic infections, impact gut microbiome composition and metabolite production. Using a multi-omics approach on 850 fecal samples from 263 patients with acute or chronic liver disease, we demonstrate that patients hospitalized for liver disease have reduced microbiome diversity and a paucity of bioactive metabolites. We find that patients treated with the orally administered but non-absorbable disaccharide lactulose have increased densities of intestinal Bifidobacteria and reduced incidence of systemic infections and mortality. Bifidobacteria metabolize lactulose, produce high concentrations of acetate and acidify the gut lumen, which, in combination, can reduce the growth of antibiotic-resistant pathobionts such as Vancomycin-resistant Enterococcus faecium. Our studies suggest that lactulose and Bifidobacteria serve as a synbiotic to reduce rates of infection in patients with severe liver disease.

Increasing experimental evidence suggests that administering live commensal bacterial species can optimize microbiome composition and lead to reduced disease severity and enhanced health. Our understanding of the intestinal microbiome and its functions has increased over the past two decades largely due to deep sequence analyses of fecal nucleic acids, metabolomic and proteomic assays to measure nutrient use and metabolite production, and extensive studies on the metabolism and ecological interactions of a wide range of commensal bacterial species inhabiting the intestine. Herein, we review new and important findings that have emerged from this work and provide thoughts and considerations on approaches to re-establish and optimize microbiome functions by assembling and administering commensal bacterial consortia.

Longitudinal microbiome data provide valuable insight into disease states and clinical responses, but they are challenging to mine and view collectively. To address these limitations, we present TaxUMAP, a taxonomically informed visualization for displaying microbiome states in large clinical microbiome datasets. We used TaxUMAP to chart a microbiome atlas of 1,870 patients with cancer during therapy-induced perturbations. Bacterial density and diversity were positively associated, but the trend was reversed in liquid stool. Low-diversity states (dominations) remained stable after antibiotic treatment, and diverse communities had a broader range of antimicrobial resistance genes than dominations. When examining microbiome states associated with risk for bacteremia, TaxUMAP revealed that certain Klebsiella species were associated with lower risk for bacteremia localize in a region of the atlas that is depleted …

BackgroundLiver transplantation (LT) is associated with postoperative infections caused by antibiotic-resistant bacterial pathogens that reside in the intestine. An intact intestinal microbiome suppresses expansion of enteric pathogens, however patients with severe liver disease often have reduced microbiome diversity and increased density of antibiotic-resistant Enterococcus and Enterobacterales species. Experimental models have demonstrated that metabolites produced by the intestinal microbiome, including short chain fatty acids (SCFAs), secondary bile acids and indole compounds, enhance host epithelial and immune defenses against enteric pathogens. Microbiome derived metabolites likely contribute to resistance against infectious diseases in LT patients, however, this remains uninvestigated.

Whether the human fetus and the prenatal intrauterine environment (amniotic fluid and placenta) are stably colonized by microbial communities in a healthy pregnancy remains a subject of debate. Here we evaluate recent studies that characterized microbial populations in human fetuses from the perspectives of reproductive biology, microbial ecology, bioinformatics, immunology, clinical microbiology and gnotobiology, and assess possible mechanisms by which the fetus might interact with microorganisms. Our analysis indicates that the detected microbial signals are likely the result of contamination during the clinical procedures to obtain fetal samples or during DNA extraction and DNA sequencing. Furthermore, the existence of live and replicating microbial populations in healthy fetal tissues is not compatible with fundamental concepts of immunology, clinical microbiology and the derivation of germ-free …

PurposeCertain gut microbiome derived metabolites have been shown to have a protective immunomodulatory role in transplantation. We sought to investigate whether sensitization in patients undergoing heart transplantation (HT) is associated with gut metabolite concentrations.MethodsThis is a single-center prospective study of all HTs performed from July 2020 to May 2022. Stool samples were collected within two weeks peri-transplant. Shotgun metagenomics was used to analyze microbiome compositions and mass spectrometry was used to analyze gut microbiome metabolites. Sensitization was defined as calculated panel reactive antibodies class I or II >10% or class I+II >10%. Gut microbiome composition, diversity, and metabolites were compared between sensitized and non-sensitized (NS) groups.ResultsThere were 19 (27.1%) sensitized and 51 (72.9%) NS recipients. A total of 18 (25.7%) patients were …

The present invention relates to methods and compositions for reducing the risk and severity of C. difficile infection. It is based, at least in part, on the discovery that a restricted fraction of the gut microbiota, including the bacterium Clostridium scindens, contributes substantially to resistance against C. difficile infection. Without being bound by any particular theory, it is believed that this is achieved through the biosynthesis of secondary bile acids.

In the version of this article initially published, there were composition errors in the second column of Table 4, where for each age subgroup, the second set of “P-tau217” terms now shown for each subgroup were shown as entries for “P-tau181.” The table has been amended in the HTML and PDF versions of the article.

Recent advances in sequencing techniques unveiled the vast potential of ribosomally synthesized and post-translationally modified peptides (RiPPs) encoded in microbiomes. Class I lantibiotics such as nisin A, widely used as a food preservative, have been investigated for their efficacy in killing pathogens. However, the impact of nisin and nisin-like class I lantibiotics on commensal bacteria residing in the human gut remains unclear. Here, we report six gut-derived class I lantibiotics that are close homologs of nisin, four of which are novel. We applied an improved lantibiotic expression platform to produce and purify these lantibiotics for antimicrobial assays. We determined their minimal inhibitory concentration (MIC) against both Gram-positive human pathogens and gut commensals, and profiled the lantibiotic resistance genes in these pathogens and commensals. SAR studies with variants revealed key regions and residues that impact their antimicrobial properties. Our characterization and SAR studies of nisin-like lantibiotics against both pathogens and human gut commensals could shed light on the future development of lantibiotic-based therapeutics and food preservatives.

BackgroundCavernous angiomas (CAs) affect 0.5% of the population, predisposing to serious neurologic sequelae from brain bleeding. A leaky gut epithelium associated with a permissive gut microbiome, was identified in patients who develop CAs, favoring lipid polysaccharide producing bacterial species. Micro-ribonucleic acids along with plasma levels of proteins reflecting angiogenesis and inflammation were also previously correlated with CA and CA with symptomatic hemorrhage.MethodsThe plasma metabolome of CA patients and CA patients with symptomatic hemorrhage was assessed using liquid-chromatography mass spectrometry. Differential metabolites were identified using partial least squares-discriminant analysis (p < 0.05, FDR corrected). Interactions between these metabolites and the previously established CA transcriptome, microbiome, and differential proteins were queried for mechanistic …

Discerning the effect of pharmacological exposures on intestinal bacterial communities in cancer patients is challenging. Here, we deconvoluted the relationship between drug exposures and changes in microbial composition by developing and applying a new computational method, PARADIGM (parameters associated with dynamics of gut microbiota), to a large set of longitudinal fecal microbiome profiles with detailed medication-administration records from patients undergoing allogeneic hematopoietic cell transplantation. We observed that several non-antibiotic drugs, including laxatives, antiemetics, and opioids, are associated with increased Enterococcus relative abundance and decreased alpha diversity. Shotgun metagenomic sequencing further demonstrated subspecies competition, leading to increased dominant-strain genetic convergence during allo-HCT that is significantly associated with antibiotic …

Progression of chronic liver disease is precipitated by hepatocyte loss, inflammation and fibrosis. This process results in the loss of critical hepatic functions, increasing morbidity and the risk of infection. Medical interventions that treat complications of hepatic failure, including antibiotic administration for systemic infections and lactulose treatment for hepatic encephalopathy, can impact gut microbiome composition and metabolite production. Here, using shotgun metagenomic sequencing and targeted metabolomic analyses on 847 faecal samples from 262 patients with acute or chronic liver disease, we demonstrate that patients hospitalized for liver disease have reduced microbiome diversity and a paucity of bioactive metabolites, including short-chain fatty acids and bile acid derivatives, that impact immune defences and epithelial barrier integrity. We find that patients treated with the orally administered but non …

Introduction Microbial isolates from culture can be identified using 16S or whole-genome sequencing which generates substantial costs and requires time and expertise. Protein fingerprinting via Matrix-assisted Laser Desorption Ionization–time of flight mass spectrometry (MALDI-TOF MS) is widely used for rapid bacterial identification in routine diagnostics but shows a poor performance and resolution on commensal bacteria due to currently limited database entries. The aim of this study was to develop a MALDI-TOF MS plugin database (CLOSTRI-TOF) allowing for rapid identification of non-pathogenic human commensal gastrointestinal bacteria. Methods We constructed a database containing mass spectral profiles (MSP) from 142 bacterial strains representing 47 species and 21 genera within the class Clostridia. Each strain-specific MSP was constructed using >20 raw spectra measured on a microflex Biotyper system (Bruker-Daltonics) from two independent cultures. Results For validation, we used 58 sequence-confirmed strains and the CLOSTRI-TOF database successfully identified 98 and 93% of the strains, respectively, in two independent laboratories. Next, we applied the database to 326 isolates from stool of healthy Swiss volunteers and identified 264 (82%) of all isolates (compared to 170 (52.1%) with the Bruker-Daltonics library alone), thus classifying 60% of the formerly unknown isolates. Discussion We describe a new open-source MSP database for fast and accurate identification of the Clostridia class from the human gut microbiota. CLOSTRI-TOF expands the number of species which can be rapidly identified by MALDI-TOF …

The impact of Clostridioides difficile strain diversity on the severity of intestinal infection and diarrhea remains unclear. The RT027/ST1 strain is highly prevalent and has been associated with more severe disease and increased toxin production. Previous studies using antibiotic-treated mice, however, have demonstrated that the severity of diarrhea and colonic inflammation caused by clinical RT027/ST1 C. difficile isolates cultured from different patients is isolate-specific and varies from avirulent to lethal. Herein we demonstrate that increased flagellar expression is associated with increased in vivo virulence. While sequencing the flagellar operon did not identify differences between high and low virulence isolates, high virulence was associated with strains encoding higher proportions of the phase variable flagellar switch in the ON mode. We found that the proportion of bacteria with the switch in the ON mode correlates with maximum weight loss, a readout for virulence in mice. Further analysis of flagellar switch sequences identified variant inverted repeat (IR) sequences, with 40% of isolates having lost one A or T in the IR compared to the genome of C. difficile R20291. The isolates with the R20291 IR sequence have increased virulence compared to those with variant IR (p = 3.2e-05) and these isolates have markedly reduced ability to invert the flagellar switch. Our results suggest that a restricted capacity to invert the flagellar switch during infection is associated with reduced virulence of C. difficile RT027/ST1 strains and may account for some of the inconsistent associations between C. difficile infection and disease severity in patients.

In the original article, there was an error in the Data availability statement. The dataset deposited on the Zenodo link was incomplete and the MALDI spectra were named with the old taxonomy. We have now corrected these errors, added a few strains and taken out two strains with ambiguous spectra. We have uploaded the ClostriTof version 2.0 database plugin on Zenodo. The correct Data availability statement appears below.“The datasets presented in this study can be found on Zenodo under the following link: https://zenodo. org/record/7773644#. ZCny2y8Rrfc.” In the published article, there was an imprecision in the Conflict of interest. This sentence previously stated:“The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.” The correct Conflict of interest appears below.

PurposeGut microbial dysbiosis has been correlated to solid organ and stem cell transplant rejection and death. The HeartCare lab test (CareDx) is increasingly used as routine surveillance for heart transplant (HT) injury and rejection. We investigated whether the microbiome can serve as a noninvasive marker of immune activation and allograft injury among HT recipients.MethodsWe conducted a single-center, prospective cohort study of single organ HT recipients from 2020-2021. Shotgun metagenomic sequencing was performed on peri-HT stool samples. Gut microbial diversity and composition were correlated with the highest abnormal AlloSure or AlloMap obtained within 6 months post-HT.ResultsThirty-eight HT recipients were included. Stool samples were collected 5.3 ± 7.4 days from HT. The highest HeartCare lab values were measured 72 days (IQR [41, 103]) post-HT. Seven HT recipients had high …

Provided herein is a method of treating an individual afflicted with an inflammatory bowel disease utilizing Candida abundance as a biomarker of responsiveness. The method comprises determining levels of Candida in a sample from the gastrointestinal tract of an individual, and if the level of Candida is higher than a reference level, identifying the individual as suitable for microbiota transplantation therapy (MTT), and optionally, administering to such an individual the MTT, and in individuals having gastrointestinal tract Candida levels lower than a reference level, increasing the Candida levels prior to prior to administration of MTT.

The present disclosure relates to novel lantibiotics, lantibi otic pharmaceutical compositions, isolated and recombinant lantibiotic-producing bacteria, bacterial pharmaceutical compositions, methods of producing novel lantibiotics from lantibiotic-producing bacteria, and methods of using such lantibiotics, lantibiotic pharmaceutical compositions, and bacterial pharmaceutical compositions to treat gram-positive bacteria infections, including vancomycin resistant entero cocci infections, in patients, and to treat food and other objects to avoid gram-positive bacteria contamination.

Anti-CD19 chimeric antigen receptor (CAR) T cell therapy has led to unprecedented responses in patients with high-risk hematologic malignancies. However, up to 60% of patients still experience disease relapse and up to 80% of patients experience CAR-mediated toxicities, such as cytokine release syndrome or immune effector cell-associated neurotoxicity syndrome. We investigated the role of the intestinal microbiome on these outcomes in a multicenter study of patients with B cell lymphoma and leukemia. We found in a retrospective cohort (n = 228) that exposure to antibiotics, in particular piperacillin/tazobactam, meropenem and imipenem/cilastatin (P-I-M), in the 4 weeks before therapy was associated with worse survival and increased neurotoxicity. In stool samples from a prospective cohort of CAR T cell recipients (n = 48), the fecal microbiome was altered at baseline compared to healthy controls. Stool …

Hospitalized patients receiving hematopoietic cell transplants provide a unique opportunity to study the human gut microbiome. We previously compiled a large-scale longitudinal dataset of fecal microbiota and associated metadata, but we had limited that analysis to taxonomic composition of bacteria from 16S rRNA gene sequencing. Here we augment those data with shotgun metagenomics. The compilation amounts to a nested subset of 395 samples compiled from different studies at Memorial Sloan Kettering. Shotgun metagenomics describes the microbiome at the functional level, particularly in antimicrobial resistances and virulence factors. We provide accession numbers that link each sample to the paired-end sequencing files deposited in a public repository, which can be directly accessed by the online services of PATRIC to be analyzed without the users having to download or transfer the files. Then, we …

Respiratory failure and mortality from COVID-19 result from virus- and inflammation-induced lung tissue damage. The intestinal microbiome and associated metabolites are implicated in immune responses to respiratory viral infections, however their impact on progression of severe COVID-19 remains unclear. We prospectively enrolled 71 patients with COVID-19 associated critical illness, collected fecal specimens within 3 days of medical intensive care unit admission, defined microbiome compositions by shotgun metagenomic sequencing, and quantified microbiota-derived metabolites (NCT #04552834). Of the 71 patients, 39 survived and 32 died. Mortality was associated with increased representation of Proteobacteria in the fecal microbiota and decreased concentrations of fecal secondary bile acids and desaminotyrosine (DAT). A microbiome metabolic profile (MMP) that accounts for fecal secondary bile acids …

The present invention relates to methods and compositions for reducing the risk and severity of vancomycin-resistant Enterococci infection or colonization. It is based, at least in part, on the discovery that a restricted fraction of the gut microbiota, including the bacteria Clostridium scindens and/or the bacteria Blautia producta contribute substantially to resistance against vancomycin-resistant Enterococci infection or colonization. Without being bound by any particular theory, it is believed that this is achieved through the biosynthesis of secondary bile acids in the case of Clostridium scindens.

SSATA b st ra ct s high volume (HV) centers, especially the median operative time. Conclusion Transition to CPD at our community cancer center led to significantly shorter operative times and decreased length of stay. These, as well as many of our secondary outcomes, compared favorably to other HV centers. Adoption of CPD at may offset the procedure’ s known risks. 769 IS NEOADJUVANT CHEMOTHERAPY BEFORE CYTOREDUCTION ASSOCIATED WITH IMPROVED SURVIVAL IN APPENDICEAL/COLORECTAL ADENOCARCINOMA WITH PERITONEAL METASTASES? Stephanie Young, Siu-Yuan Huang, Melanie Goldfarb, Victoria O'Connor, Anna Leung Objective: Investigate the association of neoadjuvant chemotherapy (NAC) and survival in patients with appendiceal or colorectal adenocarcinoma with peritoneal metastasis (PM) undergoing cytoreductive surgery (CRS). Background: Randomized …

Background.Fecal microbiota transplantation (FMT) is an effective treatment of recurrent Clostridioides difficile infections (rCDI), but has more limited efficacy in treating either ulcerative colitis (UC) or Crohn’s disease (CD), two major forms of inflammatory bowel diseases (IBD). We hypothesize that FMT recipients with rCDI and/or IBD have baseline fecal bile acid (BA) compositions that differ significantly from that of their healthy donors and that FMT will normalize the BA compositions.Aim.To study the effect of single colonoscopic FMT on microbial composition and function in four recipient groups: 1.) rCDI patients without IBD (rCDI− IBD); 2.) rCDI with IBD (rCDI+ IBD); 3.) UC patients without rCDI (UC− rCDI); 4.) CD patients without rCDI (CD− rCDI).Methods.We performed 16S rRNA gene sequence, shotgun DNA sequence and quantitative bile acid metabolomic analyses on stools collected from 55 pairs of subjects …

Rationale COVID-19 critical illness has been associated with an abnormal fecal microbiota and dysregulated immune response. A healthy microbiome and its associated metabolome regulate the systemic immune system and may contribute to the course of COVID-19. Here we investigate whether an abnormal fecal microbiota and reduced metabolite production is associated with progressive COVID-19 respiratory failure and death. Methods This prospective single-center observational study enrolled 102 patients with COVID-19 admitted to the intensive care unit with respiratory failure or shock. To examine the role of the microbiome early in the course of critical illness we limited the analysis to patients who provided a fecal specimen within 3 days of ICU admission (n= 71). Fecal samples underwent shotgun metagenomic DNA sequencing to define microbiome composition and metabolomic assays to determine …

BackgroundFecal microbiota transplantation (FMT) is an effective treatment of recurrent Clostridioides difficile infections (rCDI). In comparison, FMT has more limited efficacy in treating either ulcerative colitis (UC) or Crohn’s disease (CD), two major forms of inflammatory bowel diseases (IBD). We hypothesize that FMT recipients with rCDI and/or IBD have baseline fecal bile acid (BA) compositions that differ significantly from that of their healthy donors and may be normalized by FMT.AimTo study the effect of single colonoscopic FMT on the microbial composition and function of recipients with rCDI and/or IBD.MethodsMulti-omic analysis was performed on stools from 55 pairs of subjects and donors enrolled in two prospective single arm FMT clinical trials [ClinicalTrials.gov ID:NCT03268213, 479696, (IND) 15642, ClinicalTrials.gov ID: NCT03267238, IND 16795]. Fitted linear mixed models were used to examine the effects of four recipient groups (rCDI - IBD, rCDI + IBD, UC - rCDI, CD - rCDI), FMT status (Donor, pre-FMT, 1-week post-FMT, 3-months post-FMT) and first order Group*FMT interactions.ResultsFMT was effective in preventing rCDI for up to one year in 92% of the rCDI - IBD group and 75% of the rCDI + IBD recipients. The donor-recipient Sørensen similarity index was < 0.6 in all donor-CDI recipient pairs but > 0.6 in some donor-IBD only recipient pairs at baseline. Increasing post-FMT similarity indices > 0.6 in IBD recipients, was not clearly associated with reduced fecal calprotectin levels. Fecal secondary BA levels were lower in rCDI ± IBD and CD – rCDI recipients compared to donors. FMT restored secondary BA levels in these …

Extensive research has elucidated the influence of the gut microbiota on human health and disease susceptibility and resistance. We review recent clinical and laboratory-based experimental studies associating the gut microbiota with certain human diseases. We also highlight ongoing translational advances that manipulate the gut microbiota to treat human diseases and discuss opportunities and challenges in translating microbiome research from and to the bedside.

PurposeRecent evidence suggest that the gut microbiome may influence tacrolimus dosing requirements, potentially through direct metabolism. The impact of the gut microbiome on tacrolimus requirements among heart transplant (HT) recipients during medication initiation is unknown. We aimed to evaluate the effect of the gut microbiome on tacrolimus dosing requirements among HT recipients in the peri-HT period.MethodsWe conducted a prospective, observational cohort study of all single organ HT recipients at a single center from 2020-2021. Stool samples were collected within 2 weeks of HT and underwent shotgun metagenomic analysis. Measures of microbial diversity, composition, and metabolomics were correlated to the ratio of tacrolimus serum level (L) to the total 24-hour dose (D) at time of post-HT discharge. HT recipients were further divided into 2 groups: above-median L/D ratio (slow metabolizers …

The disclosure relates to a therapeutic composition for treating L. monocytogenes infection or L. monocytogenes colonization, the composition including at least one, at least two, at least three, or all of an isolated C. saccharogumia bacteria, an isolated C. ramosum bacteria, an isolated C. hathewayi bacteria, and/or an isolated B. producta bacteria in a formulation suitable for administration to a subject. The disclosure further provides similar compositions lacking an isolated C. saccharogumia bacteria. The disclosure additionally provides methods of treating L. monocytogenes infection or colonization using such compositions.

Schistosome infection is recognized as a potentially modifiable risk factor for HIV in women by the World Health Organization. Alterations in cervicovaginal bacteria have been associated with HIV acquisition and have not been studied in schistosome infection. We collected cervical swabs from Tanzanian women with and without S. mansoni and S. haematobium to determine effects on cervicovaginal microbiota. Infected women were treated, and follow-up swabs were collected after 3 months. 16S rRNA sequencing was performed on DNA extracted from swabs. We compared 39 women with S. mansoni with 52 uninfected controls, and 16 with S. haematobium with 27 controls. S. mansoni-infected women had increased abundance of Peptostreptococcus (p = 0.026) and presence of Prevotella timonesis (p = 0.048) compared to controls. High-intensity S. haematobium infection was associated with more …

Introduction: Cellular immunotherapy with CD19-targeted chimeric antigen receptor (CAR) T cells has provided new therapeutic options for patients with high-risk hematologic malignancies. Following this therapy, patients may experience disease relapse or CAR-mediated toxicity due to cytokine release syndrome (CRS) or immune effector cell-associated neurotoxicity syndrome (ICANS). Recent studies have confirmed that the intestinal microbiome can modulate the anti-tumor immune response to chemotherapy, immune checkpoint blockade, graft-versus-host disease after allogeneic hematopoietic cell transplantation, and adoptive cellular therapy. The contribution of the intestinal microbiome on the function of CAR T cells in vivo both with respect to their anti-tumor function and their propensity to induce toxicities is not known. Hence, in a multi-center study we analyzed the association between clinical outcomes …

Gram-negative pathogens, such as Klebsiella pneumoniae, remodel their outer membrane (OM) in response to stress to maintain its integrity as an effective barrier and thus to promote their survival in the host. The emergence of carbapenem-resistant K. pneumoniae (CR-Kp) strains that are resistant to virtually all antibiotics is an increasing clinical problem and OM impermeability has limited development of antimicrobial agents because higher molecular weight antibiotics cannot access sites of activity. Here, we demonstrate that TAM (translocation and assembly module) deletion increases CR-Kp OM permeability under stress conditions and enhances sensitivity to high-molecular weight antimicrobials. SILAC-based proteomic analyses revealed mis-localization of membrane proteins in the TAM deficient strain. Stress-induced sensitization enhances clearance of TAM-deficient CR-Kp from the gut lumen following fecal microbiota transplantation and from infection sites following pulmonary or systemic infection. Our study suggests that TAM, as a regulator of OM permeability, represents a potential target for development of agents that enhance the effectiveness of existing antibiotics.

The impact of the gut microbiota in human health is affected by several factors including its composition, drug administrations, therapeutic interventions and underlying diseases. Unfortunately, many human microbiota datasets available publicly were collected to study the impact of single variables, and typically consist of outpatients in cross-sectional studies, have small sample numbers and/or lack metadata to account for confounders. These limitations can complicate reusing the data for questions outside their original focus. Here, we provide comprehensive longitudinal patient dataset that overcomes those limitations: a collection of fecal microbiota compositions (> 10,000 microbiota samples from> 1,000 patients) and a rich description of the “hospitalome” experienced by the hosts, ie, their drug exposures and other metadata from patients with cancer, hospitalized to receive allogeneic hematopoietic cell …

BackgroundLiver transplant (LT) recipients have abnormal microbiota before and after transplantation.(1, 2) Associations between fecal microbiota, microbial metabolites, and clinical outcomes in liver transplantation are not well established. We correlated fecal microbiota composition and metabolite concentrations with early LT outcomes, including infection.MethodsIn a prospective observational study, we collected peri-transplant fecal samples and determined microbiota composition by 16S ribosomal RNA gene sequencing in LT recipients. Fecal short chain fatty acid (SCFA) and bile acid concentrations were measured by targeted GC-and LC-MS analyses, respectively. Inverse Simpson index was used to determine microbiota alpha-diversity in subjects and healthy controls. Clinical outcomes including length of stay, ICU admission, liver function, antibiotic use, immunosuppressive requirement and post-operative …

PurposeThe contribution of the intestinal microbiome to alloimmunity in heart transplantation (HT) is unknown. We examined fecal microbiota of HT recipients at time of transplantation and characterized microbiota composition, diversity, and metabolite production.MethodsIn a prospective, observational, pilot study, pre and post-HT stool samples were collected and microbiota composition determined by 16S ribosomal RNA gene sequencing. Fecal short chain fatty acid (SCFA) concentrations were determined by targeted metabolomics. HT samples were compared to those of healthy controls (HC) and liver transplant (LT) subjects.Results52 fecal samples were analyzed from 9 HT recipients (1 heart-kidney, 1 heart-liver, 1 heart-liver-kidney) and compared to 15 HC and 8 LT subjects. A measure of within-sample microbial diversity, the inverse Simpson index was lower among HT recipients before and after …

Clostridioides difficile is the leading cause of healthcare-associated infectious diarrhoea. However, it is increasingly appreciated that healthcare-associated infections derive from both community and healthcare environments, and that the primary sites of C. difficile transmission may be strain-dependent. We conducted a multisite genomic epidemiology study to assess differential genomic evidence of healthcare vs community spread for two of the most common C. difficile strains in the USA: sequence type (ST) 1 (associated with ribotype 027) and ST2 (associated with ribotype 014/020). We performed whole-genome sequencing and phylogenetic analyses on 382 ST1 and ST2 C. difficile isolates recovered from stool specimens collected during standard clinical care at 3 geographically distinct US medical centres between 2010 and 2017. ST1 and ST2 isolates both displayed some evidence of phylogenetic …

We previously described clinically relevant reductions in fecal microbiota diversity in patients undergoing allogeneic hematopoietic cell transplantation (allo-HCT). Recipients of high-dose chemotherapy and autologous HCT (auto-HCT) incur similar antibiotic exposures and nutritional alterations. To characterize the fecal microbiota in the auto-HCT population, we analyzed 1161 fecal samples collected from 534 adult recipients of auto-HCT for lymphoma, myeloma, and amyloidosis in an observational study conducted at 2 transplantation centers in the United States. By using 16S ribosomal gene sequencing, we assessed fecal microbiota composition and diversity, as measured by the inverse Simpson index. At both centers, the diversity of early pretransplant fecal microbiota was lower in patients than in healthy controls and decreased further during the course of transplantation. Loss of diversity and domination …

• In a prospective observational study, we collected peritransplant and post-transplant fecal samples• We determined microbiota composition by 16S rRNA sequencing and characterized metabolism by measuring short chain fatty acids (SCFA) and bile acid metabolites.• Microbiota composition was compared to healthy controls• Outcomes including length of stay, ICU care, graft function, anastomosis failure, antibiotic use, rejection, and post operative (post-op) infection were collected and correlated with microbiota composition and metabolism• 69 patients were enrolled, 70 LT were performed and 307 fecal samples were collected and analyzed• Compared to healthy controls, the fecal microbiota of LT recipients had reduced α-diversity (p< 0.0001),• Beneficial SCFA (p< 0.0001) and secondary bile acids (p< 0.0001) were also lower compared to controls• Three health promoting taxa Bacteroidetes …

The gut microbiota produces metabolites that regulate host immunity, thereby impacting disease resistance and susceptibility. The extent to which commensal bacteria reciprocally respond to immune activation, however, remains largely unexplored. Herein, we colonized mice with four anaerobic symbionts and show that acute immune responses result in dramatic transcriptional reprogramming of these commensals with minimal changes in their relative abundance. Transcriptomic changes include induction of stress-response mediators and downregulation of carbohydrate-degrading factors such as polysaccharide utilization loci (PULs). Flagellin and anti-CD3 antibody, two distinct immune stimuli, induced similar transcriptional profiles, suggesting that commensal bacteria detect common effectors or activate shared pathways when facing different host responses. Immune activation altered the intestinal metabolome …

Rationale The fecal microbiota of critically ill patients has reduced diversity, with progressive loss of healthpromoting symbiotic bacterial populations during the patients’ admission to the intensive care unit (ICU). The microbiota produces a wide range of metabolites that influence T cell differentiation and provide resistance against intestinal pathogens, including short chain fatty acids (SCFAs) and secondary bile acids. The impact of ICU hospitalization on microbiota-derived metabolites is unknown. Methods Critically ill patients with respiratory failure or shock were enrolled in a clinical study at a single academic center. Fecal specimens, if produced, were collected following ICU admission and every other day until discharge. Fecal specimens were extracted using the QIAamp PowerFecal Pro DNA Kit and the V4-5 region of 16s RNA genes was amplified and sequenced on the Illumina MiSeq platform using 2x 250 …

Background Gram-negative bloodstream infections (BSIs) represent a significant complication facing allogeneic hematopoietic cell transplant (allo-HCT) recipients, as a result of intestinal translocation during neutropenia. In this study we sought to better understand how the composition of the intestinal microbiota is connected to risk of gram-negative BSIs, expanding on our prior work in these patients. Methods Fecal specimens were collected from recipients of allo-HCT and analyzed using 16S ribosomal RNA gene sequencing. Samples and clinical data extending from the pretransplant conditioning period through stem cell engraftment were used in the analysis. Intestinal domination (relative abundance ≥ 30%) by gram-negative bacteria was used as predictor of gram-negative BSI using Cox proportional hazards modeling. Further analysis of microbiota composition was …

The impact of the gut microbiota in human health is affected by several factors including its composition, drug administrations, therapeutic interventions and underlying diseases. Unfortunately, many human microbiota datasets available publicly were collected to study the impact of single variables, and typically consist of outpatients in cross-sectional studies, have small sample numbers and/or lack metadata to account for confounders. These limitations can complicate reusing the data for questions outside their original focus. Here, we provide comprehensive longitudinal patient dataset that overcomes those limitations: a collection of fecal microbiota compositions (>10,000 microbiota samples from >1,000 patients) and a rich description of the “hospitalome” experienced by the hosts, i.e., their drug exposures and other metadata from patients with cancer, hospitalized to receive allogeneic hematopoietic cell …

The complex bacterial populations that constitute the gut microbiota can harbor antibiotic resistance genes (ARGs), including those encoding β-lactamase enzymes (BLA), which degrade commonly prescribed antibiotics such as ampicillin. The prevalence of such genes in commensal bacteria has been increased in recent years by the wide use of antibiotics in human populations and in livestock. While transfer of ARGs between bacterial species has well-established dramatic public health implications, these genes can also function in trans within bacterial consortia, where antibiotic-resistant bacteria can provide antibiotic-sensitive neighbors with leaky protection from drugs, as shown both in vitro and in vivo, in models of lung and subcutaneous coinfection. However, whether the expression of ARGs by harmless commensal bacterial species can destroy antibiotics in the intestinal lumen and shield antibiotic …

Bacteria belonging to the Lachnospiraceae family are abundant, obligate anaerobic members of the microbiota in healthy humans. Lachnospiraceae impact their hosts by producing short-chain fatty acids, converting primary to secondary bile acids, and facilitating colonization resistance against intestinal pathogens. To increase our understanding of genomic and functional diversity between members of this family, we cultured 273 Lachnospiraceae isolates representing 11 genera and 27 species from human donors and performed whole-genome sequencing assembly and annotation. This analysis revealed substantial inter- and intra-species diversity in pathways that likely influence an isolate's ability to impact host health. These differences are likely to impact colonization resistance through lantibiotic expression or intestinal acidification, influence host mucosal immune cells and enterocytes via butyrate …

Clostridium difficile (reclassified as “Clostridioides”) is the leading cause of hospital-acquired infections in the United States, and is associated with high-patient mortality and high rates of recurrence. Inflammasome priming and activation by the bacterial toxins, TcdA, TcdB, and C. difficile transferase (CDT), initiates a potent immune response that is characterized by interleukin- (IL) 8, IL-1β, and neutrophil recruitment, and is required for pathogen killing. However, it is becoming clearer that a strong inflammatory response during C. difficile infection can result in host tissue damage, and is associated with worse patient outcome. Recent work has begun to show that a type-2 immune response, most often associated with helminth infections, allergy, and asthma, may be protective during C. difficile infection. While the mechanisms through how this response protect are still unclear, there is evidence that it is mediated …

Studies of the relationship between the gastrointestinal microbiota and outcomes in allogeneic hematopoietic stem cell transplantation (allo-HCT) have thus far largely focused on early complications, predominantly infection and acute graft-versus-host disease (GVHD). We examined the potential relationship of the microbiome with chronic GVHD (cGVHD) by analyzing stool and plasma samples collected late after allo-HCT using a case-control study design. We found lower circulating concentrations of the microbe-derived short-chain fatty acids (SCFAs) propionate and butyrate in day 100 plasma samples from patients who developed cGVHD, compared with those who remained free of this complication, in the initial case-control cohort of transplant patients and in a further cross-sectional cohort from an independent transplant center. An additional cross-sectional patient cohort from a third transplant center was …

Background Relationships between microbiota composition and clinical outcomes after allogeneic hematopoietic-cell transplantation have been described in single-center studies. Geographic variations in the composition of human microbial communities and differences in clinical practices across institutions raise the question of whether these associations are generalizable. Methods The microbiota composition of fecal samples obtained from patients who were undergoing allogeneic hematopoietic-cell transplantation at four centers was profiled by means of 16S ribosomal RNA gene sequencing. In an observational study, we examined associations between microbiota diversity and mortality using Cox proportional-hazards analysis. For stratification of the cohorts into higher- and lower-diversity groups, the median diversity value that was observed at the study center in New York was used. In the analysis of …

BackgroundMonocytes are an essential cellular component of the innate immune system that support the host’s effectiveness to combat a range of infectious pathogens. Hemopoietic cell transplantation (HCT) results in transient monocyte depletion, but the factors that regulate recovery of monocyte populations are not fully understood. In this study, we investigated whether the composition of the gastrointestinal microbiota is associated with the recovery of monocyte homeostasis after HCT.MethodsWe performed a single-center, prospective, pilot study of 18 recipients of either autologous or allogeneic HCT. Serial blood and stool samples were collected from each patient during their HCT hospitalization. Analysis of the gut microbiota was done using 16S rRNA gene sequencing, and flow cytometric analysis was used to characterize the phenotypic composition of monocyte populations.ResultsDynamic fluctuations in …

Clostridioides difficile is an enteric pathogen that can cause significant clinical disease in both humans and animals. However, clinical disease arises most commonly after treatment with broad-spectrum antibiotics. The organism's ability to cause naturally occurring disease in mice is rare, and little is known about its clinical significance in highly immunocompromised mice. We report on 2 outbreaks of diarrhea associated with C. difficile in mice. In outbreak 1, 182 of approximately 2, 400 NOD.Cg-Prkdcscid Il2rgtm1Wjl /SzJ (NSG) and related strains of mice became clinically ill after cessation of a 14-d course of 0.12% amoxicillin feed to control an increase in clinical signs associated with Corynebacterium bovis infection. Most mice had been engrafted with human tumors; the remainder were experimentally naïve. Affected animals exhibited 1 of 3 clinical syndromes: 1) peracute death; 2) severe diarrhea leading to …

Burnet postulated that the diversity of T-cell receptors (TCR) allows T cells to protect against the development of cancers that display antigens with a similar, seemingly endless diversity. To test this hypothesis, we developed a strategy in which a single breeding pair of mice gives rise to four groups of sibling mice. Three of the four groups had a similar number of CD8+ T cells, but TCR diversity was either broad, significantly reduced, or absent when expressing only one type of TCR. The fourth group had no T cells. All mice shared the same housing, and, therefore, their microbial environment was similar. Only slight differences in the intestinal flora were observed under these conditions. An undisturbed broad TCR repertoire was required for the rejection of inoculated cancers displaying the natural antigenic heterogeneity of primary tumors, whereas even one type of TCR was sufficient to protect …

MethodsWe evaluated 16S stool profiles of 849 samples from 215 recipients of unmodified allo-HCT. Patients were classified in four groups according to aGVHD organ involvement: upper GI only (UGI, n= 53), lower GI with/without upper GI (LGI, n= 56), no GI involvement (non-GI, n= 30) and no GVHD (n= 76). Samples were grouped into pre-onset (day− 20 to 0) and post-onset (day 1 to 20) aGVHD.ResultsPre-onset, LGI patients showed a decreased strict anaerobes to facultative anaerobes (A/F) ratio vs. non-GI (p= 0.036) and a low A/F ratio was associated with reduced overall survival (p= 0.004) from aGVHD onset. After aGVHD onset, LGI patients had reduced microbial alpha diversity, abundance of predicted butyrate-producing (BP) bacteria and A/F ratio vs. non-GI patients (p= 0.017, p= 0.003 and p= 0.020, respectively). LGI patients also had less BP bacteria, members of genus Blautia, and lower A/F ratio (p= 0 …

BackgroundClostridioides difficile is a toxin-producing bacterium that is the foremost cause of healthcare-associated diarrhea in the United States. Recent epidemiologic and genomic evidence indicates that divergent C. difficile strains have varying propensities for transmission within healthcare settings. We investigated whether and how these differences are reflected in the genomic epidemiology of 2 common C. difficile strains—sequence type (ST) 1 (analogous to Ribotype 027) and ST2 (associated with Ribotypes 014/020)—across 3 geographically distinct US medical centers. Methods Between 2011 and 2017, a convenience sample of ST1 and ST2 C. difficile clinical isolates were collected from 3 US sites: The University of Michigan Medical Center, Texas Medical Center Hospitals, and Memorial Sloan Kettering Cancer Center. Isolates underwent whole-genome sequencing and in silico multilocus sequence …

Background:The intestinal microbiota contributes to the pathogenesis of obesity and metabolic disorders. People living with HIV (PLWH) have a higher risk for the development of visceral adiposity with accompanying worsened cardiovascular risk.Setting:Convenience sample from an HIV clinic and research unit.Methods:To understand the relationship between adiposity and intestinal dysbiosis, we compared the gut microbiota and inflammatory markers in a cross-sectional study of viscerally obese, generally obese, and lean PLWH. Fecal intestinal microbiota was characterized by 16S ribosomal DNA sequencing. Abdominal CTs quantified subcutaneous adipose tissue and visceral adipose tissue (SAT; VAT). Serum high sensitivity C-reactive protein, adiponectin, leptin, IL-6, MCP-1, and sCD14 were assayed.Results:We studied 15, 9, and 11 participants with visceral obesity, general obesity, and lean body type …

Tissue resident memory CD8+ T cells (Trm) are poised for immediate reactivation at sites of pathogen entry and provide optimal protection of mucosal surfaces. The intestinal tract represents a portal of entry for many infectious agents; however, to date specific strategies to enhance Trm responses at this site are lacking. Here, we present TMDI (Transient Microbiota Depletion-boosted Immunization), an approach that leverages antibiotic treatment to temporarily restrain microbiota-mediated colonization resistance, and favor intestinal expansion to high densities of an orally-delivered Listeria monocytogenes strain carrying an antigen of choice. By augmenting the local chemotactic gradient as well as the antigenic load, this procedure generates a highly expanded pool of functional, antigen-specific intestinal Trm, ultimately enhancing protection against infectious re-challenge in mice. We propose that TMDI is a useful …

Antibiotic treatment of patients undergoing complex medical treatments can deplete commensal bacterial strains from the intestinal microbiota, thereby reducing colonization resistance against a wide range of antibiotic-resistant pathogens. Loss of colonization resistance can lead to marked expansion of vancomycin-resistant Enterococcus faecium (VRE), Klebsiella pneumoniae, and Escherichia coli in the intestinal lumen, predisposing patients to bloodstream invasion and sepsis. The impact of intestinal domination by these antibiotic-resistant pathogens on mucosal immune defenses and epithelial and mucin-mediated barrier integrity is unclear. We used a mouse model to study the impact of intestinal domination by antibiotic-resistant bacterial species and strains on the colonic mucosa. Intestinal colonization with K. pneumoniae, Proteus mirabilis, or Enterobacter cloacae promoted greater recruitment of …