keyword
https://read.qxmd.com/read/38496653/comprehensive-analyses-of-a-large-human-gut-bacteroidales-culture-collection-reveal-species-and-strain-level-diversity-and-evolution
#1
Zhenrun J Zhang, Cody G Cole, Michael J Coyne, Huaiying Lin, Nicholas Dylla, Rita C Smith, Emily Waligurski, Ramanujam Ramaswamy, Che Woodson, Victoria Burgo, Jessica C Little, David Moran, Amber Rose, Mary McMillin, Emma McSpadden, Anitha Sundararajan, Ashley M Sidebottom, Eric G Pamer, Laurie E Comstock
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...
March 9, 2024: bioRxiv
https://read.qxmd.com/read/38293740/activity-of-gut-derived-nisin-like-lantibiotics-against-human-gut-pathogens-and-commensals
#2
JOURNAL ARTICLE
Zhenrun J Zhang, Chunyu Wu, Ryan Moreira, Darian Dorantes, Téa Pappas, Anitha Sundararajan, Huaiying Lin, Eric G Pamer, Wilfred A van der Donk
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...
January 31, 2024: ACS Chemical Biology
https://read.qxmd.com/read/38234830/exposure-and-resistance-to-lantibiotics-impact-microbiota-composition-and-function
#3
Zhenrun J Zhang, Cody Cole, Huaiying Lin, Chunyu Wu, Fidel Haro, Emma McSpadden, Wilfred A van der Donk, Eric G Pamer
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...
December 30, 2023: bioRxiv
https://read.qxmd.com/read/38177297/dietary-and-host-derived-metabolites-are-used-by-diverse-gut-bacteria-for-anaerobic-respiration
#4
JOURNAL ARTICLE
Alexander S Little, Isaac T Younker, Matthew S Schechter, Paola Nol Bernardino, Raphaël Méheust, Joshua Stemczynski, Kaylie Scorza, Michael W Mullowney, Deepti Sharan, Emily Waligurski, Rita Smith, Ramanujam Ramanswamy, William Leiter, David Moran, Mary McMillin, Matthew A Odenwald, Anthony T Iavarone, Ashley M Sidebottom, Anitha Sundararajan, Eric G Pamer, A Murat Eren, Samuel H Light
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...
January 2024: Nature Microbiology
https://read.qxmd.com/read/38105970/an-evolution-based-framework-for-describing-human-gut-bacteria
#5
Benjamin A Doran, Robert Y Chen, Hannah Giba, Vivek Behera, Bidisha Barat, Anitha Sundararajan, Huaiying Lin, Ashley Sidebottom, Eric G Pamer, Arjun S Raman
UNLABELLED: 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...
December 5, 2023: bioRxiv
https://read.qxmd.com/read/38103544/fecal-metabolite-profiling-identifies-liver-transplant-recipients-at-risk-for-postoperative-infection
#6
JOURNAL ARTICLE
Christopher J Lehmann, Nicholas P Dylla, Matthew Odenwald, Ravi Nayak, Maryam Khalid, Jaye Boissiere, Jackelyn Cantoral, Emerald Adler, Matthew R Stutz, Mark Dela Cruz, Angelica Moran, Huaiying Lin, Ramanujam Ramaswamy, Anitha Sundararajan, Ashley M Sidebottom, Jessica Little, Eric G Pamer, Andrew Aronsohn, John Fung, Talia B Baker, Aalok Kacha
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...
December 9, 2023: Cell Host & Microbe
https://read.qxmd.com/read/37845315/bifidobacteria-metabolize-lactulose-to-optimize-gut-metabolites-and-prevent-systemic-infection-in-patients-with-liver-disease
#7
JOURNAL ARTICLE
Matthew A Odenwald, Huaiying Lin, Christopher Lehmann, Nicholas P Dylla, Cody G Cole, Jake D Mostad, Téa E Pappas, Ramanujam Ramaswamy, Angelica Moran, Alan L Hutchison, Matthew R Stutz, Mark Dela Cruz, Emerald Adler, Jaye Boissiere, Maryam Khalid, Jackelyn Cantoral, Fidel Haro, Rita A Oliveira, Emily Waligurski, Thomas G Cotter, Samuel H Light, Kathleen G Beavis, Anitha Sundararajan, Ashley M Sidebottom, K Gautham Reddy, Sonali Paul, Anjana Pillai, Helen S Te, Mary E Rinella, Michael R Charlton, Eric G Pamer, Andrew I Aronsohn
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...
October 16, 2023: Nature Microbiology
https://read.qxmd.com/read/37523264/virulence-and-genomic-diversity-among-clinical-isolates-of-st1-bi-nap1-027-clostridioides-difficile
#8
JOURNAL ARTICLE
Qiwen Dong, Huaiying Lin, Marie-Maude Allen, Julian R Garneau, Jonathan K Sia, Rita C Smith, Fidel Haro, Tracy McMillen, Rosemary L Pope, Carolyn Metcalfe, Victoria Burgo, Che Woodson, Nicholas Dylla, Claire Kohout, Anitha Sundararajan, Evan S Snitkin, Vincent B Young, Louis-Charles Fortier, Mini Kamboj, Eric G Pamer
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...
July 30, 2023: Cell Reports
https://read.qxmd.com/read/37329880/the-taxumap-atlas-efficient-display-of-large-clinical-microbiome-data-reveals-ecological-competition-in-protection-against-bacteremia
#9
JOURNAL ARTICLE
Jonas Schluter, Ana Djukovic, Bradford P Taylor, Jinyuan Yan, Caichen Duan, Grant A Hussey, Chen Liao, Sneh Sharma, Emily Fontana, Luigi A Amoretti, Roberta J Wright, Anqi Dai, Jonathan U Peled, Ying Taur, Miguel-Angel Perales, Benjamin A Siranosian, Ami S Bhatt, Marcel R M van den Brink, Eric G Pamer, Joao B Xavier
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...
June 12, 2023: Cell Host & Microbe
https://read.qxmd.com/read/37295406/high-resolution-analyses-of-associations-between-medications-microbiome-and-mortality-in-cancer-patients
#10
JOURNAL ARTICLE
Chi L Nguyen, Kate A Markey, Oriana Miltiadous, Anqi Dai, Nicholas Waters, Keimya Sadeghi, Teng Fei, Roni Shouval, Bradford P Taylor, Chen Liao, John B Slingerland, Ann E Slingerland, Annelie G Clurman, Molly A Maloy, Lauren Bohannon, Paul A Giardina, Daniel G Brereton, Gabriel K Armijo, Emily Fontana, Ana Gradissimo, Boglarka Gyurkocza, Anthony D Sung, Nelson J Chao, Sean M Devlin, Ying Taur, Sergio A Giralt, Miguel-Angel Perales, Joao B Xavier, Eric G Pamer, Jonathan U Peled, Antonio L C Gomes, Marcel R M van den Brink
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...
June 8, 2023: Cell
https://read.qxmd.com/read/37283928/corrigendum-a-maldi-tof-ms-library-for-rapid-identification-of-human-commensal-gut-bacteria-from-the-class-clostridia
#11
Paul Tetteh Asare, Chi-Hsien Lee, Vera Hürlimann, Youzheng Teo, Aline Cuénod, Nermin Akduman, Cordula Gekeler, Afrizal Afrizal, Myriam Corthesy, Claire Kohout, Vincent Thomas, Tomas de Wouters, Gilbert Greub, Thomas Clavel, Eric G Pamer, Adrian Egli, Lisa Maier, Pascale Vonaesch
[This corrects the article DOI: 10.3389/fmicb.2023.1104707.].
2023: Frontiers in Microbiology
https://read.qxmd.com/read/37054670/assembling-symbiotic-bacterial-species-into-live-therapeutic-consortia-that-reconstitute-microbiome-functions
#12
REVIEW
Rita A Oliveira, Eric G Pamer
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...
April 12, 2023: Cell Host & Microbe
https://read.qxmd.com/read/36896425/a-maldi-tof-ms-library-for-rapid-identification-of-human-commensal-gut-bacteria-from-the-class-clostridia
#13
JOURNAL ARTICLE
Paul Tetteh Asare, Chi-Hsien Lee, Vera Hürlimann, Youzheng Teo, Aline Cuénod, Nermin Akduman, Cordula Gekeler, Afrizal Afrizal, Myriam Corthesy, Claire Kohout, Vincent Thomas, Tomas de Wouters, Gilbert Greub, Thomas Clavel, Eric G Pamer, Adrian Egli, Lisa Maier, Pascale Vonaesch
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...
2023: Frontiers in Microbiology
https://read.qxmd.com/read/36869161/plasma-metabolites-with-mechanistic-and-clinical-links-to-the-neurovascular-disease-cavernous-angioma
#14
JOURNAL ARTICLE
Abhinav Srinath, Bingqing Xie, Ying Li, Je Yeong Sone, Sharbel Romanos, Chang Chen, Anukriti Sharma, Sean Polster, Pieter C Dorrestein, Kelly C Weldon, Dorothy DeBiasse, Thomas Moore, Rhonda Lightle, Janne Koskimäki, Dongdong Zhang, Agnieszka Stadnik, Kristina Piedad, Matthew Hagan, Abdallah Shkoukani, Julián Carrión-Penagos, Dehua Bi, Le Shen, Robert Shenkar, Yuan Ji, Ashley Sidebottom, Eric Pamer, Jack A Gilbert, Mark L Kahn, Mark D'Souza, Dinanath Sulakhe, Issam A Awad, Romuald Girard
BACKGROUND: Cavernous 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. METHODS: The plasma metabolome of CA patients and CA patients with symptomatic hemorrhage was assessed using liquid-chromatography mass spectrometry...
March 3, 2023: Commun Med (Lond)
https://read.qxmd.com/read/36711955/virulence-and-genomic-diversity-among-clinical-isolates-of-st1-bi-nap1-027-clostridioides-difficile
#15
Qiwen Dong, Huaiying Lin, Marie-Maude Allen, Julian R Garneau, Jonathan K Sia, Rita C Smith, Fidel Haro, Tracy McMillen, Rosemary L Pope, Carolyn Metcalfe, Victoria Burgo, Che Woodson, Nicholas Dylla, Claire Kohout, Anitha Sundararajan, Evan S Snitkin, Vincent B Young, Louis-Charles Fortier, Mini Kamboj, Eric G Pamer
Clostridioides difficile (C. difficile) , a leading cause of nosocomial infection, produces toxins that damage the colonic epithelium and results in colitis that varies from mild to fulminant. Variation in disease severity is poorly understood and has been attributed to host factors (age, immune competence and intestinal microbiome composition) and/or virulence differences between C. difficile strains, with some, such as the epidemic BI/NAP1/027 (MLST1) strain, being associated with greater virulence. We tested 23 MLST1(ST1) C...
January 12, 2023: bioRxiv
https://read.qxmd.com/read/36697862/questioning-the-fetal-microbiome-illustrates-pitfalls-of-low-biomass-microbial-studies
#16
REVIEW
Katherine M Kennedy, Marcus C de Goffau, Maria Elisa Perez-Muñoz, Marie-Claire Arrieta, Fredrik Bäckhed, Peer Bork, Thorsten Braun, Frederic D Bushman, Joel Dore, Willem M de Vos, Ashlee M Earl, Jonathan A Eisen, Michal A Elovitz, Stephanie C Ganal-Vonarburg, Michael G Gänzle, Wendy S Garrett, Lindsay J Hall, Mathias W Hornef, Curtis Huttenhower, Liza Konnikova, Sarah Lebeer, Andrew J Macpherson, Ruth C Massey, Alice Carolyn McHardy, Omry Koren, Trevor D Lawley, Ruth E Ley, Liam O'Mahony, Paul W O'Toole, Eric G Pamer, Julian Parkhill, Jeroen Raes, Thomas Rattei, Anne Salonen, Eran Segal, Nicola Segata, Fergus Shanahan, Deborah M Sloboda, Gordon C S Smith, Harry Sokol, Tim D Spector, Michael G Surette, Gerald W Tannock, Alan W Walker, Moran Yassour, Jens Walter
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...
January 2023: Nature
https://read.qxmd.com/read/36618438/metagenomic-and-bile-acid-metabolomic-analysis-of-fecal-microbiota-transplantation-for-recurrent-clostridiodes-difficile-and-or-inflammatory-bowel-diseases
#17
JOURNAL ARTICLE
Rubin Jf Ramos, Chencan Zhu, Dimitri F Joseph, Shubh Thaker, Joseph F Lacomb, Katherine Markarian, Hannah J Lee, Jessica C Petrov, Farah Monzur, Jonathan M Buscaglia, Anupama Chawla, Leslie Small-Harary, Grace Gathungu, Jeffrey A Morganstern, Jie Yang, Jinyu Li, Eric G Pamer, Charles E Robertson, Daniel N Frank, Justin R Cross, Ellen Li
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...
October 31, 2022: Medical Research Archives
https://read.qxmd.com/read/36329015/immunomodulatory-fecal-metabolites-are-associated-with-mortality-in-covid-19-patients-with-respiratory-failure
#18
JOURNAL ARTICLE
Matthew R Stutz, Nicholas P Dylla, Steven D Pearson, Paola Lecompte-Osorio, Ravi Nayak, Maryam Khalid, Emerald Adler, Jaye Boissiere, Huaiying Lin, William Leiter, Jessica Little, Amber Rose, David Moran, Michael W Mullowney, Krysta S Wolfe, Christopher Lehmann, Matthew Odenwald, Mark De La Cruz, Mihai Giurcanu, Anne S Pohlman, Jesse B Hall, Jean-Luc Chaubard, Anitha Sundararajan, Ashley Sidebottom, John P Kress, Eric G Pamer, Bhakti K Patel
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)...
November 3, 2022: Nature Communications
https://read.qxmd.com/read/36253610/author-correction-gut-microbiome-correlates-of-response-and-toxicity-following-anti-cd19-car-t-cell-therapy
#19
Melody Smith, Anqi Dai, Guido Ghilardi, Kimberly V Amelsberg, Sean M Devlin, Raymone Pajarillo, John B Slingerland, Silvia Beghi, Pamela S Herrera, Paul Giardina, Annelie Clurman, Emmanuel Dwomoh, Gabriel Armijo, Antonio L C Gomes, Eric R Littmann, Jonas Schluter, Emily Fontana, Ying Taur, Jae H Park, Maria Lia Palomba, Elizabeth Halton, Josel Ruiz, Tania Jain, Martina Pennisi, Aishat Olaide Afuye, Miguel-Angel Perales, Craig W Freyer, Alfred Garfall, Shannon Gier, Sunita Nasta, Daniel Landsburg, James Gerson, Jakub Svoboda, Justin Cross, Elise A Chong, Sergio Giralt, Saar I Gill, Isabelle Riviere, David L Porter, Stephen J Schuster, Michel Sadelain, Noelle Frey, Renier J Brentjens, Carl H June, Eric G Pamer, Jonathan U Peled, Andrea Facciabene, Marcel R M van den Brink, Marco Ruella
No abstract text is available yet for this article.
October 17, 2022: Nature Medicine
https://read.qxmd.com/read/35759806/global-trends-in-gut-microbiota-and-clostridioides-difficile-infection-research-a-visualized-study
#20
JOURNAL ARTICLE
Zitong Li, Haoran Ke, Qianyun Lin, Zefeng Shen, Ye Chen
BACKGROUND: Clostridioides (clostridium) difficile infection (CDI) is the most common cause of nosocomial diarrheal disease, which has become a public health problem worldwide; gut dysbiosis plays a central role in its pathophysiology. This study conducted a bibliometric analysis of publications on gut microbiota and CDI to summarize the current status of research including research hotspots. METHODS: Relevant publications from January 2004 to February 2022 were identified from the Web of Science Core Collection...
July 2022: Journal of Infection and Public Health
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