Stock Ticker

Experimental glycopeptide antibiotic EVG7 prevents recurrent Clostridioides difficile infection by sparing members of the Lachnospiraceae family

  • Feuerstadt, P., Theriault, N. & Tillotson, G. The burden of CDI in the United States: a multifactorial challenge. BMC Infect. Dis. 23, 132 (2023).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • European Centre for Disease Control and Prevention. Clostridioides difficile infections – Annual Epidemiological Report for 2018−2020; 2024. Available from: https://www.ecdc.europa.eu/en/publications-data/clostridioides-difficile-infections-annual-epidemiological-report-2018-2020.

  • Guh, A.Y. et al. Trends in U.S. Burden of Clostridioides difficile Infection and Outcomes. N. Engl. J. Med. 382, 1320–1330 (2020).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Czepiel, J. et al. Clostridium difficile infection: review. Eur. J. Clin. Microbiol. Infect. Dis. 38, 1211–1221 (2019).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Feuerstadt, P. et al. Healthcare resource utilization and direct medical costs associated with index and recurrent Clostridioides difficile infection: a real-world data analysis. J. Med. Econ. 23, 603–609 (2020).

    Article 
    PubMed 

    Google Scholar
     

  • Bartlett, J. G. & Gerding, D. N. Clinical Recognition and Diagnosis of Clostridium difficile Infection. Clin. Infect. Dis. 46, S12–S18 (2008).

    Article 
    PubMed 

    Google Scholar
     

  • Zhu, D., Sorg, J. A. & Sun, X. Clostridioides difficile Biology: Sporulation, Germination, and Corresponding Therapies for C. difficile Infection. Front. Cell. Infect. Microbiol. 8, 29 (2018).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Baktash, A. et al. Mechanistic Insights in the Success of Fecal Microbiota Transplants for the Treatment of Clostridium difficile Infections. Front. Microbiol. 9, 1242 (2018).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • McDonald, L. C. et al. Clinical Practice Guidelines for Clostridium difficile Infection in Adults and Children: 2017 Update by the Infectious Diseases Society of America (IDSA) and Society for Healthcare Epidemiology of America (SHEA). Clin. Infect. Dis. 66, 987–994 (2018).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Johnson, S. et al. Clinical Practice Guideline by the Infectious Diseases Society of America (IDSA) and Society for Healthcare Epidemiology of America (SHEA): 2021 Focused Update Guidelines on Management of Clostridioides difficile Infection in Adults. Clin. Infect. Dis. 73, e1029–e1044 (2021).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Al-Jashaami, L. S. & DuPont, H. L. Management of Clostridium difficile Infection. Gastroenterol. Hepatol. 12, 609–616 (2016).


    Google Scholar
     

  • Tsigrelis, C. Recurrent Clostridioides difficile infection: Recognition, management, prevention. Clevel. Clin. J. Med. 87, 347–359 (2020).

    Article 

    Google Scholar
     

  • Wang, R. Clostridioides difficile infection: microbe-microbe interactions and live biotherapeutics. Front. Microbiol. 14, 1182612 (2023).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Gonzales-Luna, A. J. et al. Reduced Susceptibility to Metronidazole Is Associated With Initial Clinical Failure in Clostridioides difficile Infection. Open Forum Infect. Dis. 8, ofab365 (2021).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • van Prehn, J. et al. European Society of Clinical Microbiology and Infectious Diseases: 2021 update on the treatment guidance document for Clostridioides difficile infection in adults. Clin. Microbiol. Infect. 27, S1–S21 (2021).

    Article 
    PubMed 

    Google Scholar
     

  • Freeman, J. et al. Antimicrobial susceptibility testing of Clostridioides difficile: a dual-site study of three different media and three therapeutic antimicrobials. Clin. Microbiol. Infect. 6, 1011–1017 (2025).

    Article 

    Google Scholar
     

  • Marchandin, H. et al. In vivo emergence of a still uncommon resistance to fidaxomicin in the urgent antimicrobial resistance threat Clostridioides difficile. J. Antimicrobial Chemother. 78, 1992–1999 (2023).

    Article 
    CAS 

    Google Scholar
     

  • Smits, W. K., Garey, K. W., Riley, T. V. & Johnson, S. Clostridioides difficile is a bacterial priority pathogen. Anaerobe 93, 102965 (2025).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Eubank, T. A. et al. Reduced Vancomycin Susceptibility in Clostridioides difficile Is Associated With Lower Rates of Initial Cure and Sustained Clinical Response. Clin. Infect. Dis. 79, 15–21 (2024).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Fishbein, S. et al. Randomized Controlled Trial of Oral Vancomycin Treatment in Clostridioides difficile-Colonized Patients. mSphere 6, e00936–00920 (2021).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Benech, N. et al. Update on microbiota-derived therapies for recurrent Clostridioides difficile infections. Clin. Microbiol. Infect. 30, 462–468 (2024).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Pribyl, A. L., Hugenholtz, P. & Cooper, M. A. A decade of advances in human gut microbiome-derived biotherapeutics. Nat. Microbiol. 10, 301–312 (2025).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Wang, Y., Hunt, A., Danziger, L. & Drwiega, E. N. A Comparison of Currently Available and Investigational Fecal Microbiota Transplant Products for Recurrent Clostridioides difficile Infection. Antibiotics 13, 436 (2024).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • McMillan, A. S. & Theriot, C. M. Bile acids impact the microbiota, host, and C. difficile dynamics providing insight into mechanisms of efficacy of FMTs and microbiota-focused therapeutics. Gut Microbes 16, 2393766 (2024).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Birch, C. R. et al. Cost-effectiveness of faecal microbiota transplantation compared with vancomycin monotherapy for early Clostridioides difficile infection: economic evaluation alongside a randomized controlled trial. J. Hospital Infect. 155, 145–149 (2025).

    Article 
    CAS 

    Google Scholar
     

  • Baunwall, S. M. D. et al. Faecal microbiota transplantation for first or second Clostridioides difficile infection (EarlyFMT): a randomised, double-blind, placebo-controlled trial. Lancet Gastroenterol. Hepatol. 7, 1083–1091 (2022).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • OpenBiome. FMT Update & Future Directions. [Press Release]; 2024. Available from https://openbiome.org/feature/fmt-update-future-directions/.

  • Davidson, J. OpenBiome No Longer Distributing FMT For Recurrent C. difficile Infections. [Gastroenterology & Endoscopy News]; 2024. Available from https://www.gastroendonews.com/PRN/Article/12-24/OpenBiome-No-Longer-Distributing-FMT-For-Recurrent-C-difficile-Infections/75606.

  • Jain, N., Umar, T. P., Fahner, A.-F. & Gibietis, V. Advancing therapeutics for recurrent clostridioides difficile infections: an overview of vowst’s FDA approval and implications. Gut Microbes 15, 2232137 (2023).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Mullard, A. FDA approves second microbiome-based C. difficile therapy. Nat. Rev. Drug Discov. 22, 436 (2023).

    PubMed 

    Google Scholar
     

  • Shirley, D.-A., Tornel, W., Warren, C. A. & Moonah, S. Clostridioides difficile Infection in Children: Recent Updates on Epidemiology, Diagnosis, Therapy. Pediatrics 152, e2023062307 (2023).

    Article 
    PubMed 

    Google Scholar
     

  • Carlson, T. J., Gonzales-Luna, A. J. & Garey, K. W. Fulminant Clostridioides difficile Infection: A Review of Treatment Options for a Life-Threatening Infection. Semin. Respiratory Crit. Care Med. 43, 028–038 (2022).

    Article 

    Google Scholar
     

  • van Groesen, E. et al. Semisynthetic guanidino lipoglycopeptides with potent in vitro and in vivo antibacterial activity. Sci. Transl. Med. 16, eabo4736 (2024).

    Article 
    PubMed 

    Google Scholar
     

  • Theriot, C. M. et al. Cefoperazone-treated mice as an experimental platform to assess differential virulence of Clostridium difficile strains. Gut Microbes 2, 326–334 (2011).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Blake, S. et al. Salicylanilide Analog Minimizes Relapse of Clostridioides difficile Infection in Mice. J. Medicinal Chem. 63, 6898–6908 (2020).

    Article 
    CAS 

    Google Scholar
     

  • Seekatz, A. M. et al. Fecal Microbiota Transplantation Eliminates Clostridium difficile in a Murine Model of Relapsing Disease. Infect. Immun. 83, 3838–3846 (2015).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Hou, K. et al. Microbiota in health and diseases. Signal Transduct. Target. Ther. 7, 135 (2022).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Seekatz, A. M. & Young, V. B. Clostridium difficile and the microbiota. J. Clin. Investig. 124, 4182–4189 (2014).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Theriot, C. M., Bowman, A. A. & Young, V. B. Antibiotic-Induced Alterations of the Gut Microbiota Alter Secondary Bile Acid Production and Allow for Clostridium difficile Spore Germination and Outgrowth in the Large Intestine. mSphere 1, e00045–00015 (2016).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • McMillan, A. S. et al. Metagenomic, metabolomic, and lipidomic shifts associated with fecal microbiota transplantation for recurrent Clostridioides difficile infection. mSphere 9, e00706–e00724 (2024).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Buffie, C. G. et al. Precision microbiome reconstitution restores bile acid mediated resistance to Clostridium difficile. Nature 517, 205–208 (2015).

    Article 
    ADS 
    CAS 
    PubMed 

    Google Scholar
     

  • Girinathan, B. P. et al. In vivo commensal control of Clostridioides difficile virulence. Cell Host Microbe 29, 1693–1708.e1697 (2021).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Kang, J. D. et al. Bile Acid 7α-Dehydroxylating Gut Bacteria Secrete Antibiotics that Inhibit Clostridium difficile: Role of Secondary Bile Acids. Cell Chem. Biol. 26, 27–34.e24 (2019).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Fishbein, S. R. S. et al. Commensal-pathogen dynamics structure disease outcomes during Clostridioides difficile colonization. Cell Host Microbe 33, 30–41.e36 (2025).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Aguirre, A. M. et al. Bile acid-independent protection against Clostridioides difficile infection. PLOS Pathog. 17, e1010015 (2021).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Walsh, C. T. et al. Bacterial resistance to vancomycin: Five genes and one missing hydrogen bond tell the story. Chem. Biol. 3, 21–28 (1996).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • van Groesen, E. et al. Vancomyxins: Vancomycin-Polymyxin Nonapeptide Conjugates That Retain Anti-Gram-Positive Activity with Enhanced Potency against Gram-Negative Strains. ACS Infect. Dis. 7, 2746–2754 (2021).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Li, Q. et al. Outer-membrane-acting peptides and lipid II-targeting antibiotics cooperatively kill Gram-negative pathogens. Commun. Biol. 4, 31 (2021).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Antonoplis, A. et al. Vancomycin-Arginine Conjugate Inhibits Growth of Carbapenem-Resistant E. coli and Targets Cell-Wall Synthesis. ACS Chem. Biol. 14, 2065–2070 (2019).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Sarkar, P. et al. Vancomycin Derivative Inactivates Carbapenem-resistant Acinetobacter baumannii and Induces Autophagy. ACS Chem. Biol. 15, 884–889 (2020).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Bian, X. et al. Single Amine or Guanidine Modification on Norvancomycin and Vancomycin to Overcome Multidrug-Resistance through Augmented Lipid II Binding and Increased Membrane Activity. J. Medicinal Chem. 67, 20639–20663 (2024).

    Article 
    CAS 

    Google Scholar
     

  • Babakhani, F. et al. Fidaxomicin Inhibits Spore Production in Clostridium difficile. Clin. Infect. Dis. 55, S162–S169 (2012).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Yamaguchi, T. et al. The gut microbiome diversity of Clostridioides difficile-inoculated mice treated with vancomycin and fidaxomicin. J. Infect. Chemother. 26, 483–491 (2020).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Louie, T. J. et al. OPT-80 Eliminates Clostridium difficile and Is Sparing of Bacteroides Species during Treatment of C. difficile Infection. Antimicrobial Agents Chemother. 53, 261–263 (2009).

    Article 
    CAS 

    Google Scholar
     

  • Louie, T. J. et al. Fidaxomicin versus Vancomycin for Clostridium difficile Infection. N. Engl. J. Med. 364, 422–431 (2011).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • van Eijk, E. et al. Complete genome sequence of the Clostridium difficile laboratory strain 630Δerm reveals differences from strain 630, including translocation of the mobile element CTn5. BMC Genomics 16, 31 (2015).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Hussain, H. A., Roberts, A. P. & Mullany, P. Generation of an erythromycin-sensitive derivative of Clostridium difficile strain 630 (630Δerm) and demonstration that the conjugative transposon Tn916ΔE enters the genome of this strain at multiple sites. J. Med. Microbiol. 54, 137–141 (2005).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Kassam, Z., Lee, C. H. & Hunt, R. H. Review of the Emerging Treatment of Clostridium difficile Infection with Fecal Microbiota Transplantation and Insights into Future Challenges. Clin. Lab. Med. 34, 787–798 (2014).

    Article 
    PubMed 

    Google Scholar
     

  • Rohlke, F. & Stollman, N. Fecal microbiota transplantation in relapsing Clostridium difficile infection. Therapeutic Adv. Gastroenterol. 5, 403–420 (2012).

    Article 

    Google Scholar
     

  • Blair, H. A. SER-109 (VOWST™): A Review in the Prevention of Recurrent Clostridioides difficile Infection. Drugs 84, 329–336 (2024).

    Article 
    PubMed 

    Google Scholar
     

  • DeFilipp, Z. et al. Drug-Resistant E. coli Bacteremia Transmitted by Fecal Microbiota Transplant. N. Engl. J. Med. 381, 2043–2050 (2019).

    Article 
    PubMed 

    Google Scholar
     

  • Tan, X. & Johnson, S. Fecal microbiota transplantation (FMT) for C. difficile infection, just say ‘No’. Anaerobe 60, 102092 (2019).

    Article 
    PubMed 

    Google Scholar
     

  • Peery, A. F. et al. AGA Clinical Practice Guideline on Fecal Microbiota–Based Therapies for Select Gastrointestinal Diseases. Gastroenterology 166, 409–434 (2024).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Peixoto, R. S. et al. Harnessing the microbiome to prevent global biodiversity loss. Nat. Microbiol. 7, 1726–1735 (2022).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Khosravi, A. & Mazmanian, S. K. Disruption of the gut microbiome as a risk factor for microbial infections. Curr. Opin. Microbiol. 16, 221–227 (2013).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Durack, J. & Lynch, S. V. The gut microbiome: Relationships with disease and opportunities for therapy. J. Exp. Med. 216, 20–40 (2019).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Afzaal, M. et al. Human gut microbiota in health and disease: Unveiling the relationship. Front. Microbiol. 13, 999001 (2022).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Carlson, T. J. & Gonzales-Luna, A. J. Antibiotic Treatment Pipeline for Clostridioides difficile Infection (CDI): A Wide Array of Narrow-Spectrum Agents. Curr. Infect. Dis. Rep. 22, 20 (2020).

    Article 

    Google Scholar
     

  • Quan, M. et al. Fighting against Clostridioides difficile infection: Current medications. Int. J. Antimicrobial Agents 64, 107198 (2024).

    Article 
    CAS 

    Google Scholar
     

  • World Health Organization. 2023 Antibacterial agents in clinical and preclinical development: an overview and analysis. Available from https://www.who.int/publications/i/item/9789240094000 (2024).

  • Okhuysen, P. C. et al. A Randomized, Double-Blind, Phase 3 Safety and Efficacy Study of Ridinilazole Versus Vancomycin for Treatment of Clostridioides difficile Infection: Clinical Outcomes With Microbiome and Metabolome Correlates of Response. Clin. Infect. Dis. 78, 1462–1472 (2024).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Taylor, N. P. Summit makes case for changes to antibiotic R&D after sharing data from failed phase 3 trial. 2022. Available from https://www.fiercebiotech.com/biotech/summit-makes-case-changes-antibiotic-rd-after-sharing-data-failed-phase-3-trial.

  • DEINOVE – Update on the receivership proceedings. [Press release]; 2023. Available from https://firstwordpharma.com/story/5697000.

  • Lomeli, B. K. et al. Multiple-Ascending-Dose Phase 1 Clinical Study of the Safety, Tolerability, and Pharmacokinetics of CRS3123, a Narrow-Spectrum Agent with Minimal Disruption of Normal Gut Microbiota. Antimicrobial Agents Chemother. 64, e01395–01319 (2019).

    Article 

    Google Scholar
     

  • Crestone Inc. Crestone Announces Positive Data from Phase 2 Clinical Trial of CRS3123 for C. Difficile Infections (CDI). [Press release]; 2024. Available from https://crestonepharma.com/positive-data-phase-2-clinical-trial-crs3123/.

  • Eubank, T. A. et al. P-1109. A phase 2, randomized, double-blind study of ibezapolstat compared with vancomycin for the treatment of Clostridioides difficile infection: clinical and microbiome evaluation. Open Forum Infect. Dis. 12, ofae631.1297 (2025).

    Article 
    PubMed Central 

    Google Scholar
     

  • MGB Biopharma. MGB Biopharma Announces Successful Outcome from Phase II Clinical Study with MGB-BP-3 – a Potential New Gold Standard, First-Line Treatment for Clostridium difficile Infection (CDI). [Press release]; 2020. Available from https://www.mgb-biopharma.com/mgb-biopharma-announces-successful-outcome-from-phase-ii-clinical-study-with-mgb-bp-3-a-potential-new-gold-standard-first-line-treatment-for-clostridium-difficile-infection-cdi/.

  • Critchley, I. A. et al. Spectrum of activity and mode of action of REP3123, a new antibiotic to treat Clostridium difficile infections. J. Antimicrobial Chemother. 63, 954–963 (2009).

    Article 
    CAS 

    Google Scholar
     

  • Murray, B. et al. In vitro activity of the novel antibacterial agent ibezapolstat (ACX-362E) against Clostridioides difficile. J. Antimicrobial Chemother. 75, 2149–2155 (2020).

    CAS 

    Google Scholar
     

  • Citron, D. M. et al. Comparative in vitro activity of REP3123 against Clostridium difficile and other anaerobic intestinal bacteria. J. Antimicrobial Chemother. 63, 972–976 (2009).

    Article 
    CAS 

    Google Scholar
     

  • Garey, K. W. et al. Efficacy, Safety, Pharmacokinetics, and Microbiome Changes of Ibezapolstat in Adults with Clostridioides difficile Infection: A Phase 2a Multicenter Clinical Trial. Clin. Infect. Dis. 75, 1164–1170 (2022).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • McPherson, J. K. et al. The microbiome-restorative potential of ibezapolstat for the treatment of Clostridioides difficile infection is predicted through variant PolC-type DNA polymerase III in Lachnospiraceae and Oscillospiraceae. Antimicrobial Agents Chemother. 69, e01679–01624 (2025).

    Article 

    Google Scholar
     

  • Vacca, M. et al. The Controversial Role of Human Gut Lachnospiraceae. Microorganisms 8, 573 (2020).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Reeves, A. E., Koenigsknecht, M. J., Bergin, I. L. & Young, V. B. Suppression of Clostridium difficile in the Gastrointestinal Tracts of Germfree Mice Inoculated with a Murine Isolate from the Family Lachnospiraceae. Infect. Immun. 80, 3786–3794 (2012).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Tejada, J. N. et al. Prevention and cure of murine C. difficile infection by a Lachnospiraceae strain. Gut Microbes 16, 2392872 (2024).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Zaplana, T., Miele, S. & Tolonen, A. C. Lachnospiraceae are emerging industrial biocatalysts and biotherapeutics. Front. Bioeng. Biotechnol. 11, 1324396 (2024).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Feuerstadt, P. et al. SER-109, an Oral Microbiome Therapy for Recurrent Clostridioides difficile Infection. N. Engl. J. Med. 386, 220–229 (2022).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Knetsch, C. W. et al. Comparative analysis of an expanded Clostridium difficile reference strain collection reveals genetic diversity and evolution through six lineages. Infect., Genet. Evolution 12, 1577–1585 (2012).

    Article 

    Google Scholar
     

  • Baktash, A. et al. Comparison of Whole-Genome Sequence-Based Methods and PCR Ribotyping for Subtyping of Clostridioides difficile. J. Clin. Microbiol. 60, e01737–01721 (2022).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Winston, J. A., Thanissery, R., Montgomery, S. A. & Theriot, C. M. Cefoperazone-treated Mouse Model of Clinically-relevant Clostridium difficile Strain R20291. J. Vis. Exp. 118, e54850 (2016).


    Google Scholar
     

  • Perez, J., Springthorpe, V. S. & Sattar, S. A. Clospore: A Liquid Medium for Producing High Titers of Semi-purified Spores of Clostridium difficile. J. AOAC Int. 94, 618–626 (2011).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Warren, C. A. et al. Amixicile, a Novel Inhibitor of Pyruvate:Ferredoxin Oxidoreductase, Shows Efficacy against Clostridium difficile in a Mouse Infection Model. Antimicrobial Agents Chemother. 56, 4103–4111 (2012).

    Article 
    CAS 

    Google Scholar
     

  • Bolger, A. M., Lohse, M. & Usadel, B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30, 2114–2120 (2014).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Bolyen, E. et al. Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. Nat. Biotechnol. 37, 852–857 (2019).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Callahan, B. J. et al. DADA2: High-resolution sample inference from Illumina amplicon data. Nat. Methods 13, 581–583 (2016).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Bokulich, N. A. et al. Optimizing taxonomic classification of marker-gene amplicon sequences with QIIME 2’s q2-feature-classifier plugin. Microbiome 6, 90 (2018).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Robeson, M. S. et al. RESCRIPt: Reproducible sequence taxonomy reference database management. PLoS Computational Biol. 17, e1009581 (2021).

    Article 

    Google Scholar
     

  • Quast, C. et al. The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res. 41, D590–D596 (2012).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • R Core Team. R: A language and environment for statistical computing. R Foundation for Statistical Computing. https://www.R-project.org/ (2021).

  • McMurdie, P. J. & Holmes, S. phyloseq: An R Package for Reproducible Interactive Analysis and Graphics of Microbiome Census Data. PLoS ONE 8, e61217 (2013).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Lahti, L. & Shetty, S. microbiome R package. https://doi.org/10.18129/B9.bioc.microbiome

  • Barnett, D. J. M., Arts, I. C. W. & Penders, J. microViz: an R package for microbiome data visualization and statistics. J. Open Source Softw. 6, 3201 (2021).

    Article 
    ADS 

    Google Scholar
     

  • Oksanen, J. et al. vegan: Community Ecology Package. R package version 2.6-4 https://CRAN.R-project.org/package=vegan (2022).

  • Simpson, G. L. & Oksanen, J. ggvegan: ‘ggplot2’ Plots for the ‘vegan’ Package. R package version 0.1.999 https://gavinsimpson.r-universe.dev/ggvegan/ggvegan.pdf (2023).

  • Wickham, H. ggplot2: Elegant Graphics for Data Analysis. https://doi.org/10.1007/978-0-387-98141-3 (Springer-Verlag, 2009).

  • Ducarmon, Q. R. et al. Clostridioides difficile infection with isolates of cryptic clade C-II: a genomic analysis of polymerase chain reaction ribotype 151. Clin. Microbiol. Infect. 29, 538.e531–538.e536 (2023).

    Article 

    Google Scholar
     

  • Source link

    Get RawNews Daily

    Stay informed with our RawNews daily newsletter email

    Liverpool defender left out of World Cup squad

    Madonna Covering Rent For Musicians Working At Her Old NYC Rehearsal Space

    Up 16.5%! Here’s why Hollywood Bowl stock smashed the FTSE 250 today

    Trump says Iran would not get sanctions relief in exchange for giving up enriched uranium