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• Journal article
  Mullish BH, Michael DR, Dabcheva M, Webberley TS, Coates N, John DA, Wang D, Luo Y, Plummer SF, Marchesi JRet al., 2024,

  Authors' reply to letter: He who controls Clostridia and Bacteroidia controls the gut microbiome: The concept of targeted probiotics to restore the balance of keystone taxa in irritable bowel syndrome

  , Neurogastroenterology & Motility, Vol: n/a, ISSN: 1350-1925
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• Journal article
  Perry RW, Mullish BH, Alexander JL, Shah R, Danckert NP, Blanco JM, Roberts L, Liu Z, Chrysostomou D, Radhakrishnan ST, Balarajah S, Barry R, Hicks LC, Williams HR, Marchesi Jet al., 2024,

  Sa1889 3D Printed rectal swabs for assessing the gut microbiome, metabolome, and inflammation

  , Gastroenterology, Vol: 166, Pages: S566-S567, ISSN: 0016-5085
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• Conference paper
  Radhakrishnan ST, Alexander JL, Mullish BH, Valdivia-Garcia M, Danckert NP, Serrano-Contreras JI, Balarajah S, Perry RW, Gallagher KI, Hicks LC, Powell N, Li JV, Marchesi J, Williams HRet al., 2024,

  Sa1871 THE COMPOSITION AND FUNCTION OF THE GUT MICROBIOTA IN A TREATMENT NAIVE INCEPTION COHORT OF INFLAMMATORY BOWEL DISEASE (IBD) CAN ACCURATELY DIFFERENTIATE IBD PHENOTYPE.

  , Publisher: Elsevier BV, Pages: S-559, ISSN: 0016-5085
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• Conference paper
  King OG, Yip AY, Horrocks V, Blanco JM, Marchesi J, Mullish BH, Clarke TB, McDonald JAet al., 2024,

  Sa1927 ANTIBIOTIC TREATMENT PROMOTES THE INTESTINAL COLONISATION OF VANCOMYCIN-RESISTANT ENTEROCOCCUS BY KILLING MEMBERS OF THE GUT MICROBIOTA AND DECREASING NUTRIENT COMPETITION

  , Publisher: Elsevier BV, Pages: S-584, ISSN: 0016-5085
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• Journal article
  Pitashny M, Kao D, Ianiro G, Mullish B, Nagy G, Urbonas T, Kesten I, Stabholz Y, Kupcinskas J, Franz R, Rondinella D, Tamburini S, Tudlik Z, Masucci L, Quaranta G, Fusco W, Cammarota G, Skieceviciene J, Wong K, Segata N, Paul M, Bar-Yoseph Het al., 2024,

  Lyophilized fecal microbiome transfer for primary Clostridioides difficile infection: a multicenter randomized controlled trial (DONATE Study)

  , Open Research Europe, Vol: 4, Pages: 61-61

  <ns3:p>Background Primary Clostridioides difficile infection (pCDI) carries high recurrence and mortality rates and is globally spread. pCDI is often a consequence of exposure to antibiotics, disrupting the healthy intestinal microbiota composition. Not surprisingly, in this antibiotic-associated infection, failure of the standard antibiotic treatment is high. Frozen fecal microbiota transplantation (FMT), the introduction of the microbial community from a healthy donor, has been shown to be safe and highly effective in cases of recurrent CDI, reaching &gt;90% cumulative success rate. Importantly, FMT has shown potential for intestinal decolonization of multidrug-resistant organisms (MDRO), and/or mitigation of their ability to cause invasive infection. The use of FMT for pCDI, has been tested in small studies, showing promising results. The use of frozen FMT graft is often administered via colonoscopy or enteral (naso-jejunal) tubes, which are invasive procedures, placing significant burden on these often frail patients and the institutions providing the services. Moreover, frozen FMT is hampered by storage needs which limit accessibility and spread. Methods We have developed a lyophilized FMT product (Lyo-FMT - a dry compound that does not need freezing) that retains viability, prolongs the shelf time of the product and improves patient acceptance. In a randomized controlled multicenter trial, we aim to assess the efficacy of Lyo-FMT for pCDI in comparison to standard antibiotic therapy. Expected results This easy-to-administer product will restore the microbial community, fight the infective agent and reduce the overall antibiotic-resistant gene burden. This, in turn, will lower the recurrence rate and decrease carriage of other MDRO, coupled with a reduction in antibiotic use. Data on microbial shifts during treatment will shed light on our understanding of the pathophysiology of the disease. Clinicaltrials.gov registration <ns3:bold>NCT05709184

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• Conference paper
  Ghani R, Mullish B, Ghazy A, Corbett R, Duncan N, Satta G, Gilchrist M, Williams H, Pavlu J, Innes A, MacDonald J, Miguens Blanco J, Danckert N, Davies F, Marchesi Jet al., 2024,

  P3438 – Intestinal microbiota transplantation for patients colonised with multidrug-resistant organisms have an improvement in clinical outcomes associated with a significant increase in alpha-diversity metrics of the gastrointestinal microbiota

  , ESCMID Global, Publisher: Elsevier
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• Journal article
  Routy B, Lenehan JG, Miller Jr WH, Jamal R, Messaoudene M, Daisley BA, Hes C, Al KF, Martinez-Gili L, Puncochar M, Ernst S, Logan D, Belanger K, Esfahani K, Richard C, Ninkov M, Piccinno G, Armanini F, Pinto F, Krishnamoorthy M, Figueredo R, Thebault P, Takis P, Magrill J, Ramsay L, Derosa L, Marchesi JR, Parvathy SN, Elkrief A, Watson IR, Lapointe R, Segata N, Haeryfar SMM, Mullish BH, Silverman MS, Burton JP, Vareki SMet al., 2024,

  Fecal microbiota transplantation plus anti-PD-1 immunotherapy in advanced melanoma: a phase I trial (vol 29, pg 2121, 2023 )

  , NATURE MEDICINE, Vol: 30, Pages: 604-604, ISSN: 1078-8956
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• Journal article
  Kragsnaes MS, Jensen JRB, Nilsson AC, Malik MI, Munk HL, Pedersen JK, Horn HC, Kruhoffer M, Kristiansen K, Mullish BH, Marchesi JR, Kjeldsen J, Roettger R, Ellingsen Tet al., 2024,

  Dynamics of inflammation-associated plasma proteins following faecal microbiota transplantation in patients with psoriatic arthritis and healthy controls: exploratory findings from the FLORA trial

  , RMD OPEN, Vol: 10, ISSN: 2056-5933
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• Journal article
  Forlano R, Martinez-Gili L, Takis P, Miguens-Blanco J, Liu T, Triantafyllou E, Skinner C, Loomba R, Thursz M, Marchesi JR, Mullish BH, Manousou Pet al., 2024,

  Disruption of gut barrier integrity and host-microbiome interactions underlie MASLD severity in patients with type-2 diabetes mellitus.

  , Gut Microbes, Vol: 16

  Aberration of the "gut-liver axis" contributes to the development and progression of metabolic dysfunction-associated steatotic liver disease (MASLD). Here, we use multi-omics to analyze the gut microbiota composition and metabolic profile of patients with type-2 diabetes mellitus (T2DM). T2DM patients were screened for liver disease by blood tests, ultrasound, and liver stiffness measurements. Stool microbiota was analyzed by 16S rRNA gene sequencing; metabolomic profiling by Nuclear Magnetic Resonance spectroscopy and Ultra-High Performance-Mass Spectrometry. Microbiome and metabolic signatures were analyzed in the whole cohort and in matched subsets to identify signatures specific for steatosis (MASLD±) or fibrosis (Fibrosis±). Gut permeability was assessed in-vitro using monolayers of MDCK cells and trans-epithelial electric resistance (TEER). Cytokine profile was assessed in serum and stools.Overall, 285 patients were enrolled: 255 serum, 252 urine and 97 stool samples were analyzed. Anaeroplasma and Escherichia/Shigella ASVs were higher, while Butyricicoccus ASVs were lower in those with normal liver. In MASLD±, Butyricicoccus ASV was significantly higher in those with steatosis. In the Fibrosis±, Butyricicoccus ASV was significantly lower in those with fibrosis. Glycochenodeoxycholic acid-3-sulfate (G-UDCA-3S) appeared to be higher in MASLD with fibrosis. Fecal water from patients with MASLD and fibrosis caused the greatest drop in the TEER vs those with normal liver; this was reversed with protease inhibitors. Finally, fecal IL-13 was lower in MASLD with fibrosis. We identified microbiome signatures which were specific for steatosis and fibrosis and independent of other metabolic risk factors. Moreover, we conclude that protease-related gut permeability plays a role in those MASLD patients with fibrosis, and that disease progression is linked to a gut-liver axis which is at least partially independent of T2DM.

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• Journal article
  Ghani R, Chrysostomou D, Roberts LA, Pandiaraja M, Marchesi JR, Mullish BHet al., 2024,

  Faecal (or intestinal) microbiota transplant: a tool for repairing the gut microbiome.

  , Gut Microbes, Vol: 16

  Faecal/intestinal microbiota transplant (FMT/IMT) is an efficacious treatment option for recurrent Clostridioides difficile infection, which has prompted substantial interest in FMT's potential role in the management of a much broader range of diseases associated with the gut microbiome. Despite its promise, the success rates of FMT in these other settings have been variable. This review critically evaluates the current evidence on the impact of clinical, biological, and procedural factors upon the therapeutic efficacy of FMT, and identifies areas that remain nebulous. Due to some of these factors, the optimal therapeutic approach remains unclear; for example, the preferred timing of FMT administration in a heavily antibiotic-exposed hematopoietic cell transplant recipient is not standardized, with arguments that can be made in alternate directions. We explore how these factors may impact upon more informed selection of donors, potential matching of donors to recipients, and aspects of clinical care of FMT recipients. This includes consideration of how gut microbiome composition and functionality may strategically inform donor selection criteria. Furthermore, we review how the most productive advances within the FMT space are those where clinical and translational outcomes are assessed together, and where this model has been used productively in recent years to better understand the contribution of the gut microbiome to human disease, and start the process toward development of more targeted microbiome therapeutics.

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