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Ventero MP, Espinosa N, Jover R, Guillen Y, Merino E, Rodríguez JC. Evolution of intestinal microbiome in a process of faecal microbiota transfer (FMT) in a patient with Clostridioides difficile infection: NGS analysis with different software programs. Enferm Infecc Microbiol Clin 2020; 39:184-187. [PMID: 32680797 DOI: 10.1016/j.eimc.2020.05.023] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Revised: 04/30/2020] [Accepted: 05/16/2020] [Indexed: 11/26/2022]
Abstract
INTRODUCTION Clostridioides difficile infection (CDI) has become a global healthcare challenge due to increases in its incidence and mortality rates. Faecal microbiota transfer (FMT) is postulated as a protocol to prevent CDI recurrence. MATERIAL AND METHODS A donor faecal sample and patient faecal samples (pre-FMT and post-FMT) were analysed. The r16S gene was amplified and sequenced by NGS, and its diversity and taxonomy composition were examined. RESULTS Microbial richness increased in post-FMT samples, and the β diversity studies grouped the samples into two clusters. One included the non-pathological samples (donor and pre-FMT samples), and the other included the pathological sample. The results obtained by Qiime2 and Bioconductor were similar. CONCLUSION The analysis showed an increase in taxonomic diversity after the FMT, which suggests its usefulness. Moreover, these results showed that standardisation of bioinformatics analysis is key.
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Affiliation(s)
- María Paz Ventero
- Servicio de Microbiología. Hospital General Universitario de Alicante. Instituto de Investigación Sanitaria y Biomédica de Alicante-ISABIAL, Alicante, España.
| | - Noelia Espinosa
- Servicio de Microbiología. Hospital General Universitario de Alicante. Instituto de Investigación Sanitaria y Biomédica de Alicante-ISABIAL, Alicante, España
| | - Rodrigo Jover
- Servicio Digestivo. Hospital General Universitario de Alicante. Instituto de Investigación Sanitaria y Biomédica de Alicante-ISABIAL, Alicante, España
| | | | - Esperanza Merino
- Unidad de Enfermedades infecciosas. Hospital General Universitario de Alicante. Instituto de Investigación Sanitaria y Biomédica de Alicante-ISABIAL, Alicante, España
| | - Juan Carlos Rodríguez
- Servicio de Microbiología. Hospital General Universitario de Alicante. Instituto de Investigación Sanitaria y Biomédica de Alicante-ISABIAL, Alicante, España; Departamento de Producción Vegetal y Microbiología. Universidad Miguel Hernández de Elche (Alicante), Elche, España
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O'Connor KM, Lucking EF, Golubeva AV, Strain CR, Fouhy F, Cenit MC, Dhaliwal P, Bastiaanssen TFS, Burns DP, Stanton C, Clarke G, Cryan JF, O'Halloran KD. Manipulation of gut microbiota blunts the ventilatory response to hypercapnia in adult rats. EBioMedicine 2019; 44:618-638. [PMID: 30898652 PMCID: PMC6606895 DOI: 10.1016/j.ebiom.2019.03.029] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Revised: 03/08/2019] [Accepted: 03/11/2019] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND It is increasingly evident that perturbations to the diversity and composition of the gut microbiota have significant consequences for the regulation of integrative physiological systems. There is growing interest in the potential contribution of microbiota-gut-brain signalling to cardiorespiratory control in health and disease. METHODS In adult male rats, we sought to determine the cardiorespiratory effects of manipulation of the gut microbiota following a 4-week administration of a cocktail of antibiotics. We subsequently explored the effects of administration of faecal microbiota from pooled control (vehicle) rat faeces, given by gavage to vehicle- and antibiotic-treated rats. FINDINGS Antibiotic intervention depressed the ventilatory response to hypercapnic stress in conscious animals, owing to a reduction in the respiratory frequency response to carbon dioxide. Baseline frequency, respiratory timing variability, and the expression of apnoeas and sighs were normal. Microbiota-depleted rats had decreased systolic blood pressure. Faecal microbiota transfer to vehicle- and antibiotic-treated animals also disrupted the gut microbiota composition, associated with depressed ventilatory responsiveness to hypercapnia. Chronic antibiotic intervention or faecal microbiota transfer both caused significant disruptions to brainstem monoamine neurochemistry, with increased homovanillic acid:dopamine ratio indicative of increased dopamine turnover, which correlated with the abundance of several bacteria of six different phyla. INTERPRETATION Chronic antibiotic administration and faecal microbiota transfer disrupt gut microbiota, brainstem monoamine concentrations and the ventilatory response to hypercapnia. We suggest that aberrant microbiota-gut-brain axis signalling has a modulatory influence on respiratory behaviour during hypercapnic stress. FUND: Department of Physiology and APC Microbiome Ireland, University College Cork, Ireland.
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Affiliation(s)
- Karen M O'Connor
- Department of Physiology, School of Medicine, College of Medicine & Health, University College Cork, Cork, Ireland; Department of Anatomy & Neuroscience, School of Medicine, College of Medicine & Health, University College Cork, Cork, Ireland; APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Eric F Lucking
- Department of Physiology, School of Medicine, College of Medicine & Health, University College Cork, Cork, Ireland
| | - Anna V Golubeva
- APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Conall R Strain
- Teagasc Food Research Centre, Moorepark, Fermoy, County Cork, Ireland
| | - Fiona Fouhy
- APC Microbiome Ireland, University College Cork, Cork, Ireland; Teagasc Food Research Centre, Moorepark, Fermoy, County Cork, Ireland
| | - María C Cenit
- Department of Anatomy & Neuroscience, School of Medicine, College of Medicine & Health, University College Cork, Cork, Ireland; Institute of Agrochemistry and Food Technology (IATA), National Council for Scientific Research (CSIC), Valencia, Spain
| | - Pardeep Dhaliwal
- Department of Physiology, School of Medicine, College of Medicine & Health, University College Cork, Cork, Ireland
| | - Thomaz F S Bastiaanssen
- Department of Anatomy & Neuroscience, School of Medicine, College of Medicine & Health, University College Cork, Cork, Ireland; APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - David P Burns
- Department of Physiology, School of Medicine, College of Medicine & Health, University College Cork, Cork, Ireland
| | - Catherine Stanton
- APC Microbiome Ireland, University College Cork, Cork, Ireland; Teagasc Food Research Centre, Moorepark, Fermoy, County Cork, Ireland
| | - Gerard Clarke
- APC Microbiome Ireland, University College Cork, Cork, Ireland; Department of Psychiatry and Neurobehavioural Science, School of Medicine, College of Medicine & Health, University College Cork, Cork, Ireland
| | - John F Cryan
- Department of Anatomy & Neuroscience, School of Medicine, College of Medicine & Health, University College Cork, Cork, Ireland; APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Ken D O'Halloran
- Department of Physiology, School of Medicine, College of Medicine & Health, University College Cork, Cork, Ireland; APC Microbiome Ireland, University College Cork, Cork, Ireland.
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Terveer EM, van Beurden YH, Goorhuis A, Seegers JFML, Bauer MP, van Nood E, Dijkgraaf MGW, Mulder CJJ, Vandenbroucke-Grauls CMJE, Verspaget HW, Keller JJ, Kuijper EJ. How to: Establish and run a stool bank. Clin Microbiol Infect 2017; 23:924-930. [PMID: 28529025 DOI: 10.1016/j.cmi.2017.05.015] [Citation(s) in RCA: 103] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2017] [Revised: 05/12/2017] [Accepted: 05/13/2017] [Indexed: 12/15/2022]
Abstract
BACKGROUND Since 2013, several stool banks have been developed following publications reporting on clinical success of 'faecal microbiota transplantation' (FMT) for recurrent Clostridium difficile infections (CDI). However, protocols for donor screening, faecal suspension preparation, and transfer of the faecal suspension differ between countries and institutions. Moreover, no European consensus exists regarding the legislative aspects of the faecal suspension product. Internationally standardized recommendations about the above mentioned aspects have not yet been established. OBJECTIVE In 2015, the Netherlands Donor Feces Bank (NDFB) was founded with the primary aim of providing a standardized product for the treatment of patients with recurrent CDI in the Netherlands. Standard operation procedures for donor recruitment, donor selection, donor screening, and production, storage, and distribution of frozen faecal suspensions for FMT were formulated. RESULTS AND DISCUSSION Our experience summarized in this review addresses current donor recruitment and screening, preparation of the faecal suspension, transfer of the faecal microbiota suspension, and the experiences and follow-up of the patients treated with donor faeces from the NDFB.
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Affiliation(s)
- E M Terveer
- Dept. of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands.
| | - Y H van Beurden
- Dept. of Medical Microbiology & Infection Control, VU University Medical Center, Amsterdam, The Netherlands; Dept. of Gastroenterology, VU University Medical Center, Amsterdam, The Netherlands
| | - A Goorhuis
- Dept. of Internal Medicine, Academic Medical Center, Amsterdam, The Netherlands
| | - J F M L Seegers
- Dept. of Internal Medicine, Academic Medical Center, Amsterdam, The Netherlands
| | - M P Bauer
- Dept. of Internal Medicine, Leiden University Medical Center, Leiden, The Netherlands
| | - E van Nood
- Dept. of Internal Medicine, Havenziekenhuis, Rotterdam, The Netherlands
| | - M G W Dijkgraaf
- Clinical Research Unit, Academic Medical Center, Amsterdam, The Netherlands
| | - C J J Mulder
- Dept. of Gastroenterology, VU University Medical Center, Amsterdam, The Netherlands
| | | | - H W Verspaget
- Dept. of Biobanking and Gastroenterology, Leiden University Medical Center, Leiden, The Netherlands
| | - J J Keller
- Dept. of Gastroenterology, MC Haaglanden, The Hague, The Netherlands; Dept. of Gastroenterology, Leiden University Medical Center, Leiden, The Netherlands.
| | - E J Kuijper
- Dept. of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands
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