|
1
|
Moutsoglou D, Ramakrishnan P, Vaughn BP. Microbiota transplant therapy in inflammatory bowel disease: advances and mechanistic insights. Gut Microbes 2025; 17:2477255. [PMID: 40062406 PMCID: PMC11901402 DOI: 10.1080/19490976.2025.2477255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/06/2024] [Revised: 01/27/2025] [Accepted: 03/04/2025] [Indexed: 03/14/2025] Open
Abstract
Microbiota transplant therapy is an emerging therapy for inflammatory bowel disease, but factors influencing its efficacy and mechanism remain poorly understood. In this narrative review, we outline key elements affecting therapeutic outcomes, including donor factors (such as age and patient relationship), recipient factors, control selection, and elements impacting engraftment and its correlation with clinical response. We also examine potential mechanisms through inflammatory bowel disease trials, focusing on the interplay between the microbiota, host, and immune system. Finally, we briefly explore potential future directions for microbiota transplant therapy and promising emerging treatments.
Collapse
Affiliation(s)
- Daphne Moutsoglou
- Gastroenterology Section, Minneapolis VA Health Care System, Minneapolis, MN, USA
- Department of Medicine, University of Minnesota, Minneapolis, MN, USA
| | | | - Byron P. Vaughn
- Division of Gastroenterology, Hepatology, and Nutrition, University of Minnesota, Minneapolis, MN, USA
| |
Collapse
|
|
2
|
Ahmadi S, Hasani A, Khabbaz A, Poortahmasbe V, Hosseini S, Yasdchi M, Mehdizadehfar E, Mousavi Z, Hasani R, Nabizadeh E, Nezhadi J. Dysbiosis and fecal microbiota transplant: Contemplating progress in health, neurodegeneration and longevity. Biogerontology 2024; 25:957-983. [PMID: 39317918 DOI: 10.1007/s10522-024-10136-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2024] [Accepted: 08/30/2024] [Indexed: 09/26/2024]
Abstract
The gut-brain axis plays an important role in mental health. The intestinal epithelial surface is colonized by billions of commensal and transitory bacteria, known as the Gut Microbiota (GM). However, potential pathogens continuously stimulate intestinal immunity when they find the place. The last two decades have witnessed several studies revealing intestinal bacteria as a key factor in the health-disease balance of the gut, as well as disease-emergent in other parts of the body. Various neurological processes, such as cognition, learning, and memory, could be affected by dysbiosis in GM. Additionally, the aging process and longevity are related to systemic inflammation caused by dysbiosis. Commensal GM affects brain development, behavior, and healthy aging suggesting that building changes in GM might be a potential therapeutic method. The innovation in GM dysbiosis is intervention by Fecal Microbiota Transplantation (FMT), which has been confirmed as a therapy for recurrent Clostridium difficile infections and is promising for other clinical disorders, such as Parkinson's disease, Multiple Sclerosis (MS), Alzheimer's disease, and depression. Additionally, FMT may be possible to promote healthy aging, and extend longevity. This review aims to connect dysbiosis, neurological disorders, and aging and the potential of FMT as a therapeutic strategy to treat these disorders, and to enhance the quality of life in the elderly.
Collapse
Affiliation(s)
- Somayeh Ahmadi
- Infectious and Tropical Diseases Research Center, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
- Students Research Committee, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Alka Hasani
- Infectious and Tropical Diseases Research Center, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran.
- Clinical Research Development Unit, Sina Educational, Research and Treatment Center, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran.
| | - Aytak Khabbaz
- Neurosciences Research Center, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Vahdat Poortahmasbe
- Infectious and Tropical Diseases Research Center, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Samaneh Hosseini
- Neurosciences Research Center, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Mohammad Yasdchi
- Neurosciences Research Center, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Elham Mehdizadehfar
- Neurosciences Research Center, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Zahra Mousavi
- Department of Psychology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Roqaiyeh Hasani
- School of Medicine, Istanbul Okan University, Tuzla, 34959, Istanbul, Turkey
| | - Edris Nabizadeh
- Infectious and Tropical Diseases Research Center, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Javad Nezhadi
- Infectious and Tropical Diseases Research Center, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| |
Collapse
|
|
3
|
Long AE, Pitta D, Hennessy M, Indugu N, Vecchiarelli B, Luethy D, Aceto H, Hurcombe S. Assessment of fecal bacterial viability and diversity in fresh and frozen fecal microbiota transplant (FMT) product in horses. BMC Vet Res 2024; 20:306. [PMID: 38987780 PMCID: PMC11234551 DOI: 10.1186/s12917-024-04166-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 07/01/2024] [Indexed: 07/12/2024] Open
Abstract
BACKGROUND Currently, lack of standardization for fecal microbiota transplantation (FMT) in equine practice has resulted in highly variable techniques, and there is no data on the bacterial metabolic activity or viability of the administered product. The objectives of this study were to compare the total and potentially metabolically active bacterial populations in equine FMT, and assess the effect of different frozen storage times, buffers, and temperatures on an equine FMT product. Fresh feces collected from three healthy adult horses was subjected to different storage methods. This included different preservation solutions (saline plus glycerol or saline only), temperature (-20 °C or -80 °C), and time (fresh, 30, 60, or 90 days). Samples underwent DNA extraction to assess total bacterial populations (both live and dead combined) and RNA extraction followed by reverse transcription to cDNA as a proxy to assess viable bacteria, then 16s rRNA gene amplicon sequencing using the V1-V2 region. RESULTS The largest difference in population indices and taxonomic composition at the genus level was seen when evaluating the results of DNA-based (total) and cDNA-based (potentially metabolically active) extraction method. At the community level, alpha diversity (observed species, Shannon diversity) was significantly decreased in frozen samples for DNA-based analysis (P < 0.05), with less difference seen for cDNA-based sequencing. Using DNA-based analysis, length of storage had a significant impact (P < 0.05) on the bacterial community profiles. For potentially metabolically active populations, storage overall had less of an effect on the bacterial community composition, with a significant effect of buffer (P < 0.05). Individual horse had the most significant effect within both DNA and cDNA bacterial communities. CONCLUSIONS Frozen storage of equine FMT material can preserve potentially metabolically active bacteria of the equine fecal microbiome, with saline plus glycerol preservation more effective than saline alone. Larger studies are needed to determine if these findings apply to other individual horses. The ability to freeze FMT material for use in equine patients could allow for easier clinical use of fecal transplant in horses with disturbances in their intestinal microbiome.
Collapse
Affiliation(s)
- Alicia E Long
- Department of Clinical Studies, New Bolton Center, University of Pennsylvania, Kennett Square, PA, USA.
| | - Dipti Pitta
- Department of Clinical Studies, New Bolton Center, University of Pennsylvania, Kennett Square, PA, USA
| | - Meagan Hennessy
- Department of Clinical Studies, New Bolton Center, University of Pennsylvania, Kennett Square, PA, USA
| | - Nagaraju Indugu
- Department of Clinical Studies, New Bolton Center, University of Pennsylvania, Kennett Square, PA, USA
| | - Bonnie Vecchiarelli
- Department of Clinical Studies, New Bolton Center, University of Pennsylvania, Kennett Square, PA, USA
| | - Daniela Luethy
- Department of Clinical Studies, New Bolton Center, University of Pennsylvania, Kennett Square, PA, USA
| | - Helen Aceto
- Department of Clinical Studies, New Bolton Center, University of Pennsylvania, Kennett Square, PA, USA
| | - Samuel Hurcombe
- Department of Clinical Studies, New Bolton Center, University of Pennsylvania, Kennett Square, PA, USA
- Veterinary Innovative Partners, New York, NY, USA
| |
Collapse
|
|
4
|
Mehra P, Kumar A. Emerging importance of stool preservation methods in OMICS studies with special focus on cancer biology. Cell Biochem Funct 2024; 42:e4063. [PMID: 38961596 DOI: 10.1002/cbf.4063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Revised: 05/12/2024] [Accepted: 05/18/2024] [Indexed: 07/05/2024]
Abstract
The intricate consortium of microorganisms in the human gut plays a crucial role in different physiological functions. The complex known-unknown elements of the gut microbiome are perplexing and the absence of standardized procedures for collecting and preserving samples has hindered continuous research in comprehending it. The technological bias produced because of lack of standard protocols has affected the reproducibility of results. The complex nature of diseases like colorectal cancer, gastric cancer, hepatocellular carcinoma and breast cancer require a thorough understanding of its etiology for an efficient and timely diagnosis. The designated protocols for collection and preservation of stool specimens have great variance, hence generate inconsistencies in OMICS studies. Due to the complications associated to the nature of sample, it is important to preserve the sample to be studied later in a laboratory or to be used in the future research purpose. Stool preservation is gaining importance due to the increased use of treatment options like fecal microbiota transplantation to cure conditions like recurrent Clostridium difficile infections and for OMICS studies including metagenomics, metabolomics and culturomics. This review provides an insight into the importance of omics studies for the identification and development of novel biomarkers for quick and noninvasive diagnosis of various diseases.
Collapse
Affiliation(s)
- Parul Mehra
- Gene Regulation Laboratory, National Institute of Immunology, New Delhi, India
| | - Anil Kumar
- Gene Regulation Laboratory, National Institute of Immunology, New Delhi, India
| |
Collapse
|
|
5
|
Bottino P, Vay D, Leli C, Ferrara L, Pizzo V, Gotta F, Raiteri A, Rapallo F, Roveta A, Maconi A, Rocchetti A. Evaluation of Bacterial Viability for Fecal Microbiota Transplantation: Impact of Thawing Temperature and Storage Time. Microorganisms 2024; 12:1294. [PMID: 39065063 PMCID: PMC11278783 DOI: 10.3390/microorganisms12071294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2024] [Revised: 06/17/2024] [Accepted: 06/20/2024] [Indexed: 07/28/2024] Open
Abstract
Fecal Microbiota Transplantation (FMT) represents a promising therapeutic tool under study for several purposes and is currently applied to the treatment of recurrent Clostridioides difficile infection. However, since the use of fresh stool was affected by several issues linked to donor screening, the development of a frozen stool bank is a reliable option to standardize FMT procedures. Nevertheless, different environmental factors impact microbial viability. Herein, we report the effect of different thawing temperatures and storage conditions on bacterial suspensions in the FMT procedure. In total, 20 stool samples were divided into aliquots and tested across a combination of different storing periods (15, 30; 90 days) and thawing procedures (4 °C overnight, room temperature for 1 h; 37 °C for 5 min). Focusing on storage time, our data showed a significant reduction in viability for aerobic and anaerobic bacteria after thawing for 15 days, while no further reductions were observed until after 90 days. Instead, among the different thawing procedures, no significant differences were observed for aerobic bacteria, while for anaerobes, thawing at 37 °C for 5 min was more effective in preserving the bacterial viability. In conclusion, the frozen fecal microbiota remained viable for at least three months, with an excellent recovery rate in all three thawing conditions.
Collapse
Affiliation(s)
- Paolo Bottino
- Microbiology and Virology Laboratory, Azienda Ospedaliera Universitaria “SS. Antonio e Biagio e C. Arrigo”, 15121 Alessandria, Italy; (D.V.); (C.L.); (L.F.); (V.P.); (F.G.); (A.R.)
| | - Daria Vay
- Microbiology and Virology Laboratory, Azienda Ospedaliera Universitaria “SS. Antonio e Biagio e C. Arrigo”, 15121 Alessandria, Italy; (D.V.); (C.L.); (L.F.); (V.P.); (F.G.); (A.R.)
| | - Christian Leli
- Microbiology and Virology Laboratory, Azienda Ospedaliera Universitaria “SS. Antonio e Biagio e C. Arrigo”, 15121 Alessandria, Italy; (D.V.); (C.L.); (L.F.); (V.P.); (F.G.); (A.R.)
| | - Lidia Ferrara
- Microbiology and Virology Laboratory, Azienda Ospedaliera Universitaria “SS. Antonio e Biagio e C. Arrigo”, 15121 Alessandria, Italy; (D.V.); (C.L.); (L.F.); (V.P.); (F.G.); (A.R.)
| | - Valentina Pizzo
- Microbiology and Virology Laboratory, Azienda Ospedaliera Universitaria “SS. Antonio e Biagio e C. Arrigo”, 15121 Alessandria, Italy; (D.V.); (C.L.); (L.F.); (V.P.); (F.G.); (A.R.)
| | - Franca Gotta
- Microbiology and Virology Laboratory, Azienda Ospedaliera Universitaria “SS. Antonio e Biagio e C. Arrigo”, 15121 Alessandria, Italy; (D.V.); (C.L.); (L.F.); (V.P.); (F.G.); (A.R.)
| | - Alessio Raiteri
- Department of Science and Technological Innovation, University of Eastern Piedmont, 15121 Alessandria, Italy;
| | - Fabio Rapallo
- Department of Economics, University of Genova, 16126 Genova, Italy;
| | - Annalisa Roveta
- Research Training Innovation Infrastructure, Research and Innovation Department (DAIRI), Azienda Ospedaliera Universitaria “SS. Antonio e Biagio e C. Arrigo”, 15121 Alessandria, Italy; (A.R.); (A.M.)
| | - Antonio Maconi
- Research Training Innovation Infrastructure, Research and Innovation Department (DAIRI), Azienda Ospedaliera Universitaria “SS. Antonio e Biagio e C. Arrigo”, 15121 Alessandria, Italy; (A.R.); (A.M.)
| | - Andrea Rocchetti
- Microbiology and Virology Laboratory, Azienda Ospedaliera Universitaria “SS. Antonio e Biagio e C. Arrigo”, 15121 Alessandria, Italy; (D.V.); (C.L.); (L.F.); (V.P.); (F.G.); (A.R.)
| |
Collapse
|
|
6
|
Chen S, Cai X, Lao L, Wang Y, Su H, Sun H. Brain-Gut-Microbiota Axis in Amyotrophic Lateral Sclerosis: A Historical Overview and Future Directions. Aging Dis 2024; 15:74-95. [PMID: 37307822 PMCID: PMC10796086 DOI: 10.14336/ad.2023.0524] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Accepted: 05/24/2023] [Indexed: 06/14/2023] Open
Abstract
Amyotrophic Lateral Sclerosis (ALS) is a devastating neurodegenerative disease which is strongly associated with age. The incidence of ALS increases from the age of 40 and peaks between the ages of 65 and 70. Most patients die of respiratory muscle paralysis or lung infections within three to five years of the appearance of symptoms, dealing a huge blow to patients and their families. With aging populations, improved diagnostic methods and changes in reporting criteria, the incidence of ALS is likely to show an upward trend in the coming decades. Despite extensive researches have been done, the cause and pathogenesis of ALS remains unclear. In recent decades, large quantities of studies focusing on gut microbiota have shown that gut microbiota and its metabolites seem to change the evolvement of ALS through the brain-gut-microbiota axis, and in turn, the progression of ALS will exacerbate the imbalance of gut microbiota, thereby forming a vicious cycle. This suggests that further exploration and identification of the function of gut microbiota in ALS may be crucial to break the bottleneck in the diagnosis and treatment of this disease. Hence, the current review summarizes and discusses the latest research advancement and future directions of ALS and brain-gut-microbiota axis, so as to help relevant researchers gain correlative information instantly.
Collapse
Affiliation(s)
- Shilan Chen
- Clinical Biobank Center, Microbiome Medicine Center, Department of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou 510280, China.
- Neurosurgery Center, The National Key Clinical Specialty, The Engineering Technology Research Center of Education Ministry of China on Diagnosis and Treatment of Cerebrovascular Disease, Guangdong Provincial Key Laboratory on Brain Function Repair and Regeneration, The Neurosurgery Institute of Guangdong Province, Zhujiang Hospital, Southern Medical University, Guangzhou 510280, China.
| | - Xinhong Cai
- Clinical Biobank Center, Microbiome Medicine Center, Department of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou 510280, China.
- Neurosurgery Center, The National Key Clinical Specialty, The Engineering Technology Research Center of Education Ministry of China on Diagnosis and Treatment of Cerebrovascular Disease, Guangdong Provincial Key Laboratory on Brain Function Repair and Regeneration, The Neurosurgery Institute of Guangdong Province, Zhujiang Hospital, Southern Medical University, Guangzhou 510280, China.
| | - Lin Lao
- Clinical Biobank Center, Microbiome Medicine Center, Department of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou 510280, China.
- Neurosurgery Center, The National Key Clinical Specialty, The Engineering Technology Research Center of Education Ministry of China on Diagnosis and Treatment of Cerebrovascular Disease, Guangdong Provincial Key Laboratory on Brain Function Repair and Regeneration, The Neurosurgery Institute of Guangdong Province, Zhujiang Hospital, Southern Medical University, Guangzhou 510280, China.
| | - Yuxuan Wang
- Clinical Biobank Center, Microbiome Medicine Center, Department of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou 510280, China.
- Neurosurgery Center, The National Key Clinical Specialty, The Engineering Technology Research Center of Education Ministry of China on Diagnosis and Treatment of Cerebrovascular Disease, Guangdong Provincial Key Laboratory on Brain Function Repair and Regeneration, The Neurosurgery Institute of Guangdong Province, Zhujiang Hospital, Southern Medical University, Guangzhou 510280, China.
| | - Huanxing Su
- Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Taipa, Macau.
| | - Haitao Sun
- Clinical Biobank Center, Microbiome Medicine Center, Department of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou 510280, China.
- Neurosurgery Center, The National Key Clinical Specialty, The Engineering Technology Research Center of Education Ministry of China on Diagnosis and Treatment of Cerebrovascular Disease, Guangdong Provincial Key Laboratory on Brain Function Repair and Regeneration, The Neurosurgery Institute of Guangdong Province, Zhujiang Hospital, Southern Medical University, Guangzhou 510280, China.
- Key Laboratory of Mental Health of the Ministry of Education, Guangdong-Hong Kong-Macao Greater Bay Area Center for Brain Science and Brain-Inspired Intelligence, Southern Medical University, Guangzhou, China.
| |
Collapse
|
|
7
|
Thilakarathna SH, Chui L. A Pilot Study to Detect Viable Salmonella spp. in Diarrheal Stool Using Viability Real-Time PCR as a Culture-Independent Diagnostic Tool in a Clinical Setting. Int J Mol Sci 2023; 24:9979. [PMID: 37373127 DOI: 10.3390/ijms24129979] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Accepted: 06/08/2023] [Indexed: 06/29/2023] Open
Abstract
Frontline laboratories are adopting culture-independent diagnostic testing (CIDT) such as nucleic acid amplification tests (NAATs) due to numerous advantages over culture-based testing methods. Paradoxically, the viability of pathogens, a crucial factor determining active infections, cannot be confirmed with current NAATs alone. A recent development of viability PCR (vPCR) was introduced to mitigate this limitation associated with real-time PCR (qPCR) by using a DNA-intercalating dye to remove residual and dead cell DNA. This study assessed the applicability of the vPCR assay on diarrheal stools. Eighty-five diarrheal stools confirmed for Salmonellosis were tested via qPCR and vPCR using in-house primers and probe targeting the invA gene. vPCR-negative stools (Ct cut off > 31) were enriched in mannitol selenite broth (MSB) to verify low bacterial loads. vPCR assay showed ~89% sensitivity (qPCR- and vPCR-positive stools: 76/85). vPCR-negative stools (9/85; qPCR-positive: 5; qPCR-negative: 4) were qPCR- and culture-positive post-MSB-enrichment and confirmed the presence of low viable bacterial loads. Random sampling error, low bacterial loads, and receiving stools in batches could contribute to false negatives. This is a pilot study and further investigations are warranted to explore vPCR to assess pathogen viability in a clinical setting, especially when culture-based testing is unavailable.
Collapse
Affiliation(s)
- Surangi H Thilakarathna
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, AB T6G 1C9, Canada
| | - Linda Chui
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, AB T6G 1C9, Canada
- Alberta Precision Laboratories, Public Health Laboratory (ProvLab), Edmonton, AB T6G 2J2, Canada
| |
Collapse
|
|
8
|
Liu F, Lu H, Dong B, Huang X, Cheng H, Qu R, Hu Y, Zhong L, Guo Z, You Y, Xu ZZ. Systematic Evaluation of the Viable Microbiome in the Human Oral and Gut Samples with Spike-in Gram+/– Bacteria. mSystems 2023; 8:e0073822. [PMID: 36971593 PMCID: PMC10134872 DOI: 10.1128/msystems.00738-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/29/2023] Open
Abstract
The functions and phenotypes of microbial communities are largely defined by viable microbes. Through advanced nucleic acid sequencing technologies and downstream bioinformatic analyses, we gained an insight into the high-resolution microbial community composition of human saliva and feces, yet we know very little about whether such community DNA sequences represent viable microbes.
Collapse
|
|
9
|
Zhang X, Ishikawa D, Ohkusa T, Fukuda S, Nagahara A. Hot topics on fecal microbiota transplantation for the treatment of inflammatory bowel disease. Front Med (Lausanne) 2022; 9:1068567. [PMID: 36530877 PMCID: PMC9755187 DOI: 10.3389/fmed.2022.1068567] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Accepted: 11/21/2022] [Indexed: 11/04/2023] Open
Abstract
Inflammatory bowel disease (IBD) is a chronic intestinal mucosal inflammatory disease with complex etiology. Traditional anti-inflammatory treatment regimens have yielded unsatisfactory results. As research continues to deepen, it has been found that the gut microbiota of patients with IBD is generally altered. The presence of microorganisms in the human gastrointestinal tract is inextricably linked to the regulation of health and disease. Disruption of the microbiotic balance of microbiota in the gastrointestinal tract is called dysbiosis, which leads to disease. Therefore, in recent years, the exploration of therapeutic methods to restore the homeostasis of the gut microbiota has attracted attention. Moreover, the use of the well-established fecal microbiota transplantation (FMT) regimen for the treatment of Clostridioides difficile infection has attracted the interest of IBD researchers. Therefore, there are an increasing number of clinical studies regarding FMT for IBD treatment. However, a series of questions regarding FMT in the treatment of IBD warrants further investigation and discussion. By reviewing published studies, this review explored hot topics such as the efficacy, safety, and administration protocol flow of FMT in the treatment of IBD. Different administration protocols have generally shown reassuring results with significant efficacy and safety. However, the FMT treatment regimen needs to be further optimized. We believe that in the future, individual customized or standard FMT implementation will further enhance the relevance of FMT in the treatment of IBD.
Collapse
Affiliation(s)
- Xiaochen Zhang
- Department of Gastroenterology, Juntendo University School of Medicine, Tokyo, Japan
| | - Dai Ishikawa
- Department of Gastroenterology, Juntendo University School of Medicine, Tokyo, Japan
- Department of Regenerative Microbiology, Juntendo University School of Medicine, Tokyo, Japan
| | - Toshifumi Ohkusa
- Department of Microbiota Research, Juntendo University Graduate School of Medicine, Tokyo, Japan
- Department of Gastroenterology and Hepatology, The Jikei University Kashiwa Hospital, Chiba, Japan
| | - Shinji Fukuda
- Department of Regenerative Microbiology, Juntendo University School of Medicine, Tokyo, Japan
| | - Akihito Nagahara
- Department of Gastroenterology, Juntendo University School of Medicine, Tokyo, Japan
- Department of Regenerative Microbiology, Juntendo University School of Medicine, Tokyo, Japan
| |
Collapse
|
|
10
|
Wang Y, Zhang Z, Liu B, Zhang C, Zhao J, Li X, Chen L. A study on the method and effect of the construction of a humanized mouse model of fecal microbiota transplantation. Front Microbiol 2022; 13:1031758. [PMID: 36466673 PMCID: PMC9709132 DOI: 10.3389/fmicb.2022.1031758] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Accepted: 10/20/2022] [Indexed: 02/11/2024] Open
Abstract
The gestation period is critical for the health of the mother and fetus. Malnutrition or over nutrition during pregnancy may cause gestational diseases that can result in adverse pregnancy outcomes. Fecal microbiota transplantation (FMT) can be used to re-establish new gut microbiota to treat a variety of diseases and construct a model to investigate the nutritional health during pregnancy. Therefore, this study investigated whether human-derived gut microbiota during pregnancy could colonize the intestines of mice. Moreover, we determined the time and method of intervention for FMT. Based on this information, a humanized mouse model of FMT was constructed to simulate the human intestinal microecology during pregnancy, and serve as a useful animal model for the study of nutritional health and disease during pregnancy. Germ-free (GF) and specific pathogen free (SPF) C57BL/6J mice were selected for humanized gestational FMT and the transplantation outcomes were evaluated. The results demonstrated that the gestational intestinal microbiota colonized the intestines of mice, allowing researchers to construct a humanized mouse model of gestational FMT. The main intestinal flora of the gestational period were transplanted into GF mice, with the gestational flora being similar to the flora of GF mice after transplantation. However, antibiotics could not eliminate the original microbial flora in SPF mice, and the flora was complex and variable after FMT with little increase in abundance. Background flora had a significant impact on the outcomes assessment. The results were better in GF mice than in SPF mice, and after microbiota transplantation, a superior effect was observed on day 21 compared to days 7 and 14.
Collapse
Affiliation(s)
- Yaru Wang
- School of Biological Engineering, Dalian Polytechnic University, Liaoning, Dalian, China
- National Engineering Research Center of Dairy Health for Maternal and Child, Beijing Sanyuan Foods Co. Ltd., Beijing, China
- Beijing Engineering Research Center of Dairy, Beijing Technical Innovation Center of Human Milk Research, Beijing Sanyuan Foods Co. Ltd., Beijing, China
| | - Zhenzhen Zhang
- National Engineering Research Center of Dairy Health for Maternal and Child, Beijing Sanyuan Foods Co. Ltd., Beijing, China
- Beijing Engineering Research Center of Dairy, Beijing Technical Innovation Center of Human Milk Research, Beijing Sanyuan Foods Co. Ltd., Beijing, China
| | - Bin Liu
- National Engineering Research Center of Dairy Health for Maternal and Child, Beijing Sanyuan Foods Co. Ltd., Beijing, China
- Beijing Engineering Research Center of Dairy, Beijing Technical Innovation Center of Human Milk Research, Beijing Sanyuan Foods Co. Ltd., Beijing, China
| | - Chunzhi Zhang
- School of Biological Engineering, Dalian Polytechnic University, Liaoning, Dalian, China
| | - Junying Zhao
- National Engineering Research Center of Dairy Health for Maternal and Child, Beijing Sanyuan Foods Co. Ltd., Beijing, China
- Beijing Engineering Research Center of Dairy, Beijing Technical Innovation Center of Human Milk Research, Beijing Sanyuan Foods Co. Ltd., Beijing, China
| | - Xianping Li
- National Engineering Research Center of Dairy Health for Maternal and Child, Beijing Sanyuan Foods Co. Ltd., Beijing, China
- Beijing Engineering Research Center of Dairy, Beijing Technical Innovation Center of Human Milk Research, Beijing Sanyuan Foods Co. Ltd., Beijing, China
| | - Lijun Chen
- National Engineering Research Center of Dairy Health for Maternal and Child, Beijing Sanyuan Foods Co. Ltd., Beijing, China
- Beijing Engineering Research Center of Dairy, Beijing Technical Innovation Center of Human Milk Research, Beijing Sanyuan Foods Co. Ltd., Beijing, China
| |
Collapse
|
|
11
|
Hosokawa M, Endoh T, Kamata K, Arikawa K, Nishikawa Y, Kogawa M, Saeki T, Yoda T, Takeyama H. Strain-level profiling of viable microbial community by selective single-cell genome sequencing. Sci Rep 2022; 12:4443. [PMID: 35292746 PMCID: PMC8924182 DOI: 10.1038/s41598-022-08401-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 03/08/2022] [Indexed: 11/09/2022] Open
Abstract
Culture-independent analysis with high-throughput sequencing has been widely used to characterize bacterial communities. However, signals derived from non-viable bacteria and non-cell DNA may inhibit its characterization. Here, we present a method for viable bacteria-targeted single-cell genome sequencing, called PMA-SAG-gel, to obtain comprehensive whole-genome sequences of surviving uncultured bacteria from microbial communities. PMA-SAG-gel uses gel matrixes that enable sequential enzymatic reactions for cell lysis and genome amplification of viable single cells from the microbial communities. PMA-SAG-gel removed the single-amplified genomes (SAGs) derived from dead bacteria and enabled selective sequencing of viable bacteria in the model samples of Escherichia coli and Bacillus subtilis. Next, we demonstrated the recovery of near-complete SAGs of eight oxygen-tolerant bacteria, including Bacteroides spp. and Phocaeicola spp., from 1331 human feces SAGs. We found the presence of two different strains in each species and identified their specific genes to investigate the metabolic functions. The survival profile of an entire population at the strain level will provide the information for understanding the characteristics of the surviving bacteria under the specific environments or sample processing and insights for quality assessment of live bacterial products or fecal microbiota transplantation and for understanding the effect of antimicrobial treatments.
Collapse
Affiliation(s)
- Masahito Hosokawa
- Department of Life Science and Medical Bioscience, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo, 162-8480, Japan. .,Research Organization for Nano and Life Innovation, Waseda University, 513 Wasedatsurumaki-cho, Shinjuku-ku, Tokyo, 162-0041, Japan. .,bitBiome, Inc., 513 Wasedatsurumaki-cho, Shinjuku-ku, Tokyo, 162-0041, Japan. .,Computational Bio Big-Data Open Innovation Laboratory, National Institute of Advanced Industrial Science and Technology, 3-4-1 Okubo, Shinjuku-ku, Tokyo, 169-8555, Japan. .,Institute for Advanced Research of Biosystem Dynamics, Waseda Research Institute for Science and Engineering, 3-4-1 Okubo, Shinjuku-ku, Tokyo, 169-8555, Japan.
| | - Taruho Endoh
- bitBiome, Inc., 513 Wasedatsurumaki-cho, Shinjuku-ku, Tokyo, 162-0041, Japan
| | - Kazuma Kamata
- bitBiome, Inc., 513 Wasedatsurumaki-cho, Shinjuku-ku, Tokyo, 162-0041, Japan
| | - Koji Arikawa
- bitBiome, Inc., 513 Wasedatsurumaki-cho, Shinjuku-ku, Tokyo, 162-0041, Japan
| | - Yohei Nishikawa
- Research Organization for Nano and Life Innovation, Waseda University, 513 Wasedatsurumaki-cho, Shinjuku-ku, Tokyo, 162-0041, Japan.,Computational Bio Big-Data Open Innovation Laboratory, National Institute of Advanced Industrial Science and Technology, 3-4-1 Okubo, Shinjuku-ku, Tokyo, 169-8555, Japan
| | - Masato Kogawa
- Research Organization for Nano and Life Innovation, Waseda University, 513 Wasedatsurumaki-cho, Shinjuku-ku, Tokyo, 162-0041, Japan
| | - Tatsuya Saeki
- bitBiome, Inc., 513 Wasedatsurumaki-cho, Shinjuku-ku, Tokyo, 162-0041, Japan
| | - Takuya Yoda
- bitBiome, Inc., 513 Wasedatsurumaki-cho, Shinjuku-ku, Tokyo, 162-0041, Japan
| | - Haruko Takeyama
- Department of Life Science and Medical Bioscience, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo, 162-8480, Japan.,Research Organization for Nano and Life Innovation, Waseda University, 513 Wasedatsurumaki-cho, Shinjuku-ku, Tokyo, 162-0041, Japan.,Computational Bio Big-Data Open Innovation Laboratory, National Institute of Advanced Industrial Science and Technology, 3-4-1 Okubo, Shinjuku-ku, Tokyo, 169-8555, Japan.,Institute for Advanced Research of Biosystem Dynamics, Waseda Research Institute for Science and Engineering, 3-4-1 Okubo, Shinjuku-ku, Tokyo, 169-8555, Japan
| |
Collapse
|
|
12
|
Fecal Microbiota Transplants for Inflammatory Bowel Disease Treatment: Synthetic- and Engineered Communities-Based Microbiota Transplants Are the Future. Gastroenterol Res Pract 2022; 2022:9999925. [PMID: 35140783 PMCID: PMC8820897 DOI: 10.1155/2022/9999925] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Accepted: 01/12/2022] [Indexed: 12/21/2022] Open
Abstract
The human intestine harbors a huge number of diverse microorganisms where a variety of complex interactions take place between the microbes as well as the host and gut microbiota. Significant long-term variations in the gut microbiota (dysbiosis) have been associated with a variety of health conditions including inflammatory bowel disease (IBD). Conventional fecal microbiota transplantations (FMTs) have been utilized to treat IBD and have been proved promising. However, various limitations such as transient results, pathogen transfer, storage, and reproducibility render conventional FMT less safe and less sustainable. Defined synthetic microbial communities (SynCom) have been used to dissect the host-microbiota-associated functions using gnotobiotic animals or in vitro cell models. This review focuses on the potential use of SynCom in IBD and its advantages and relative safety over conventional FMT. Additionally, this review reinforces how various technological advances could be combined with SynCom to have a better understanding of the complex microbial interactions in various gut inflammatory diseases including IBD. Some technological advances including the availability of a gut-on-a-chip system, intestinal organoids, ex vivo intestinal cultures, AI-based refining of the microbiome structural and functional data, and multiomic approaches may help in making more practical in vitro models of the human host. Additionally, an increase in the cultured diversity from gut microbiota and the availability of their genomic information would further make the design and utilization of SynCom more feasible. Taken together, the combined use of the available knowledge of the gut microbiota in health and disease and recent technological advances and the development of defined SynCom seem to be a promising, safe, and sustainable alternative to conventional FMT in treating IBD.
Collapse
|
|
13
|
Secombe KR, Al-Qadami GH, Subramaniam CB, Bowen JM, Scott J, Van Sebille YZ, Snelson M, Cowan C, Clarke G, Gheorghe CE, Cryan JF, Wardill HR. Guidelines for reporting on animal fecal transplantation (GRAFT) studies: recommendations from a systematic review of murine transplantation protocols. Gut Microbes 2022; 13:1979878. [PMID: 34586011 PMCID: PMC8489962 DOI: 10.1080/19490976.2021.1979878] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Fecal microbiota transplant (FMT) is a powerful tool used to connect changes in gut microbial composition with a variety of disease states and pathologies. While FMT enables potential causal relationships to be identified, the experimental details reported in preclinical FMT protocols are highly inconsistent and/or incomplete. This limitation reflects a current lack of authoritative guidance on reporting standards that would facilitate replication efforts and ultimately reproducible science. We therefore systematically reviewed all FMT protocols used in mouse models with the goal of formulating recommendations on the reporting of preclinical FMT protocols. Search strategies were applied across three databases (PubMed, EMBASE, and Ovid Medline) until June 30, 2020. Data related to donor attributes, stool collection, processing/storage, recipient preparation, administration, and quality control were extracted. A total of 1753 papers were identified, with 241 identified for data extraction and analysis. Of the papers included, 92.5% reported a positive outcome with FMT intervention. However, the vast majority of studies failed to address core methodological aspects including the use of anaerobic conditions (91.7% of papers lacked information), storage (49.4%), homogenization (33.6%), concentration (31.5%), volume (19.9%) and administration route (5.3%). To address these reporting limitations, we developed theGuidelines for Reporting Animal Fecal Transplant (GRAFT) that guide reporting standards for preclinical FMT. The GRAFT recommendations will enable robust reporting of preclinical FMT design, and facilitate high-quality peer review, improving the rigor and translation of knowledge gained through preclinical FMT studies.
Collapse
Affiliation(s)
- Kate R. Secombe
- School of Biomedicine, Adelaide Medical School, University of Adelaide, Adelaide, SA, Australia,CONTACT Kate R. Secombe The University of Queensland, Australia
| | - Ghanyah H. Al-Qadami
- School of Biomedicine, Adelaide Medical School, University of Adelaide, Adelaide, SA, Australia
| | - Courtney B. Subramaniam
- School of Biomedicine, Adelaide Medical School, University of Adelaide, Adelaide, SA, Australia
| | - Joanne M. Bowen
- School of Biomedicine, Adelaide Medical School, University of Adelaide, Adelaide, SA, Australia
| | - Jacqui Scott
- School of Biomedicine, Adelaide Medical School, University of Adelaide, Adelaide, SA, Australia,Precision Medicine Theme (Cancer), South Australian Health and Medical Research Institute, Adelaide, SA, Australia
| | | | - Matthew Snelson
- Department of Diabetes, Central Clinical School, Monash University, Melbourne, VIC, Australia
| | - Caitlin Cowan
- School of Psychology and Brain and Mind Centre, University of Sydney, Sydney, NSW, Australia
| | - Gerard Clarke
- Department of Psychiatry and Neurobehavioural Science, Department of Anatomy and Neuroscience, and APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Cassandra E. Gheorghe
- Department of Psychiatry and Neurobehavioural Science and APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - John F. Cryan
- Department of Anatomy and Neuroscience and APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Hannah R. Wardill
- School of Biomedicine, Adelaide Medical School, University of Adelaide, Adelaide, SA, Australia,Precision Medicine Theme (Cancer), South Australian Health and Medical Research Institute, Adelaide, SA, Australia
| |
Collapse
|
|
14
|
Bokoliya SC, Dorsett Y, Panier H, Zhou Y. Procedures for Fecal Microbiota Transplantation in Murine Microbiome Studies. Front Cell Infect Microbiol 2021; 11:711055. [PMID: 34621688 PMCID: PMC8490673 DOI: 10.3389/fcimb.2021.711055] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Accepted: 08/24/2021] [Indexed: 12/11/2022] Open
Abstract
Fecal microbiota transplantation (FMT) has been widely recognized as an approach to determine the microbiome’s causal role in gut dysbiosis-related disease models and as a novel disease-modifying therapy. Despite potential beneficial FMT results in various disease models, there is a variation and complexity in procedural agreement among research groups for performing FMT. The viability of the microbiome in feces and its successful transfer depends on various aspects of donors, recipients, and lab settings. This review focuses on the technical practices of FMT in animal studies. We first document crucial factors required for collecting, handling, and processing donor fecal microbiota for FMT. Then, we detail the description of gut microbiota depletion methods, FMT dosages, and routes of FMT administrations in recipients. In the end, we describe assessments of success rates of FMT with sustainability. It is critical to work under the anaerobic condition to preserve as much of the viability of bacteria. Utilization of germ- free mice or depletion of recipient gut microbiota by antibiotics or polyethylene glycol are two common recipient preparation approaches to achieve better engraftment. Oral-gastric gavage preferred by most researchers for fast and effective administration of FMT in mice. Overall, this review highlights various methods that may lead to developing the standard and reproducible protocol for FMT.
Collapse
Affiliation(s)
- Suresh C Bokoliya
- Department of Medicine, University of Connecticut (UConn) Health, Farmington, CT, United States
| | - Yair Dorsett
- Department of Medicine, University of Connecticut (UConn) Health, Farmington, CT, United States
| | - Hunter Panier
- Department of Medicine, University of Connecticut (UConn) Health, Farmington, CT, United States
| | - Yanjiao Zhou
- Department of Medicine, University of Connecticut (UConn) Health, Farmington, CT, United States
| |
Collapse
|
|
15
|
Baunwall SMD, Dahlerup JF, Engberg JH, Erikstrup C, Helms M, Juel MA, Kjeldsen J, Nielsen HL, Nilsson AC, Rode AA, Vinter-Jensen L, Hvas CL. Danish national guideline for the treatment of Clostridioides difficile infection and use of faecal microbiota transplantation (FMT). Scand J Gastroenterol 2021; 56:1056-1077. [PMID: 34261379 DOI: 10.1080/00365521.2021.1922749] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Aim: This Danish national guideline describes the treatment of adult patients with Clostridioides (formerly Clostridium) difficile (CD) infection and the use of faecal microbiota transplantation (FMT). It suggests minimum standard for implementing an FMT service.Method: Four scientific societies appointed members for a working group which conducted a systematic literature review and agreed on the text and recommendations. All clinical recommendations were evalluated for evidence level and grade of recommendation.Results: In CD infection, the use of marketed and experimental antibiotics as well as microbiota-based therapies including FMT are described. An algorithm for evaluating treatment effect is suggested. The organisation of FMT, donor recruitment and screening, laboratory preparation, clinical application and follow-up are described.Conclusion: Updated evidence for the treatment of CD infection and the use of FMT is provided.
Collapse
Affiliation(s)
| | - Jens Frederik Dahlerup
- Department of Hepatology and Gastroenterology, Aarhus University Hospital, Aarhus, Denmark
| | | | - Christian Erikstrup
- Department of Clinical Immunology, Aarhus University Hospital, Aarhus, Denmark
| | - Morten Helms
- Department of Infectious Diseases, Hvidovre Hospital, Hvidovre, Denmark
| | | | - Jens Kjeldsen
- Department of Gastroenterology, Odense University Hospital, Odense, Denmark
| | - Hans Linde Nielsen
- Department of Clinical Microbiology, Aalborg University Hospital, Aalborg, Denmark
| | | | - Anne Abildtrup Rode
- Department of Internal Medicine, Zealand University Hospital, Roskilde, Denmark
| | - Lars Vinter-Jensen
- Department of Gastroenterology, Aalborg University Hospital, Aalborg, Denmark
| | - Christian Lodberg Hvas
- Department of Hepatology and Gastroenterology, Aarhus University Hospital, Aarhus, Denmark
| |
Collapse
|
|
16
|
Abstract
The use of germ-free mice is integral to the understanding of host-gut microbiome relationships. Such models rely on faithful replication of the donor microbiome to establish causal effects of the gut microbiota on host pathophysiology. This protocol describes the preparation and transfer of donor microbiota, focusing on strict anaerobic processing methods and multiple instillations by gavage for optimal gut microbiota recovery. For complete details on the generation and use of this protocol, please refer to Choo and Rogers (2021).
Collapse
Affiliation(s)
- Jocelyn M Choo
- Microbiome and Host Health, South Australia Health and Medical Research Institute, Adelaide 5000, Australia.,Microbiome Research Laboratory, College of Medicine and Public Health, Flinders University, Bedford Park 5042, Australia
| | - Geraint B Rogers
- Microbiome and Host Health, South Australia Health and Medical Research Institute, Adelaide 5000, Australia.,Microbiome Research Laboratory, College of Medicine and Public Health, Flinders University, Bedford Park 5042, Australia
| |
Collapse
|
|
17
|
Keller JJ, Ooijevaar RE, Hvas CL, Terveer EM, Lieberknecht SC, Högenauer C, Arkkila P, Sokol H, Gridnyev O, Mégraud F, Kump PK, Nakov R, Goldenberg SD, Satokari R, Tkatch S, Sanguinetti M, Cammarota G, Dorofeev A, Gubska O, Laniro G, Mattila E, Arasaradnam RP, Sarin SK, Sood A, Putignani L, Alric L, Baunwall SMD, Kupcinskas J, Link A, Goorhuis AG, Verspaget HW, Ponsioen C, Hold GL, Tilg H, Kassam Z, Kuijper EJ, Gasbarrini A, Mulder CJJ, Williams HRT, Vehreschild MJGT. A standardised model for stool banking for faecal microbiota transplantation: a consensus report from a multidisciplinary UEG working group. United European Gastroenterol J 2021; 9:229-247. [PMID: 33151137 PMCID: PMC8259288 DOI: 10.1177/2050640620967898] [Citation(s) in RCA: 89] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Accepted: 09/27/2020] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Faecal microbiota transplantation is an emerging therapeutic option, particularly for the treatment of recurrent Clostridioides difficile infection. Stool banks that organise recruitment and screening of faeces donors are being embedded within the regulatory frameworks described in the European Union Tissue and Cells Directive and the technical guide to the quality and safety of tissue and cells for human application, published by the European Council. OBJECTIVE Several European and international consensus statements concerning faecal microbiota transplantation have been issued. While these documents provide overall guidance, we aim to provide a detailed description of all processes that relate to the collection, handling and clinical application of human donor stool in this document. METHODS Collaborative subgroups of experts on stool banking drafted concepts for all domains pertaining to stool banking. During a working group meeting in the United European Gastroenterology Week 2019 in Barcelona, these concepts were discussed and finalised to be included in our overall guidance document about faecal microbiota transplantation. RESULTS A guidance document for all domains pertaining to stool banking was created. This document includes standard operating manuals for several processes involved with stool banking, such as handling of donor material, storage and donor screening. CONCLUSION The implementation of faecal microbiota transplantation by stool banks in concordance with our guidance document will enable quality assurance and guarantee the availability of donor faeces preparations for patients.
Collapse
|
|
18
|
Wang Y, Yan Y, Thompson KN, Bae S, Accorsi EK, Zhang Y, Shen J, Vlamakis H, Hartmann EM, Huttenhower C. Whole microbial community viability is not quantitatively reflected by propidium monoazide sequencing approach. MICROBIOME 2021; 9:17. [PMID: 33478576 PMCID: PMC7819323 DOI: 10.1186/s40168-020-00961-3] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Accepted: 12/06/2020] [Indexed: 05/11/2023]
Abstract
BACKGROUND High-throughput sequencing provides a powerful window into the structural and functional profiling of microbial communities, but it is unable to characterize only the viable portion of microbial communities at scale. There is as yet not one best solution to this problem. Previous studies have established viability assessments using propidium monoazide (PMA) treatment coupled with downstream molecular profiling (e.g., qPCR or sequencing). While these studies have met with moderate success, most of them focused on the resulting "viable" communities without systematic evaluations of the technique. Here, we present our work to rigorously benchmark "PMA-seq" (PMA treatment followed by 16S rRNA gene amplicon sequencing) for viability assessment in synthetic and realistic microbial communities. RESULTS PMA-seq was able to successfully reconstruct simple synthetic communities comprising viable/heat-killed Escherichia coli and Streptococcus sanguinis. However, in realistically complex communities (computer screens, computer mice, soil, and human saliva) with E. coli spike-in controls, PMA-seq did not accurately quantify viability (even relative to variability in amplicon sequencing), with its performance largely affected by community properties such as initial biomass, sample types, and compositional diversity. We then applied this technique to environmental swabs from the Boston subway system. Several taxa differed significantly after PMA treatment, while not all microorganisms responded consistently. To elucidate the "PMA-responsive" microbes, we compared our results with previous PMA-based studies and found that PMA responsiveness varied widely when microbes were sourced from different ecosystems but were reproducible within similar environments across studies. CONCLUSIONS This study provides a comprehensive evaluation of PMA-seq exploring its quantitative potential in synthetic and complex microbial communities, where the technique was effective for semi-quantitative purposes in simple synthetic communities but provided only qualitative assessments in realistically complex community samples. Video abstract.
Collapse
Affiliation(s)
- Ya Wang
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Harvard University, 655 Huntington Avenue, Boston, MA 02115 USA
- Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142 USA
| | - Yan Yan
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Harvard University, 655 Huntington Avenue, Boston, MA 02115 USA
- Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142 USA
| | - Kelsey N. Thompson
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Harvard University, 655 Huntington Avenue, Boston, MA 02115 USA
- Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142 USA
| | - Sena Bae
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Harvard University, 655 Huntington Avenue, Boston, MA 02115 USA
- Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142 USA
| | - Emma K. Accorsi
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Harvard University, 655 Huntington Avenue, Boston, MA 02115 USA
| | - Yancong Zhang
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Harvard University, 655 Huntington Avenue, Boston, MA 02115 USA
- Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142 USA
| | - Jiaxian Shen
- Department of Civil and Environmental Engineering, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208 USA
| | - Hera Vlamakis
- Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142 USA
| | - Erica M. Hartmann
- Department of Civil and Environmental Engineering, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208 USA
| | - Curtis Huttenhower
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Harvard University, 655 Huntington Avenue, Boston, MA 02115 USA
- Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142 USA
- Department of Immunology and Infectious Diseases, Harvard TH Chan School of Public Health, Harvard University, 655 Huntington Avenue, Boston, MA 02115 USA
| |
Collapse
|
|
19
|
Kopper JJ, Alexander TL, Kogan CJ, Berreta AR, Burbick CR. In Vitro Evaluation of the Effect of Storage at -20°C and Proximal Gastrointestinal Conditions on Viability of Equine Fecal Microbiota Transplant. J Equine Vet Sci 2020; 98:103360. [PMID: 33663713 DOI: 10.1016/j.jevs.2020.103360] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 12/04/2020] [Accepted: 12/07/2020] [Indexed: 11/18/2022]
Abstract
Fecal microbiota transplant (FMT), a technique used to restore normal intestinal microbial communities, has been successful in treating humans with Clostridioides difficile colitis. Subsequently, FMT is being used in veterinary patients with suspected intestinal dysbiosis. Unfortunately, little data are available regarding best practices for FMT in horses. The objective of this study was to evaluate the effects of storing manure prepared for equine FMT (MP-FMT) at -20°C for up to 4 weeks and passage through a simulated proximal gastrointestinal (GI) tract on the viability of MP-FMT. The results of this study indicate that storage at -20°C for greater than 1 week and exposure to conditions consistent with the proximal GI tract significantly decreased viability of the microbial population, with gram-negative enteric bacteria most significantly impacted. This preliminary evaluation indicates that further work is necessary to determine best practices to preserve the viability MP-FMT in horses.
Collapse
Affiliation(s)
- Jamie J Kopper
- Department of Veterinary Clinical Sciences, Washington State University, Pullman, WA.
| | - Trevor L Alexander
- Washington Animal Disease Diagnostic Laboratory, Washington State University, Pullman, WA
| | - Clark J Kogan
- Center for Interdisciplinary Statistical Education and Research, Washington State University, Pullman, WA
| | - Ana R Berreta
- Department of Veterinary Clinical Sciences, Washington State University, Pullman, WA
| | - Claire R Burbick
- Washington Animal Disease Diagnostic Laboratory, Washington State University, Pullman, WA; Department of Veterinary Microbiology and Pathology, Washington State University, Pullman, WA
| |
Collapse
|
|
20
|
Vendrik KEW, Terveer EM, Kuijper EJ, Nooij S, Boeije-Koppenol E, Sanders IMJG, van Lingen E, Verspaget HW, Berssenbrugge EKL, Keller JJ, van Prehn J. Periodic screening of donor faeces with a quarantine period to prevent transmission of multidrug-resistant organisms during faecal microbiota transplantation: a retrospective cohort study. THE LANCET. INFECTIOUS DISEASES 2020; 21:711-721. [PMID: 33275940 DOI: 10.1016/s1473-3099(20)30473-4] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Revised: 04/24/2020] [Accepted: 05/27/2020] [Indexed: 02/07/2023]
Abstract
BACKGROUND On June 13, 2019, the US Food and Drug Administration issued a warning after transfer of faeces containing an extended-spectrum β-lactamase (ESBL)-producing Escherichia coli by faecal microbiota transplantation led to bacteraemia in two immunocompromised patients. Consequently, we evaluated the effectiveness of the faeces donor-screening protocol of the Netherlands Donor Faeces Bank, which consists of screening of donors for multidrug-resistant organisms every 3 months, combined with additional screening on indication (eg, after travelling abroad) and application of a quarantine period for all faecal suspensions delivered within those 3 months. METHODS We did a retrospective cohort study of data collected between Jan 1, 2015, and Oct 14, 2019, on the multidrug-resistant organism testing results of donor faeces. Additionally, we tested previously quarantined faecal suspensions approved for faecal microbiota transplantation between Dec 12, 2016, and May 1, 2019, for the presence of multidrug-resistant organisms using both aselective and selective broth enrichment media. Whole-genome sequencing with core-genome multilocus sequence typing (cgMLST) was done on all multidrug-resistant isolates. FINDINGS Among initial screenings, six (9%) of 66 tested individuals were positive for multidrug-resistant organisms and 11 (17%) of 66 tested individuals were positive for multidrug-resistant organisms at any timepoint. Multidrug-resistant organisms were detected in four (25%) of 16 active donors, who had a median donation duration of 268 days (IQR 92 to 366). Among all screening results, 14 (74%) of 19 detected multidrug-resistant organisms were ESBL-producing E coli. 170 (49%) of 344 approved faecal suspensions had corresponding research faeces aliquots available and were tested (from 11 active donors with a median of eight [IQR five to 26] suspensions per donor). No multidrug-resistant organisms were detected in the 170 approved faecal suspensions (one-sided 95% CI 0 to 1·7). cgMLST revealed that all multidrug-resistant organisms were genetically different. INTERPRETATION Healthy faeces donors can become colonised with multidrug-resistant organisms during donation activities. Our screening protocol did not result in approval of multidrug-resistant organism-positive faecal suspensions for microbiota transplantation. FUNDING None.
Collapse
Affiliation(s)
- Karuna E W Vendrik
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, Netherlands
| | - Elisabeth M Terveer
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, Netherlands
| | - Ed J Kuijper
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, Netherlands.
| | - Sam Nooij
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, Netherlands
| | - Eline Boeije-Koppenol
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, Netherlands
| | - Ingrid M J G Sanders
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, Netherlands
| | - Emilie van Lingen
- Department of Gastroenterology and Hepatology, Leiden University Medical Center, Leiden, Netherlands
| | - Hein W Verspaget
- Department of Gastroenterology and Hepatology, Leiden University Medical Center, Leiden, Netherlands; Department of Biobanking, Leiden University Medical Center, Leiden, Netherlands
| | - Eric K L Berssenbrugge
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, Netherlands
| | - Josbert J Keller
- Department of Gastroenterology and Hepatology, Leiden University Medical Center, Leiden, Netherlands; Department of Gastroenterology, Haaglanden Medical Center, The Hague, Netherlands
| | - Joffrey van Prehn
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, Netherlands
| | | |
Collapse
|
|
21
|
Nicco C, Paule A, Konturek P, Edeas M. From Donor to Patient: Collection, Preparation and Cryopreservation of Fecal Samples for Fecal Microbiota Transplantation. Diseases 2020; 8:diseases8020009. [PMID: 32326509 PMCID: PMC7349373 DOI: 10.3390/diseases8020009] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 04/03/2020] [Accepted: 04/10/2020] [Indexed: 12/26/2022] Open
Abstract
Fecal Microbiota Transplantation (FMT) is suggested as an efficacious therapeutic strategy for restoring intestinal microbial balance, and thus for treating disease associated with alteration of gut microbiota. FMT consists of the administration of fresh or frozen fecal microorganisms from a healthy donor into the intestinal tract of diseased patients. At this time, in according to healthcare authorities, FMT is mainly used to treat recurrent Clostridium difficile. Despite the existence of a few existing stool banks worldwide and many studies of the FMT, there is no standard method for producing material for FMT, and there are a multitude of factors that can vary between the institutions. The main constraints for the therapeutic uses of FMT are safety concerns and acceptability. Technical and logistical issues arise when establishing such a non-standardized treatment into clinical practice with safety and proper governance. In this context, our manuscript describes a process of donor safety screening for FMT compiling clinical and biological examinations, questionnaires and interviews of donors. The potential risk of transmission of SARS-CoV-2 virus by the use of fecal microbiota for transplantation must be taken urgently into consideration. We discuss a standardized procedure of collection, preparation and cryopreservation of fecal samples through to the administration of material to patients, and explore the risks and limits of this method of FMT. The future success of medicine employing microbiota transplantation will be tightly related to its modulation and manipulation to combat dysbiosis. To achieve this goal, standard and strict methods need to be established before performing any type of FMT.
Collapse
Affiliation(s)
- Carole Nicco
- Cochin Institute, INSERM U1016, University Paris Descartes, Development, Reproduction and Cancer, Cochin Hospital, 75014 Paris, France;
| | - Armelle Paule
- International Society of Microbiota, 75002 Paris, France;
| | - Peter Konturek
- Teaching Hospital of the University of Jena, Thuringia-Clinic Saalfeld, 07318 Saalfeld, Germany;
| | - Marvin Edeas
- Cochin Institute, INSERM U1016, University Paris Descartes, Development, Reproduction and Cancer, Cochin Hospital, 75014 Paris, France;
- Correspondence:
| |
Collapse
|
|
22
|
Dorsaz S, Charretier Y, Girard M, Gaïa N, Leo S, Schrenzel J, Harbarth S, Huttner B, Lazarevic V. Changes in Microbiota Profiles After Prolonged Frozen Storage of Stool Suspensions. Front Cell Infect Microbiol 2020; 10:77. [PMID: 32185143 PMCID: PMC7058979 DOI: 10.3389/fcimb.2020.00077] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Accepted: 02/17/2020] [Indexed: 12/12/2022] Open
Abstract
Introduction: Fecal microbiota transplantation (FMT) is recommended as safe and effective treatment for recurrent Clostridioides difficile infections. Freezing the FMT preparation simplifies the process, allowing a single stool sample to be used for multiple receivers and over an extended period of time. We aimed to assess the effect of long-term frozen storage on bacterial taxonomic profiles of a stool suspension prepared for FMT. Methods: DNA was extracted from a stool suspension before freezing and sequentially during the 18-month storage period at -80°C. Two different protocols were used for DNA extraction. The first relied on a classical mechanical and chemical cell disruption to extract both intra- and extracellular DNA; the second included specific pre-treatments aimed at removing free DNA and DNA from human and damaged bacterial cells. Taxonomic profiling of bacterial communities was performed by sequencing of V3-V4 16S rRNA gene amplicons. Results: Microbiota profiles obtained by whole DNA extraction procedure remained relatively stable during frozen storage. When DNA extraction procedure included specific pre-treatments, microbiota similarity between fresh and frozen samples progressively decreased with longer frozen storage times; notably, the abundance of Bacteroidetes decreased in a storage duration-dependent manner. The abundance of Firmicutes, the main butyrate producers in the colon, were not much affected by frozen storage for up to 1 year. Conclusion: Our data show that metataxonomic analysis of frozen stool suspensions subjected to specific pre-treatments prior to DNA extractions might provide an interesting indication of bacterial resistance to stress conditions and thus of chances of survival in FMT recipients.
Collapse
Affiliation(s)
- Stéphane Dorsaz
- Genomic Research Laboratory, Division of Infectious Diseases, Department of Medicine, Geneva University Hospitals and Faculty of Medicine, Geneva, Switzerland
| | - Yannick Charretier
- Genomic Research Laboratory, Division of Infectious Diseases, Department of Medicine, Geneva University Hospitals and Faculty of Medicine, Geneva, Switzerland
| | - Myriam Girard
- Genomic Research Laboratory, Division of Infectious Diseases, Department of Medicine, Geneva University Hospitals and Faculty of Medicine, Geneva, Switzerland
| | - Nadia Gaïa
- Genomic Research Laboratory, Division of Infectious Diseases, Department of Medicine, Geneva University Hospitals and Faculty of Medicine, Geneva, Switzerland
| | - Stefano Leo
- Genomic Research Laboratory, Division of Infectious Diseases, Department of Medicine, Geneva University Hospitals and Faculty of Medicine, Geneva, Switzerland
| | - Jacques Schrenzel
- Genomic Research Laboratory, Division of Infectious Diseases, Department of Medicine, Geneva University Hospitals and Faculty of Medicine, Geneva, Switzerland.,Bacteriology Laboratory, Division of Laboratory Medicine, Department of Diagnostics, Geneva University Hospitals and Faculty of Medicine, Geneva, Switzerland
| | - Stephan Harbarth
- Infection Control Program, Division of Infectious Diseases, Geneva University Hospitals and Faculty of Medicine, Geneva, Switzerland
| | - Benedikt Huttner
- Infection Control Program, Division of Infectious Diseases, Geneva University Hospitals and Faculty of Medicine, Geneva, Switzerland
| | - Vladimir Lazarevic
- Genomic Research Laboratory, Division of Infectious Diseases, Department of Medicine, Geneva University Hospitals and Faculty of Medicine, Geneva, Switzerland
| |
Collapse
|
|
23
|
Flux MC, Lowry CA. Finding intestinal fortitude: Integrating the microbiome into a holistic view of depression mechanisms, treatment, and resilience. Neurobiol Dis 2020; 135:104578. [PMID: 31454550 PMCID: PMC6995775 DOI: 10.1016/j.nbd.2019.104578] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2019] [Revised: 06/27/2019] [Accepted: 08/14/2019] [Indexed: 02/07/2023] Open
Abstract
Depression affects at least 322 million people globally, or approximately 4.4% of the world's population. While the earnestness of researchers and clinicians to understand and treat depression is not waning, the number of individuals suffering from depression continues to increase over and above the rate of global population growth. There is a sincere need for a paradigm shift. Research in the past decade is beginning to take a more holistic approach to understanding depression etiology and treatment, integrating multiple body systems into whole-body conceptualizations of this mental health affliction. Evidence supports the hypothesis that the gut microbiome, or the collective trillions of microbes inhabiting the gastrointestinal tract, is an important factor determining both the risk of development of depression and persistence of depressive symptoms. This review discusses recent advances in both rodent and human research that explore bidirectional communication between the gut microbiome and the immune, endocrine, and central nervous systems implicated in the etiology and pathophysiology of depression. Through interactions with circulating inflammatory markers and hormones, afferent and efferent neural systems, and other, more niche, pathways, the gut microbiome can affect behavior to facilitate the development of depression, exacerbate current symptoms, or contribute to treatment and resilience. While the challenge of depression may be the direst mental health crisis of our age, new discoveries in the gut microbiome, when integrated into a holistic perspective, hold great promise for the future of positive mental health.
Collapse
Affiliation(s)
- M C Flux
- Department of Psychology and Neuroscience, University of Colorado Boulder, Boulder, CO 80309, USA.
| | - Christopher A Lowry
- Department of Integrative Physiology, Center for Neuroscience, and Center for Microbial Exploration, University of Colorado Boulder, Boulder, CO 80309, USA; Department of Physical Medicine & Rehabilitation and Center for Neuroscience, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA; Veterans Health Administration, Rocky Mountain Mental Illness Research Education and Clinical Center (MIRECC), Rocky Mountain Regional Veterans Affairs Medical Center (RMRVAMC), Aurora, CO 80045, USA; Military and Veteran Microbiome: Consortium for Research and Education (MVM-CoRE), Aurora, CO 80045, USA; Senior Fellow, VIVO Planetary Health, Worldwide Universities Network (WUN), West New York, NJ 07093, USA.
| |
Collapse
|
|
24
|
Quaranta G, Sanguinetti M, Masucci L. Fecal Microbiota Transplantation: A Potential Tool for Treatment of Human Female Reproductive Tract Diseases. Front Immunol 2019; 10:2653. [PMID: 31827467 PMCID: PMC6890827 DOI: 10.3389/fimmu.2019.02653] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Accepted: 10/28/2019] [Indexed: 12/16/2022] Open
Abstract
The gastro-intestinal tract is an extensive organ involved in several activities, with a crucial role in immunity. Billions of commensal and transient microorganisms, known as the gut microbiota, and potential pathogens, which are constantly stimulating intestinal immunity, colonize the intestinal epithelial surface. The gut microbiota may be regarded as analogous to a solid organ with multiple different functions. In the last decade, many studies have demonstrated that intestinal bacteria can be a decisive factor in the health-disease balance of the intestine, and they can also be responsible for illnesses in other locations. For this reason, fecal microbiota transplantation (FMT) represents an important therapeutic option for Clostridium difficile infections and hold promise for different clinical conditions, such as multiple sclerosis, autism, obesity, and other systemic diseases. FMT consists of the infusion of a fecal suspension from a healthy donor to a recipient in order to restore gut flora alterations. Similar to the gut, the female reproductive tract is an example of a very complex biological ecosystem. Recent studies indicate a possible relationship between the gut and female tract microbiota, associating specific intestinal bacteria patterns with genital female diseases, such as polycystic ovary syndrome (PCOS), endometriosis and bacterial vaginosis (BV). FMT could represent a potential innovative treatment option in this field.
Collapse
Affiliation(s)
- Gianluca Quaranta
- Istituto di Microbiologia, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Maurizio Sanguinetti
- Istituto di Microbiologia, Università Cattolica del Sacro Cuore, Rome, Italy.,Dipartimento Scienze di Laboratorio e Infettivologiche, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - Luca Masucci
- Istituto di Microbiologia, Università Cattolica del Sacro Cuore, Rome, Italy.,Dipartimento Scienze di Laboratorio e Infettivologiche, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| |
Collapse
|