@article {pmid31116134,
year = {2019},
author = {Revolinski, SL and Munoz-Price, LS},
title = {Clostridioides difficile in transplant patients: early diagnosis, treatment, and prevention.},
journal = {Current opinion in infectious diseases},
volume = {},
number = {},
pages = {},
doi = {10.1097/QCO.0000000000000560},
pmid = {31116134},
issn = {1473-6527},
abstract = {PURPOSE OF REVIEW: Clostridioides difficile infection is common in solid organ transplant and hematopoietic stem-cell transplant recipients and is associated with significant morbidity and mortality. These populations are also underrepresented in clinical trials, making optimal management difficult. Because of this, management of these populations follows national guideline recommendations. This review aims to summarize the recent relevant literature pertaining to the clinical management of C. difficile infection in transplant patients, with a particular focus on diagnosis, treatment, and prevention.

RECENT FINDINGS: Early diagnosis of C. difficile colonization may mitigate both horizontal and vertical transmission (progression from colonization to colitis) of infection. Once diagnosed, recent literature suggests antibiotic treatment should align with that recommended by national guidelines. Fecal microbiota transplant is an emerging therapy for recurrent C. difficile infection, and recent data have demonstrated safety and efficacy. Prevention strategies including antimicrobial stewardship, probiotic administration, antibiotic administration, and bezlotoxumab may be beneficial in transplant populations, but more data are needed to confirm recent findings.

SUMMARY: Studies evaluating C. difficile infection in transplant patients are only recently starting to emerge. Further research is needed to identify optimal treatment and prevention strategies, and to examine novel strategies such as microbiome manipulation.},
}

@article {pmid31113785,
year = {2019},
author = {Krensky, C and Poutanen, SM and Hota, SS},
title = {Diarrhea after fecal microbiota transplantation for recurrent Clostridioides difficile infection.},
journal = {CMAJ : Canadian Medical Association journal = journal de l'Association medicale canadienne},
volume = {191},
number = {20},
pages = {E559-E561},
doi = {10.1503/cmaj.181193},
pmid = {31113785},
issn = {1488-2329},
}

@article {pmid30601771,
year = {2019},
author = {Mankal, PK and Abed, J and Latte-Naor, S and Grinspan, A and Kotler, DP},
title = {Fidaxomicin and Fecal Microbiota Transplants for Severe Clostridium difficile Colitis.},
journal = {American journal of therapeutics},
volume = {26},
number = {1},
pages = {e115-e117},
doi = {10.1097/MJT.0000000000000573},
pmid = {30601771},
issn = {1536-3686},
mesh = {Anti-Bacterial Agents/*therapeutic use ; Clostridium difficile/*isolation & purification ; Enterocolitis, Pseudomembranous/microbiology/*therapy ; *Fecal Microbiota Transplantation ; Fidaxomicin/*therapeutic use ; Humans ; Male ; Middle Aged ; Treatment Outcome ; },
}

Anti-Bacterial Agents/*therapeutic use
Clostridium difficile/*isolation & purification
Enterocolitis, Pseudomembranous/microbiology/*therapy
*Fecal Microbiota Transplantation
Fidaxomicin/*therapeutic use
Humans
Male
Middle Aged
Treatment Outcome

@article {pmid30193113,
year = {2018},
author = {Suez, J and Zmora, N and Zilberman-Schapira, G and Mor, U and Dori-Bachash, M and Bashiardes, S and Zur, M and Regev-Lehavi, D and Ben-Zeev Brik, R and Federici, S and Horn, M and Cohen, Y and Moor, AE and Zeevi, D and Korem, T and Kotler, E and Harmelin, A and Itzkovitz, S and Maharshak, N and Shibolet, O and Pevsner-Fischer, M and Shapiro, H and Sharon, I and Halpern, Z and Segal, E and Elinav, E},
title = {Post-Antibiotic Gut Mucosal Microbiome Reconstitution Is Impaired by Probiotics and Improved by Autologous FMT.},
journal = {Cell},
volume = {174},
number = {6},
pages = {1406-1423.e16},
doi = {10.1016/j.cell.2018.08.047},
pmid = {30193113},
issn = {1097-4172},
support = {/HHMI/Howard Hughes Medical Institute/United States ; },
mesh = {Adolescent ; Adult ; Aged ; Animals ; Anti-Bacterial Agents/*pharmacology ; Fecal Microbiota Transplantation ; Feces/microbiology ; Female ; Gastrointestinal Microbiome/*drug effects ; Humans ; Intestinal Mucosa/drug effects/microbiology ; Lactobacillus/drug effects/genetics/isolation & purification ; Lactococcus/genetics/isolation & purification ; Male ; Mice ; Mice, Inbred C57BL ; Middle Aged ; Probiotics/*administration & dosage ; RNA, Ribosomal, 16S/analysis/genetics/metabolism ; Young Adult ; },
abstract = {Probiotics are widely prescribed for prevention of antibiotics-associated dysbiosis and related adverse effects. However, probiotic impact on post-antibiotic reconstitution of the gut mucosal host-microbiome niche remains elusive. We invasively examined the effects of multi-strain probiotics or autologous fecal microbiome transplantation (aFMT) on post-antibiotic reconstitution of the murine and human mucosal microbiome niche. Contrary to homeostasis, antibiotic perturbation enhanced probiotics colonization in the human mucosa but only mildly improved colonization in mice. Compared to spontaneous post-antibiotic recovery, probiotics induced a markedly delayed and persistently incomplete indigenous stool/mucosal microbiome reconstitution and host transcriptome recovery toward homeostatic configuration, while aFMT induced a rapid and near-complete recovery within days of administration. In vitro, Lactobacillus-secreted soluble factors contributed to probiotics-induced microbiome inhibition. Collectively, potential post-antibiotic probiotic benefits may be offset by a compromised gut mucosal recovery, highlighting a need of developing aFMT or personalized probiotic approaches achieving mucosal protection without compromising microbiome recolonization in the antibiotics-perturbed host.},
}

Adolescent
Adult
Aged
Animals
Anti-Bacterial Agents/*pharmacology
Fecal Microbiota Transplantation
Feces/microbiology
Female
Gastrointestinal Microbiome/*drug effects
Humans
Intestinal Mucosa/drug effects/microbiology
Lactobacillus/drug effects/genetics/isolation & purification
Lactococcus/genetics/isolation & purification
Male
Mice
Mice, Inbred C57BL
Middle Aged
Probiotics/*administration & dosage
RNA, Ribosomal, 16S/analysis/genetics/metabolism
Young Adult

@article {pmid31105766,
year = {2019},
author = {Saha, S and Khanna, S},
title = {Management of Clostridioides difficile colitis: insights for the gastroenterologist.},
journal = {Therapeutic advances in gastroenterology},
volume = {12},
number = {},
pages = {1756284819847651},
doi = {10.1177/1756284819847651},
pmid = {31105766},
issn = {1756-283X},
abstract = {Clostridioides difficile infection (CDI) is a common cause of diarrhea in both inpatient and outpatient settings. The last few years have seen major changes in the treatment spectrum of CDI, most notably, recommendations against using metronidazole for initial CDI, the addition of fidaxomicin and bezlotoxumab, and emergence of microbial replacement therapies. Several other therapies are undergoing clinical trials. This narrative review focuses on the treatment of CDI with a summary of literature on the newer modalities and the treatment guidelines issued by Infectious Diseases Society of America and European Society of Clinical Microbiology and Infectious Diseases.},
}

@article {pmid31105675,
year = {2019},
author = {Wang, J and Lang, T and Shen, J and Dai, J and Tian, L and Wang, X},
title = {Core Gut Bacteria Analysis of Healthy Mice.},
journal = {Frontiers in microbiology},
volume = {10},
number = {},
pages = {887},
doi = {10.3389/fmicb.2019.00887},
pmid = {31105675},
issn = {1664-302X},
abstract = {Previous studies revealed that there existed great individual variations of gut microbiota in mice, and the gut bacteria of mice were changed with the occurrence and development of diseases. To identify the core gut bacteria in healthy mice and explore their relationships with the host phenotypes would help to understand the underlying mechanisms. In this study, we identified 37 genus-level core bacteria from feces of 101 healthy mice with different ages, sexes, and mouse strains in three previous studies. They collectively represented nearly half of the total sequences, and predominantly included carbohydrate- and amino acids-metabolizing bacteria and immunomodulatory bacteria. Among them, Anaerostipes indwelt the gut of all healthy mice. Co-abundance analysis showed that these core genera were clustered into five groups (Group C1-C5), which were ecologically related. For example, the abundances of Group C2 including probiotics Bifidobacterium and Lactobacillus slightly positively correlated with those of Group C1. Principal component analysis (PCA) and multivariate analysis of variance test revealed that these core gut genera were distinguished with age and sex, and also associated with their health/disease state. Linear discriminant analysis effect size (LEfSe) method showed that bacteria in Group C1 and C2/C3 increased with the age in infancy and early adulthood, and were more abundant in female mice than in male ones. The metabolic syndrome (MS) induced by high fat diet (HFD) and accelerated postnatal growth would decrease Group C2 genera, whereas probiotics intervention would reverse HFD-induced reduction of Group C2. Spearman correlation analysis indicated that the principal components based on the abundance of the 37 core genera were significantly correlated with host characteristic parameters of MS. These results demonstrated that the 37 core genera in five co-abundance groups from healthy mice were related to host phenotypes. It was indicated that these prevalent gut bacterial genera could be representative of the healthy gut microbiome in gnotobiotic animal models, and might also be candidates of probiotics and fecal microbiota transplantation.},
}

@article {pmid29449660,
year = {2018},
author = {Shono, Y and van den Brink, MRM},
title = {Gut microbiota injury in allogeneic haematopoietic stem cell transplantation.},
journal = {Nature reviews. Cancer},
volume = {18},
number = {5},
pages = {283-295},
pmid = {29449660},
issn = {1474-1768},
mesh = {Anti-Bacterial Agents/adverse effects ; Dysbiosis/etiology ; Fecal Microbiota Transplantation ; *Gastrointestinal Microbiome/drug effects ; Graft vs Host Disease/etiology/*microbiology ; Hematologic Neoplasms/therapy ; Hematopoietic Stem Cell Transplantation/*adverse effects/mortality ; Humans ; Infection/etiology/*microbiology ; Prebiotics ; Probiotics/pharmacology ; Transplantation, Homologous/*adverse effects/mortality ; },
abstract = {Allogeneic haematopoietic stem cell transplantation (allo-HSCT) is considered to be the strongest curative immunotherapy for various malignancies (primarily, but not limited to, haematologic malignancies). However, application of allo-HSCT is limited owing to its life-threatening major complications, such as graft-versus-host disease (GVHD), relapse and infections. Recent advances in large-scale DNA sequencing technology have facilitated rapid identification of the microorganisms that make up the microbiota and evaluation of their interactions with host immunity in various diseases, including cancer. This has resulted in renewed interest regarding the role of the intestinal flora in patients with haematopoietic malignancies who have received an allo-HSCT and in whether the microbiota affects clinical outcomes, including GVHD, relapse, infections and transplant-related mortality. In this Review, we discuss the potential role of intestinal microbiota in these major complications after allo-HSCT, summarize clinical trials evaluating the microbiota in patients who have received allo-HSCT and discuss how further studies of the microbiota could inform the development of strategies that improve outcomes of allo-HSCT.},
}

Anti-Bacterial Agents/adverse effects
Dysbiosis/etiology
Fecal Microbiota Transplantation
*Gastrointestinal Microbiome/drug effects
Graft vs Host Disease/etiology/*microbiology
Hematologic Neoplasms/therapy
Hematopoietic Stem Cell Transplantation/*adverse effects/mortality
Humans
Infection/etiology/*microbiology
Prebiotics
Probiotics/pharmacology
Transplantation, Homologous/*adverse effects/mortality

@article {pmid31103793,
year = {2019},
author = {Dailey, FE and Turse, EP and Daglilar, E and Tahan, V},
title = {The dirty aspects of fecal microbiota transplantation: a review of its adverse effects and complications.},
journal = {Current opinion in pharmacology},
volume = {49},
number = {},
pages = {29-33},
doi = {10.1016/j.coph.2019.04.008},
pmid = {31103793},
issn = {1471-4973},
abstract = {Fecal microbiota transplantation is becoming a growing therapy for a variety of indications, including recurrent or refractory Clostridium difficile infection (CDI), as well as many other gastrointestinal and extra-intestinal diseases. In fact, fecal microbiota transplantation is now strongly recommended as the treatment of choice for multiple recurrences of CDI, given its strong efficacy and a favorable short-term side effect profile. As the application of this therapy expands, awareness of its adverse events has also developed. The purpose of this review is to bring to light the side effects and complications associated with fecal microbiota transplantation, with an emphasis on findings from recently published studies.},
}

@article {pmid29659775,
year = {2018},
author = {Peter, J and Zeitz, J and Stallmach, A},
title = {Ustekinumab Rescue Therapy in a Patient With Chronic Refractory Pouchitis.},
journal = {Journal of Crohn's & colitis},
volume = {12},
number = {8},
pages = {1008-1009},
doi = {10.1093/ecco-jcc/jjy037},
pmid = {29659775},
issn = {1876-4479},
mesh = {Adult ; Anti-Inflammatory Agents/administration & dosage ; Colitis, Ulcerative/diagnosis/surgery ; Crohn Disease/*diagnosis ; Diagnosis, Differential ; Drug Resistance, Multiple ; Endoscopy, Gastrointestinal/methods ; Fecal Microbiota Transplantation/*adverse effects/methods ; Humans ; *Intestinal Mucosa/diagnostic imaging/pathology ; Male ; Patient Care Management/methods ; *Pouchitis/diagnosis/etiology/physiopathology/therapy ; Prednisolone/*administration & dosage ; Proctocolectomy, Restorative/*adverse effects/methods ; Recurrence ; Severity of Illness Index ; Treatment Outcome ; Ustekinumab/*administration & dosage ; },
}

Adult
Anti-Inflammatory Agents/administration & dosage
Colitis, Ulcerative/diagnosis/surgery
Crohn Disease/*diagnosis
Diagnosis, Differential
Drug Resistance, Multiple
Endoscopy, Gastrointestinal/methods
Fecal Microbiota Transplantation/*adverse effects/methods
Humans
*Intestinal Mucosa/diagnostic imaging/pathology
Male
Patient Care Management/methods
*Pouchitis/diagnosis/etiology/physiopathology/therapy
Prednisolone/*administration & dosage
Proctocolectomy, Restorative/*adverse effects/methods
Recurrence
Severity of Illness Index
Treatment Outcome
Ustekinumab/*administration & dosage

@article {pmid31095511,
year = {2019},
author = {Sasmita, AO},
title = {Modification of the gut microbiome to combat neurodegeneration.},
journal = {Reviews in the neurosciences},
volume = {},
number = {},
pages = {},
doi = {10.1515/revneuro-2019-0005},
pmid = {31095511},
issn = {0334-1763},
abstract = {The gut microbiome was extensively researched for its biological variety and its potential role in propagating diseases outside of the gastrointestinal (GI) tract. Recently, a lot of effort was focused on comprehending the gut-brain axis and the bizarre communication between the GI system and the nervous system. Ample amount of studies being carried out also revealed the involvement of the gut microbiome in enhancing the degree of many neurological disorders, including neurodegenerative diseases. It was widely observed that there were distinct microbiome profiles and dysbiosis within patients suffering from Alzheimer's disease, Parkinson's disease, amyotrophic lateral sclerosis, and multiple sclerosis. Various approaches to re-establish the balance of the gut microbiome, from antibiotic therapy, fecal microbiota transplant, or ingestion of psychobiotics, are discussed within this review within the specific context of combating neurodegenerative diseases. Present studies and clinical trials indicate that although there is an immense potential of gut microbiome modification to be preventive or therapeutic, there are still many intercalated components of the gut-brain axis at play and thus, more research needs to be carried out to delineate microbiome factors that may potentially alleviate symptoms of neurodegeneration.},
}

@article {pmid31091761,
year = {2019},
author = {Noce, A and Marrone, G and Di Daniele, F and Ottaviani, E and Wilson Jones, G and Bernini, R and Romani, A and Rovella, V},
title = {Impact of Gut Microbiota Composition on Onset and Progression of Chronic Non-Communicable Diseases.},
journal = {Nutrients},
volume = {11},
number = {5},
pages = {},
doi = {10.3390/nu11051073},
pmid = {31091761},
issn = {2072-6643},
abstract = {In recent years, mounting scientific evidence has emerged regarding the evaluation of the putative correlation between the gut microbiota composition and the presence of chronic non-communicable diseases (NCDs), such as diabetes mellitus, chronic kidney disease, and arterial hypertension. The aim of this narrative review is to examine the current literature with respect to the relationship between intestinal dysbiosis and the insurgence/progression of chronic NCDs, analyzing the physiopathological mechanisms that can induce microbiota modification in the course of these pathologies, and the possible effect induced by microbiota alteration upon disease onset. Therapy based on probiotics, prebiotics, synbiotics, postbiotics, and fecal microbiota transplant can represent a useful therapeutic tool, as has been highlighted on animal studies. To this moment, clinical studies that intended to demonstrate the beneficial effect induced by this kind of oral supplementation on the gut microbiota composition, and subsequent amelioration of signs and symptoms of chronic NCDs have been conducted on limited sample populations for a limited follow-up period. Therefore, to fully evaluate the therapeutic value of this kind of intervention, it would be ideal to design ample population; randomized clinical trials with a lengthy follow up period.},
}

@article {pmid31085417,
year = {2019},
author = {Turse, EP and Dailey, FE and Ghouri, YA and Tahan, V},
title = {Fecal microbiota transplantation donation: the gift that keeps on giving.},
journal = {Current opinion in pharmacology},
volume = {49},
number = {},
pages = {24-28},
doi = {10.1016/j.coph.2019.04.009},
pmid = {31085417},
issn = {1471-4973},
abstract = {Fecal microbiota transplantation (FMT) is being studied and utilized for various medical conditions including Clostridium difficile colitis, inflammatory bowel diseases (IBD), obesity, myasthenia gravis, and so on. Yet, FMT donation, whether from an individual or a stool bank, can be challenging given the numerous requirements and donor costs. Furthermore, data outcomes on recipients of FMT regarding donor's health co-morbidities, age, and weight are limited but emerging. The purpose of this review is to evaluate cost, safety, and accessibility in FMT donation.},
}

@article {pmid31088542,
year = {2019},
author = {Prevel, R and Boyer, A and M'Zali, F and Lasheras, A and Zahar, JR and Rogues, AM and Gruson, D},
title = {Is systematic fecal carriage screening of extended-spectrum beta-lactamase-producing Enterobacteriaceae still useful in intensive care unit: a systematic review.},
journal = {Critical care (London, England)},
volume = {23},
number = {1},
pages = {170},
doi = {10.1186/s13054-019-2460-3},
pmid = {31088542},
issn = {1466-609X},
abstract = {BACKGROUND: Extended-spectrum beta-lactamase-producing Enterobacteriaceae (ESBL-E) are disseminating worldwide leading to increased hospital length of stay and mortality in intensive care units (ICU). ESBL-E dissemination was first due to outbreaks in hospital settings which led to the implementation of systematic fecal carriage screening to improve hygiene procedures by contact precautions. ESBLs have since spread in the community, and the relevance of contact precautions is questioned. ESBL-E dissemination led to an overuse of carbapenems triggering the emergence of carbapenem-resistant Enterobacteriaceae. Empirical antimicrobial therapy based on ESBL-E fecal carriage has been proposed but is debated as it could increase the consumption of carbapenems among ESBL-E carriers without any clinical benefit. Finally, selective decontamination among ESBL-E fecal carriers is evoked to decrease the risk for subsequent ESBL-E infection, but its efficacy remains debated. We propose to systematically review the evidence to recommend or not such systematic ESBL-E fecal carriage screening in adult ICU.

METHODS: Every article focusing on ESBL-E and ICU available on the MEDLINE database was assessed. Articles were included if focusing on cross-transmission, efficacy of hygiene procedures, link between ESBL-E colonization and infection or guidance of empirical therapy or selective decontamination efficacy.

RESULTS: Among 330 articles referenced on PubMed, 39 abstracts were selected for full-text assessment and 25 studies were included. Systematic screening of ESBL-E fecal carriage to guide contact precautions do not seem to decrease the rate of ESBL-E cross-transmission. It has a very good negative predictive value for subsequent ESBL-E infections but a positive predictive value between 40 and 50% and so does not help to spare carbapenems. Cessation of ESBL-E carriage systematic screening could decrease the use of carbapenems in ICU without any clinical harm. Nevertheless, further studies are needed to validate these results from monocentric before-after study. Selective decontamination strategy applied to ESBL-E fecal carriers could be helpful, but available data are conflicting.

CONCLUSION: Current knowledge lacks of high-quality evidence to strongly recommend in favor of or against a systematic ESBL-E fecal carriage screening policy for ICU patients in a non-outbreak situation. Further evaluation of selective decontamination or fecal microbiota transplantation among ESBL-E fecal carriers is needed.},
}

@article {pmid31082878,
year = {2019},
author = {Shaukat, A and Brenner, DM},
title = {Fecal Microbiota Transplant for Irritable Bowel Syndrome: Panacea or Placebo?.},
journal = {The American journal of gastroenterology},
volume = {},
number = {},
pages = {},
doi = {10.14309/ajg.0000000000000259},
pmid = {31082878},
issn = {1572-0241},
abstract = {Irritable bowel syndrome (IBS) is a common disorder of heterogeneous pathogenesis, and alterations in the gut microbiome/dysbiosis play a role in the development of symptoms in a subset of individuals with IBS. Consequently, it stands to reason that modulation of the microbiome via fecal microbial transplant (FMT) may serve as an effective treatment strategy because this has proven effective for treating other illnesses such as Clostridium difficile colitis. Small studies completed to date have offered conflicting results and the strains used, route of administration, and IBS subtypes may all play a role in treatment outcomes. A better understanding of the altered microbiome of patients with IBS and more rigorous trials are warranted before the utility of fecal microbial transplant for IBS symptoms can be determined.},
}

@article {pmid30694953,
year = {2019},
author = {Rancich, M and Roman, C},
title = {Updated guidelines for diagnosing and managing Clostridium difficile.},
journal = {JAAPA : official journal of the American Academy of Physician Assistants},
volume = {32},
number = {2},
pages = {48-50},
doi = {10.1097/01.JAA.0000552734.33929.01},
pmid = {30694953},
issn = {1547-1896},
mesh = {Anti-Bacterial Agents/*standards/therapeutic use ; *Clostridium difficile ; Enterocolitis, Pseudomembranous/diagnosis/microbiology/*therapy ; Fecal Microbiota Transplantation/*standards ; Humans ; Metronidazole/*standards/therapeutic use ; Practice Guidelines as Topic ; },
abstract = {The updated Infectious Disease Society of America guidelines for managing Clostridium difficile infections remove metronidazole as first-line therapy and add fecal microbiota transplants to the treatment options. This article reviews the new guidelines and strategies for diagnosis and infection control.},
}

Anti-Bacterial Agents/*standards/therapeutic use
*Clostridium difficile
Enterocolitis, Pseudomembranous/diagnosis/microbiology/*therapy
Fecal Microbiota Transplantation/*standards
Humans
Metronidazole/*standards/therapeutic use
Practice Guidelines as Topic

@article {pmid30643289,
year = {2019},
author = {Feehley, T and Plunkett, CH and Bao, R and Choi Hong, SM and Culleen, E and Belda-Ferre, P and Campbell, E and Aitoro, R and Nocerino, R and Paparo, L and Andrade, J and Antonopoulos, DA and Berni Canani, R and Nagler, CR},
title = {Healthy infants harbor intestinal bacteria that protect against food allergy.},
journal = {Nature medicine},
volume = {25},
number = {3},
pages = {448-453},
doi = {10.1038/s41591-018-0324-z},
pmid = {30643289},
issn = {1546-170X},
support = {UL1 TR000430/TR/NCATS NIH HHS/United States ; P30 DK042086/DK/NIDDK NIH HHS/United States ; P30 CA014599/CA/NCI NIH HHS/United States ; R56 AI134923/AI/NIAID NIH HHS/United States ; UL1 TR002389/TR/NCATS NIH HHS/United States ; R01 AI106302/AI/NIAID NIH HHS/United States ; },
mesh = {Anaphylaxis/*microbiology ; Animals ; Clostridiales/genetics ; *Fecal Microbiota Transplantation ; Female ; Food Hypersensitivity/microbiology ; Gastrointestinal Microbiome/*genetics ; Germ-Free Life ; Healthy Volunteers ; Humans ; Ileum/microbiology ; Infant ; Male ; Mice ; Milk Hypersensitivity/*microbiology ; },
abstract = {There has been a striking generational increase in life-threatening food allergies in Westernized societies1,2. One hypothesis to explain this rising prevalence is that twenty-first century lifestyle practices, including misuse of antibiotics, dietary changes, and higher rates of Caesarean birth and formula feeding have altered intestinal bacterial communities; early-life alterations may be particularly detrimental3,4. To better understand how commensal bacteria regulate food allergy in humans, we colonized germ-free mice with feces from healthy or cow's milk allergic (CMA) infants5. We found that germ-free mice colonized with bacteria from healthy, but not CMA, infants were protected against anaphylactic responses to a cow's milk allergen. Differences in bacterial composition separated the healthy and CMA populations in both the human donors and the colonized mice. Healthy and CMA colonized mice also exhibited unique transcriptome signatures in the ileal epithelium. Correlation of ileal bacteria with genes upregulated in the ileum of healthy or CMA colonized mice identified a clostridial species, Anaerostipes caccae, that protected against an allergic response to food. Our findings demonstrate that intestinal bacteria are critical for regulating allergic responses to dietary antigens and suggest that interventions that modulate bacterial communities may be therapeutically relevant for food allergy.},
}

Anaphylaxis/*microbiology
Animals
Clostridiales/genetics
*Fecal Microbiota Transplantation
Female
Food Hypersensitivity/microbiology
Gastrointestinal Microbiome/*genetics
Germ-Free Life
Healthy Volunteers
Humans
Ileum/microbiology
Infant
Male
Mice
Milk Hypersensitivity/*microbiology

@article {pmid31054313,
year = {2019},
author = {Khanna, S and Gerding, DN},
title = {Current and future trends in clostridioides (clostridium) difficile infection management.},
journal = {Anaerobe},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.anaerobe.2019.04.010},
pmid = {31054313},
issn = {1095-8274},
abstract = {Current and future management of Clostridioides difficile infection (CDI) including antibiotic treatment is increasingly focused on preventive strategies, either prevention of recurrent CDI (rCDI) or primary prevention of CDI. In addition to newer narrow spectrum antibiotics and pulse dosing of antibiotic treatment, multiple widely differing approaches to prevention of CDI and rCDI are under clinical development or recently approved for clinical use. They include immunologics, both passive monoclonal antibodies and active vaccines targeted at C. difficile toxins, approaches to reduce antibiotic dysbiosis in the gut, microbiome restoration using fecal microbiome transplants (FMT) or biotherapeutic bacterial derivatives, and substitution of non-toxigenic C. difficile (NTCD) for toxigenic C. difficile. Newer antibiotics, monoclonal antibodies, and FMT are targeted at reducing rCDI whereas vaccines and reduction of antibiotic dysbiosis in the gut are targeted at prevention of primary CDI. Biotherapeutics may be used for prevention of either primary CDI or rCDI. Approaches such as monoclonal antibodies, FMT, and biotherapeutics provide rapid but transient preventive benefits, whereas vaccines require weeks to months to be effective, but will presumably provide long term prevention. More rapid but transient prevention strategies such as FMT and biotherapeutics could be used in combination with vaccines to provide both rapid and durable CDI prevention.},
}

@article {pmid31076926,
year = {2019},
author = {Lin, C and Wan, J and Lu, Y and Zhang, H and Chen, X and Su, Y and Zhu, W},
title = {Active bacterial communities of pig fecal microbiota transplantation suspension prepared and preserved under different conditions.},
journal = {AMB Express},
volume = {9},
number = {1},
pages = {63},
doi = {10.1186/s13568-019-0787-4},
pmid = {31076926},
issn = {2191-0855},
support = {31572414//National Natural Science Foundation of China/ ; 3187130113//National Natural Science Foundation of China/ ; 2018YFD0500404//National Key R & D Program of China/ ; },
abstract = {Although fecal microbiota transplantation (FMT) has become a research hotspot, studies on comparison of the active fecal bacteria suspension under different preparation conditions are limited. This study investigated the abundances of active bacterial community in pig FMT suspension that produced under different oxygen concentrations or cryopreservation conditions. Fecal samples from a Landrace × Yorkshire sow were used to prepare fecal bacteria suspension under the anaerobic (AN group) and aerobic conditions (AE group), respectively. And then half of the anaerobic fecal bacteria suspension was cryopreservation in - 80 °C (AN-CR group) for 1 week. The microbial RNA in the fecal bacteria suspension was extracted before and after cryopreservation, and reverse transcribed into cDNA. MiSeq sequencing 16S rRNA gene of bacterial cDNA showed that the bacterial diversity in the AN group was significantly higher than that in the AE group. Comparing with the sows' fecal sample, the relative abundances of Lactobacillus johnsonii, Lactobacillus coleohominis and Parabacteroides merdae in AN, AE and AN-CR groups were reduced. The short-term cryopreservation had low impact on the structure of the active bacterial community in the fecal bacterial suspension. These results suggest that fecal bacteria suspension can be better prepared under strict anaerobic condition, and that fecal bacteria suspension can be cryopreserved in - 80 °C for a short time.},
}

@article {pmid31073525,
year = {2019},
author = {Jia, Q and Zhang, L and Zhang, J and Pei, F and Zhu, S and Sun, Q and Duan, L},
title = {Fecal Microbiota of Diarrhea-Predominant Irritable Bowel Syndrome Patients Causes Hepatic Inflammation of Germ-Free Rats and Berberine Reverses It Partially.},
journal = {BioMed research international},
volume = {2019},
number = {},
pages = {4530203},
doi = {10.1155/2019/4530203},
pmid = {31073525},
issn = {2314-6141},
abstract = {Effects of the microbiome associated with diarrhea-predominant irritable bowel syndrome (IBS-D) on the gut have been reported, but no study has reported the effects of the IBS-D gut microbiome on the liver. We transplanted the fecal microbiota from an IBS-D patient and from a healthy volunteer to GF rats. The hepatic inflammation, serum biochemical parameters and metabolome, fecal microbiota profile, fecal short-chain fatty acids (SCFAs), and correlations among them before and after berberine intervention were assessed. Compared with the healthy control fecal microbiome transplantation (FMT) rats, the fecal microbiota of IBS-D patients induces significant Kupffer cell hyperplasia, hepatic sinusoid hypertrophy, and elevated levels of hepatic tumor necrosis factor-α and interferon-γ and decreases the synthesis of ALB in GF rats. This is possibly related to Faecalibacterium and Bifidobacterium attributable to fecal formate, acetate, and propionate levels, which are associated with the host linoleic acid pathway. Berberine can partially reverse the Kupffer cell hyperplasia, Faecalibacterium, fecal formate, acetate, and propionate by modulating the gut microbiome composition. These results may imply that IBS-D not only is an intestinal functional disorder but can cause liver inflammation, thus providing some implications regarding the clinical cognition and treatment of IBS-D.},
}

@article {pmid30728535,
year = {2019},
author = {Chakradhar, S},
title = {Positive selection.},
journal = {Nature medicine},
volume = {25},
number = {2},
pages = {192-194},
doi = {10.1038/s41591-019-0351-4},
pmid = {30728535},
issn = {1546-170X},
mesh = {Bacteria/isolation & purification/*metabolism ; Fecal Microbiota Transplantation ; Feces/microbiology ; Humans ; Probiotics/pharmacology ; },
}

Bacteria/isolation & purification/*metabolism
Fecal Microbiota Transplantation
Feces/microbiology
Humans
Probiotics/pharmacology

@article {pmid29942096,
year = {2018},
author = {Hoyles, L and Fernández-Real, JM and Federici, M and Serino, M and Abbott, J and Charpentier, J and Heymes, C and Luque, JL and Anthony, E and Barton, RH and Chilloux, J and Myridakis, A and Martinez-Gili, L and Moreno-Navarrete, JM and Benhamed, F and Azalbert, V and Blasco-Baque, V and Puig, J and Xifra, G and Ricart, W and Tomlinson, C and Woodbridge, M and Cardellini, M and Davato, F and Cardolini, I and Porzio, O and Gentileschi, P and Lopez, F and Foufelle, F and Butcher, SA and Holmes, E and Nicholson, JK and Postic, C and Burcelin, R and Dumas, ME},
title = {Molecular phenomics and metagenomics of hepatic steatosis in non-diabetic obese women.},
journal = {Nature medicine},
volume = {24},
number = {7},
pages = {1070-1080},
pmid = {29942096},
issn = {1546-170X},
support = {MR/L01632X/1//Medical Research Council/United Kingdom ; MR/M501797/1//Medical Research Council/United Kingdom ; },
mesh = {Animals ; Cells, Cultured ; Cohort Studies ; Confounding Factors (Epidemiology) ; Diabetes Mellitus/*genetics ; Fecal Microbiota Transplantation ; Female ; Hepatocytes/metabolism ; Humans ; Metabolome ; Metabolomics ; *Metagenomics ; Mice ; Microbiota ; Non-alcoholic Fatty Liver Disease/*genetics ; Obesity/*genetics ; Phenotype ; Transcriptome/genetics ; },
abstract = {Hepatic steatosis is a multifactorial condition that is often observed in obese patients and is a prelude to non-alcoholic fatty liver disease. Here, we combine shotgun sequencing of fecal metagenomes with molecular phenomics (hepatic transcriptome and plasma and urine metabolomes) in two well-characterized cohorts of morbidly obese women recruited to the FLORINASH study. We reveal molecular networks linking the gut microbiome and the host phenome to hepatic steatosis. Patients with steatosis have low microbial gene richness and increased genetic potential for the processing of dietary lipids and endotoxin biosynthesis (notably from Proteobacteria), hepatic inflammation and dysregulation of aromatic and branched-chain amino acid metabolism. We demonstrated that fecal microbiota transplants and chronic treatment with phenylacetic acid, a microbial product of aromatic amino acid metabolism, successfully trigger steatosis and branched-chain amino acid metabolism. Molecular phenomic signatures were predictive (area under the curve = 87%) and consistent with the gut microbiome having an effect on the steatosis phenome (>75% shared variation) and, therefore, actionable via microbiome-based therapies.},
}

Animals
Cells, Cultured
Cohort Studies
Confounding Factors (Epidemiology)
Diabetes Mellitus/*genetics
Fecal Microbiota Transplantation
Female
Hepatocytes/metabolism
Humans
Metabolome
Metabolomics
*Metagenomics
Mice
Microbiota
Non-alcoholic Fatty Liver Disease/*genetics
Obesity/*genetics
Phenotype
Transcriptome/genetics

@article {pmid31070838,
year = {2019},
author = {Huang, HL and Chen, HT and Luo, QL and Xu, HM and He, J and Li, YQ and Zhou, YL and Yao, F and Nie, YQ and Zhou, YJ},
title = {Relief of irritable bowel syndrome by fecal microbiota transplantation is associated with changes in diversity and composition of the gut microbiota.},
journal = {Journal of digestive diseases},
volume = {},
number = {},
pages = {},
doi = {10.1111/1751-2980.12756},
pmid = {31070838},
issn = {1751-2980},
abstract = {AIM: To evaluate the efficacy and safety of fecal microbiota transplantation (FMT) for refractory irritable bowel syndrome (IBS).

METHODS: Microbiota suspensions from feces donors were injected into the intestines of 30 Chinese patients with IBS. Microbiota composition analysis and genomic DNA extraction were performed on fecal samples obtained from these patients at baseline and 1 month after FMT. FMT's clinical efficacy and safety were assessed using questionnaires covering four aspects of IBS therapeutic efficacy and assessment of adverse effects during a 6-month follow-up.

RESULTS: Analytical data showed that FMT could change the gut microbiota composition, improve gastrointestinal symptoms, and alleviate depression and anxiety by restoring microbial diversity. The questionnaire scores confirmed that the maintained clinical response is 3-6 months after the first FMT.

CONCLUSIONS: FMT could be an effective and safe therapeutic strategy for IBS treatment, warranting comprehensive investigation.},
}

@article {pmid31068891,
year = {2019},
author = {Xia, GH and You, C and Gao, XX and Zeng, XL and Zhu, JJ and Xu, KY and Tan, CH and Xu, RT and Wu, QH and Zhou, HW and He, Y and Yin, J},
title = {Stroke Dysbiosis Index (SDI) in Gut Microbiome Are Associated With Brain Injury and Prognosis of Stroke.},
journal = {Frontiers in neurology},
volume = {10},
number = {},
pages = {397},
doi = {10.3389/fneur.2019.00397},
pmid = {31068891},
issn = {1664-2295},
abstract = {Background: Significant dysbiosis occurs in the gut microbiome of stroke patients. Condensing these broad, complex changes into one index would greatly facilitate the clinical usage of gut microbiome data. Here, we formulated a gut microbiota index in patients with acute ischemic stroke based on their gut microbiota dysbiosis patterns and tested whether the index was correlated with brain injury and early outcome. Methods: A total of 104 patients with acute ischemic stroke and 90 healthy individuals were recruited, and their gut microbiotas were compared and to model a Stroke Dysbiosis Index (SDI), which representing stroke-associated dysbiosis patterns overall. Another 83 patients and 70 controls were recruited for validation. The association of SDI with stroke severity (National Institutes of Health Stroke Scale [NIHSS] score) and outcome (modified Rankin scale [mRS] score: favorable, 0-2; unfavorable, >2) at discharge was also assessed. A middle cerebral artery occlusion (MCAO) model was used in human flora-associated (HFA) animals to explore the causal relationship between gut dysbiosis and stroke outcome. Results: Eighteen genera were significantly different between stroke patients and healthy individuals. The SDI formula was devised based on these microbiome differences; SDI was significantly higher in stroke patients than in healthy controls. SDI alone discriminated stroke patients from controls with AUCs of 74.9% in the training cohort and 84.3% in the validation cohort. SDI was significantly and positively correlated with NIHSS score on admission and mRS score at discharge. Logistic regression analysis showed that SDI was an independent predictor of severe stroke (NIHSS ≥8) and early unfavorable outcome (mRS >2). Mice receiving fecal transplants from high-SDI patients developed severe brain injury with elevated IL-17+ γδ T cells in gut compared to mice receiving transplants from low-SDI patients (all P < 0.05). Conclusions: We developed an index to measure gut microbiota dysbiosis in stroke patients; this index was significantly correlated with patients' outcome and was causally related to outcome in a mouse model of stroke. Our model facilitates the potential clinical application of gut microbiota data in stroke and adds quantitative evidence linking the gut microbiota to stroke.},
}

@article {pmid31066530,
year = {2019},
author = {Gilbert, B and Schrenzel, J},
title = {[Fecal microbiota transplantation : current status and prospects].},
journal = {Revue medicale suisse},
volume = {15},
number = {650},
pages = {976-983},
pmid = {31066530},
issn = {1660-9379},
abstract = {Fecal microbiota transplantation (FMT) is approved as a safe and effective treatment of recurrent Clostridium difficile infections. The technique is now being studied for other indications, usually involving chronic inflammation, metabolic disorders, or autoimmunity, for which the gut microbiota appears to play a key role. We detail thereafter, according to their degree of evidence, the potential future indications, in which FMT has already been tried on Humans. Except for ulcerative colitis and metabolic syndrome, the methodology of the published trials is often insufficiently described and inhomogeneous. Further randomized placebo-controlled trials and standardization of practice will be needed to confirm these preliminary but encouraging results.},
}

@article {pmid31065565,
year = {2019},
author = {Galloway-Peña, JR and Peterson, CB and Malik, F and Sahasrabhojane, PV and Shah, DP and Brumlow, CE and Carlin, LG and Chemaly, RF and Im, JS and Rondon, G and Felix, E and Veillon, L and Lorenzi, PL and Alousi, AM and Jenq, RR and Kontoyiannis, DP and Shpall, EJ and Shelburne, SA and Okhuysen, PC},
title = {Fecal Microbiome, Metabolites, and Stem Cell Transplant Outcomes: A Single-Center Pilot Study.},
journal = {Open forum infectious diseases},
volume = {6},
number = {5},
pages = {ofz173},
doi = {10.1093/ofid/ofz173},
pmid = {31065565},
issn = {2328-8957},
abstract = {Background: Accumulating evidence suggests that the intestinal microbiome may dramatically affect the outcomes of hematopoietic stem cell transplant (HSCT) recipients. Providing 16S ribosomal RNA based microbiome characterization in a clinically actionable time frame is currently problematic. Thus, determination of microbial metabolites as surrogates for microbiome composition could offer practical biomarkers.

Methods: Longitudinal fecal specimens (n = 451) were collected from 44 patients before HSCT through 100 days after transplantation, as well as 1-time samples from healthy volunteers (n = 18) as controls. Microbiota composition was determined using 16S ribosomal RNA V4 sequencing. Fecal indole and butyrate levels were determined using liquid chromatography tandem mass spectrometry.

Results: Among HSCT recipients, both fecal indole and butyrate levels correlated with the Shannon diversity index at baseline (P = .02 and P = .002, respectively) and directly after transplantation (P = .006 and P < .001, respectively). Samples with high butyrate levels were enriched for Clostridiales, whereas samples containing high indole were also enriched for Bacteroidales. A lower Shannon diversity index at the time of engraftment was associated with increased incidence of acute intestinal graft-vs-host disease (iGVHD) (P = .02) and transplant-related deaths (P = .03). Although fecal metabolites were not associated with acute iGVHD or overall survival, patients contracting bloodstream infections within 30 days after transplantation had significantly lower levels of fecal butyrate (P = .03).

Conclusions: Longitudinal analysis of fecal microbiome and metabolites after HSCT identified butyrate and indole as potential surrogate markers for microbial diversity and specific taxa. Further studies are needed to ascertain whether fecal metabolites can be used as biomarkers of acute iGVHD or bacteremia after HSCT.},
}

@article {pmid31064848,
year = {2019},
author = {Buchta Rosean, C and Bostic, RR and Ferey, JCM and Feng, TY and Azar, FN and Tung, KS and Dozmorov, MG and Smirnova, E and Bos, PD and Rutkowski, MR},
title = {Pre-existing commensal dysbiosis is a host-intrinsic regulator of tissue inflammation and tumor cell dissemination in hormone receptor-positive breast cancer.},
journal = {Cancer research},
volume = {},
number = {},
pages = {},
doi = {10.1158/0008-5472.CAN-18-3464},
pmid = {31064848},
issn = {1538-7445},
abstract = {It is unknown why some patients with hormone receptor-positive (HR+) breast cancer present with more aggressive and invasive disease. Metastatic dissemination occurs early in disease and is facilitated by crosstalk between the tumor and tissue environment, suggesting that undefined host-intrinsic factors enhance early dissemination and the probability of developing metastatic disease. Here we have identified commensal dysbiosis as a host-intrinsic factor associated with metastatic dissemination. Using a mouse model of HR+ mammary cancer, we demonstrate that a pre-established disruption of commensal homeostasis results in enhanced circulating tumor cells and subsequent dissemination to the tumor-draining lymph nodes and lungs. Commensal dysbiosis promoted early inflammation within the mammary gland that was sustained during HR+ mammary tumor progression. Furthermore, dysbiosis enhanced fibrosis and collagen deposition both systemically and locally within the tumor microenvironment and induced significant myeloid infiltration into the mammary gland and breast tumor. These effects were recapitulated both by directly targeting gut microbes using non-absorbable antibiotics and by fecal microbiota transplantation of dysbiotic cecal contents, demonstrating the direct impact of gut dysbiosis on mammary tumor dissemination. This study identifies dysbiosis as a pre-existing, host-intrinsic regulator of tissue inflammation, myeloid recruitment, fibrosis, and dissemination of tumor cells in HR+ breast cancer.},
}

@article {pmid31059962,
year = {2019},
author = {Zhang, F and Zhang, T and Zhu, H and Borody, TJ},
title = {Evolution of fecal microbiota transplantation in methodology and ethical issues.},
journal = {Current opinion in pharmacology},
volume = {49},
number = {},
pages = {11-16},
doi = {10.1016/j.coph.2019.04.004},
pmid = {31059962},
issn = {1471-4973},
abstract = {Fecal microbiota transplantation (FMT), the core therapy for remodeling the gut microbiota with a long medical history, has gained great attention worldwide in recent years. Increasing studies have explored its indications, methodology, efficacy, safety, and ethics. Purified forms of FMT, using an automated method for the purification of fecal microbiota from stool, has become a reality. Colonic transendoscopic enteral tubing makes frequent FMT delivery into the whole colon feasible. This review focuses on the recent progress in laboratory preparation, updated clinical strategies, novel delivery methods, and ethical issues surrounding FMT in clinical studies.},
}

@article {pmid31057522,
year = {2019},
author = {Fiedorová, K and Radvanský, M and Němcová, E and Grombiříková, H and Bosák, J and Černochová, M and Lexa, M and Šmajs, D and Freiberger, T},
title = {The Impact of DNA Extraction Methods on Stool Bacterial and Fungal Microbiota Community Recovery.},
journal = {Frontiers in microbiology},
volume = {10},
number = {},
pages = {821},
doi = {10.3389/fmicb.2019.00821},
pmid = {31057522},
issn = {1664-302X},
abstract = {Our understanding of human gut microbiota in health and disease depends on accurate and reproducible microbial data acquisition. The critical step in this process is to apply an appropriate methodology to extract microbial DNA, since biases introduced during the DNA extraction process may result in inaccurate microbial representation. In this study, we attempted to find a DNA extraction protocol which could be effectively used to analyze both the bacterial and fungal community. We evaluated the effect of five DNA extraction methods (QIAamp DNA Stool Mini Kit, PureLinkTM Microbiome DNA Purification Kit, ZR Fecal DNA MiniPrepTM Kit, NucleoSpin® DNA Stool Kit, and IHMS protocol Q) on bacterial and fungal gut microbiome recovery using (i) a defined system of germ-free mice feces spiked with bacterial or fungal strains, and (ii) non-spiked human feces. In our experimental setup, we confirmed that the examined methods significantly differed in efficiency and quality, which affected the identified stool microbiome composition. In addition, our results indicated that fungal DNA extraction might be prone to be affected by reagent/kit contamination, and thus an appropriate blank control should be included in mycobiome research. Overall, standardized IHMS protocol Q, recommended by the International Human Microbiome Consortium, performed the best when considering all the parameters analyzed, and thus could be applied not only in bacterial, but also in fungal microbiome research.},
}

@article {pmid31055584,
year = {2019},
author = {Lynch, SM and Mu, J and Grady, JJ and Stevens, RG and Devers, TJ},
title = {Fecal Microbiota Transplantation for Clostridium difficile Infection: A One-Center Experience.},
journal = {Digestive diseases (Basel, Switzerland)},
volume = {},
number = {},
pages = {1-6},
doi = {10.1159/000499873},
pmid = {31055584},
issn = {1421-9875},
abstract = {BACKGROUND: Clostridium difficile is a gram-positive, anaerobic, and spore-forming bacillus, which is responsible for the majority of antibiotic-associated diarrhea and colitis.

OBJECTIVE: Determine if fecal microbiota transplantation (FMT) is effective in a population sample from Connecticut.

METHODS: We report the clinical experience of 92 consecutive patients from one gastroenterology practice in central Connecticut treated by colonoscopy with FMT for infection with Clostridium difficile from 2012 to 2017. The analyses are based on clinical follow-up up to 3 months after the FMT procedure and on medical chart review.

RESULTS: Overall, complete recovery occurred in 86% of patients. As previously reported in a limited number of previous studies, community-acquired cases were more common than hospital-acquired cases, and community-acquired cases were more likely to be female.

CONCLUSIONS: Consistent with some previous reports, we found the following: the source of the donor for FMT did not make a difference in recovery: material from nonrelatives was as effective as from close relatives; and the presence of multiple comorbidities did not make a difference in recovery: patients with 2 or more comorbidities did as well as those with one or none.},
}

@article {pmid31049232,
year = {2019},
author = {Zhang, J and Ren, G and Li, M and Lu, P and Yi, S},
title = {The Effects of Fecal Donors with Different Feeding Patterns on Diarrhea in a Patient Undergoing Hematopoietic Stem Cell Transplantation.},
journal = {Case reports in hematology},
volume = {2019},
number = {},
pages = {4505238},
doi = {10.1155/2019/4505238},
pmid = {31049232},
issn = {2090-6560},
abstract = {Almost 90% of patients undergoing hematopoietic stem cell transplantation (HSCT) experience diarrheal episodes, which represent a severe, often life-threatening complication for these patients. Although fecal microbiota transplantation (FMT) represents an alternative treatment option for infection-related diarrhea, the application of FMT in HSCT patients is greatly restricted for safety reasons. Furthermore, the therapeutic outcomes of FMT as a diarrhea treatment are somewhat related to the choice of the FMT donor. Here, we comprehensively profiled the dynamic changes in the intestinal microbiota after FMT from two donors with different feeding patterns and the same severely diarrheal recipient undergoing HSCT via a 45-day clinical observation. Importantly, no adverse events attributed to FMT were observed. The stool volume and frequency of the patient were reduced when we used feces from donor #1 (mixed feeding), but these changes were not observed after FMT from donor #2 (exclusive breastfeeding). Interestingly, no obvious differences in overall diversity (Shannon) or richness (Chao1) between the two donors were observed. Additionally, Bifidobacterium accounted for 29.9% and 18.1% of OTUs in the stools of donors #1 and #2, respectively. Lactobacillus accounted for 16.3% and 2.9% of the stools of donors #1 and #2, respectively. Furthermore, through longitudinal monitoring of the patient, we identified 6 OTUs that were particularly sensitive to the different FMT complements. Together, we present a case report suggesting that the overall diversity of the intestinal microbiota may not be the only important element in the selection of an effective FMT donor.},
}

@article {pmid31046972,
year = {2019},
author = {Lavelle, A and Hill, C},
title = {Gut Microbiome in Health and Disease: Emerging Diagnostic Opportunities.},
journal = {Gastroenterology clinics of North America},
volume = {48},
number = {2},
pages = {221-235},
doi = {10.1016/j.gtc.2019.02.003},
pmid = {31046972},
issn = {1558-1942},
abstract = {The gut microbiome is fundamental to human health and development. Altered microbiomes have been associated with many diseases. However, variation between individuals, environmental effects, and a lack of standardization across studies makes differentiation between health and disease challenging. Large-scale population cohorts in different countries will be required to match disease subjects with healthy controls, whereas standardized, reproducible pipelines for analysis are required to compare findings between studies. Despite this, several conditions have already demonstrated great promise for developing microbiome-based biomarkers as well as providing a gateway into integrated personalized medicine.},
}

@article {pmid30249750,
year = {2018},
author = {Lee, KW and Kim, M and Lee, CH},
title = {Treatment of Dextran Sulfate Sodium-Induced Colitis with Mucosa-Associated Lymphoid Tissue Lymphoma Translocation 1 Inhibitor MI-2 Is Associated with Restoration of Gut Immune Function and the Microbiota.},
journal = {Infection and immunity},
volume = {86},
number = {12},
pages = {},
pmid = {30249750},
issn = {1098-5522},
mesh = {Acetanilides/*pharmacology ; Animals ; Cells, Cultured ; Colitis/chemically induced/*immunology/microbiology/*therapy ; Cytokines/immunology ; Dextran Sulfate ; Fecal Microbiota Transplantation ; Feces/microbiology ; Female ; Gastrointestinal Microbiome/*drug effects ; Humans ; Inflammation ; Intestines/drug effects/*immunology/microbiology ; Macrophages ; Mice ; Mice, Inbred C57BL ; Monocytes ; Mucosa-Associated Lymphoid Tissue Lymphoma Translocation 1 Protein/*antagonists & inhibitors/immunology ; Triazoles/*pharmacology ; },
abstract = {Disruption of the healthy intestinal microbiome and homeostasis of the intestinal immune system, which are closely interactive, are two key factors for ulcerative colitis. Here, we show that MI-2, a selective inhibitor of mucosa-associated lymphoid tissue lymphoma translocation-1 (MALT1), alleviated excessive inflammatory responses and was associated with restoration of healthy intestinal microbiome in mice suffering from dextran sulfate sodium (DSS)-induced colitis. We found that the diversity of intestinal microbiome of mice with DSS-induced colitis was significantly lower than that of healthy mice. However, MI-2 treatment in mice with DSS-induced colitis resulted in restored microbially diverse populations. To understand the possibility of the beneficial effect of the restored microbially diverse populations of MI-2-treated mice with DSS-induced colitis, we showed that inserting fecal microbiota from MI-2-treated mice with DSS-induced colitis and healthy control mice into mice with DSS-induced colitis could alleviate symptoms of colitis. The possibility of MI-2 treatment in DSS-induced colitis, associated with restoration of healthy microbially diverse populations in addition to reshaping host immune modulating capacity by reducing inflammatory cytokines (tumor necrosis factor alpha, interleukin-1β [IL-1β], IL-17α, and IL-22), may be considered therapeutic for ulcerative colitis.},
}

Acetanilides/*pharmacology
Animals
Cells, Cultured
Colitis/chemically induced/*immunology/microbiology/*therapy
Cytokines/immunology
Dextran Sulfate
Fecal Microbiota Transplantation
Feces/microbiology
Female
Gastrointestinal Microbiome/*drug effects
Humans
Inflammation
Intestines/drug effects/*immunology/microbiology
Macrophages
Mice
Mice, Inbred C57BL
Monocytes
Mucosa-Associated Lymphoid Tissue Lymphoma Translocation 1 Protein/*antagonists & inhibitors/immunology
Triazoles/*pharmacology

@article {pmid31037552,
year = {2019},
author = {Vujkovic-Cvijin, I and Somsouk, M},
title = {HIV and the Gut Microbiota: Composition, Consequences, and Avenues for Amelioration.},
journal = {Current HIV/AIDS reports},
volume = {},
number = {},
pages = {},
doi = {10.1007/s11904-019-00441-w},
pmid = {31037552},
issn = {1548-3576},
abstract = {PURPOSE OF REVIEW: We discuss recent advances in understanding of gut bacterial microbiota composition in HIV-infected subjects and comment on controversies. We discuss the putative effects of microbiota shifts on systemic inflammation and HIV disease progression and potential mechanisms, as well as ongoing strategies being developed to modulate the gut microbiota in humans for amelioration of infectious and inflammatory diseases.

RECENT FINDINGS: Lifestyle and behavioral factors relevant to HIV infection studies have independent effects on the microbiota. Microbial metabolism of immunomodulatory compounds and direct immune stimulation by translocation of microbes are putative mechanisms contributing to HIV disease. Fecal microbiota transplantation, microbial enzyme inhibition, phage therapy, and rationally selected probiotic cocktails have emerged as promising strategies for microbiota modulation. Numerous surveys of the HIV gut microbiota matched for lifestyle factors suggest consistent shifts in gut microbiota composition among HIV-infected subjects. Evidence exists for a complex pathogenic role of the gut microbiota in HIV disease progression, warranting further study.},
}

@article {pmid30525949,
year = {2019},
author = {Wing, AC and Kremenchutzky, M},
title = {Multiple sclerosis and faecal microbiome transplantation: are you going to eat that?.},
journal = {Beneficial microbes},
volume = {10},
number = {1},
pages = {27-32},
doi = {10.3920/BM2018.0029},
pmid = {30525949},
issn = {1876-2891},
mesh = {Dysbiosis/immunology/microbiology/*therapy ; *Fecal Microbiota Transplantation ; Gastrointestinal Microbiome/*immunology ; Host Microbial Interactions/immunology ; Humans ; Intestines/immunology/microbiology ; Multiple Sclerosis/immunology/microbiology/*therapy ; Probiotics/therapeutic use ; },
abstract = {Gut microbiome interaction goes beyond commensal function as vitamin production or support nutrients digestion. It also interplays with the host immune system and may be related to the development of immune-mediated diseases. Multiple sclerosis patients have dysbiosis compared to healthy individuals. But how this relates to disease development and severity is still uncertain. Dietary change including probiotic mixtures or ketogenic regimen has proven to change microbiome in multiple sclerosis (MS) subjects to one similar to healthy controls. However, proof of clinical benefits is lacking. We dissert on current knowledge about immune system and gut bacteria interactions. We discuss faecal microbial transplantation as a potential intervention to ameliorate gut dysbiosis in MS as well as the caveats of a clinical trial design.},
}

Dysbiosis/immunology/microbiology/*therapy
*Fecal Microbiota Transplantation
Gastrointestinal Microbiome/*immunology
Host Microbial Interactions/immunology
Humans
Intestines/immunology/microbiology
Multiple Sclerosis/immunology/microbiology/*therapy
Probiotics/therapeutic use

@article {pmid30510995,
year = {2019},
author = {Kiyohara, H and Sujino, T and Teratani, T and Miyamoto, K and Arai, MM and Nomura, E and Harada, Y and Aoki, R and Koda, Y and Mikami, Y and Mizuno, S and Naganuma, M and Hisamatsu, T and Kanai, T},
title = {Toll-Like Receptor 7 Agonist-Induced Dermatitis Causes Severe Dextran Sulfate Sodium Colitis by Altering the Gut Microbiome and Immune Cells.},
journal = {Cellular and molecular gastroenterology and hepatology},
volume = {7},
number = {1},
pages = {135-156},
pmid = {30510995},
issn = {2352-345X},
mesh = {Animals ; B-Lymphocytes/immunology ; Cell Movement ; Colitis/chemically induced/*immunology/*microbiology/pathology ; Dermatitis/*complications/immunology ; Dextran Sulfate ; Disease Progression ; Fecal Microbiota Transplantation ; Female ; *Gastrointestinal Microbiome ; Hematopoietic Stem Cells/metabolism ; Imiquimod/adverse effects ; Immunoglobulin D/metabolism ; Immunoglobulin M/metabolism ; Intestines/immunology/pathology ; Lactobacillus/physiology ; Lymph Nodes/pathology ; Lymphocyte Depletion ; Mice, Inbred C57BL ; Permeability ; Psoriasis/complications/immunology ; Toll-Like Receptor 7/*agonists ; },
abstract = {Background & Aims: Psoriasis and inflammatory bowel disease (IBD) are both chronic inflammatory diseases occurring in the skin and gut, respectively. It is well established that psoriasis and IBD have high concordance rates, and similar changes in immune cells and microbiome composition have been reported in both conditions. To study this connection, we used a combination murine model of psoriatic dermatitis and colitis in which mice were treated topically with the Toll-like receptor 7 agonist imiquimod (IMQ) and fed dextran sulfate sodium (DSS).

Methods: We applied IMQ topically to B6 mice (IMQ mice) and subsequently fed them 2% DSS in their drinking water. Disease activity and immune cell phenotypes were analyzed, and the microbial composition of fecal samples was investigated using 16S ribosomal RNA sequencing. We transplanted feces from IMQ mice to germ-free IQI/Jic (IQI) mice and fed them DSS to assess the effect of the gut microbiome on disease.

Results: We first confirmed that IMQ mice showed accelerated DSS colitis. IMQ mice had decreased numbers of IgD+ and IgM+ B cells and increased numbers of non-cytokine-producing macrophages in the gut. Moreover, the gut microbiomes of IMQ mice were perturbed, with significant reductions of Lactobacillus johnsonii and Lactobacillus reuteri populations. Germ-free mice transplanted with feces from IMQ mice, but not with feces from untreated mice, also developed exacerbated DSS colitis.

Conclusions: These results suggest that skin inflammation may contribute to pathogenic conditions in the gut via immunologic and microbiological changes. Our finding of a novel potential skin-gut interaction provides new insights into the coincidence of psoriasis and IBD.},
}

Animals
B-Lymphocytes/immunology
Cell Movement
Colitis/chemically induced/*immunology/*microbiology/pathology
Dermatitis/*complications/immunology
Dextran Sulfate
Disease Progression
Fecal Microbiota Transplantation
Female
*Gastrointestinal Microbiome
Hematopoietic Stem Cells/metabolism
Imiquimod/adverse effects
Immunoglobulin D/metabolism
Immunoglobulin M/metabolism
Intestines/immunology/pathology
Lactobacillus/physiology
Lymph Nodes/pathology
Lymphocyte Depletion
Mice, Inbred C57BL
Permeability
Psoriasis/complications/immunology
Toll-Like Receptor 7/*agonists

@article {pmid31019401,
year = {2019},
author = {Campbell, CT and Poisson, MO and Hand, EO},
title = {An Updated Review of Clostridium difficile Treatment in Pediatrics.},
journal = {The journal of pediatric pharmacology and therapeutics : JPPT : the official journal of PPAG},
volume = {24},
number = {2},
pages = {90-98},
doi = {10.5863/1551-6776-24.2.90},
pmid = {31019401},
issn = {1551-6776},
abstract = {Clostridium difficile infection (CDI) continues to have clinical and economic impact across all health care settings. Pediatrics accounts for a small percentage of worldwide infection; however, screening and diagnosis are confounded by asymptomatic colonization in young infants. Metronidazole and oral vancomycin have historically been the agents used to manage CDI in both pediatrics and adults. Newer agents and alternative therapies, such as fecal microbiota transplantation, may offer additional benefit. Recent guidelines updates from the Infectious Diseases Society of America and the Society for Healthcare Epidemiology of America separate pediatric and adult recommendations for epidemiology, diagnosis, and treatment. This review will discuss the risk factors, management, prevention, and updated guideline recommendations for CDI in the pediatric population.},
}

@article {pmid29556726,
year = {2018},
author = {Verstockt, B and Ferrante, M and Vermeire, S and Van Assche, G},
title = {New treatment options for inflammatory bowel diseases.},
journal = {Journal of gastroenterology},
volume = {53},
number = {5},
pages = {585-590},
pmid = {29556726},
issn = {1435-5922},
mesh = {Antibodies, Monoclonal, Humanized/therapeutic use ; Cell Adhesion Molecules/antagonists & inhibitors ; Fecal Microbiota Transplantation ; Gastrointestinal Agents/*therapeutic use ; Humans ; Inflammatory Bowel Diseases/*therapy ; Interleukin-12/antagonists & inhibitors ; Interleukin-23/antagonists & inhibitors ; Janus Kinase Inhibitors/therapeutic use ; Mesenchymal Stem Cell Transplantation ; Ustekinumab/*therapeutic use ; },
abstract = {The advent of anti-TNF agents has dramatically changed the treatment algorithms for IBD in the last 15 years, but primarily and more importantly secondary loss of response is often observed. Fortunately , new treatment options have been actively explored and some have already entered our clinical practice. In the class of anti-cytokine agents, the anti-IL12/IL23 monoclonal antibodies (mAbs) have entered clinical practice with the anti-p40 mAb ustekinumab in Crohn's disease (CD). Also, more selective anti-IL23 agents (anti-p19) have shown efficacy and are being further developed, in contrast to agents inhibiting IL-17 downstream which have failed in clinical trials despite their clear efficacy in psoriasis (Verstockt et al. in Expert Opin Biol Ther 17(1):31-47, 2017; Verstockt et al. in Expert Opin Drug Saf 16(7):809-821, 2017). Following up on the efficacy of the anti-adhesion molecule vedolizumab, etrolizumab (anti-beta-7 integrin) and PF-00547659, an anti-MadCam mAb, are being developed (Lobaton et al. in Aliment Pharmacol Ther 39(6):579-594, 2014). Oral anti-trafficking agents, such as ozanimod, targeting the S1P receptor responsible for the efflux of T-cells from the lymph nodes, have also shown efficacy in patients with ulcerative colitis (UC) (Sandborn et al. in N Engl J Med 374(18):1754-1762, 2016). Oral agents inhibiting cell signaling have been explored successfully in IBD. Tofacitinib, a non-selective oral Janus kinase (JAK) inhibitor, is effective in patients with UC and several other more or less selective Jak1, 2 and 3 inhibitors are being developed for the treatment of CD and UC (Sandborn et al. in N Engl J Med 376(18):1723-1736, 2017; Vermeire et al. in Lancet 389(10066):266-275, 2017; De Vries et al. in J Crohns Colitis 11(7):885-93, 2017). Finally, despite initial disappointing results with systemic administration of mesenchymal stem cells, Alofisel, adipose tissue derived, allogeneic mesenchymal stem cells, locally injected in perianal fistula tracts, induce long-lasting beneficial effects and the drug has been approved in Europe (Panes et al. in Gastroenterology, 2017). In summary, the quest for new treatment options in IBD is very active and justified by the high medical need and unresolved problems patients are facing.},
}

Antibodies, Monoclonal, Humanized/therapeutic use
Cell Adhesion Molecules/antagonists & inhibitors
Fecal Microbiota Transplantation
Gastrointestinal Agents/*therapeutic use
Humans
Inflammatory Bowel Diseases/*therapy
Interleukin-12/antagonists & inhibitors
Interleukin-23/antagonists & inhibitors
Janus Kinase Inhibitors/therapeutic use
Mesenchymal Stem Cell Transplantation
Ustekinumab/*therapeutic use

@article {pmid31017741,
year = {2019},
author = {Hsu, WH and Wang, JY and Kuo, CH},
title = {Current applications of fecal microbiota transplantation in intestinal disorders.},
journal = {The Kaohsiung journal of medical sciences},
volume = {},
number = {},
pages = {},
doi = {10.1002/kjm2.12069},
pmid = {31017741},
issn = {2410-8650},
support = {KMUH103-3M02//Kaohsiung Medical University Hospital, Taiwan/ ; MOHW107-TDU-B-212-113006//Ministry of Health and Welfare/ ; },
abstract = {Fecal microbiota transplantation (FMT) had been an ancient remedy for severe illness several centuries ago. Under modern medical analysis and evidence-based research, it has been proved as an alternative treatment for recurrent Clostridium difficile infection and recent randomized control study also showed that FMT could be an adjuvant treatment for inflammatory bowel disease. As we get a better understanding of the relationship between gut microbiota and systemic disease, FMT became a potential treatment to explore. This article summarized procedures such as donor selection, fecal material preparation, transplantation delivery methods, and adverse events. We also review the present evidence about FMT in clinical practice.},
}

@article {pmid31009795,
year = {2019},
author = {Nicholson, MR and Mitchell, PD and Alexander, E and Ballal, S and Bartlett, M and Becker, P and Davidovics, Z and Docktor, M and Dole, M and Felix, G and Gisser, J and Hourigan, SK and Jensen, MK and Kaplan, JL and Kelsen, J and Kennedy, M and Khanna, S and Knackstedt, E and Leier, M and Lewis, J and Lodarek, A and Michail, S and Oliva-Hemker, M and Patton, T and Queliza, K and Russell, GH and Singh, N and Solomon, A and Suskind, DL and Werlin, S and Kellermayer, R and Kahn, SA},
title = {Efficacy of Fecal Microbiota Transplantation for Clostridium difficile Infection in Children.},
journal = {Clinical gastroenterology and hepatology : the official clinical practice journal of the American Gastroenterological Association},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cgh.2019.04.037},
pmid = {31009795},
issn = {1542-7714},
abstract = {BACKGROUND & AIMS: Fecal microbiota transplantation (FMT) is commonly used to treat Clostridium difficile infection (CDI). CDI is an increasing cause of diarrheal illness in pediatric patients, but the effects of FMT have not been well studied in children. We performed a multi-center retrospective cohort study of pediatric and young adult patients to evaluate the efficacy, safety, and factors associated with a successful FMT for the treatment of CDI.

METHODS: We performed a retrospective study of 372 patients, 11 months to 23 years old, who underwent FMTs at 18 pediatric centers, from February 1, 2004 to February 28, 2017; 2-month outcome data were available from 335 patients. Successful FMT was defined as no recurrence of CDI in the 2 months following FMT. We performed stepwise logistic regression to identify factors associated with successful FMT.

RESULTS: Of 335 patients who underwent FMT and were followed for 2 months or more, 271 (81%) had a successful outcome following a single FMT and 86.6% had a successful outcome following a first or repeated FMT. Patients who received FMT with fresh donor stool (odds ratio [OR], 2.66; 95% CI, 1.39-5.08), underwent FMT via colonoscopy (OR, 2.41; 95% CI, 1.26-4.61), did not have a feeding tube (OR, 2.08; 95% CI, 1.05-4.11), or had 1 less episode of CDI before FMT (OR, 1.20; 95% CI, 1.04-1.39) had increased odds for successful FMT. Seventeen patients (4.7%) had a severe adverse event during the 3-month follow-up period, including 10 hospitalizations.

CONCLUSION: Based on the findings from a large multi-center retrospective cohort, FMT is effective and safe for the treatment of CDI in children and young adults. Further studies are required to optimize the timing and method of FMT for pediatric patients-factors associated with success differ from those of adult patients.},
}

@article {pmid31005136,
year = {2019},
author = {Misch, EA and Safdar, N},
title = {Clostridioides difficile Infection in the Stem Cell Transplant and Hematologic Malignancy Population.},
journal = {Infectious disease clinics of North America},
volume = {33},
number = {2},
pages = {447-466},
doi = {10.1016/j.idc.2019.02.010},
pmid = {31005136},
issn = {1557-9824},
abstract = {Clostridioides difficile infection (CDI) is common in the stem cell transplant (SCT) and hematologic malignancy (HM) population and mostly occurs in the early posttransplant period. Treatment of CDI in SCT/HM is the same as for the general population, with the exception that fecal microbiota transplant (FMT) has not been widely adopted because of safety concerns. Several case reports, small series, and retrospective studies have shown that FMT is effective and safe. A randomized controlled trial of FMT for prophylaxis of CDI in SCT patients is underway. In addition, an abundance of novel therapeutics for CDI is currently in development.},
}

@article {pmid31004524,
year = {2019},
author = {Xie, Y and Matsumoto, H and Kennedy, S and Newberry, EP and Moritz, W and DeBosch, BJ and Moley, KH and Rubin, DC and Warner, BW and Kau, AL and Tarr, PI and Wylie, TN and Wylie, KM and Davidson, NO},
title = {Impaired chylomicron assembly modifies hepatic metabolism through bile acid dependent and transmissible microbial adaptations.},
journal = {Hepatology (Baltimore, Md.)},
volume = {},
number = {},
pages = {},
doi = {10.1002/hep.30669},
pmid = {31004524},
issn = {1527-3350},
abstract = {The mechanisms by which alterations in intestinal bile acid (BA) metabolism improve systemic glucose tolerance and hepatic metabolic homeostasis are incompletely understood. Here we examined metabolic adaptations in mice with conditional intestinal deletion of the abetalipoproteinemia (ABL) gene microsomal triglyceride transfer protein (Mttp-IKO), which blocks chylomicron assembly and impairs intestinal lipid transport. Mttp-IKO mice exhibit improved hepatic glucose metabolism and augmented insulin signaling, without weight loss. These adaptations included decreased BA excretion, increased pool size, altered BA composition and increased Fgf15 production. Mttp-IKO mice absorb fructose normally, but are protected against dietary fructose-induced hepatic steatosis, without weight loss or changes in energy expenditure. In addition, Mttp-IKO mice exhibit altered cecal microbial communities, both at baseline and also following fructose feeding, including increased abundance of Bacteroides and Lactobacillus genera. Transplantation of cecal microbiota from chow-fed Mttp-IKO mice into antibiotic-treated wild-type recipients conferred transmissible protection against fructose-induced hepatic steatosis in association with a bloom in Akkermansia and increased Clostridium XIVa genera, whose abundance was positively correlated with fecal coprostanol and total neutral sterol excretion in recipient mice. However, antibiotic treated Mttp-IKO mice were still protected against fructose induced hepatic steatosis, suggesting that changes in microbiota are not required for this phenotype. Nevertheless, we found increased abundance of fecal Akkermansia from two adult ABL subjects with MTTP mutations, compared to their heterozygous parents and within the range noted in six healthy control subjects. Furthermore, Akkermansia abundance across all subjects was positively correlated with fecal coprostanol excretion. CONCLUSION: The findings collectively suggest multiple adaptive pathways of metabolic regulation following blocked chylomicron assembly, including shifts in BA signaling and altered microbial composition that confer a transmissible phenotype. This article is protected by copyright. All rights reserved.},
}

@article {pmid31004464,
year = {2019},
author = {Toral, M and Robles-Vera, I and de la Visitación, N and Romero, M and Sánchez, M and Gómez-Guzmán, M and Rodriguez-Nogales, A and Yang, T and Jiménez, R and Algieri, F and Gálvez, J and Raizada, MK and Duarte, J},
title = {Role of the immune system in vascular function and blood pressure control induced by fecal microbiota transplantation in rats.},
journal = {Acta physiologica (Oxford, England)},
volume = {},
number = {},
pages = {e13285},
doi = {10.1111/apha.13285},
pmid = {31004464},
issn = {1748-1716},
abstract = {AIM: High blood pressure (BP) is associated with gut microbiota dysbiosis. The aim of this study was to investigate whether changes in gut microbiota induced by exchanging the gut microbiota between spontaneously hypertensive rats (SHR) and normotensive Wistar-Kyoto (WKY) alter the gut-immune system interaction inducing changes in vascular function and BP.

METHODS: Twenty-week-old recipient WKY and SHR were orally gavaged with donor fecal contents from WKY or SHR. In additional experiments, we used a design to determine whether blockade of B7-dependent costimulation with CTLA4-Ig or blockade of IL-17 with IL-17-neutralizing antibody could prevent hypertension caused by fecal microbiota transplantation (FMT) from SHR to WKY.

RESULTS: Correlation analyses identified the bacterial abundance of Turicibacter and S24-7_g that, respectively, positively and negatively correlated with systolic BP. FMT from WKY rats to SHR rats reduced basal systolic BP, restored the imbalance between Th17/Treg in mesenteric lymph nodes (MLNs) and aorta, and improved endothelial dysfunction and vascular oxidative status found in SHR transplanted with SHR faeces. FMT from SHR to WKY increased CD80 and CD86 mRNA levels and T cells activation in MLNs, circulating T cells, aortic T cell infiltration, impaired endothelial function and increased basal SBP. These effects were abolished by blockade of B7-dependent costimulation with CTLA4-Ig. IL-17a neutralizing antibody reduced SBP and improved endothelial dysfunction induced by FMT from SHR to WKY.

CONCLUSION: Gut microbiota is an important factor involved in the control of BP, as a consequence of its effect in T-cell activation in gut immune system and vascular T-cells accumulation. This article is protected by copyright. All rights reserved.},
}

@article {pmid30999462,
year = {2019},
author = {Jones, EW and Carlson, JM},
title = {Steady-state reduction of generalized Lotka-Volterra systems in the microbiome.},
journal = {Physical review. E},
volume = {99},
number = {3-1},
pages = {032403},
doi = {10.1103/PhysRevE.99.032403},
pmid = {30999462},
issn = {2470-0053},
abstract = {The generalized Lotka-Volterra (gLV) equations, a classic model from theoretical ecology, describe the population dynamics of a set of interacting species. As the number of species in these systems grow in number, their dynamics become increasingly complex and intractable. We introduce steady-state reduction (SSR), a method that reduces a gLV system of many ecological species into two-dimensional subsystems that each obey gLV dynamics and whose basis vectors are steady states of the high-dimensional model. We apply this method to an experimentally-derived model of the gut microbiome in order to observe the transition between "healthy" and "diseased" microbial states. Specifically, we use SSR to investigate how fecal microbiota transplantation, a promising clinical treatment for dysbiosis, can revert a diseased microbial state to health.},
}

@article {pmid30997086,
year = {2019},
author = {Nishida, A and Imaeda, H and Inatomi, O and Bamba, S and Sugimoto, M and Andoh, A},
title = {The efficacy of fecal microbiota transplantation for patients with chronic pouchitis: A case series.},
journal = {Clinical case reports},
volume = {7},
number = {4},
pages = {782-788},
doi = {10.1002/ccr3.2096},
pmid = {30997086},
issn = {2050-0904},
abstract = {Pouchitis is one of the most common complications that develop after restorative proctocolectomy with ileal pouch-anal anastomosis for ulcerative colitis. Single fecal microbiota transplantation (FMT) by colonoscopy was performed safely on three patients with pouchitis. However, the efficacy of FMT on pouchitis was limited.},
}

@article {pmid30987771,
year = {2019},
author = {Abreu Y Abreu, AT and Velarde-Ruiz Velasco, JA and Zavala-Solares, MR and Remes-Troche, JM and Carmona-Sánchez, RI and Aldana-Ledesma, JM and Camacho-Ortiz, A and Contreras-Omaña, R and Díaz-Seoane, R and Elizondo-Vázquez, CT and Garza-González, E and Grajales-Figueroa, G and Gómez-Escudero, O and Jacobo-Karam, JS and Morales-Arámbula, M and Olivares-Guzmán, LO and Sifuentes-Osornio, J and Siu-Moguel, AG and Soto-Solís, R and Valdovinos-García, LR and Valdovinos-Díaz, MA and Vázquez-Elizondo, G and Lazo-de la Vega Jasso, SA},
title = {Consensus on the prevention, diagnosis, and treatment of Clostridium difficile infection.},
journal = {Revista de gastroenterologia de Mexico},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.rgmx.2018.12.001},
pmid = {30987771},
issn = {0375-0906},
abstract = {In recent decades, Clostridium difficile infection (CDI) has become a worldwide health problem. Mexico is no exception, and therefore the Asociación Mexicana de Gastroenterología brought together a multidisciplinary group (gastroenterologists, endoscopists, internists, infectious disease specialists, and microbiologists) to carry out the "Consensus on the prevention, diagnosis, and treatment of Clostridium difficile infection", establishing useful recommendations (in relation to the adult population) for the medical community. Said recommendations are presented herein. Among them, it was recognized that CDI should be suspected in subjects with diarrhea that have a history of antibiotic and/or immunosuppressant use, but that it can also be a community-acquired infection. A 2-step diagnostic algorithm was proposed, in which a highly sensitive test, such as glutamate dehydrogenase (GDH), is first utilized, and if positive, confirmed by the detection of toxins through immunoassay or nucleic acid detection tests. Another recommendation was that CDI based on clinical evaluation be categorized as mild-moderate, severe, and complicated severe, given that such a classification enables better therapeutic decisions to be made. In mild-moderate CDI, oral vancomycin is the medication of choice, and metronidazole is recommended as an alternative treatment. In addition, fecal microbiota transplantation was recognized as an efficacious option in patients with recurrence or in the more severe cases of infection, and surgery should be reserved for patients with severe colitis (toxic megacolon), in whom all medical treatment has failed.},
}

@article {pmid30986885,
year = {2019},
author = {Stallmach, A and Grunert, P and Pieper, D and Steube, A},
title = {[Ulcerative colitis: Does the modulation of gut microbiota induce long-lasting remission?].},
journal = {Zeitschrift fur Gastroenterologie},
volume = {},
number = {},
pages = {},
doi = {10.1055/a-0874-6603},
pmid = {30986885},
issn = {1439-7803},
abstract = {Although the pathogenesis of ulcerative colitis (UC) remains elusive, substantial progress in understanding its development and progression has been achieved in the past decades, and novel effective treatment strategies have been developed. Changes in gut microbiota, environmental triggers, deregulation of immunological responses, and genetic predisposition have been identified as pathogenic key factors. There are several lines of clinical observations, which support a close connection of altered gut microbiota with the development and course of UC. Despite a plethora of microbiota alterations in UC, it is currently unclear whether the observed changes in inflammation are cause or effect of the altered microbiota state.Fecal microbiota transplantation (FMT) provides a novel, perhaps complementary, strategy to restore gut microbial diversity, bacterial richness, and microbial homeostasis in UC. FMT is an already established treatment option for recurrent Clostridioides difficile infection, and several case series and randomized controlled trials have described its use in UC. In this review, we evaluate recent efficacy and safety data on FMT for UC, discuss possible pitfalls and show possible areas of future development. Although FMT could become a promising treatment modality for UC, based on currently available data, FMT should be only performed in clinical trials as controlled studies focusing on long-term outcomes and safety are warranted.},
}

@article {pmid30986562,
year = {2019},
author = {Saha, S and Tariq, R and Tosh, PK and Pardi, DS and Khanna, S},
title = {Fecal Microbiota Transplantation for Eradicating Carriage of Multidrug-Resistant Organisms: A Systematic Review.},
journal = {Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cmi.2019.04.006},
pmid = {30986562},
issn = {1469-0691},
abstract = {BACKGROUND: Multidrug resistant (MDR) microorganism development in the gut is frequently secondary to inappropriate antibiotic use. Fecal microbiota transplantation (FMT) restores normal gut microbiota in patients with C difficile infection; we hypothesized that it may help in decolonizing MDR organisms (MDROs) and in preventing recurrent MDR infections.

OBJECTIVES: To assess FMT efficacy (eradication rate) for decolonizing MDROs and preventing recurrent MDR infections.

DATA SOURCES: MEDLINE, EMBASE, and Web of Science (inception through February 11, 2019).

STUDY ELIGIBILITY CRITERIA: Clinical trials, retrospective studies, case reports, and case series.

PARTICIPANTS: Patients with MDR infections or MDRO colonization treated with FMT.

INTERVENTIONS: FMT.

METHODS: Systematic review.

RESULTS: Twenty-one studies (1 randomized clinical trial, 7 uncontrolled clinical trials, 2 retrospective cohort studies, 2 case series, 9 case reports) with 192 patients were included. Three studies assessed FMT efficacy in preventing MDR infections; 16 assessed its effect on MDRO colonization; 2 assessed both. Data from 151 patients were included in the final analyses. In studies with low to moderate risk of bias, the eradication rate was 37.5% to 87.5%. Efficacy was similar in studies looking at infection or colonization and did not differ by length of follow-up. No serious adverse events from FMT were reported. Seven patients died of other causes.

CONCLUSIONS: FMT could be used as a treatment for eradicating MDR colonization and, possibly, preventing recurrent MDR infections, once more supporting efficacy and safety data are available. Larger, well-designed randomized controlled trials are needed to further explore this therapy.},
}

@article {pmid30977692,
year = {2019},
author = {Belga, S and Chiang, D and Kabbani, D and Abraldes, JG and Cervera, C},
title = {The direct and indirect effects of vancomycin-resistant enterococci colonization in liver transplant candidates and recipients.},
journal = {Expert review of anti-infective therapy},
volume = {},
number = {},
pages = {},
doi = {10.1080/14787210.2019.1607297},
pmid = {30977692},
issn = {1744-8336},
abstract = {INTRODUCTION: Vancomycin-resistant enterococci (VRE) colonization and subsequent infection results in increased morbidity, mortality and use of healthcare resources. The burden of VRE colonization in liver transplant candidates and recipients is significant. VRE colonization is a marker of gut dysbiosis and its impact on the microbiota-liver axis, may negatively affect graft function and result in negative outcomes pre- and post-transplantation. Areas covered: In this article we describe the epidemiology of VRE colonization, risk factors for VRE infection, healthcare costs associated with VRE, with a focus on the impact of VRE colonization on liver transplant recipients' fecal microbiota, the therapeutic strategies for VRE decolonization and proposed pathophysiologic mechanisms of VRE colonization in liver transplant recipients. Expert opinion: VRE colonization results in a significant loss of bacterial microbiome diversity. This may have metabolic consequences, with low production of short-chain fatty acids which may, in turn, result in immunological dysregulation. As antibiotics have failed to decolonize the gut, alternative strategies such as fecal microbiota transplantation (FMT), stimulation of intestinal antimicrobial peptides and phage therapy warrant future studies.},
}

@article {pmid30972640,
year = {2019},
author = {Ding, X and Li, Q and Li, P and Zhang, T and Cui, B and Ji, G and Lu, X and Zhang, F},
title = {Long-Term Safety and Efficacy of Fecal Microbiota Transplant in Active Ulcerative Colitis.},
journal = {Drug safety},
volume = {},
number = {},
pages = {},
doi = {10.1007/s40264-019-00809-2},
pmid = {30972640},
issn = {1179-1942},
support = {81600417//National Natural Science Foundation of China/ ; 81670495//National Natural Science Foundation of China/ ; LGY2017080//Top-notch Talent Research Projects/ ; 201502026//Project of National Health and Family Planning Commission/ ; 2015BAI13B07//National Clinical Research Center for Digestive Diseases, Xi'an, China/ ; },
abstract = {INTRODUCTION AND OBJECTIVE: The therapeutic role of fecal microbiota transplantation in ulcerative colitis varies across different reports. This study aims to evaluate the long-term safety and efficacy of a strategy called step-up fecal microbiota transplantation for ulcerative colitis.

METHODS: Two clinical trials (NCT01790061, NCT02560727) for moderate-to-severe ulcerative colitis (Mayo score range 6-12) were performed from November 2012 to July 2017. Both studies were pooled for analysis on the safety and efficacy of fecal microbiota transplantation in patients with ulcerative colitis over a 1-year follow-up. The step-up fecal microbiota transplantation strategy included step 1: single fecal microbiota transplantation; step 2: two or more fecal microbiota transplantations; and step 3: fecal microbiota transplantations followed by immunosuppressants. Long-term clinical efficacy and adverse events were assessed, and multiple factors related to fecal microbiota transplantation were evaluated.

RESULTS: Of 134 eligible patients in this real-word study, 81.3% (109/134) were included for analysis. The follow-up ranged from 1 to 5 years. Fecal microbiota transplantation-related adverse events were observed in 17.4% (43/247) of fecal microbiota transplantation procedures including one serious adverse event (myasthenia gravis) and 56 non-serious adverse events. Multivariable logistic regression analysis showed that both the method of preparation of microbiota from stool using the automatic system and the delivery method of colonic transendoscopic enteral tubing were associated with a lower rate of fecal microbiota transplantation-related adverse events (p = 0.023, p = 0.017, respectively). In total, 74.3% (81/109) and 51.4% (56/109) of patients achieved clinical response at 1 month and 3 months after step-up fecal microbiota transplantation, respectively.

CONCLUSIONS: Fecal microbiota transplantation should be a safe and promising therapy for ulcerative colitis. The improved fecal microbiota preparation and colonic transendoscopic enteral tubing might reduce the rate of adverse events in ulcerative colitis.

TRIAL REGISTRATION: ClinicalTrials.gov NCT01790061, NCT02560727.},
}

@article {pmid30969490,
year = {2019},
author = {Galperine, TK and Guery, B},
title = {[Customised infectiology - Fecal microbiota transplantation : following the Clostridioides difficile pathway].},
journal = {Revue medicale suisse},
volume = {15},
number = {646},
pages = {776-779},
pmid = {30969490},
issn = {1660-9379},
abstract = {Fecal microbiota transplantation (FMT) raised, in the recent years, a growing interest, mostly in Clostridioides difficile infections (CDI). The concept of FMT is quite simple based on the administration of fecal matter from a healthy donor to a patient with a disease related to the gut microbiota imbalance (dysbiosis). Although the theory seems straightforward, the fine mechanisms are multiple and not yet completely understood. In Switzerland, FMT is considered as a drug under the pharmacist responsibility. The only official indication for FMT is multi-recurrent CDI. For practical reasons, most of the FMT are performed with fresh stools, but development of frozen forms and capsules should considerably enhance treatment delivery. Other indications are currently investigated but not yet in the clinical routine.},
}

@article {pmid30969003,
year = {2019},
author = {Alukal, J and Dutta, SK and Surapaneni, BK and Le, M and Tabbaa, O and Philips, L and Mattar, MC},
title = {Safety and Efficacy of Fecal Microbiota Transplant in 9 Critically Ill Patients with Severe and Complicated Clostridium Difficile Infection with Impending Colectomy: A Case Series.},
journal = {Journal of digestive diseases},
volume = {},
number = {},
pages = {},
doi = {10.1111/1751-2980.12750},
pmid = {30969003},
issn = {1751-2980},
abstract = {BACKGROUND AND AIMS: There is significant data that support the efficacy and safety of Fecal Microbiota Transplant (FMT) in Recurrent Clostridium Difficile Infection (RCDI). The objective of our study was to determine the success rate of FMT in patients diagnosed with severe and complicated CDI with impending colectomy in the ICU setting.

METHODS: This was a 2 center study, which consisted of 9 patients who met criteria of severe and complicated CDI and had impending colectomy. All 9 patients failed conventional antibiotic therapy and were deemed too unstable to undergo colectomy. Hence, FMT was considered as the next step in management.

RESULTS: Following FMT there was marked improvement in clinical status with resolution of diarrhea, reduced vasopressor requirement, reduction in abdominal distention and pain.The primary cure rate of our study after a single round of FMT was 78% (7/9). 8 out of the 9 patients (88.88%) avoided a colectomy during the same hospital admission. CDI related death was 12.5% (1/9) and non CDI death was 12.5% (1/9).

CONCLUSION: Our success with FMT in fulminant CDI shows that this therapeutic modality is a promising alternative and could be a potential bowel saving intervention. This article is protected by copyright. All rights reserved.},
}

@article {pmid30967971,
year = {2019},
author = {Mrazek, K and Bereswill, S and Heimesaat, MM},
title = {Fecal Microbiota Transplantation Decreases Intestinal Loads of Multi-Drug Resistant Pseudomonas aeruginosa in Murine Carriers.},
journal = {European journal of microbiology & immunology},
volume = {9},
number = {1},
pages = {14-22},
doi = {10.1556/1886.2019.00002},
pmid = {30967971},
issn = {2062-509X},
abstract = {Intestinal carriage of multi-drug resistant (MDR) Gram-negative bacteria including Pseudomonas aeruginosa (Psae) constitutes a pivotal prerequisite for subsequent fatal endogenous infections in patients at risk. We here addressed whether fecal microbiota transplantation (FMT) could effectively combat MDR-Psae carriage. Therefore, secondary abiotic mice were challenged with MDR-Psae by gavage. One week later, mice were subjected to peroral FMT from either murine or human donors on 3 consecutive days. Irrespective of murine or human origin of fecal transplant, intestinal MDR-Psae loads decreased as early as 24 h after the initial FMT. Remarkably, the murine FMT could lower intestinal MDR-Psae burdens by approximately 4 log orders of magnitude within 1 week. In another intervention study, mice harboring a human gut microbiota were perorally challenged with MDR-Psae and subjected to murine FMT on 3 consecutive days, 1 week later. Strikingly, within 5 days, murine FMT resulted in lower loads and carrier rates of MDR-Psae in mice with a human gut microbiota. In conclusion, FMT might be a promising antibiotics-independent option to combat intestinal MDR-Psae carriage and thus prevent from future endogenous infections of patients at risk.},
}

@article {pmid30967875,
year = {2019},
author = {Bereswill, S and Escher, U and Grunau, A and Kühl, AA and Dunay, IR and Tamas, A and Reglodi, D and Heimesaat, MM},
title = {Pituitary Adenylate Cyclase-Activating Polypeptide-A Neuropeptide as Novel Treatment Option for Subacute Ileitis in Mice Harboring a Human Gut Microbiota.},
journal = {Frontiers in immunology},
volume = {10},
number = {},
pages = {554},
doi = {10.3389/fimmu.2019.00554},
pmid = {30967875},
issn = {1664-3224},
abstract = {The neuropeptide Pituitary adenylate cyclase-activating polypeptide (PACAP) is well-known for its important functions in immunity and inflammation. Data regarding anti-inflammatory properties of PACAP in the intestinal tract are limited, however. In our present preclinical intervention study we addressed whether PACAP treatment could alleviate experimental subacute ileitis mimicking human gut microbiota conditions. Therefore, secondary abioitic mice were subjected to human fecal microbiota transplantation (FMT) and perorally infected with low-dose Toxoplasma gondii to induce subacute ileitis on day 0. From day 3 until day 8 post-infection, mice were either treated with synthetic PACAP38 or placebo. At day 9 post-infection, placebo, but not PACAP treated mice exhibited overt macroscopic sequelae of intestinal immunopathology. PACAP treatment further resulted in less distinct apoptotic responses in ileal and colonic epithelia that were accompanied by lower T cell numbers in the mucosa and lamina propria and less secretion of pro-inflammatory cytokines in intestinal ex vivo biopsies. Notably, ileitis-associated gut microbiota shifts were less distinct in PACAP as compared to placebo treated mice. Inflammation-ameliorating effects of PACAP were not restricted to the intestines, but could also be observed in extra-intestinal including systemic compartments as indicated by lower apoptotic cell counts and less pro-inflammatory cytokine secretion in liver and lungs taken from PACAP treated as compared to placebo control mice, which also held true for markedly lower serum TNF and IL-6 concentrations in the former as compared to the latter. Our preclinical intervention study provides strong evidence that synthetic PACAP alleviates subacute ileitis and extra-intestinal including systemic sequelae of T cell-driven immunopathology. These findings further support PACAP as a novel treatment option for intestinal inflammation including inflammatory bowel diseases (IBD).},
}

@article {pmid30967657,
year = {2019},
author = {Kang, DW and Adams, JB and Coleman, DM and Pollard, EL and Maldonado, J and McDonough-Means, S and Caporaso, JG and Krajmalnik-Brown, R},
title = {Long-term benefit of Microbiota Transfer Therapy on autism symptoms and gut microbiota.},
journal = {Scientific reports},
volume = {9},
number = {1},
pages = {5821},
doi = {10.1038/s41598-019-42183-0},
pmid = {30967657},
issn = {2045-2322},
abstract = {Many studies have reported abnormal gut microbiota in individuals with Autism Spectrum Disorders (ASD), suggesting a link between gut microbiome and autism-like behaviors. Modifying the gut microbiome is a potential route to improve gastrointestinal (GI) and behavioral symptoms in children with ASD, and fecal microbiota transplant could transform the dysbiotic gut microbiome toward a healthy one by delivering a large number of commensal microbes from a healthy donor. We previously performed an open-label trial of Microbiota Transfer Therapy (MTT) that combined antibiotics, a bowel cleanse, a stomach-acid suppressant, and fecal microbiota transplant, and observed significant improvements in GI symptoms, autism-related symptoms, and gut microbiota. Here, we report on a follow-up with the same 18 participants two years after treatment was completed. Notably, most improvements in GI symptoms were maintained, and autism-related symptoms improved even more after the end of treatment. Important changes in gut microbiota at the end of treatment remained at follow-up, including significant increases in bacterial diversity and relative abundances of Bifidobacteria and Prevotella. Our observations demonstrate the long-term safety and efficacy of MTT as a potential therapy to treat children with ASD who have GI problems, and warrant a double-blind, placebo-controlled trial in the future.},
}

@article {pmid30967260,
year = {2019},
author = {He, Y and Yu, H and Ge, Y and Li, X and Jiang, M and Liu, Y and Li, X and Wang, Y and Guo, M and Qin, X and Wang, X},
title = {Bacterial β-glucuronidase alleviates dextran sulfate sodium-induced colitis in mice: A possible crucial new diagnostic and therapeutic target for inflammatory bowel disease.},
journal = {Biochemical and biophysical research communications},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.bbrc.2019.03.196},
pmid = {30967260},
issn = {1090-2104},
abstract = {OBJECTIVE: Inflammatory bowel diseases (IBD) including ulcerative colitis and Crohn's disease are devastating diseases of the gut. At present, all the treatments are mainly targeting symptoms like inflammation. The disease remains regarded as incurable, largely due to lacking of knowledge on its etiology. Our previous studies suggested that impaired inactivation of digestive proteases by deconjugated bilirubin in experimental colitis, thus bacterial β-glucuronidase for catalyzing the reaction, may have played critical role in the pathogenesis of IBD.

METHODS: We first analyzed β-glucuronidase activity in gut tissue and feces of mice by a colitis model. Then the effect of β-glucuronidase on experimental colitis was investigated in detail by administration of β-glucuronidase (from E. coli) and fecal material transplantation to mice with 3% DSS in drinking water for 7 days.

RESULTS: Mice with colitis showed unchanged activity of β-glucuronidase in colon tissue but decreased activity in feces. Treatment with bacterial β-glucuronidase at 100 U or above alleviated DSS-induced colitis as demonstrated by the less body weight loss, less disease activity score, increased expression of tight junction proteins and decreased gut permeability, decreases in MPO, TNF-α, IL-1β, TLR-4 and MyD88, and increase in IL-10 and IκBα in gut, restored fecal β-glucuronidase and gut microbiota along with decreases in fecal digestive proteases. Transplantation of fecal material from control to colitis mice showed similar effects as treatment with β-glucuronidase.

CONCLUSIONS: Bacterial β-glucuronidase showed strong inhibition on colitis along with the reduction in fecal digestive proteases, which may be a crucial diagnostic and therapeutic target for IBD.},
}

@article {pmid30957161,
year = {2019},
author = {Tariq, R and Pardi, DS and Bartlett, MG and Khanna, S},
title = {Low Cure Rates in Controlled Trials of Fecal Microbiota Transplantation for Recurrent Clostridium difficile Infection: A Systematic Review and Meta-analysis.},
journal = {Clinical infectious diseases : an official publication of the Infectious Diseases Society of America},
volume = {68},
number = {8},
pages = {1351-1358},
doi = {10.1093/cid/ciy721},
pmid = {30957161},
issn = {1537-6591},
abstract = {BACKGROUND: Fecal microbiota transplantation (FMT) is highly effective for treating recurrent Clostridium difficile infection (CDI) in observational studies (>90%), but cure rates in clinical trials are lower. We performed a systematic review and meta-analysis to assess the efficacy of FMT for recurrent CDI in open-label studies and clinical trials .

METHODS: A systematic search from January 1978 to March 2017 was performed to include clinical trials of FMT for CDI. We analyzed CDI resolution by calculating weighted pooled rates (WPRs).

RESULTS: Thirteen trials were included, comprising 610 patients with CDI treated with single FMT. Overall, 439 patients had clinical cure (WPR, 76.1%; 95% confidence interval (CI), 66.4%-85.7%). There was significant heterogeneity among studies (I2 = 91.35%). Cure rates were lower in randomized trials (139/216 patients; WPR, 67.7%; 95% CI, 54.2%-81.3%) than in open-label studies (300/394 patients; WPR, 82.7%; 71.1%-94.3%) (P < .001). Subgroup analysis by FMT delivery modality showed lower cure rates with enema than colonoscopy (WPR, 66.3% vs 87.4%; P < .001) but no difference between colonoscopy and oral delivery (WPR, 87.4% vs 81.4%; P = .17). Lower rates were seen for studies including both recurrent and refractory CDI than for those including only recurrent CDI (WPR, 63.9% vs 79%; P < .001).

CONCLUSIONS: FMT was associated with lower cure rates in randomized trials than in open-label and in observational studies. Colonoscopy and oral route are more effective than enema for stool delivery. The efficacy also seems to be higher for recurrent than for refractory CDI.},
}

@article {pmid30946615,
year = {2019},
author = {Cold, F and Browne, PD and Günther, S and Halkjaer, SI and Petersen, AM and Al-Gibouri, Z and Hansen, LH and Christensen, AH},
title = {Multidonor FMT capsules improve symptoms and decrease fecal calprotectin in ulcerative colitis patients while treated - an open-label pilot study.},
journal = {Scandinavian journal of gastroenterology},
volume = {},
number = {},
pages = {1-8},
doi = {10.1080/00365521.2019.1585939},
pmid = {30946615},
issn = {1502-7708},
abstract = {BACKGROUND: Growing evidence indicates that gut dysbiosis is a factor in the pathogenesis of ulcerative colitis (UC). Fecal microbiota transplantation (FMT) appears to be promising in inducing UC remission, but there are no reports regarding administration using capsules.

METHODS: Seven patients with active UC, aged 27-50 years, were treated with 25 multidonor FMT capsules daily for 50 days as a supplement to their standard treatment in an open-label pilot study. The primary objective was to follow symptoms through the Simple Clinical Colitis Activity Index (SCCAI). Secondary objectives were to follow changes in fecal calprotectin and microbial diversity through fecal samples and quality of life through the Inflammatory Bowel Disease Questionnaire (IBDQ). Participants were followed through regular visits for six months.

RESULTS: From a median of 6 at baseline, the SCCAI of all participants decreased, with median decreases of 5 (p = .001) and 6 (p = .001) after 4 and 8 weeks, respectively. Three of the seven patients had flare-up/relapse of symptoms after the active treatment period. The median F-calprotectin of ≥1800 mg/kg at baseline decreased significantly during the treatment period, but increased again in the follow-up period. The median IBDQ improved at all visits compared to baseline. The fecal microbiota α-diversity did not increase in the study period compared to baseline. All participants completed the treatment and no serious adverse events were reported.

CONCLUSION: Fifty days of daily multidonor FMT capsules temporarily improved symptoms and health-related life quality and decreased F-calprotectin in patients with active UC.},
}

@article {pmid30945014,
year = {2019},
author = {Czepiel, J and Dróżdż, M and Pituch, H and Kuijper, EJ and Perucki, W and Mielimonka, A and Goldman, S and Wultańska, D and Garlicki, A and Biesiada, G},
title = {Clostridium difficile infection: review.},
journal = {European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s10096-019-03539-6},
pmid = {30945014},
issn = {1435-4373},
abstract = {Clostridium difficile (C. difficile) is a Gram-positive, spore-forming, anaerobic bacillus, which is widely distributed in the intestinal tract of humans and animals and in the environment. In the last decade, the frequency and severity of C. difficile infection has been increasing worldwide to become one of the most common hospital-acquired infections. Transmission of this pathogen occurs by the fecal-oral route and the most important risk factors include antibiotic therapy, old age, and hospital or nursing home stay. The clinical picture is diverse and ranges from asymptomatic carrier status, through various degrees of diarrhea, to the most severe, life threatening colitis resulting with death. Diagnosis is based on direct detection of C. difficile toxins in feces, most commonly with the use of EIA assay, but no single test is suitable as a stand-alone test confirming CDI. Antibiotics of choice are vancomycin, fidaxomicin, and metronidazole, though metronidazole is considered as inferior. The goal of this review is to update physicians on current scientific knowledge of C. difficile infection, focusing also on fecal microbiota transplantation which is a promising therapy.},
}

@article {pmid30940601,
year = {2019},
author = {Wardill, HR and Secombe, KR and Bryant, RV and Hazenberg, MD and Costello, SP},
title = {Adjunctive fecal microbiota transplantation in supportive oncology: Emerging indications and considerations in immunocompromised patients.},
journal = {EBioMedicine},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.ebiom.2019.03.070},
pmid = {30940601},
issn = {2352-3964},
abstract = {FMT has gained enormous momentum in the treatment of acute inflammatory and infectious diseases. Despite an encouraging safety profile, FMT has been met with caution in the oncological setting due to perceived infectious risks in immunocompromised patients. Theoretical risks aside, the application of FMT in oncology may stand to benefit patients, via modulation of treatment efficacy and the mitigation of treatment complications. Here, we summarize most recent safety data of FMT in immunocompromised cohorts, including people with cancer, highlighting that FMT may actually provide protection against bacterial translocation via introduction of a diverse microbiome and restoration of epithelial defenses. We also discuss the emerging translational applications of FMT within supportive oncology, including the prevention and treatment of graft vs. host disease and sepsis, treatment of immunotherapy-induced colitis and restoration of the gut microbiome in survivors of childhood cancer.},
}

@article {pmid30936486,
year = {2019},
author = {Ingle, H and Lee, S and Ai, T and Orvedahl, A and Rodgers, R and Zhao, G and Sullender, M and Peterson, ST and Locke, M and Liu, TC and Yokoyama, CC and Sharp, B and Schultz-Cherry, S and Miner, JJ and Baldridge, MT},
title = {Viral complementation of immunodeficiency confers protection against enteric pathogens via interferon-λ.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41564-019-0416-7},
pmid = {30936486},
issn = {2058-5276},
support = {R01 AI141478/AI/NIAID NIH HHS/United States ; R01 AI139314/AI/NIAID NIH HHS/United States ; R01 AI127552/AI/NIAID NIH HHS/United States ; K22 AI127846/AI/NIAID NIH HHS/United States ; R03 AI126101/AI/NIAID NIH HHS/United States ; T32 AI106688/AI/NIAID NIH HHS/United States ; T32 AI007163/AI/NIAID NIH HHS/United States ; P30 DK052574/DK/NIDDK NIH HHS/United States ; K08 AR070918/AR/NIAMS NIH HHS/United States ; },
abstract = {Commensal microbes profoundly impact host immunity to enteric viral infections1. We have shown that the bacterial microbiota and host antiviral cytokine interferon-λ (IFN-λ) determine the persistence of murine norovirus in the gut2,3. However, the effects of the virome in modulating enteric infections remain unexplored. Here, we report that murine astrovirus can complement primary immunodeficiency to protect against murine norovirus and rotavirus infections. Protection against infection was horizontally transferable between immunocompromised mouse strains by co-housing and fecal transplantation. Furthermore, protection against enteric pathogens corresponded with the presence of a specific strain of murine astrovirus in the gut, and this complementation of immunodeficiency required IFN-λ signalling in gut epithelial cells. Our study demonstrates that elements of the virome can protect against enteric pathogens in an immunodeficient host.},
}

@article {pmid30930793,
year = {2019},
author = {Toral, M and Robles-Vera, I and de la Visitación, N and Romero, M and Yang, T and Sánchez, M and Gómez-Guzmán, M and Jiménez, R and Raizada, MK and Duarte, J},
title = {Critical Role of the Interaction Gut Microbiota - Sympathetic Nervous System in the Regulation of Blood Pressure.},
journal = {Frontiers in physiology},
volume = {10},
number = {},
pages = {231},
doi = {10.3389/fphys.2019.00231},
pmid = {30930793},
issn = {1664-042X},
abstract = {Association between gut dysbiosis and neurogenic diseases, such as hypertension, has been described. The aim of this study was to investigate whether changes in the gut microbiota alter gut-brain interactions inducing changes in blood pressure (BP). Recipient normotensive Wistar-Kyoto (WKY) and spontaneously hypertensive rats (SHR) were orally gavaged with donor fecal contents from SHR and WKY. We divided the animals into four groups: WKY transplanted with WKY microbiota (W-W), SHR with SHR (S-S), WKY with SHR (W-S) and SHR with WKY (S-W). Basal systolic BP (SBP) and diastolic BP (DBP) were reduced with no change in heart rate as a result of fecal microbiota transplantation (FMT) from WKY rats to SHR. Similarly, FMT from SHR to WKY increased basal SBP and DBP. Increases in both NADPH oxidase-driven reactive oxygen species production and proinflammatory cytokines in brain paraventricular nucleus linked to higher BP drop with pentolinium and plasmatic noradrenaline (NA) levels were found in the S-S group as compared to the W-W group. These parameters were reduced by FMT from WKY to SHR. Increased levels of pro-inflammatory cytokines, tyrosine hydroxylase mRNA levels and NA content in the proximal colon, whereas reduced mRNA levels of gap junction proteins, were found in the S-S group as compared to the W-W group. These changes were inhibited by FMT from WKY to SHR. According to our correlation analyses, the abundance of Blautia and Odoribacter showed a negative correlation with high SBP. In conclusion, in SHR gut microbiota is an important factor involved in BP control, at least in part, as consequence of its effect on neuroinflammation and the sympathetic nervous system activity.},
}

@article {pmid30929665,
year = {2019},
author = {Caesar, R},
title = {Pharmacologic and Nonpharmacologic Therapies for the Gut Microbiota in Type 2 Diabetes.},
journal = {Canadian journal of diabetes},
volume = {43},
number = {3},
pages = {224-231},
doi = {10.1016/j.jcjd.2019.01.007},
pmid = {30929665},
issn = {2352-3840},
abstract = {The gut microbiota is an important regulator of host metabolism. Metagenome analyses have demonstrated that the gut microbiota differs between patients with type 2 diabetes and healthy subjects, and several studies have shown that impaired glucose metabolism is associated with decreased levels of butyrate-producing bacteria. Gut microbiota-produced metabolites, such as short-chain fatty acids, amino acid derivatives and secondary bile acids, participate in metabolic and immunologic processes and, hence, pose putative links between the gut microbiota and glucose homeostasis. Strategies to prevent and treat type 2 diabetes through manipulation of the gut microbiota are being developed. These include replacement of the gut microbiota by fecal transplantation, consumption of fibres to promote the function and growth of beneficial bacteria and treatment with probiotic bacterial strains. Furthermore, it has been shown that many drugs, including drugs used for treatment of diabetes, have major impacts on gut microbiota and, thereby, potentially on glucose metabolism. In particular, the commonly used drug metformin has been shown to influence the functional capacity of the gut microbiota, and recent evidence indicates that this may contribute to the antidiabetes effect of metformin.},
}

@article {pmid30924853,
year = {2019},
author = {Suzumura, EA and Bersch-Ferreira, ÂC and Torreglosa, CR and da Silva, JT and Coqueiro, AY and Kuntz, MGF and Chrispim, PP and Weber, B and Cavalcanti, AB},
title = {Effects of oral supplementation with probiotics or synbiotics in overweight and obese adults: a systematic review and meta-analyses of randomized trials.},
journal = {Nutrition reviews},
volume = {},
number = {},
pages = {},
doi = {10.1093/nutrit/nuz001},
pmid = {30924853},
issn = {1753-4887},
abstract = {CONTEXT: Recent evidence suggests that modulation of the gut microbiota may contribute to body weight control.

OBJECTIVE: This systematic review aimed to assess the effects of oral supplementation with probiotics or synbiotics on body weight, body mass index (BMI), and waist circumference in overweight and obese adults (BMI ≥ 25 kg/m2).

DATA SOURCES: Five electronic databases-PubMed, Embase, Cochrane Library/CENTRAL, LILACS, and Web of Science-were searched from inception to August 2017. No language restrictions were applied.

STUDY SELECTION: Randomized and quasi-randomized parallel trials that assessed the effects of oral supplementation with probiotics or synbiotics vs any other intervention but bariatric surgery or fecal transplantation in overweight or obese adults were selected.

DATA EXTRACTION: Three teams of 2 authors independently assessed risk of bias and extracted data from the included trials. Data were pooled using inverse-variance random-effects meta-analyses. The quality of evidence was assessed using the GRADE (Grading of Recommendations Assessment, Development and Evaluation) system.

RESULTS: Nineteen randomized trials (28 publications, 1412 participants) were included. There were no differences in mean body weight change [mean difference (MD), -0.54 kg; 95%CI, -1.09 to 0.01; I2 = 0%; moderate quality of evidence) or mean BMI change (MD, -0.19 kg/m2; 95%CI, -0.43 to 0.04; I2 = 51%; low quality of evidence) between groups who received probiotics or synbiotics and control groups. Oral supplementation with probiotics or synbiotics reduced mean waist circumference compared with control (MD, -0.82 cm; 95%CI, -1.43 to -0.21; I2 = 46%; low quality of evidence).

CONCLUSIONS: The findings suggest that oral supplementation with probiotics or synbiotics has a small effect to reduce waist circumference but no effect on body weight or BMI, although the quality of evidence is low to moderate. Therefore, the current evidence is not definitive. Large-scale trials are needed and may help to better inform clinical practice.

PROSPERO registration number CRD42018075126.},
}

@article {pmid30922964,
year = {2019},
author = {Liao, X and Song, L and Zeng, B and Liu, B and Qiu, Y and Qu, H and Zheng, Y and Long, M and Zhou, H and Wang, Y and Du, Y and Xu, J and Shen, R and Tong, Q and Cai, L and Li, X and Guo, S and Yang, G and Zhu, Z and Pu, X and Wei, H and Zheng, H},
title = {Alteration of gut microbiota induced by DPP-4i treatment improves glucose homeostasis.},
journal = {EBioMedicine},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.ebiom.2019.03.057},
pmid = {30922964},
issn = {2352-3964},
abstract = {BACKGROUND: Increasing evidence indicates that the gut microbiota contributes to the occurrence and development of metabolic diseases. However, little is known about the effects of commonly used antidiabetic agents on the gut microbiota. In this study, we investigated the roles of dipeptidyl peptidase-4 inhibitors (DPP-4i) and α-glucosidase inhibitor in modulating the gut microbiota.

METHODS: 16S-rDNA sequencing was performed to analyse the effects of DPP-4i and acarbose on the gut microbiota in mice fed a high-fat diet (HFD). Fecal microbiota transplantation (FMT) from type 2 diabetes patients to germ-free mice was performed to investigate the contribution of the altered microbiome to antidiabetic effects of the drugs. Fecal metabolomics was also analysed by untargeted and targeted GC-MS systems.

FINDINGS: Although DPP-4i and α-glucosidase inhibitor both altered the gut microbial composition, only the microbiome modulation of DPP-4i contributed to its hypoglycemic effect. Specifically, the changes of 68.6% genera induced by HFD were rescued by DPP-4i. FMT showed that the DPP-4i-altered microbiome improved glucose tolerance in colonized mice, while acarbose did not. Moreover, DPP-4i increased the abundance of Bacteroidetes, and also promoted a functional shift in the gut microbiome, especially increasing the production of succinate.

INTERPRETATION: Our findings demonstrate an important effect of DPP-4i on the gut microbiota, revealing a new hypoglycemic mechanism and an additional benefit of it. Furthermore, modulating the microbial composition, and the functional shift arising from changes in the microbiome, might be a potential strategy for improving glucose homeostasis. FUND: This work was supported by grants from the National Natural Science Foundation of China (No. 81700757, No. 81471039, No. 81700714 and No. 81770434), the National Key R&D Program of China (No. 2017YFC1309602, No. 2016YFC1101100, No. 2017YFD0500503 and No. 2017YFD0501001), and the Natural Science Foundation of Chongqing (No. cstc2014jcyjjq10006, No. cstc2016jcyjA0093 and No. cstc2016jcyjA0518).},
}

@article {pmid30920413,
year = {2019},
author = {Bajaj, JS and Hays, RA},
title = {Manipulation of the Gut-Liver Axis Using Microbiome Restoration Therapy in Primary Sclerosing Cholangitis.},
journal = {The American journal of gastroenterology},
volume = {},
number = {},
pages = {},
doi = {10.14309/ajg.0000000000000191},
pmid = {30920413},
issn = {1572-0241},
abstract = {Alteration of the normal gut-liver axis is important in primary sclerosing cholangitis (PSC). Lack of effective medical therapy for PSC makes microbiome restoration an alluring therapeutic target. Allegretti et al. performed an open-label safety trial of fecal microbiota transplant (FMT) in noncirrhotic PSC patients with inflammatory bowel disease in remission on minimal therapy. FMT was safe in this population, and after FMT, there was a stable, early increase in microbial diversity and donor engraftment with mixed effects on alkaline phosphatase but no significant change in fecal bile acid profile. Further trials are needed to find whether FMT has a role to play in PSC therapy.},
}

@article {pmid30919462,
year = {2019},
author = {Matsuo, K and Haku, A and Bi, B and Takahashi, H and Kamada, N and Yaguchi, T and Saijo, S and Yoneyama, M and Goto, Y},
title = {Fecal microbiota transplantation prevents Candida albicans from colonizing the gastrointestinal tract.},
journal = {Microbiology and immunology},
volume = {},
number = {},
pages = {},
doi = {10.1111/1348-0421.12680},
pmid = {30919462},
issn = {1348-0421},
abstract = {Gut microbes symbiotically colonize the gastrointestinal (GI) tract, interacting with each other and their host to maintain GI tract homeostasis. Recent reports have shown that gut microbes help protect the gut from colonization by pathogenic microbes. Here, we report that commensal microbes prevent colonization of the pathogenic fungus, Candida albicans, in the GI tract. Wild-type specific pathogen-free (SPF) mice are resistant to C. albicans colonization in the GI tract. However, administering certain antibiotics to SPF mice enables C. albicans colonization. Quantitative kinetics of commensal bacteria are inversely correlated with the number of C. albicans in the gut. Here, we provide further evidence that fecal microbiota transplantation effectively prevents Candida colonization in the GI tract. These data demonstrate the importance of commensal bacteria as a barrier of the GI tract surface, and highlight the potential clinical applications of commensal bacteria for preventing pathogenic fungal infections. This article is protected by copyright. All rights reserved.},
}

@article {pmid30919208,
year = {2019},
author = {Adler, E and Tabaa, A and Kassam, Z and Zydek, M and Terdiman, J and El-Nachef, N},
title = {Capsule-Delivered Fecal Microbiota Transplant Is Safe and Well Tolerated in Patients with Ulcerative Colitis.},
journal = {Digestive diseases and sciences},
volume = {},
number = {},
pages = {},
doi = {10.1007/s10620-019-05596-5},
pmid = {30919208},
issn = {1573-2568},
}

@article {pmid30909689,
year = {2019},
author = {Kim, KO and Gluck, M},
title = {Fecal Microbiota Transplantation: An Update on Clinical Practice.},
journal = {Clinical endoscopy},
volume = {52},
number = {2},
pages = {137-143},
doi = {10.5946/ce.2019.009},
pmid = {30909689},
issn = {2234-2400},
abstract = {Fecal microbiota transplantation (FMT) is an infusion in the colon, or the delivery through the upper gastrointestinal tract, of stool from a healthy donor to a recipient with a disease believed to be related to an unhealthy gut microbiome. FMT has been successfully used to treat recurrent Clostridium difficile infection (rCDI). The short-term success of FMT in rCDI has led to investigations of its application to other gastrointestinal disorders and extra-intestinal diseases with presumed gut dysbiosis. Despite the promising results of FMT in these conditions, several barriers remain, including determining the characteristics of a healthy microbiome, ensuring the safety of the recipient with respect to long-term outcomes, adequate monitoring of the recipient of fecal material, achieving high-quality control, and maintaining reasonable costs. For these reasons, establishing uniform protocols for stool preparation, finding the best modes of FMT administration, maintaining large databases of donors and recipients, and assuring that oral ingestion is equivalent to the more widely accepted colonoscopic infusion are issues that need to be addressed.},
}

@article {pmid30908299,
year = {2019},
author = {Xu, D and Chen, VL and Steiner, CA and Berinstein, JA and Eswaran, S and Waljee, AK and Higgins, PDR and Owyang, C},
title = {Efficacy of Fecal Microbiota Transplantation in Irritable Bowel Syndrome: A Systematic Review and Meta-Analysis.},
journal = {The American journal of gastroenterology},
volume = {},
number = {},
pages = {},
doi = {10.14309/ajg.0000000000000198},
pmid = {30908299},
issn = {1572-0241},
abstract = {OBJECTIVES: Irritable bowel syndrome (IBS) is a common gastrointestinal condition with a heterogeneous pathophysiology. An altered gut microbiome has been identified in some IBS patients, and fecal microbiota transplantation (FMT) has been suggested to treat IBS. We performed meta-analyses and systematic review of available randomized controlled trials (RCTs) to evaluate the efficacy of FMT in IBS.

METHODS: We performed a systematic literature search of MEDLINE, EMBASE, Cochrane Central Register of Controlled Trials, and Web of Science. Selection criteria included RCTs of FMT vs placebo using FMT excipients or autologous FMT in IBS. Meta-analyses were conducted to evaluate the summary relative risk (RR) and 95% confidence intervals (CIs) of combined studies for primary outcome of improvement in global IBS symptoms as measured by accepted integrative symptom questionnaires or dichotomous responses to questions of overall symptom improvement.

RESULTS: Among 742 citations identified, 7 were deemed to be potentially relevant, of which 4 studies involving 254 participants met eligibility. No significant difference in global improvement of IBS symptoms was observed at 12 weeks in FMT vs placebo (RR = 0.93; 95% CI 0.48-1.79). Heterogeneity among studies was significant (I = 79%). Subgroup analyses revealed benefits of single-dose FMT using colonoscopy and nasojejunal tubes in comparison with autologous FMT for placebo treatment (number needed to treat = 5, RR = 1.59; 95% CI 1.06-2.39; I = 0%) and a reduction in likelihood of improvement of multiple-dose capsule FMT RCTs (number needed to harm = 3, RR = 0.54; 95% CI 0.34-0.85; I = 13%). Placebo response was 33.7% in nonoral FMT RCTs and 67.8% in capsule FMT RCTs. The Grading of Recommendations Assessment, Development and Evaluation quality of the body of evidence was very low.

CONCLUSIONS: Current evidence from RCTs does not suggest a benefit of FMT for global IBS symptoms. There remain questions regarding the efficacy of FMT in IBS as well as the lack of a clean explanation on the discrepant results among RCTs in subgroup analyses.},
}

@article {pmid30906449,
year = {2019},
author = {Zhou, J and Zhou, Z and Ji, P and Ma, M and Guo, J and Jiang, S},
title = {Effect of fecal microbiota transplantation on experimental colitis in mice.},
journal = {Experimental and therapeutic medicine},
volume = {17},
number = {4},
pages = {2581-2586},
doi = {10.3892/etm.2019.7263},
pmid = {30906449},
issn = {1792-0981},
abstract = {The aim of the present study was to investigate the effect of fecal microbiota transplantation (FMT) on the acute inflammatory response in a murine model of dextran sulfate sodium (DSS)-induced colitis, and to delineate the putative underlying mechanism(s). Mice were divided into four groups, namely the normal control, DSS, 5-aminosalicylic acid (5-ASA) and FMT group. Mice in the DSS, 5-ASA and FMT groups were orally administered 3% DSS (w/v) solution for 7 days to induce colitis. On days 1, 3, 5 and 7, mice in the DSS, 5-ASA and FMT groups were respectively administered 0.5% carboxymethylcellulose sodium, 5-ASA suspension and fecal suspension by enema. The disease activity index of each mouse was calculated on a daily basis. All mice were sacrificed on day 8, and the length of their colons was measured. Myeloperoxidase (MPO) activity, and the levels of tumor necrosis factor α (TNF-α), interleukin (IL)-1β and IL-10 in the colon tissues of each group were also measured. Compared with that in the DSS group, FMT ameliorated the severity of inflammation due to ulcerative colitis in mice, which was accompanied by a significantly decreased MPO activity, reduced levels of TNF-α and IL-1β, and an increased level of IL-10 in colon tissue (all P<0.05). Taken together, these results demonstrated that FMT exerted a therapeutic effect on experimental colitis in mice, and the associated mechanism is likely to involve the remodeling of the intestinal flora and regulation of intestinal T-cell immunity homeostasis.},
}

@article {pmid30906424,
year = {2019},
author = {Levy, AN and Allegretti, JR},
title = {Insights into the role of fecal microbiota transplantation for the treatment of inflammatory bowel disease.},
journal = {Therapeutic advances in gastroenterology},
volume = {12},
number = {},
pages = {1756284819836893},
doi = {10.1177/1756284819836893},
pmid = {30906424},
issn = {1756-283X},
abstract = {Fecal microbiota transplantation (FMT) has changed the treatment landscape of Clostridium difficile infection (CDI). Emerging evidence has shown that FMT can also be an effective and safe treatment strategy in CDI with underlying inflammatory bowel disease (IBD). Recently, randomized controlled trials of FMT in ulcerative colitis support its expanding role in restoring gut homeostasis in this disease. However, heterogeneous study designs leave several questions yet to be answered, including how to best position this novel therapy in the treatment approach of Crohn's disease and pouchitis. Additional studies are needed to validate whether FMT can assume a complementary role in the standard treatment of IBD.},
}

@article {pmid30905818,
year = {2019},
author = {Wu, X and Zhang, T and Chen, X and Ji, G and Zhang, F},
title = {Microbiota transplantation: Targeting cancer treatment.},
journal = {Cancer letters},
volume = {452},
number = {},
pages = {144-151},
doi = {10.1016/j.canlet.2019.03.010},
pmid = {30905818},
issn = {1872-7980},
abstract = {Mounting evidence have demonstrated that gut microbiota plays a critical role in cancer patients' therapeutic responses to chemotherapy, radiotherapy and immunotherapy, including clinical efficacy and sensitivity to toxicity. These fascinating findings evoke a possibility of manipulating gut microbiota to optimize anti-cancer treatment from bench to beside. Microbiota transplantation (MT), including fecal microbiota transplantation (FMT) and selective microbiota transplantation (SMT), may improve the effect of anti-cancer treatment and/or reduce the related side effects. The safety and efficacy of MT in cancer treatment are the core of translational research in this promising field, which inspire us to focus on the MT technology and mechanism of MT targeting anti-cancer treatment. To perform clean FMT based on automatic methods by machine in exclusive laboratory has become true. Colonic transendoscopic enteral tubing as a novel delivering way for MT should bring convenience for frequent delivering in practice and feasible tool for confirming the therapeutic effect in research. The present review focuses on the recent findings on role of microbiota on chemotherapy, radiotherapy and immunotherapy, and the methodology, feasibility and challenges of MT in anti-cancer treatment.},
}

@article {pmid30899209,
year = {2019},
author = {Fischer, M},
title = {Recent Research on Fecal Microbiota Transplantation in Inflammatory Bowel Disease Patients.},
journal = {Gastroenterology & hepatology},
volume = {15},
number = {1},
pages = {44-47},
pmid = {30899209},
issn = {1554-7914},
}

@article {pmid30899006,
year = {2019},
author = {Wang, W and Lin, L and Du, Y and Song, Y and Peng, X and Chen, X and Yang, CJ},
title = {Assessing the viability of transplanted gut microbiota by sequential tagging with D-amino acid-based metabolic probes.},
journal = {Nature communications},
volume = {10},
number = {1},
pages = {1317},
doi = {10.1038/s41467-019-09267-x},
pmid = {30899006},
issn = {2041-1723},
mesh = {Amino Acids/*administration & dosage/chemistry ; Animals ; Anti-Bacterial Agents/pharmacology ; Fecal Microbiota Transplantation/*methods ; Feces/microbiology ; Fluorescent Dyes/chemistry ; Gastrointestinal Microbiome/*drug effects/genetics ; Gastrointestinal Tract/*microbiology ; Male ; Mice ; Mice, Inbred C57BL ; Microbial Viability/drug effects ; RNA, Ribosomal, 16S/*genetics ; Staining and Labeling/*methods ; Stereoisomerism ; },
abstract = {Currently, there are more than 200 fecal microbiota transplantation (FMT) clinical trials worldwide. However, our knowledge of this microbial therapy is still limited. Here we develop a strategy using sequential tagging with D-amino acid-based metabolic probes (STAMP) for assessing the viabilities of transplanted microbiotas. A fluorescent D-amino acid (FDAA) is first administered to donor mice to metabolically label the gut microbiotas in vivo. The labeled microbiotas are transplanted to recipient mice, which receive a second FDAA with a different color. The surviving transplants should incorporate both FDAAs and can be readily distinguished by presenting two colors simultaneously. Isolation of surviving bacteria and 16S rDNA sequencing identify several enriched genera, suggesting the importance of specific bacteria in FMT. In addition, using STAMP, we evaluate the effects on transplant survival of pre-treating recipients using different antibiotics. We propose STAMP as a versatile tool for deciphering the complex biology of FMT, and potentially improving its treatment efficacy.},
}

Amino Acids/*administration & dosage/chemistry
Animals
Anti-Bacterial Agents/pharmacology
Fecal Microbiota Transplantation/*methods
Feces/microbiology
Fluorescent Dyes/chemistry
Gastrointestinal Microbiome/*drug effects/genetics
Gastrointestinal Tract/*microbiology
Male
Mice
Mice, Inbred C57BL
Microbial Viability/drug effects
RNA, Ribosomal, 16S/*genetics
Staining and Labeling/*methods
Stereoisomerism

@article {pmid30893082,
year = {2019},
author = {Alsahhar, JS and Rahimi, RS},
title = {Updates on the pathophysiology and therapeutic targets for hepatic encephalopathy.},
journal = {Current opinion in gastroenterology},
volume = {35},
number = {3},
pages = {145-154},
doi = {10.1097/MOG.0000000000000527},
pmid = {30893082},
issn = {1531-7056},
abstract = {PURPOSE OF REVIEW: Hepatic encephalopathy is one of the most debilitating clinical manifestations of cirrhosis and associated with increased morbidity and mortality. Treatment modalities available include the nonabsorbable disaccharides (lactulose) and the nonabsorbable antibiotics (rifaximin).

RECENT FINDINGS: Newer therapeutic targets under evaluation include ammonia scavengers (ornithine phenylacetate) and modulation of gut microbiota (fecal microbiota transplantation).

SUMMARY: This review will focus on the pathophysiology of hepatic encephalopathy along with an update on therapeutic targets under investigation.},
}

@article {pmid30890952,
year = {2019},
author = {Wan, JJ and Lin, CH and Ren, ED and Su, Y and Zhu, WY},
title = {Effects of Early Intervention With Maternal Fecal Bacteria and Antibiotics on Liver Metabolome and Transcription in Neonatal Pigs.},
journal = {Frontiers in physiology},
volume = {10},
number = {},
pages = {171},
doi = {10.3389/fphys.2019.00171},
pmid = {30890952},
issn = {1664-042X},
abstract = {The establishment of a stable bacterial flora in early life is associated with host metabolism. Studies of fecal microbiota transplantation (FMT) and antibiotics on neonatal pig mainly focused on intestinal development and mucosal immunity, but the information on metabolism is lacking. The objective of this study was to investigate the responses of metabolome and transcriptome in the livers of neonatal piglets that were orally inoculated with maternal fecal bacteria suspension and amoxicillin (AM) solution. Five litters of Duroc × Landrace × Yorkshire neonatal piglets were used as five replicates and nine piglets in each litter were randomly assigned to the control (CO), AM or FMT groups. Neonatal piglets in three groups were fed with 3 mL saline (0.9%), AM solution (6.94 mg/mL) or fecal bacteria suspension (>109/mL), respectively, on days 1-6. At the age of 7 and 21 days, one piglet from each group in each litter was sacrificed, and the serum and liver were collected for analysis. The RNA sequencing analysis showed that the mRNA expressions of arachidonate 12-lipoxygenase (ALOX12), acetyl-CoA acyltransferase 2 (ACAA2), cytochrome P450 family 1 subfamily A member 2 (CYP1A2), glutamic-pyruvic transaminase 2 (GPT2) and argininosuccinate synthase 1 (ASS1) were downregulated (P < 0.05) by AM on day 7, and that the mRNA expressions of arachidonate 15-lipoxygenase (ALOX15), CYP1A2 and GPT2 were downregulated (P < 0.05) by FMT on day 7. GC-MS analysis showed that AM and FMT treatments mainly affected fatty acid metabolism and amino acid metabolism on days 7 and 21. AM and FMT both reduced (P < 0.05) the blood levels of triglycerides and low density lipoprotein cholesterol (LDL-C) on day 7. AM reduced (P < 0.05) the blood level of cholesterol on day 21, and FMT reduced the blood levels of cholesterol, triglycerides and LDL-C on day 21. These results indicate that early intervention with FMT or AM can reduce fatty acid oxidative catabolism and amino acid biosynthesis of neonatal piglets, which provides a reference for regulation host metabolism through early intervention in animal production and even human health.},
}

@article {pmid30889205,
year = {2019},
author = {Ohara, T},
title = {Identification of the microbial diversity after fecal microbiota transplantation therapy for chronic intractable constipation using 16s rRNA amplicon sequencing.},
journal = {PloS one},
volume = {14},
number = {3},
pages = {e0214085},
doi = {10.1371/journal.pone.0214085},
pmid = {30889205},
issn = {1932-6203},
abstract = {BACKGROUND: Fecal microbiota transplantation (FMT) is an effective therapeutic approach for the treatment of functional gastrointestinal disease by restoring gut microbiota; however, there is a lack of sufficient understanding regarding which microbial populations successfully colonize the recipient gut. This study characterized microbial composition and diversity in patients diagnosed with chronic constipation at 1 month and 1 year after FMT.

METHODS: We explored the microbial diversity of pre- and posttransplant stool specimens from patients using 16S rRNA gene sequencing, followed by functional analysis.

RESULTS: The results identified 22 species of microorganisms colonized in the recipients from the donors at 1 month after FMT. One-year follow-up of the patient identified the colonization of 18 species of microorganisms, resulting in identification of species in significant abundance, including Bacteroides fragilis and Hungatella hathewayi in the recipient at 1 month after FMT and Dialister succinatiphilus, Coprococcus catus, and Sutterella stercoricanis at 1 year after FMT. The majority of the colonized species belong to the phylum Firmicutes and carry genes related to polysaccharide metabolism and that enhance the energy-harvesting efficiency of the host.

CONCLUSION: These results suggest that FMT is effective for the treatment of chronic constipation through the restoration and colonization of donor microbiota in the recipient gut up to 1 year after FMT.},
}

@article {pmid30886607,
year = {2019},
author = {Liu, Z and Wang, N and Ma, Y and Wen, D},
title = {Hydroxytyrosol Improves Obesity and Insulin Resistance by Modulating Gut Microbiota in High-Fat Diet-Induced Obese Mice.},
journal = {Frontiers in microbiology},
volume = {10},
number = {},
pages = {390},
doi = {10.3389/fmicb.2019.00390},
pmid = {30886607},
issn = {1664-302X},
abstract = {Obesity is a common chronic metabolic disease that is harmful to human health and predisposes the affected individuals to a cluster of pathologies. Insulin resistance (IR) is one of the most frequent complications of obesity. Hydroxytyrosol (HT) may reduce obesity and IR in high-fat diet (HFD)-fed mice; however, the mechanism underlying is still unknown. Systemic low-grade inflammation and intestinal dysfunction are thought to be associated with obesity and IR. In this study, we found that HFD feeding for 8 weeks altered the intestinal microbiota, injured intestinal barrier function, increased endotoxin release into the blood, enhanced the expression of inflammatory factors (TNF-α, IL-1β, IL-6) and lipid accumulation in liver, caused obesity, and aggravated IR via the JNK/IRS (Ser 307) pathway in HFD mice. We also found that HT gavage could reverse those effects and the beneficial effects of HT were transferable through fecal microbiota transplantation. Our data indicate that HT can improve obesity and IR by altering the composition of the intestinal microbiota and improving integrity of the intestinal wall. We propose that HT replenishment may be used as a dietary intervention strategy to prevent obesity and IR.},
}

@article {pmid30882536,
year = {2019},
author = {Allegretti, JR and Kassam, Z and Fischer, M and Kelly, C and Chan, WW},
title = {Risk Factors for Gastrointestinal Symptoms Following Successful Eradication of Clostridium difficile by Fecal Microbiota Transplantation (FMT).},
journal = {Journal of clinical gastroenterology},
volume = {},
number = {},
pages = {},
doi = {10.1097/MCG.0000000000001194},
pmid = {30882536},
issn = {1539-2031},
abstract = {BACKGROUND: Fecal microbiota transplantation (FMT) is a promising therapy for recurrent Clostridioides difficile infection (CDI). Many patients report altered bowel habits including constipation, bloating, gas and loose stool post-FMT despite resolution of CDI, and the etiology remains unclear.

METHODS: This was a prospective cohort study of adult patients with recurrent CDI who underwent FMT (1) via colonoscopy with patient-selected donor stool, (2) via colonoscopy from a universal stool bank donor, or (3) via capsules from a universal stool bank. Reassessment occurred 8 weeks post-FMT. Those cured were assessed for gastrointestinal symptoms (bloating, loose stools, constipation). Multivariate logistic regression was performed to assess predictors of post-FMT gastrointestinal symptoms.

RESULTS: A total of 150 subjects underwent FMT for recurrent CDI, of which 68.7% (103) were female, mean age was 61.5 years±18.1 and 31 patients (20.7%) had preexisting irritable bowel syndrome. Thirty-six had FMT via colonoscopy with a patient-selected donor, 67 via colonoscopy with stool bank donors, and 47 via FMT capsules from stool bank donors. Among those cured, 41 (31.2%) had gastrointestinal symptoms post-FMT. The factors associated with symptoms included younger age (57.2 vs. 64.1 y, P=0.03), a baseline history of irritable bowel syndrome (36.6% vs. 13.3%, P=0.002) and preexisting inflammatory bowel disease (31.7% vs. 10%, P=0.002). Small bowel exposure to donor stool was not related to symptoms (63.4% vs. 62.2%, P=0.89).

CONCLUSIONS: Altered bowel habits are a consequence of CDI and are common after FMT. This study suggests that donor type and FMT delivery modality are not related to the presence of irregular gastrointestinal symptoms after FMT.},
}

@article {pmid30877020,
year = {2019},
author = {Uchiyama, K and Naito, Y and Takagi, T},
title = {Intestinal microbiome as a novel therapeutic target for local and systemic inflammation.},
journal = {Pharmacology & therapeutics},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.pharmthera.2019.03.006},
pmid = {30877020},
issn = {1879-016X},
abstract = {Recently, the pathogenesis of systemic inflammatory disease such as inflammatory bowel disease (IBD), multiple sclerosis (MS), systemic inflammatory arthritis, asthma, and non-alcoholic fatty liver disease has been reported to be related to the dysbiosis of gut microbiota. The contribution of special bacteria for the development of those diseases has been elucidated by disease animal models such as germ-free mice. Besides, the contribution by several bacteria for the pathogenesis of those diseases has been suggested by detailed analysis of the 16 small ribosomal subunit RNA (16S rRNA) from stool samples of the patients. Gut microbiota-targeted treatment for systemic inflammatory diseases such as fecal microbiota transplant (FMT), and probiotics has been now reported. Though there are several issues to be understood, these treatments have been highlighted as an innovative approach to intractable systemic inflammatory disease. In the present review, recent reports regarding the relation between gut microbiota and systemic inflammatory diseases are discussed with treatments to target gut microbiota.},
}

@article {pmid30876614,
year = {2019},
author = {Ramesh, MS and Yee, J},
title = {Clostridioides difficile Infection in Chronic Kidney Disease/End-Stage Renal Disease.},
journal = {Advances in chronic kidney disease},
volume = {26},
number = {1},
pages = {30-34},
doi = {10.1053/j.ackd.2019.01.001},
pmid = {30876614},
issn = {1548-5609},
abstract = {Clostridioides difficile infection (CDI) is a major health-care burden and increasingly seen in patients with chronic kidney disease (CKD) and end-stage renal disease (ESRD). Increased antibiotic use, alteration in host defenses, and gastric acid suppression are some of the etiologies for increased risk of CDI in these populations. Patients with CKD/ESRD have a higher risk of initial episode, recurrence, and development of severe CDI than those without CKD or ESRD. Diagnosis and management of CDI in patients with CKD/ESRD are similar to that in the general population. The mortality, length of stay, and health-care costs are higher in patients with CDI and CKD/ESRD. Antimicrobial stewardship with reduction in antibiotic use along with infection-control measures such as contact isolation and hand hygiene with soap and water is essential in the control and prevention of CDI in patients with CKD/ESRD.},
}

@article {pmid30873549,
year = {2019},
author = {Sood, A and Mahajan, R and Singh, A and Midha, V and Mehta, V and Narang, V and Singh, T and Pannu, AS},
title = {Role of Fecal Microbiota Transplantation for Maintenance of Remission in Patients with Ulcerative Colitis: A Pilot Study.},
journal = {Journal of Crohn's & colitis},
volume = {},
number = {},
pages = {},
doi = {10.1093/ecco-jcc/jjz060},
pmid = {30873549},
issn = {1876-4479},
abstract = {OBJECTIVES: To study the role of fecal microbiota transplantation (FMT) in maintenance of remission in ulcerative colitis (UC).

METHODS: In this pilot study, patients with UC in clinical remission after multi-session FMT were randomly allocated to either maintenance FMT or placebo colonoscopic infusion every 8 weeks, for 48 weeks. The standard of care (SOC) therapy was continued in all patients. The primary end point was maintenance of steroid-free clinical remission (Mayo score ≤2, all sub scores ≤ 1) at week 48. Secondary end points were achievement of endoscopic remission (endoscopic Mayo score 0) and histological remission (Nancy grade 0, 1) at week 48.

RESULTS: Sixty one patients in clinical remission were randomized to receive either FMT n=31) or placebo (n=30). The primary outcome was achieved in 27/31 (87.1%) patients allocated FMT versus 20/30 (66.7%) patients assigned placebo (p=0.111). Secondary end points of endoscopic remission [FMT: 18/31 (58.1%) versus placebo: 8/30 (26.7%), p=0.026] and histological remission [FMT: 14/31 (45.2%) versus placebo: 5/30 (16.7%), p=0. 033] were achieved in significantly higher number of patients with FMT. Three patients receiving FMT (9.7%) and 8 patients on placebo (26.7%) relapsed. There were no serious adverse events necessitating discontinuation in patients on FMT, 1 patient who relapsed on placebo required colectomy.

CONCLUSIONS: Maintenance FMT in patients who are in clinical remission may help sustain clinical, endoscopic and histological remission in patients with UC. Keywords: Inflammatory Bowel Disease; Clinical remission; Endoscopic remission; Histological remission.},
}

@article {pmid30867532,
year = {2019},
author = {Xu, X and Fukui, H and Ran, Y and Tomita, T and Oshima, T and Watari, J and Miwa, H},
title = {Alteration of GLP-1/GPR43 expression and gastrointestinal motility in dysbiotic mice treated with vancomycin.},
journal = {Scientific reports},
volume = {9},
number = {1},
pages = {4381},
doi = {10.1038/s41598-019-40978-9},
pmid = {30867532},
issn = {2045-2322},
support = {17K09363//Ministry of Education, Culture, Sports, Science and Technology (MEXT)/ ; },
abstract = {Gut microbiota plays a pivotal role in various aspects of host physiology, including metabolism, gastrointestinal (GI) motility and hormonal secretion. In the present study, we investigated the effect of antibiotic-associated dysbiosis on metabolism and GI motility in relation to colonic expression of glucagon-like peptide-1 (GLP-1) and G protein coupled receptor (GPR)43. Specific pathogen-free (SPF) mice (ICR, 6 weeks old, female) were orally administered vancomycin (0.2 mg/ml) in drinking water for 7 days. In another experiment, germ-free (GF) mice (ICR, 6 weeks old, female) were subjected to oral fecal transplantation (FT) using a fecal bacterial suspension prepared from SPF mice that had received vancomycin treatment (FT-V) or one from untreated control SPF mice (FT-C). The gastrointestinal transit time (GITT) was measured by administration of carmine red (6% w/v) solution. The expression of GLP-1 and GPR43 was examined by immunohistochemistry and realtime RT-PCR, and the plasma GLP-1 level was measured by ELISA. In vancomycin-treated SPF mice, the diversity of the gut microbiota was significantly reduced and the abundance of Lactobacillus was markedly increased. Significant increases in body weight, cecum weight, plasma GLP-1 level and colonic GLP-1/GPR43 expression were also noted relative to the controls. These alterations were reproducible in GF mice with FT-V. Moreover, FT-V GF mice showed a significantly increased food intake and a significantly prolonged GITT in comparison with FT-C GF mice. Vancomycin-induced dysbiosis promotes body weight gain and prolongs GITT, accompanied by an increase of colonic GLP-1/GPR43 expression.},
}

@article {pmid30861553,
year = {2019},
author = {Roggenbrod, S and Schuler, C and Haller, B and Sohn, M and Storr, M and Schepp, W and Gundling, F},
title = {[Patient perception and approval of fecal microbiota transplantation (FMT) as an alternative treatment option for ulcerative colitis].},
journal = {Zeitschrift fur Gastroenterologie},
volume = {57},
number = {3},
pages = {296-303},
doi = {10.1055/a-0821-7166},
pmid = {30861553},
issn = {1439-7803},
abstract = {INTRODUCTION: Fecal microbiota transplantation (FMT) represents a treatment option for recurring Clostridium difficile-associated colitis. However, there is also evidence that FMT can be effective in treating ulcerative colitis. This study examined the approval and willingness of affected patients who underwent FMT.

METHODS: A standardized questionnaire containing 27 polar and open questions was dispatched to a cohort of 262 patients suffering from UC. It included questions regarding the FMT process, donors, and possible concerns. Additionally, aspects of social background and disease activity were addressed.

RESULTS: The response rate was 31.3 % (n = 82). Forty-eight (58.5 %) patients were already aware of FMT. Forty-six (56.1 %) were willing to undergo FMT if given a respective indication. The effectiveness of the procedure (40.2 %), followed by failure of all other therapies (17.1 %), formed the principal motivation. The transmission of possible infectious agents (26.8 %), and the potential contamination of the stool graft leading to a deterioration of clinical symptoms, raised the most concerns. (20.7 %).The preferred delivery system of FMT was capsules (67.1 %), followed by colonoscopic application (47.6 %). The patients were in favour of a donor proposed by the physician (52,4 %). Willingness to undergo FMT did not differ significantly between genders (56.4 % women vs. 57.1 % men). Smokers (88.9 %), patients who did not watch television at all (77.8 %) and those with private health insurance, showed an increased willingness to undergo FMT.

CONCLUSION: For the majority of the UC patients surveyed, FMT represents a feasible treatment option. Approximately half of the respondents would consider FMT as an alternative treatment option, even inspite of a satisfactory disease response to current standard therapies. Unsurprisingly, there are concerns regarding the transmission of possible infectious agents and the hygienic implementation of FMT itself.},
}

@article {pmid30861317,
year = {2019},
author = {Joseph, J and Saha, S and Greenberg-Worisek, AJ},
title = {Fecal Microbiota Transplantation: An Ambiguous Translational Pathway for a Promising Treatment.},
journal = {Clinical and translational science},
volume = {},
number = {},
pages = {},
doi = {10.1111/cts.12621},
pmid = {30861317},
issn = {1752-8062},
}

@article {pmid30859364,
year = {2019},
author = {Wang, J and Wang, P and Li, D and Hu, X and Chen, F},
title = {Beneficial effects of ginger on prevention of obesity through modulation of gut microbiota in mice.},
journal = {European journal of nutrition},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00394-019-01938-1},
pmid = {30859364},
issn = {1436-6215},
support = {D16110500540001//Beijing Municipal Science and Technology Project/ ; },
abstract = {PURPOSE: Recent evidence has demonstrated that the gut microbiota plays a critical role in the treatment of obesity and other metabolic dysfunctions. Ginger (Zingiber officinale Roscoe), one of the most commonly used spices and dietary supplements, has been shown to exert beneficial effects against obesity and related disorders. However, to date, the mechanisms linking these effects to the gut microbiota remain unclear. This study aims to investigate the relationship between the gut microbiota and the metabolic adaptations resulting from ginger supplementation in mice.

METHODS: Four groups of mice were fed a normal chow diet (NCD) or a high-fat diet (HFD) with or without ginger supplementation for 16 weeks. Lipid profiles, proinflammatory cytokines, glucose tolerance, microbiota composition and short-chain fatty acid (SCFA) concentrations were analyzed at the end of the experiment. In addition, microbiota-depleted mice were transplanted with the fecal microbiota of mice fed a HFD or mice fed a HFD along with ginger supplementation. Glucose tolerance and microbiota composition were assessed after a 8-week fecal microbiota transplantation (FMT).

RESULTS: We observed marked decreases in body weight, liver steatosis, and low-grade inflammation as well as amelioration of insulin resistance in the HFD-fed mice treated with ginger. Furthermore, ginger supplementation modulated the gut microbiota composition and increased species belonging to the Bifidobacterium genus and SCFA-producing bacteria (Alloprevotella and Allobaculum), along with increases in fecal SCFA concentrations. The FMT experiment showed anti-obesity and microbiota-modulating effects similar to those observed in the oral ginger-feeding experiment.

CONCLUSIONS: This study suggests that modulation of the gut microbiota as a result of ginger supplementation has a therapeutic effect on obesity in mice.},
}

@article {pmid30858872,
year = {2019},
author = {Sartelli, M and Di Bella, S and McFarland, LV and Khanna, S and Furuya-Kanamori, L and Abuzeid, N and Abu-Zidan, FM and Ansaloni, L and Augustin, G and Bala, M and Ben-Ishay, O and Biffl, WL and Brecher, SM and Camacho-Ortiz, A and Caínzos, MA and Chan, S and Cherry-Bukowiec, JR and Clanton, J and Coccolini, F and Cocuz, ME and Coimbra, R and Cortese, F and Cui, Y and Czepiel, J and Demetrashvili, Z and Di Carlo, I and Di Saverio, S and Dumitru, IM and Eckmann, C and Eiland, EH and Forrester, JD and Fraga, GP and Frossard, JL and Fry, DE and Galeiras, R and Ghnnam, W and Gomes, CA and Griffiths, EA and Guirao, X and Ahmed, MH and Herzog, T and Kim, JI and Iqbal, T and Isik, A and Itani, KMF and Labricciosa, FM and Lee, YY and Juang, P and Karamarkovic, A and Kim, PK and Kluger, Y and Leppaniemi, A and Lohsiriwat, V and Machain, GM and Marwah, S and Mazuski, JE and Metan, G and Moore, EE and Moore, FA and Ordoñez, CA and Pagani, L and Petrosillo, N and Portela, F and Rasa, K and Rems, M and Sakakushev, BE and Segovia-Lohse, H and Sganga, G and Shelat, VG and Spigaglia, P and Tattevin, P and Tranà, C and Urbánek, L and Ulrych, J and Viale, P and Baiocchi, GL and Catena, F},
title = {2019 update of the WSES guidelines for management of Clostridioides (Clostridium) difficile infection in surgical patients.},
journal = {World journal of emergency surgery : WJES},
volume = {14},
number = {},
pages = {8},
doi = {10.1186/s13017-019-0228-3},
pmid = {30858872},
issn = {1749-7922},
abstract = {In the last three decades, Clostridium difficile infection (CDI) has increased in incidence and severity in many countries worldwide. The increase in CDI incidence has been particularly apparent among surgical patients. Therefore, prevention of CDI and optimization of management in the surgical patient are paramount. An international multidisciplinary panel of experts from the World Society of Emergency Surgery (WSES) updated its guidelines for management of CDI in surgical patients according to the most recent available literature. The update includes recent changes introduced in the management of this infection.},
}

@article {pmid30852592,
year = {2019},
author = {Hirten, RP and Grinspan, A and Fu, SC and Luo, Y and Suarez-Farinas, M and Rowland, J and Contijoch, EJ and Mogno, I and Yang, N and Luong, T and Labrias, PR and Peter, I and Cho, JH and Sands, BE and Colombel, JF and Faith, JJ and Clemente, JC},
title = {Microbial Engraftment and Efficacy of Fecal Microbiota Transplant for Clostridium Difficile in Patients With and Without Inflammatory Bowel Disease.},
journal = {Inflammatory bowel diseases},
volume = {},
number = {},
pages = {},
doi = {10.1093/ibd/izy398},
pmid = {30852592},
issn = {1536-4844},
abstract = {BACKGROUND: Recurrent and severe Clostridium difficile infections (CDI) are treated with fecal microbiota transplant (FMT). Uncertainty exists regarding FMT effectiveness for CDI with underlying inflammatory bowel disease (IBD) and regarding its effects on disease activity and effectiveness in transferring the donor microbiota to patients with and without IBD.

METHODS: Subjects with and without IBD who underwent FMT for recurrent or severe CDI between 2013 and 2016 at The Mount Sinai Hospital were followed for up to 6 months. The primary outcome was CDI recurrence 6 months after FMT. Secondary outcomes were (1) CDI recurrence 2 months after FMT; (2) frequency of IBD flare after FMT; (3) microbiota engraftment after FMT; (and 4) predictors of CDI recurrence.

RESULTS: One hundred thirty-four patients, 46 with IBD, were treated with FMT. Follow-up was available in 83 and 118 patients at 6 and 2 months, respectively. There was no difference in recurrence in patients with and without IBD at 6 months (38.7% vs 36.5%; P > 0.99) and 2 months (22.5% vs 17.9%; P = 0.63). Proton pump inhibitor use, severe CDI, and comorbid conditions were predictors of recurrence. Pre-FMT microbiota was not predictive of CDI recurrence. Subjects with active disease requiring medication escalation had reduced engraftment, with no difference in engraftment based on CDI recurrence or IBD endoscopic severity at FMT.

CONCLUSIONS: Inflammatory bowel disease did not affect CDI recurrence rates 6 months after FMT. Pre-FMT microbiota was not predictive of recurrence, and microbial engraftment was impacted in those requiring IBD treatment escalation, though not by CDI recurrence or IBD disease severity.},
}

@article {pmid30851429,
year = {2019},
author = {Hibbard, J and Jiang, ZD and DuPont, HL},
title = {Fecal calprotectin and fecal indole predict outcome of fecal microbiota transplantation in subjects with recurrent Clostridium difficile infection.},
journal = {Anaerobe},
volume = {56},
number = {},
pages = {102-105},
doi = {10.1016/j.anaerobe.2019.03.006},
pmid = {30851429},
issn = {1095-8274},
abstract = {Fecal calprotectin and indole were studied in 134 subjects with recurrent CDI before and after FMT. Reduced fecal calprotectin (p = 0.0353, 95% CI 0.1305-0.1439) and rising levels of indole (p < 0.0001, 95% CI < 0.0001-0.0003) predicted successful treatment. A ratio of recal calprotectin/indole may provide prognostic value for FMT (p = 0.0004, 95% CI 0.22-0.87).},
}

@article {pmid30848026,
year = {2019},
author = {Chen, CC and Chen, YN and Liou, JM and Wu, MS and , },
title = {From germ theory to germ therapy.},
journal = {The Kaohsiung journal of medical sciences},
volume = {35},
number = {2},
pages = {73-82},
doi = {10.1002/kjm2.12011},
pmid = {30848026},
issn = {2410-8650},
support = {NTUH 106-P06//National Taiwan University Hospital/ ; NTUH 104-P05//National Taiwan University Hospital/ ; 107-0210-01-19-04//Translational Innovation of Biopharmaceutical Development-Technology Supporting Platform Axis/ ; MOHW107-TDU-B-211-123 002//Ministry of Health and Welfare of Taiwan/ ; MOHW106-TDU-B-211-113 002//Ministry of Health and Welfare of Taiwan/ ; MOST 107-3017-F-002-002//Ministry of Science and Technology, Executive Yuan, ROC, Taiwan/ ; TCTC-TR2 106-2321-B-002-025//Ministry of Science and Technology, Executive Yuan, ROC, Taiwan/ ; NTU-107 L9014-1//Ministry of Education (MOE) in Taiwan/ ; },
abstract = {Germ theory of disease and Koch's postulates has been governing our understanding of the role of microbes in human health since 19th century. The discovery of Helicobacter pylori (H. pylori) and H. pylori associated diseases has typically represented the concept and framework of Koch's postulates. Eradication of H. pylori to prevent peptic ulcers recurrence and gastric cancer is the triumph of this microbiology paradigm. Advances of next generation sequencing provide great insight into the unculturable microbes and show trillions of microbes have evolved with human beings. Research into the microbiome-the microbial communities (microbiota) and the host environment that they inhabit-has changed our understanding about microbes in human health and disease. The gut microbiota, the largest reservoir of the microbiome in human, plays a critical role in our catabolic-metabolism and immunity. This review will show the changes of the view of microbes on human health. We will briefly discuss dysbiosis, the disruption of symbiotic relationship between the host and microbiota, and the associated diseases. This leads to an idea to manipulate the microbiota, either by restoring missing functions or by eliminating harmful functions, to prevent or treat a variety of diseases. Current evidences of two common germ therapies, fecal microbiota transplantation and probiotics, in treating diseases will be reviewed.},
}

@article {pmid30847461,
year = {2019},
author = {Olmedo, M and Reigadas, E and Valerio, M and Vázquez-Cuesta, S and Pajares, JA and Matilla, A and Muñoz, P and Bouza, E},
title = {Is it reasonable to perform Fecal Microbiota Transplantation for recurrent Clostridium difficile Infection in patients with liver cirrhosis?.},
journal = {Revista espanola de quimioterapia : publicacion oficial de la Sociedad Espanola de Quimioterapia},
volume = {32},
number = {2},
pages = {205-207},
pmid = {30847461},
issn = {1988-9518},
}

@article {pmid30845942,
year = {2019},
author = {Biagi, E and Zama, D and Rampelli, S and Turroni, S and Brigidi, P and Consolandi, C and Severgnini, M and Picotti, E and Gasperini, P and Merli, P and Decembrino, N and Zecca, M and Cesaro, S and Faraci, M and Prete, A and Locatelli, F and Pession, A and Candela, M and Masetti, R},
title = {Early gut microbiota signature of aGvHD in children given allogeneic hematopoietic cell transplantation for hematological disorders.},
journal = {BMC medical genomics},
volume = {12},
number = {1},
pages = {49},
doi = {10.1186/s12920-019-0494-7},
pmid = {30845942},
issn = {1755-8794},
support = {GR-2013-02357136//Ministero della Salute/ ; IG- 17200 and "5xmille"-9962//Associazione Italiana per la Ricerca sul Cancro/ ; },
abstract = {BACKGROUND: The onset of acute Graft-versus-Host Disease (aGvHD) has been correlated with the gut microbiota (GM) composition, but experimental observations are still few, mainly involving cohorts of adult patients. In the current scenario where fecal microbiota transplantation has been used as a pioneer therapeutic approach to treat steroid-refractory aGvHD, there is an urgent need to expand existing observational studies of the GM dynamics in Hematopoietic Stem Cell Transplantation (HSCT). Aim of the present study is to explore the GM trajectory in 36 pediatric HSCT recipients in relation to aGvHD onset.

METHODS: Thirty-six pediatric patients, from four transplantation centers, undergoing HSCT were enrolled in the study. Stools were collected at three time points: before HSCT, at time of engraftment and > 30 days following HSCT. Changes in the GM phylogenetic structure were studied by 16S rRNA gene Illumina sequencing and phylogenetic assignation.

RESULTS: Children developing gut aGvHD had a dysbiotic GM layout before HSCT occurred. This putative aGvHD-predisposing ecosystem state was characterized by (i) reduced diversity, (ii) lower Blautia content, (iii) increase in Fusobacterium abundance. At time of engraftment, the GM structure underwent a deep rearrangement in all patients but, regardless of the occurrence of aGvHD and its treatment, it reacquired a eubiotic configuration from day 30.

CONCLUSIONS: We found a specific GM signature before HSCT predictive of subsequent gut aGvHD occurrence. Our data may open the way to a GM-based stratification of the risk of developing aGvHD in children undergoing HSCT, potentially useful also to identify patients benefiting from prophylactic fecal transplantation.},
}

@article {pmid30844145,
year = {2019},
author = {Chang, CS and Ruan, JW and Kao, CY},
title = {An overview of microbiome based strategies on anti-obesity.},
journal = {The Kaohsiung journal of medical sciences},
volume = {35},
number = {1},
pages = {7-16},
doi = {10.1002/kjm2.12010},
pmid = {30844145},
issn = {2410-8650},
support = {106-2628-B-400-001-MY3//Ministry of Science and Technology, Taiwan (MOST)/ ; 104-2320-B-400-019-MY3//Ministry of Science and Technology, Taiwan (MOST)/ ; IM-107-PP-04//National Health Research Institutes (NHRI)/ ; },
abstract = {With the significant global obesity epidemic and emerging strong scientific evidence that connected gut microbiota to obesity, intervening obesity by targeting gut microbiota has become a trendy strategy. Particularly the application of probiotics has become remarkably popular because of their expected association with gut microbiota modulation. Although there are many literatures on the effects of probiotics in obese animal models, most of them reported the effects of probiotic bacteria on metabolic indications with limited information on anti-obesity itself. Besides, some probiotics have been shown to reduce certain metabolic symptoms but they failed to achieve weight loss. This report reviewed the current literatures on the anti-obesity effects of next-generation probiotics in various animal obesity models and discussed the beneficial potential of fecal microbiota transplantation in treating obesity in humans. The purpose of this article is to help guide further research improve the probiotic bacteria experiments in more precise animal obesity models by standardizing the anti-obesogenesis, obesity control, and treatment assays and hopefully the evidence-based investigations on harnessing gut microbiota through next-generation probiotics or fecal microbiota transplantation will develop new interventions to promote and achieve anti-obesity.},
}

@article {pmid30841760,
year = {2019},
author = {Cammarota, G and Gallo, A and Ianiro, G and Montalto, M},
title = {Emerging drugs for the treatment of clostridium difficile.},
journal = {Expert opinion on emerging drugs},
volume = {24},
number = {1},
pages = {17-28},
doi = {10.1080/14728214.2019.1591371},
pmid = {30841760},
issn = {1744-7623},
abstract = {INTRODUCTION: Clostridium difficile or Clostridioides difficile (C. difficile) infection represents the most common cause of healthcare-associated infection. Over the last decades, the incidence and severity of C. difficile infection is rapidly increasing, with a significant impact on morbidity and mortality, and burden on health care system. Orally administered vancomycin and fidaxomicin are the therapeutic options of choice for initial C. difficile infection and fecal microbiota transplant for the recurrence infection. Furthermore, in recent years several new antibiotics with narrow-spectrum activity and low intestinal resorption have been developed, including surotomycin, cadazolid, and ridinilazol, and novel toxoid vaccines are expected to be efficacious in the prevention of C. difficile infection. Areas covered: Literature review was performed to select publications about current guidelines and phase-II/III trials on emerging drugs. These include novel antibiotics, monoclonal antibodies, vaccines, and fecal microbiota transplantation. Expert opinion: We have today a wide spectrum of promising therapeutic possibilities against infection. Pivotal future clinical trials may be crucial in developing effective strategies to optimize outcomes, mainly in high-risk population.},
}

@article {pmid30840758,
year = {2019},
author = {Petito, V and Fiore, L and Lopetuso, LR and Scaldaferri, F},
title = {Commentary to "Safety, Clinical Response, and Microbiome Findings Following Fecal Microbiota Transplant in Children With Inflammatory Bowel Disease".},
journal = {Inflammatory bowel diseases},
volume = {},
number = {},
pages = {},
doi = {10.1093/ibd/izz031},
pmid = {30840758},
issn = {1536-4844},
}

@article {pmid30834334,
year = {2019},
author = {Kim, P and Gadani, A and Abdul-Baki, H and Mitre, R and Mitre, M},
title = {Fecal microbiota transplantation in recurrent Clostridium difficile infection: A retrospective single-center chart review.},
journal = {JGH open : an open access journal of gastroenterology and hepatology},
volume = {3},
number = {1},
pages = {4-9},
doi = {10.1002/jgh3.12093},
pmid = {30834334},
issn = {2397-9070},
abstract = {Background and Aim: Fecal microbiota transplantation (FMT) has been proposed as a treatment option for patients with recurrent Clostridium difficile (C. difficile) infection but remains a novel option. We examined if FMT is an effective means of treating recurrent C. difficile infection.

Methods: A retrospective review of 35 patients who underwent FMT was completed. Demographics and other variables, including the use of proton pump inhibitor therapy and history of inflammatory bowel disease, were collected.

Results: Twenty-five patients (71.4%) belonged to a high-risk population (working in a hospital setting, rehabilitation center, or nursing facility) and a total of 74.3% of patients (n = 26 patients) had no history of proton pump inhibitor use. Twenty-five patients (71.4%) had used metronidazole prior to transplantation, 35 patients (100%) had used vancomycin, and 7 patients (20%) had used fidaxomicin for prior infection. Four patients (11.4%) had used all three antibiotics during prior treatment. Of the eight patients who had a history of inflammatory bowel disease, six (75%) experienced resolution of symptoms after transplantation. A total of 30 patients (85.7%) had resolution of their symptoms 6-8 weeks' posttransplant, while 5 patients (14.3%) continued to have symptoms.

Conclusions: Our retrospective chart review supports that patients benefit from FMT in the setting of recurrent C. difficile infection.},
}

@article {pmid30832423,
year = {2019},
author = {Álvarez-Mercado, AI and Navarro-Oliveros, M and Robles-Sánchez, C and Plaza-Díaz, J and Sáez-Lara, MJ and Muñoz-Quezada, S and Fontana, L and Abadía-Molina, F},
title = {Microbial Population Changes and Their Relationship with Human Health and Disease.},
journal = {Microorganisms},
volume = {7},
number = {3},
pages = {},
doi = {10.3390/microorganisms7030068},
pmid = {30832423},
issn = {2076-2607},
support = {PI-0538-2017//Junta de Andalucía/ ; },
abstract = {Specific microbial profiles and changes in intestinal microbiota have been widely demonstrated to be associated with the pathogenesis of a number of extra-intestinal (obesity and metabolic syndrome) and intestinal (inflammatory bowel disease) diseases as well as other metabolic disorders, such as non-alcoholic fatty liver disease and type 2 diabetes. Thus, maintaining a healthy gut ecosystem could aid in avoiding the early onset and development of these diseases. Furthermore, it is mandatory to evaluate the alterations in the microbiota associated with pathophysiological conditions and how to counteract them to restore intestinal homeostasis. This review highlights and critically discusses recent literature focused on identifying changes in and developing gut microbiota-targeted interventions (probiotics, prebiotics, diet, and fecal microbiota transplantation, among others) for the above-mentioned pathologies. We also discuss future directions and promising approaches to counteract unhealthy alterations in the gut microbiota. Altogether, we conclude that research in this field is currently in its infancy, which may be due to the large number of factors that can elicit such alterations, the variety of related pathologies, and the heterogeneity of the population involved. Further research on the effects of probiotics, prebiotics, or fecal transplantations on the composition of the human gut microbiome is necessary.},
}

@article {pmid30827274,
year = {2019},
author = {Albarrak, AA and Romana, BS and Uraz, S and Yousef, MH and Al Juboori, A and Tahan, V},
title = {Clostridium difficile infection in Inflammatory Bowel Disease Patients.},
journal = {Endocrine, metabolic & immune disorders drug targets},
volume = {},
number = {},
pages = {},
doi = {10.2174/1871530319666190301120558},
pmid = {30827274},
issn = {2212-3873},
abstract = {BACKGROUND: The rising incidence of Clostridium difficile infection (CDI) in the general population has been recognized by health care organizations worldwide. The emergence of hypervirulent strains has made CDI more challenging to understand and treat. Inflammatory bowel disease (IBD) patients are at higher risk of infection, including CDI.

OBJECTIVE: A diagnostic approach for recurrent CDI has yet to be validated, particularly for IBD patients. Enzyme immunoassay (EIA) for toxins A and B, as well as glutamate dehydrogenase EIA, are both rapid testing options for the identification of CDI. Without a high index of suspicion, it is challenging to initially differentiate CDI from an IBD flare based on clinical evaluation alone.

METHOD/RESULTS: Here, we provide and up-to-date review on CDI in IBD patients. When caring for an IBD patient with suspected CDI, it is appropriate to empirically treat the presumed infection while awaiting further test results. Treatment with vancomycin or fidaxomicin, but not oral metronidazole, has been advocated by an expert review from the clinical practice update committee of the American Gastroenterology Association. Recurrent CDI is more common in IBD patients compared to non-IBD patients (32% versus 24%), thus more aggressive treatment is recommended for IBD patients along with early consideration of fecal microbiota transplant.

CONCLUSION: Although the use of infliximab during CDI has been debated, clinical experience exists supporting its use in an IBD flare, even with active CDI when needed.},
}

@article {pmid30821676,
year = {2019},
author = {Grace, E and Chahine, EB},
title = {Updates on Clostridioides (Clostridium) difficile Infection With Emphasis on Long-Term Care.},
journal = {The Senior care pharmacist},
volume = {34},
number = {1},
pages = {29-42},
doi = {10.4140/TCP.n.2019.29},
pmid = {30821676},
issn = {2639-9636},
abstract = {OBJECTIVE: To provide a review of the classification, epidemiology, risk factors, diagnosis, treatment, and prevention of Clostridioides (Clostridium) difficile (C. difficile) infection (CDI) with an emphasis on longterm care.

DATA SOURCES: PubMed and Google Scholar were searched for relevant literature using a combination of the following terms: C. difficile, classification, epidemilogy, risk factors, diagnosis, treatment, prevention, and long-term care. Sources were limited to human data.

The main article reviewed was the 2017 CDI guidelines of the Infectious Diseases Society of American and the Society for Healthcare Epidemiology of America. Other articles were reviewed for relevance to CDI in long-term care settings.

DATA SYNTHESIS: CDI is associated with significant morbidity and mortality, particularly in older adults. The primary risk factors are advanced age and receipt of antibiotics. Diagnosis is suspected based on signs and symptoms and confirmed by laboratory tests. Vancomycin and fidaxomicin have replaced metronidazole as the drugs of choice for CDI. Fidaxomicin is associated with a lower risk of recurrence than vancomycin. Fecal microbiota transplantation is reserved for patients with multiple recurrences. Bezlotoxumab can be used in addition to standard therapy to prevent CDIs in patients at high risk for recurrence. Infection control strategies and antibiotic stewardship programs are known to reduce the rates of CDIs in institutional settings.

CONCLUSION: CDI is largely iatrogenic, and diagnosis is based on clinical presentation and laboratory tests. Treatment options include vancomycin, fidaxomicin, and fecal microbiota transplantation. Prevention centers around infection control and antibiotic stewardship. More research is needed in long-term care settings.},
}

@article {pmid30820491,
year = {2019},
author = {Lam, TJ and Ye, Y},
title = {CRISPRs for Strain Tracking and Their Application to Microbiota Transplantation Data Analysis.},
journal = {The CRISPR journal},
volume = {2},
number = {1},
pages = {41-50},
doi = {10.1089/crispr.2018.0046},
pmid = {30820491},
issn = {2573-1599},
support = {R01 AI108888/AI/NIAID NIH HHS/United States ; R01 AI143254/AI/NIAID NIH HHS/United States ; },
abstract = {CRISPR-Cas systems are adaptive immune systems naturally found in bacteria and archaea. Prokaryotes use these immune systems to defend against invaders, which include phages, plasmids, and other mobile genetic elements. Relying on the integration of spacers derived from invader sequences (protospacers) into CRISPR loci (forming spacers flanked by repeats), CRISPR-Cas systems are able to store the memory of past immunological encounters. While CRISPR-Cas systems have evolved in response to invading mobile genetic elements, invaders have also developed mechanisms to avoid detection. As a result of an arms race between CRISPR-Cas systems and their targets, CRISPR arrays typically undergo rapid turnover of spacers through the acquisition and loss events. Additionally, microbiomes of different individuals rarely share spacers. Here, we present a computational pipeline, CRISPRtrack, for strain tracking based on CRISPR spacer content, and we applied it to fecal transplantation microbiome data to study the retention of donor strains in recipients. Our results demonstrate the potential use of CRISPRs as a simple yet effective tool for donor-strain tracking in fecal transplantation and as a general purpose tool for quantifying microbiome similarity.},
}