@article {pmid31316785,
year = {2019},
author = {Gutin, L and Piceno, Y and Fadrosh, D and Lynch, K and Zydek, M and Kassam, Z and LaMere, B and Terdiman, J and Ma, A and Somsouk, M and Lynch, S and El-Nachef, N},
title = {Fecal microbiota transplant for Crohn disease: A study evaluating safety, efficacy, and microbiome profile.},
journal = {United European gastroenterology journal},
volume = {7},
number = {6},
pages = {807-814},
doi = {10.1177/2050640619845986},
pmid = {31316785},
issn = {2050-6406},
abstract = {Background: Emerging trials suggest fecal microbiota transplantation (FMT) is a promising treatment for ulcerative colitis; however, there is a paucity of data in Crohn disease (CD).

Objective: The objectives of this article are to determine whether single-dose FMT improves clinical and endoscopic outcomes in CD patients and to identify meaningful changes in the microbiome in response to FMT.

Methods: We performed a prospective, open-label, single-center study. Ten CD patients underwent FMT and were evaluated for clinical response (defined as decrease in Harvey-Bradshaw Index score ≥3 at one month post-FMT) and microbiome profile (16S ribosomal RNA sequencing) at one month post-FMT.

Results: Three of 10 patients responded to FMT. Two of 10 patients had significant adverse events requiring escalation of therapy. On microbiome analysis, bacterial communities of responders had increased relative abundance of bacteria commonly found in donor gut microbiota.

Conclusions: Single-dose FMT in this cohort of CD patients showed modest effect and potential for harm. Responders tended to have lower baseline alpha diversity, suggesting baseline perturbation of microbiota may be an indicator of potential responders to FMT in this patient population. Controlled trials are needed to further assess the efficacy and safety of FMT in CD and determine whether FMT is a viable option in this patient population.Clinicaltrials.gov number: NCT02460705.},
}

@article {pmid31316751,
year = {2019},
author = {Lin, DM and Lin, HC},
title = {A theoretical model of temperate phages as mediators of gut microbiome dysbiosis.},
journal = {F1000Research},
volume = {8},
number = {},
pages = {},
doi = {10.12688/f1000research.18480.1},
pmid = {31316751},
issn = {2046-1402},
abstract = {Bacteriophages are the most prominent members of the gut microbiome, outnumbering their bacterial hosts by a factor of 10. Phages are bacteria-specific viruses that are gaining attention as highly influential regulators of the gut bacterial community. Dysregulation of the gut bacterial community contributes to dysbiosis, a microbiome disorder characterized by compositional and functional changes that contribute to disease. A role for phages in gut microbiome dysbiosis is emerging with evidence that the gut phage community is altered in dysbiosis-associated disorders such as colorectal cancer and inflammatory bowel disease. Several recent studies have linked successful fecal microbiota transplantation to uptake of the donor's gut phage community, offering some insight into why some recipients respond to treatment whereas others do not. Here, we review the literature supporting a role for phages in mediating the gut bacterial community, giving special attention to Western diet dysbiosis as a case study to demonstrate a theoretical phage-based mechanism for the establishment and maintenance of dysbiosis.},
}

@article {pmid31315214,
year = {2019},
author = {Shin, JH and Chaplin, AS and Hays, RA and Kolling, GL and Vance, S and Guerrant, RL and Archbald-Pannone, L and Warren, CA},
title = {Outcomes of a Multidisciplinary Clinic in Evaluating Recurrent Clostridioides difficile Infection Patients for Fecal Microbiota Transplant: A Retrospective Cohort Analysis.},
journal = {Journal of clinical medicine},
volume = {8},
number = {7},
pages = {},
doi = {10.3390/jcm8071036},
pmid = {31315214},
issn = {2077-0383},
support = {5T32AI007046-39//National Institute of Allergy and Infectious Diseases/ ; Buchanan Award//University of Virginia/ ; },
abstract = {Fecal microbiota transplantation (FMT) has been shown to be an effective treatment for recurrent Clostridioides difficile infections (rCDIs). We assessed the benefits of a multidisciplinary C. difficile clinic for screening FMT eligibility in patients with rCDI. Patients seen at the University of Virginia Complicated C. difficile Clinic (CCDC) underwent comprehensive evaluation for possible FMT. Patients were eligible for FMT if there was history of greater than two episodes of rCDI. Patients were evaluated for the outcome after evaluation in the clinic. A total of 113 patients were evaluated: 77 were eligible for FMT, of which 25 patients did not undergo FMT. The rate of recurrence at three months and all-cause mortality were 4.5% and 7% for patients who received FMT and 16.7% and 12.5% for eligible patients who did not receive FMT. There were 36 patients who were not eligible for FMT, with two or fewer recurrences and a recurrence rate of 8.8% and all-cause mortality of 6%. One in three patients screened for FMT had a nutritional deficiency diagnosed, with zinc deficiency being most common (20%). Additional diagnoses, including inflammatory bowel disease, were made during the evaluation. FMT is a highly effective treatment for rCDI, most notably in patients with multiple recurrences. A systematic approach for evaluating patients with rCDI helps identify patients who benefit most from FMT and those who have other conditions.},
}

@article {pmid31313610,
year = {2019},
author = {Catho, G and Huttner, BD},
title = {Strategies for the eradication of extended-spectrum beta-lactamase or carbapenemase-producing Enterobacteriaceae intestinal carriage.},
journal = {Expert review of anti-infective therapy},
volume = {},
number = {},
pages = {},
doi = {10.1080/14787210.2019.1645007},
pmid = {31313610},
issn = {1744-8336},
abstract = {Introduction: Among the multidrug resistant pathogens, extended-spectrum beta-lactamase (ESBL-E) or carbapenemase-producing Enterobacteriaceae (CPE) are currently considered the main threat due to the scarcity of therapeutic options and their rapid spread around the globe. In addition to developing new antibiotics and stopping transmission, recent research has focused on "decolonization" strategies to eradicate the carriage of ESBL-E/CPE before infection occurs. Areas covered: In this narrative review, we aim to describe the current evidence of decolonization strategies for ESBL-E or CPE intestinal carriage. We first define decolonization and highlight the issues related to the lack of standardized definition, then we summarize the available data on the natural history of colonization. Finally, we review the strategies assessed over the past 10 years for ESBL and CPE decolonization: oral antibiotics, probiotics and more recently fecal microbiota transplantation. We conclude by presenting the risks and uncertainties associated with these strategies. Expert opinion: The evidence available today is too low to recommend decolonization strategies for ESBL-E or CPE in routine clinical practice. The potential increase of resistance and the impact of microbiome manipulation should not be underestimated. Some of these decolonization strategies may nevertheless be effective, at least in temporarily suppressing colonization, which could be useful for specific populations such as high-risk patients. Effectiveness and long-term effects must be properly assessed through well-designed randomized controlled trials.},
}

@article {pmid31306634,
year = {2019},
author = {Lo, GH},
title = {The transplantation of fecal microbiota for cirrhotic patients.},
journal = {Gastroenterology},
volume = {},
number = {},
pages = {},
doi = {10.1053/j.gastro.2019.06.040},
pmid = {31306634},
issn = {1528-0012},
}

@article {pmid31306229,
year = {2019},
author = {Chen, X and Li, HY and Hu, XM and Zhang, Y and Zhang, SY},
title = {Current understanding of gut microbiota alterations and related therapeutic intervention strategies in heart failure.},
journal = {Chinese medical journal},
volume = {},
number = {},
pages = {},
doi = {10.1097/CM9.0000000000000330},
pmid = {31306229},
issn = {2542-5641},
abstract = {OBJECTIVE: The purpose of this review is to stress the complicated interactions between the microbiota and the development of heart failure. Moreover, the feasibility of modulating intestinal microbes and metabolites as novel therapeutic strategies is discussed.

DATA SOURCES: This study was based on data obtained from PubMed up to March 31, 2019. Articles were selected using the following search terms: "gut microbiota," "heart failure," "trimethylamine N-oxide (TMAO)," "short-chain fatty acid (SCFA)," "bile acid," "uremic toxin," "treatment," "diet," "probiotic," "prebiotic," "antibiotic," and "fecal microbiota transplantation."

RESULTS: Accumulated evidence has revealed that the composition of the gut microbiota varies obviously in people with heart failure compared to those with healthy status. Altered gut microbial communities contribute to heart failure through bacterial translocation or affecting multiple metabolic pathways, including the trimethylamine/TMAO, SCFA, bile acid, and uremic toxin pathways. Meanwhile, modulation of the gut microbiota through diet, pre/probiotics, fecal transplantation, and microbial enzyme inhibitors has become a potential therapeutic approach for many metabolic disorders. Specifically, a few studies have focused on the cardioprotective effects of probiotics on heart failure.

CONCLUSIONS: The composition of the gut microbiota in people with heart failure is different from those with healthy status. A reduction in SCFA-producing bacteria in patients with heart failure might be a notable characteristic for patients with heart failure. Moreover, an increase in the microbial potential to produce TMAO and lipopolysaccharides is prominent. More researches focused on the mechanisms of microbial metabolites and the clinical application of multiple therapeutic interventions is necessarily required.},
}

@article {pmid31306151,
year = {2019},
author = {Allegretti, JR and Kassam, Z},
title = {Fecal Microbiota Transplantation in Patients With Primary Sclerosing Cholangitis: The Next Steps in This Promising Story.},
journal = {The American journal of gastroenterology},
volume = {},
number = {},
pages = {},
doi = {10.14309/ajg.0000000000000317},
pmid = {31306151},
issn = {1572-0241},
}

@article {pmid31305466,
year = {2019},
author = {Sun, L and Li, J and Lan, LL and Li, XA},
title = {The effect of fecal microbiota transplantation on Hepatic myelopathy: A case report.},
journal = {Medicine},
volume = {98},
number = {28},
pages = {e16430},
doi = {10.1097/MD.0000000000016430},
pmid = {31305466},
issn = {1536-5964},
abstract = {RATIONALE: Hepatic myelopathy (HM), also known as portal-systemic myelopathy, is a rare neurological complication that occurs in patients with chronic liver disease. There is no easy and feasible treatment, liver transplantation is the only accepted therapy that may be effective for patients at early stage at present. The pathogenesis of the disease is not clear yet, and the prognosis is poor. Here we describe a reversible HM after fecal microbiota transplantation.

PATIENT CONCERNS: In this report, a middle-aged female patient with hepatitis B cirrhosis, occurred HM after transjugular intrahepatic portosystemic shunt, a progressive spastic paraparesis in both legs were the main symptoms.

DIAGNOSIS: The patient was diagnosed with HM.

INTERVENTIONS: The patient received 3 times of fecal microbiota transplantations (FMT).

OUTCOMES: The patient's muscle strength of both legs were increased at various degrees, the patient's condition improved from HM2 to HM1.

LESSONS: FMT may be another effective way to treat HM. It is cheaper, more operable, and simpler than the approved treatment and worthy of further research.},
}

@article {pmid31304425,
year = {2019},
author = {Borody, TJ and Clancy, A},
title = {Fecal microbiota transplantation for ulcerative colitis-where to from here?.},
journal = {Translational gastroenterology and hepatology},
volume = {4},
number = {},
pages = {48},
doi = {10.21037/tgh.2019.06.04},
pmid = {31304425},
issn = {2415-1289},
}

@article {pmid31302808,
year = {2019},
author = {Selvig, D and Piceno, Y and Terdiman, J and Zydek, M and Umetsu, SE and Balitzer, D and Fadrosh, D and Lynch, K and Lamere, B and Leith, T and Kassam, Z and Beck, K and Lewin, S and Ma, A and Somsouk, M and Lynch, SV and El-Nachef, N},
title = {Fecal Microbiota Transplantation in Pouchitis: Clinical, Endoscopic, Histologic, and Microbiota Results from a Pilot Study.},
journal = {Digestive diseases and sciences},
volume = {},
number = {},
pages = {},
doi = {10.1007/s10620-019-05715-2},
pmid = {31302808},
issn = {1573-2568},
abstract = {AIMS: This pilot study assessed the efficacy, safety, and microbiome dynamics of fecal microbiota transplantation (FMT) for patients with chronic pouchitis.

METHODS: A prospective open-label pilot study was performed at an academic center among pouchitis patients undergoing FMT. Patients received a minimum of a single FMT by pouchoscopy from healthy, screened donors. The primary outcome was clinical improvement in pouchitis assessed by patient survey at week 4. Secondary outcomes included decrease in total Pouchitis Disease Activity Index (PDAI) Score ≥ 3 at week 4, bowel movement frequency, ESR, CRP, fecal calprotectin, abdominal pain, and PDAI subscores including endoscopic and histologic changes. Stool samples were collected at baseline and 4 weeks post-FMT to assess bacterial microbiota using V4 16S rRNA sequencing.

RESULTS: Nineteen patients were enrolled; however, 1 patient was lost to follow-up. No patients had a major adverse event or escalation of therapy related to FMT. Total PDAI scores, endoscopic scores, and histologic scores did not decrease significantly post-FMT. However, there was a statistically significant improvement in bowel movement (BM) frequency (9.25-7.25 BM/day, p = 0.03) and trend for improvement in abdominal pain to improve post-FMT (p = 0.05). Bacterial microbiota profiling revealed no distinct community-level changes post-FMT, though a small number of specific bacterial taxa significantly differed in relative abundance.

CONCLUSIONS: A single FMT has a tolerable short-term safety profile and may be associated with a decrease in bowel movements in patients with chronic pouchitis; however, no robust endoscopic or histologic changes were observed.},
}

@article {pmid31301451,
year = {2019},
author = {Allegretti, JR and Kassam, Z and Mullish, BH and Chiang, A and Carrellas, M and Hurtado, J and Marchesi, JR and McDonald, JAK and Pechlivanis, A and Barker, GF and Blanco, JM and Garcia-Perez, I and Wong, WF and Gerardin, Y and Silverstein, M and Kennedy, K and Thompson, C},
title = {Effects of Fecal Microbiota Transplantation With Oral Capsules in Obese Patients.},
journal = {Clinical gastroenterology and hepatology : the official clinical practice journal of the American Gastroenterological Association},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cgh.2019.07.006},
pmid = {31301451},
issn = {1542-7714},
abstract = {BACKGROUND & AIMS: Studies in mice have shown that the intestinal microbiota can contribute to obesity via the anorexigenic gut hormone glucagon-like peptide 1 (GLP1) and bile acids, which affect lipid metabolism. We performed a randomized, placebo-controlled pilot study of the effects of fecal microbiota transplantation (FMT) in obese, metabolically uncompromised patients.

METHODS: We performed a double-blind study of 22 obese patients (body mass index [BMI] ≥ 35kg/m2) without a diagnosis of diabetes, non-alcoholic steatohepatitis, or metabolic syndrome. Participants were randomly assigned (1:1) to groups that received FMT by capsules (induction dose of 30 capsules at week 4 and maintenance dose of 12 capsules at week 8) or placebo capsules. FMT capsules were derived from a single, lean donor (BMI, 17.5 kg/m2). Patients were followed through week 26; the primary outcome was safety. Stool and serum samples were collected from patients at baseline and at weeks 1, 4, 6, 8 and 12 after administration of the first dose of FMT or placebo and analyzed by 16S RNA gene sequencing. Stool and serum samples were analyzed for metabolomics by liquid chromatography-mass spectrometry. Additional outcomes were change in area under the curve for GLP1 at week 12.

RESULTS: We observed no significant differences in adverse events between patients who received FMT vs placebo. There was no increase in the area under the curve of GLP1 in either group. Patients who received FMT had sustained shifts in microbiomes associated with obesity toward those of the donor (P<.001). Patients who received FMT had a sustained decrease in stool levels of taurocholic acid (P<.05), compared with baseline; bile acid profiles began to more closely resemble those of the donor. We did not observe significant changes in mean BMI at week 12 in either group.

CONCLUSIONS: In a placebo-controlled pilot study, we found that FMT capsules (derived from a lean donor) were safe but did not reduce BMI in obese metabolically uncompromised patients. The FMT capsules were well tolerated and led to sustained changes in the intestinal microbiome and bile acid profiles that were similar to those of the lean donor.},
}

@article {pmid31293718,
year = {2019},
author = {Campion, D and Giovo, I and Ponzo, P and Saracco, GM and Balzola, F and Alessandria, C},
title = {Dietary approach and gut microbiota modulation for chronic hepatic encephalopathy in cirrhosis.},
journal = {World journal of hepatology},
volume = {11},
number = {6},
pages = {489-512},
doi = {10.4254/wjh.v11.i6.489},
pmid = {31293718},
issn = {1948-5182},
abstract = {Hepatic encephalopathy (HE) is a common and serious neuropsychiatric complication of cirrhosis, acute liver failure, and porto-systemic shunting. HE largely contributes to the morbidity of patients with liver disease, severely affecting the quality of life of both patients and their relatives and being associated with poor prognosis. Its presentation is largely variable, manifesting with a broad spectrum of cognitive abnormalities ranging from subtle cognitive impairment to coma. The pathogenesis of HE is complex and has historically been linked with hyperammonemia. However, in the last years, it has become evident that the interplay of multiple actors, such as intestinal dysbiosis, gut hyperpermeability, and neuroinflammation, is of crucial importance in its genesis. Therefore, HE can be considered a result of a dysregulated gut-liver-brain axis function, where cognitive impairment can be reversed or prevented by the beneficial effects induced by "gut-centric" therapies, such as non-absorbable disaccharides, non-absorbable antibiotics, probiotics, prebiotics, and fecal microbiota transplantation. In this context dietary modifications, by modulating the intestinal milieu, can also provide significant benefit to cirrhotic patients with HE. This review will provide a comprehensive insight into the mechanisms responsible for gut-liver-brain axis dysregulation leading to HE in cirrhosis. Furthermore, it will explore the currently available therapies and the most promising future treatments for the management of patients with HE, with a special focus on the dietary approach.},
}

@article {pmid31293562,
year = {2019},
author = {Ni, J and Huang, R and Zhou, H and Xu, X and Li, Y and Cao, P and Zhong, K and Ge, M and Chen, X and Hou, B and Yu, M and Peng, B and Li, Q and Zhang, P and Gao, Y},
title = {Analysis of the Relationship Between the Degree of Dysbiosis in Gut Microbiota and Prognosis at Different Stages of Primary Hepatocellular Carcinoma.},
journal = {Frontiers in microbiology},
volume = {10},
number = {},
pages = {1458},
doi = {10.3389/fmicb.2019.01458},
pmid = {31293562},
issn = {1664-302X},
abstract = {Gut microbiota dysbiosis is closely associated with primary hepatocellular carcinoma (HCC). Recent studies have evaluated the early diagnosis of primary HCC through analysis of gut microbiota dysbiosis. However, the relationship between the degree of dysbiosis and the prognosis of primary HCC remains unclear. Because primary HCC is accompanied by dysbiosis and dysbiosis usually increases the circulatory concentrations of endotoxin and other harmful bacterial substances, which further increases liver damage, we hypothesized that level of dysbiosis associated with primary HCC increases with the stage of cancer progression. To test this hypothesis, we introduced a more integrated index referred to as the degree of dysbiosis (Ddys); and we investigated Ddys of the gut microbiota with the development of primary HCC through high-throughput sequencing of 16S rRNA gene amplicons. Our results showed that compared with healthy individuals, patients with primary HCC showed increased pro-inflammatory bacteria in their fecal microbiota. The Ddys increased significantly in patients with primary HCC compared with that in healthy controls. Moreover, there was a tendency for the Ddys to increase with the development of primary HCC, although no significant difference was detected between different stages of primary HCC. Our findings provide important insights into the use of gut microbiota analysis during the treatment of primary HCC.},
}

@article {pmid31291465,
year = {2019},
author = {Liu, T and Song, X and Khan, S and Li, Y and Guo, Z and Li, C and Wang, S and Dong, W and Liu, W and Wang, B and Cao, H},
title = {The gut microbiota at the intersection of bile acids and intestinal carcinogenesis: an old story, yet mesmerizing.},
journal = {International journal of cancer},
volume = {},
number = {},
pages = {},
doi = {10.1002/ijc.32563},
pmid = {31291465},
issn = {1097-0215},
abstract = {The prevalence of colorectal cancer (CRC) dramatically increased worldwide in the last decade. Alterations of bile acid metabolism and gut microbiota have been reported to play vital roles in intestinal carcinogenesis. About trillions of bacteria inhabited in the human gut and maintained the balance of host metabolism. Bile acids are one of numerous metabolites that are synthesized in the liver and further metabolized by the gut microbiota, and are essential in maintaining the normal gut microbiota and lipid digestion. Multiple receptors such as FXR, GPBAR1, PXR, CAR and VDR act as sensors of bile acids have been reported. In this review, we mainly discussed interplay between bile acid metabolism and gut microbiota in intestinal carcinogenesis. We then summarized the critical role of bile acids receptors involving in CRC, and also addressed the rationale of multiple interventions for CRC management by regulating bile acids-microbiota axis such as probiotics, Metformin, ursodeoxycholic acid (UDCA) and fecal microbiota transplantation (FMT). Thus, by targeting the bile acids-microbiota axis may provide novel therapeutic modalities in CRC prevention and treatment. This article is protected by copyright. All rights reserved.},
}

@article {pmid31289031,
year = {2019},
author = {Pianko, MJ and Devlin, SM and Littmann, ER and Chansakul, A and Mastey, D and Salcedo, M and Fontana, E and Ling, L and Tavitian, E and Slingerland, JB and Slingerland, AE and Clurman, A and Gomes, ALC and Taur, Y and Pamer, EG and Peled, JU and van den Brink, MRM and Landgren, O and Lesokhin, AM},
title = {Minimal residual disease negativity in multiple myeloma is associated with intestinal microbiota composition.},
journal = {Blood advances},
volume = {3},
number = {13},
pages = {2040-2044},
doi = {10.1182/bloodadvances.2019032276},
pmid = {31289031},
issn = {2473-9537},
support = {P01 CA023766/CA/NCI NIH HHS/United States ; R01 CA228308/CA/NCI NIH HHS/United States ; U01 AI124275/AI/NIAID NIH HHS/United States ; P30 CA008748/CA/NCI NIH HHS/United States ; P01 AG052359/AG/NIA NIH HHS/United States ; R01 AI095706/AI/NIAID NIH HHS/United States ; R01 CA228358/CA/NCI NIH HHS/United States ; R01 AI042135/AI/NIAID NIH HHS/United States ; L30 CA220724/CA/NCI NIH HHS/United States ; UL1 TR000457/TR/NCATS NIH HHS/United States ; },
abstract = {Patients with multiple myeloma (MM) who achieve minimal residual disease (MRD) negativity after upfront treatment have superior outcomes compared with those who remain MRD+ Recently, associations have been shown between specific commensal microbes and development of plasma cell disorders. Here, we report the association between intestinal microbiota composition and treatment outcome in MM. Microbiota composition of fecal samples collected from 34 MM patients after induction therapy and at the time of flow cytometry-based bone marrow MRD testing was determined by 16S ribosomal RNA sequencing. We observed a higher relative abundance of Eubacterium hallii in the 16 MRD- patients relative to the 18 MRD+ patients. No association was observed between microbial relative abundance and autologous stem cell transplantation history or MM paraprotein isotype. No differences in microbiota α diversity were observed between MRD- and MRD+ patients. The potential association of microbiota composition with treatment response in MM patients is an important parameter for additional correlative and clinical investigation.},
}

@article {pmid31272391,
year = {2019},
author = {Tian, Y and Zhou, Y and Huang, S and Li, J and Zhao, K and Li, X and Wen, X and Li, XA},
title = {Fecal microbiota transplantation for ulcerative colitis: a prospective clinical study.},
journal = {BMC gastroenterology},
volume = {19},
number = {1},
pages = {116},
doi = {10.1186/s12876-019-1010-4},
pmid = {31272391},
issn = {1471-230X},
support = {2016JY0090//Natural Science Foundation of Science and Technology Department of Sichuan Province/ ; 17ZD012//Science and Technology Project of The Health Planning Committee of Sichuan/ ; 16ZA0280//Natural Science Foundation of Education Department of Sichuan Province/ ; 16TD0028//Innovative Group Foundation of Education Department of Sichuan Province/ ; S16019//Foundation of the Medical Association of Sichuan Province/ ; ZYFY2017XH04//Foundation of the First Affiliated Hospital of Chengdu Medical College/ ; },
abstract = {BACKGROUND: Fecal microbiota transplantation may contribute to disease remission in ulcerative colitis; however, the factors that determine the effects of treatment remain unknown. The aim of the present study was to prospectively investigate the clinical efficacy of fecal microbiota transplantation in patients with ulcerative colitis and identify the bacterial signatures associated with clinical remission.

METHODS: A total of 20 patients with ulcerative colitis were included in this prospective and uncontrolled study. All patients underwent gastroscopy five times, once every 3 weeks. Clinical indices were used to assess the efficacy of fecal microbiota transplantation, as well as the Mayo score, a score used to evaluate the extent of intestinal mucosal lesions in patients with ulcerative colitis. The changes in intestinal flora were detected by 16S ribosomal RNA-sequencing, and the relationship between ulcerative colitis and intestinal flora was analyzed.

RESULTS: After treatment, clinical index scores for diarrhea, abdominal pain, and blood stool decreased significantly (p < 0.05). Erythrocyte sedimentation rate and C-reactive protein levels had not changed significantly; however, the clinical index score for intestinal mucosal lesions and the Mayo score decreased significantly. In addition, 16S ribosomal RNA-sequencing revealed that the intestinal flora in patients diagnosed with ulcerative colitis was different from that of donors.

CONCLUSION: Fecal microbiota transplantation has a potential therapeutic value for the treatment of ulcerative colitis as it changes the abundance of bacterial flora and improves the scores for diarrhea, abdominal pain, and mucous membrane lesions in patients with this disease.

TRIAL REGISTRATION: The clinical trial was retrospectively registered with ClinicalTrials.gov (NCT03016780) on January 11th, 2017.},
}

@article {pmid31269444,
year = {2019},
author = {Bradley, KC and Finsterbusch, K and Schnepf, D and Crotta, S and Llorian, M and Davidson, S and Fuchs, SY and Staeheli, P and Wack, A},
title = {Microbiota-Driven Tonic Interferon Signals in Lung Stromal Cells Protect from Influenza Virus Infection.},
journal = {Cell reports},
volume = {28},
number = {1},
pages = {245-256.e4},
doi = {10.1016/j.celrep.2019.05.105},
pmid = {31269444},
issn = {2211-1247},
abstract = {Type I interferon (IFNα/β) pathways are fine-tuned to elicit antiviral protection while minimizing immunopathology; however, the initiating stimuli, target tissues, and underlying mechanisms are unclear. Using models of physiological and dysregulated IFNα/β receptor (IFNAR1) surface expression, we show here that IFNAR1-dependent signals set the steady-state IFN signature in both hematopoietic and stromal cells. Increased IFNAR1 levels promote a lung environment refractory to early influenza virus replication by elevating the baseline interferon signature. Commensal microbiota drive the IFN signature specifically in lung stroma, as shown by antibiotic treatment and fecal transplantation. Bone marrow chimera experiments identify lung stromal cells as crucially important for early antiviral immunity and stroma-immune cell interaction for late antiviral resistance. We propose that the microbiota-driven interferon signature in lung epithelia impedes early virus replication and that IFNAR1 surface levels fine-tune this signature. Our findings highlight the interplay between bacterial and viral exposure, with important implications for antibiotic use.},
}

@article {pmid31266629,
year = {2019},
author = {Martel, B and Saint-Lorant, G},
title = {[Pharmaceutical system of fecal microbiota transplantation: Heterogeneous practices].},
journal = {Annales pharmaceutiques francaises},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.pharma.2019.06.001},
pmid = {31266629},
issn = {0003-4509},
abstract = {OBJECTIVE: To describe current pharmaceutical practice in French hospitals regarding fecal microbiota transplantation in terms of prescription, preparation and compounding, as well as local legislation.

MATERIAL AND METHODS: A national survey was conducted at 28 French university hospital centers followed by the sending of a GoogleForm® questionnaire from June to August 2018 in the 16 respondent centers either performing or subcontracting fecal microbiota transplant.

RESULTS: All hospitals performing or subcontracting fecal transplant (n=16,%57) report prescription indication of recurrent Clostridium difficile infection treatment, and 6 of them also as part of a clinical trial protocol. In hospitals performing fecal transplant themselves (n=11), the number of pre-donation consultations with donors varies from one (n=6) to two (n=5). Fecal sample is collected at the donor's home in 45% of cases. Route of administration for transplant is either naso-gastric administration (n=4), rectal (n=4) or both (n=5). Fecal samples for transplant are compounded either in the hospital pharmacy (n=73%) or in the laboratory (27%). Thawing methods include refrigeration between 2-8°C (50%), room temperature (25%) and water bath (25%). Billing system and reporting to health authorities are highly heterogeneous from one hospital to another.

CONCLUSION: This survey shows significant pharmaceutical practice heterogeneity within French hospitals regarding fecal microbiota transplantation despite the existence of national and European recommendations.},
}

@article {pmid31262981,
year = {2019},
author = {Morjaria, S and Schluter, J and Taylor, BP and Littmann, ER and Carter, RA and Fontana, E and Peled, JU and van den Brink, MRM and Xavier, JB and Taur, Y},
title = {Antibiotic-induced shifts in fecal microbiota density and composition during hematopoietic stem cell transplantation.},
journal = {Infection and immunity},
volume = {},
number = {},
pages = {},
doi = {10.1128/IAI.00206-19},
pmid = {31262981},
issn = {1098-5522},
abstract = {Background: Dramatic microbiota changes and loss of commensal anaerobic bacteria are associated with adverse outcomes in hematopoietic cell transplantation (HCT) recipients. In this study, we demonstrate these dynamic changes at high-resolution through daily stool sampling and assess the impact of individual antibiotics on those changes.Methods: We collected 272 longitudinal stool samples (with mostly daily frequency) from 18 patients undergoing HCT and determined their composition by multi-parallel 16S rRNA gene sequencing, as well as density of bacteria in stool by qPCR. We calculated microbiota volatility to quantify rapid shifts and developed a new dynamic systems inference method to assess the specific impact of antibiotics.Results: The greatest shifts in microbiota composition occurred between stem cell infusion and reconstitution of healthy immune cells. Piperacillin-tazobactam caused the most severe declines among obligate anaerobes.Conclusions: Our approach of daily sampling, bacterial density determination and dynamic systems modeling allowed us to infer the independent effects of specific antibiotics on the microbiota of HCT patients.},
}

@article {pmid31261545,
year = {2019},
author = {Huang, H and Xu, H and Luo, Q and He, J and Li, M and Chen, H and Tang, W and Nie, Y and Zhou, Y},
title = {Fecal microbiota transplantation to treat Parkinson's disease with constipation: A case report.},
journal = {Medicine},
volume = {98},
number = {26},
pages = {e16163},
doi = {10.1097/MD.0000000000016163},
pmid = {31261545},
issn = {1536-5964},
abstract = {RATIONALE: Fecal microbiota transplantation (FMT) is recognized as an emerging treatment through reconstruction of gut microbiota. Parkinson's disease is a neurodegenerative disorder, which is accompanied by constipation. Here we first reported a patient with Parkinson's disease and constipation that were obviously relieved after FMT.

PATIENT CONCERNS: A 71-year-old male patient presented with 7 years of resting tremor, bradykinesia (first inflicted the upper limbs and subsequently spread to lower limbs), and intractable constipation (defecation needing more than 30 minutes).

DIAGNOSES: Parkinson's disease for 7 years; constipation >3 years.

INTERVENTIONS: The patient had used madopar, pramipexole, and amantadine for anti-Parkinson and showed partially mitigation while laxative therapy for constipation failed. Finally FMT was performed.

OUTCOMES: The patient successfully defecated within 5 minutes and maintained daily unobstructed defecation until the end of follow-up. The patient's tremor in legs almost disappeared at 1 week after FMT but recurred in the right lower extremity at 2 months after FMT.

LESSONS: Gut microbiota reconstruction may have therapeutic effects for Parkinson's disease patients, especially those who have gastrointestinal symptoms and limited treatment choices.},
}

@article {pmid31258528,
year = {2019},
author = {Leshem, A and Horesh, N and Elinav, E},
title = {Fecal Microbial Transplantation and Its Potential Application in Cardiometabolic Syndrome.},
journal = {Frontiers in immunology},
volume = {10},
number = {},
pages = {1341},
doi = {10.3389/fimmu.2019.01341},
pmid = {31258528},
issn = {1664-3224},
abstract = {Newly revealed links between inflammation, obesity, and cardiometabolic syndrome have created opportunities to try previously unexplored therapeutic modalities in these common and life-risking disorders. One potential modulator of these complex disorders is the gut microbiome, which was described in recent years to be altered in patients suffering from features of cardiometabolic syndrome and to transmit cardiometabolic phenotypes upon transfer into germ-free mice. As a result, there is great interest in developing new modalities targeting the altered commensal bacteria as a means of treatment for cardiometabolic syndrome. Fecal microbiota transplantation (FMT) is one such modality in which a disease-associated microbiome is replaced by a healthy microbiome configuration. So far clinical use of FMT has been overwhelmingly successful in recurrent Clostridium difficile infection and is being extensively studied in other microbiome-associated pathologies such as cardiometabolic syndrome. This review will focus on the rationale, promises and challenges in FMT utilization in human disease. In particular, it will overview the role of the gut microbiota in cardiometabolic syndrome and the rationale, experience, and prospects of utilizing FMT treatment as a potential preventive and curative treatment of metabolic human disease.},
}

@article {pmid31258315,
year = {2019},
author = {Otrompke, J},
title = {Digestive Disease Week 2019.},
journal = {P & T : a peer-reviewed journal for formulary management},
volume = {44},
number = {7},
pages = {428-429},
pmid = {31258315},
issn = {1052-1372},
abstract = {We review selected sessions on the questionable benefits of fecal microbiota transplant; intrahepatic cholestasis of pregnancy; weight-loss drugs in combination with intragastric balloon endoscopy; and beta blockers in pancreatic cancer.},
}

@article {pmid31254675,
year = {2019},
author = {Kelly, CR and Fischer, M and Grinspan, A and Allegretti, JR},
title = {Patients Eligible for Trials of Microbe-based Therapeutics do not Represent the Population With Recurrent Clostridioides difficile Infection.},
journal = {Clinical gastroenterology and hepatology : the official clinical practice journal of the American Gastroenterological Association},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cgh.2019.06.034},
pmid = {31254675},
issn = {1542-7714},
abstract = {BACKGROUND & AIMS: Although there are many industry-funded trials of microbe-based therapeutics for Clostridioides (formerly Clostridium) difficile infection (CDI), not all patients are eligible for these trials, due to their strict enrollment criteria. Furthermore, given the widespread availability of fecal microbiota transplantation (FMT) and overwhelming evidence to support its efficacy, patients might refuse enrollment in trials with a placebo group. We analyzed willingness and eligibility of patients with recurrent CDI to participate in randomized controlled trials of microbe-based therapeutic agents.

METHODS: We performed a retrospective study of 199 patients referred to 4 tertiary referral centers for treatment of CDI from August 1, 2018 through January 31, 2019. We collected data on eligibility for FMT and enrollment in randomized controlled trials.

RESULTS: Of 130 patients deemed appropriate for FMT, 98 patients (75%) were ineligible for participation in a randomized controlled trial and 16 patients (17%) were eligible but refused to enroll. Immune compromise and inflammatory bowel diseases were the most common reasons for exclusion from trials CONCLUSIONS: Most patients with CDI who meet the guideline criteria for FMT are ineligible or unwilling to participate in randomized controlled trials of microbe-based therapeutics. Trial populations therefore do not represent the population of patients with CDI.},
}

@article {pmid31250122,
year = {2019},
author = {Aron-Wisnewsky, J and Clément, K and Nieuwdorp, M},
title = {Fecal Microbiota Transplantation: a Future Therapeutic Option for Obesity/Diabetes?.},
journal = {Current diabetes reports},
volume = {19},
number = {8},
pages = {51},
doi = {10.1007/s11892-019-1180-z},
pmid = {31250122},
issn = {1539-0829},
support = {PHRC-N Drifter//Assistance Publique - Hôpitaux de Paris/ ; PHRC Micronaria//Assistance Publique - Hôpitaux de Paris/ ; HEALTH-F4-2012-305312//Metacardis/ ; JPI MICRODIET Grant (5290510105)//Metacardis/ ; JPI MICRODIET Grant (5290510105)//Metacardis/ ; LITMUS 777377//EU Horizon 2020 grant/ ; LITMUS 777377//EU Horizon 2020 grant/ ; 17CVD01//LeDucq Foundation consortium grant/ ; 17CVD01//LeDucq Foundation consortium grant/ ; 016.146.327//ZONMW-VIDI grant 2013/ ; },
abstract = {PURPOSE OF REVIEW: The aim of this review is to summarize the current data available on the metabolic effects of fecal microbiota transplantation (FMT) including obesity and glucose metabolism in humans.

RECENT FINDINGS: Gut microbiota dysbiosis is a frequent characteristic observed in obesity and related metabolic diseases. Pieces of evidence mostly generated in mouse models suggest that rescuing this dysbiosis associates with improved metabolism. In humans, dietary or bariatric surgery interventions are often accompanied by complete or partial restoration of this dysbiosis together with weight reduction and metabolic amelioration. FMT is an interesting option to modify gut microbiota and has been associated with improved clinical outcomes, albeit only used in routine care for Clostridium difficile infection. However, there are only limited data on using FMT in the metabolic context. FMT from lean donors significantly improves insulin sensitivity in obese subjects with metabolic syndrome. However, there is a wide range of clinical responses. Interestingly in subjects with high microbial gene richness at baseline and when FMT donors that are metabolically compromised are used, no metabolic improvement is seen. Moreover, more studies evaluating the effect of FMT in patients with overt type 2 diabetes are warranted. Furthermore, interventions (in the receiver prior to FMT) aiming to enhance FMT response also need evaluation.},
}

@article {pmid31250035,
year = {2019},
author = {Wang, G and Huang, S and Wang, Y and Cai, S and Yu, H and Liu, H and Zeng, X and Zhang, G and Qiao, S},
title = {Bridging intestinal immunity and gut microbiota by metabolites.},
journal = {Cellular and molecular life sciences : CMLS},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00018-019-03190-6},
pmid = {31250035},
issn = {1420-9071},
support = {31420103908//National Natural Science Foundation of China/ ; 2017YFD0500506//Key Technologies Research and Development Program/ ; },
abstract = {The gastrointestinal tract is the site of nutrient digestion and absorption and is also colonized by diverse, highly mutualistic microbes. The intestinal microbiota has diverse effects on the development and function of the gut-specific immune system, and provides some protection from infectious pathogens. However, interactions between intestinal immunity and microorganisms are very complex, and recent studies have revealed that this intimate crosstalk may depend on the production and sensing abilities of multiple bioactive small molecule metabolites originating from direct produced by the gut microbiota or by the metabolism of dietary components. Here, we review the interplay between the host immune system and the microbiota, how commensal bacteria regulate the production of metabolites, and how these microbiota-derived products influence the function of several major innate and adaptive immune cells involved in modulating host immune homeostasis.},
}

@article {pmid31244784,
year = {2019},
author = {Chong, PP and Chin, VK and Looi, CY and Wong, WF and Madhavan, P and Yong, VC},
title = {The Microbiome and Irritable Bowel Syndrome - A Review on the Pathophysiology, Current Research and Future Therapy.},
journal = {Frontiers in microbiology},
volume = {10},
number = {},
pages = {1136},
doi = {10.3389/fmicb.2019.01136},
pmid = {31244784},
issn = {1664-302X},
abstract = {Irritable bowel syndrome (IBS) is a functional disorder which affects a large proportion of the population globally. The precise etiology of IBS is still unknown, although consensus understanding proposes IBS to be of multifactorial origin with yet undefined subtypes. Genetic and epigenetic factors, stress-related nervous and endocrine systems, immune dysregulation and the brain-gut axis seem to be contributing factors that predispose individuals to IBS. In addition to food hypersensitivity, toxins and adverse life events, chronic infections and dysbiotic gut microbiota have been suggested to trigger IBS symptoms in tandem with the predisposing factors. This review will summarize the pathophysiology of IBS and the role of gut microbiota in relation to IBS. Current methodologies for microbiome studies in IBS such as genome sequencing, metagenomics, culturomics and animal models will be discussed. The myriad of therapy options such as immunoglobulins (immune-based therapy), probiotics and prebiotics, dietary modifications including FODMAP restriction diet and gluten-free diet, as well as fecal transplantation will be reviewed. Finally this review will highlight future directions in IBS therapy research, including identification of new molecular targets, application of 3-D gut model, gut-on-a-chip and personalized therapy.},
}

@article {pmid31241182,
year = {2019},
author = {Jørgensen, SMD and Hvas, CL and Dahlerup, JF and Mikkelsen, S and Ehlers, L and Hammeken, LH and Licht, TR and Bahl, MI and Erikstrup, C},
title = {Banking feces: a new frontier for public blood banks?.},
journal = {Transfusion},
volume = {},
number = {},
pages = {},
doi = {10.1111/trf.15422},
pmid = {31241182},
issn = {1537-2995},
abstract = {Fecal microbiota transplantation (FMT) is an effective treatment for recurrent Clostridioides difficile infection and is potentially beneficial in other microbiota-related disorders. The provision of FMT in routine clinical practice requires an extensive infrastructure that is reliant on voluntary donors. Alongside an increasing demand for FMT, the logistic barriers of a large-scale donor-dependent operation and the difficulties among health authorities to regulate FMT limit the dissemination of sustainable FMT services. Blood centers are large organizations that handle a multitude of donor-dependent operations on a daily basis. Blood and feces share many of the same dependencies, and feces may present a new opportunity for the blood services to handle. In this paper, we describe how an FMT service may be established and embedded within the blood service infrastructure, and we explain the benefits of using blood donors as feces donors. We further explore the current indications of FMT, the challenges related to the lack of legislation, and the future perspectives for blood banks to meet a new and increasing demand.},
}

@article {pmid31239866,
year = {2019},
author = {Xu, Z and Liu, T and Zhou, Q and Chen, J and Yuan, J and Yang, Z},
title = {Roles of Chinese Medicine and Gut Microbiota in Chronic Constipation.},
journal = {Evidence-based complementary and alternative medicine : eCAM},
volume = {2019},
number = {},
pages = {9372563},
doi = {10.1155/2019/9372563},
pmid = {31239866},
issn = {1741-427X},
abstract = {Chronic constipation is a common gastrointestinal dysfunction, but its aetiology and pathogenesis are still unclear. Interestingly, the compositions of the gut microbiota in constipation patients and healthy controls are different. Various studies reported the different gut microbiota alterations in constipation patients, but most studies indicated that constipation patients showed the decreased beneficial bacteria and the reduced species richness of gut bacteria. Besides, the alterations in the gut microbiota may lead to constipation and constipation-related symptoms and the regulation of gut microbiota has a positive effect on gut functional diseases such as constipation. Microbial treatment methods, such as probiotics, prebiotics, synbiotics, and fecal microbiota transplantation, can be used to regulate gut microbiota. Increasing evidences have suggested that Chinese medicine (CM) has a good therapeutic effect on chronic constipation. Chinese medicine is well known for its multitarget and multimode effects on diseases as well as less side effects. In previous studies, after the treatment of constipation with CM, the gut microbiota was restored, indicating that the gut microbiota might be the target or important way for CM to exert its efficacy. In this review, we summarized the effects of microbial treatment and CM on the gut microbiota of constipation patients and discussed the relationship between CM and gut microbiota.},
}

@article {pmid31236163,
year = {2019},
author = {Singh, T and Bedi, P and Bumrah, K and Singh, J and Rai, M and Seelam, S},
title = {Updates in Treatment of Recurrent Clostridium difficile Infection.},
journal = {Journal of clinical medicine research},
volume = {11},
number = {7},
pages = {465-471},
doi = {10.14740/jocmr3854},
pmid = {31236163},
issn = {1918-3003},
abstract = {Recurrent Clostridium difficile infection (CDI) is a perpetual problem that leads to increased economic burden, higher healthcare cost, and significant morbidity and mortality. Its treatment remains a challenge. While various treatment approaches have been attempted with different levels of success, robust data establishing the superiority of one approach over the others is lacking. In this article, we review the current evidence pertaining to conventional pharmacological treatment as well as fecal microbiota transplantation (FMT) as a novel, rapidly emerging treatment modality for recurrent CDI.},
}

@article {pmid31232087,
year = {2019},
author = {Qi, X and Zhang, Y and Guo, H and Hai, Y and Luo, Y and Yue, T},
title = {Mechanism and intervention measures of iron side effects on the intestine.},
journal = {Critical reviews in food science and nutrition},
volume = {},
number = {},
pages = {1-13},
doi = {10.1080/10408398.2019.1630599},
pmid = {31232087},
issn = {1549-7852},
abstract = {Excess oral iron in the intestinal tract usually produces reactive oxygen species via Fenton and Haber-Weiss reaction, so oxidative stress is triggered. Lipid peroxidation procedurally appears, ferroptosis, apoptosis and necrosis are often induced, subsequently, mitochondrial damage, endoplasmic reticulum dysfunction and even cell death occur. As a result, the intestinal epithelial cells are destroyed, leading to the incompleteness of intestinal mechanical barrier. Simultaneously, iron supplement can change the compositions and metabolic processes of intestinal microbes, and the intestinal inflammatory may be worsened. In principle, the easier dissociation of Fe2+ from oral iron supplements is, the more serious intestinal inflammation will occur. Fortunately, some interventions have been developed to alleviate these side effects. For instance, some antioxidants e.g. VE and ferulic acid have been used to prevent the formation of free radicals or to neutralize the formed free radicals. Furthermore, some new iron supplements with the ability of slow-releasing Fe2+, e.g. ferrous citrate liposome and EDTA iron sodium, have been successfully prepared. In order to recover the intestinal micro-ecological balance, probiotics and prebiotics, bacterial consortium transplantation, and fecal microbiota transplantation have been developed. This study is meaningful for us to develop safer oral iron supplements and to maintain intestinal micro-ecological health.},
}

@article {pmid31231707,
year = {2019},
author = {Kellermayer, R},
title = {Fecal microbiota transplantation: great potential with many challenges.},
journal = {Translational gastroenterology and hepatology},
volume = {4},
number = {},
pages = {40},
doi = {10.21037/tgh.2019.05.10},
pmid = {31231707},
issn = {2415-1289},
abstract = {In January of 2019, Samuel P. Costello and colleagues published a wonderfully executed, double blind placebo-controlled trial on fecal microbiota transplantation (FMT) versus autologous stool as placebo in mild to moderately active adult ulcerative colitis [UC: one type of inflammatory bowel disease (IBD)] patients. This review-commentary examines the current state of knowledge on human gut microbiome (live microbiota + their products and surrounding environment, i.e., fecal matter) and microbial therapeutics from a gastrointestinal (GI) clinician's standpoint. The varied forms of dysbiosis as the target of FMT, recipient donor and placebo considerations are also discussed in respect to randomized control trials in IBD [and the lack thereof in Crohn's disease (CD)] with this unconventional treatment modality.},
}

@article {pmid31222022,
year = {2019},
author = {Burz, SD and Abraham, AL and Fonseca, F and David, O and Chapron, A and Béguet-Crespel, F and Cénard, S and Le Roux, K and Patrascu, O and Levenez, F and Schwintner, C and Blottière, HM and Béra-Maillet, C and Lepage, P and Doré, J and Juste, C},
title = {A Guide for Ex Vivo Handling and Storage of Stool Samples Intended for Fecal Microbiota Transplantation.},
journal = {Scientific reports},
volume = {9},
number = {1},
pages = {8897},
doi = {10.1038/s41598-019-45173-4},
pmid = {31222022},
issn = {2045-2322},
abstract = {Owing to the growing recognition of the gut microbiota as a main partner of human health, we are expecting that the number of indications for fecal microbiota transplantation (FMT) will increase. Thus, there is an urgent need for standardization of the entire process of fecal transplant production. This study provides a complete standardized procedure to prepare and store live and ready-to-use transplants that meet the standard requirements of good practices to applied use in pharmaceutical industry. We show that, if time before transformation to transplants would exceed 24 hours, fresh samples should not be exposed to temperatures above 20 °C, and refrigeration at 4 °C can be a safe solution. Oxygen-free atmosphere was not necessary and simply removing air above collected samples was sufficient to preserve viability. Transplants prepared in maltodextrin-trehalose solutions, stored in a -80 °C standard freezer and then rapidly thawed at 37 °C, retained the best revivification potential as proven by 16S rRNA profiles, metabolomic fingerprints, and flow cytometry assays over a 3-month observation period. Maltodextrin-trehalose containing cryoprotectants were also efficient in preserving viability of lyophilized transplants, either in their crude or purified form, an option that can be attractive for fecal transplant biobanking and oral formulation.},
}

@article {pmid31221971,
year = {2019},
author = {Frisbee, AL and Saleh, MM and Young, MK and Leslie, JL and Simpson, ME and Abhyankar, MM and Cowardin, CA and Ma, JZ and Pramoonjago, P and Turner, SD and Liou, AP and Buonomo, EL and Petri, WA},
title = {IL-33 drives group 2 innate lymphoid cell-mediated protection during Clostridium difficile infection.},
journal = {Nature communications},
volume = {10},
number = {1},
pages = {2712},
doi = {10.1038/s41467-019-10733-9},
pmid = {31221971},
issn = {2041-1723},
support = {R21 AI114734/AI/NIAID NIH HHS/United States ; T32 AI007496/AI/NIAID NIH HHS/United States ; 1R21AI114734//Division of Intramural Research, National Institute of Allergy and Infectious Diseases (Division of Intramural Research of the NIAID)/International ; 5R01AI124214-02//Division of Intramural Research, National Institute of Allergy and Infectious Diseases (Division of Intramural Research of the NIAID)/International ; F31 AI136421/AI/NIAID NIH HHS/United States ; R01 AI124214/AI/NIAID NIH HHS/United States ; },
mesh = {Adolescent ; Adult ; Aged ; Aged, 80 and over ; Animals ; Anti-Bacterial Agents/adverse effects ; Bacterial Toxins/immunology/metabolism ; Clostridium difficile/*immunology/pathogenicity ; Colon/cytology/immunology/microbiology/pathology ; Disease Models, Animal ; Enterocolitis, Pseudomembranous/*immunology/microbiology/mortality/therapy ; Fecal Microbiota Transplantation ; Female ; Gastrointestinal Microbiome/drug effects/immunology ; Gene Expression Profiling ; Humans ; *Immunity, Innate ; Interleukin-33/immunology/*metabolism ; Lymphocytes/*immunology/metabolism ; Male ; Mice, Inbred C57BL ; Mice, Knockout ; Middle Aged ; Up-Regulation/drug effects/immunology ; Virulence/immunology ; Young Adult ; },
abstract = {Clostridium difficile (C. difficile) incidence has tripled over the past 15 years and is attributed to the emergence of hypervirulent strains. While it is clear that C. difficile toxins cause damaging colonic inflammation, the immune mechanisms protecting from tissue damage require further investigation. Through a transcriptome analysis, we identify IL-33 as an immune target upregulated in response to hypervirulent C. difficile. We demonstrate that IL-33 prevents C. difficile-associated mortality and epithelial disruption independently of bacterial burden or toxin expression. IL-33 drives colonic group 2 innate lymphoid cell (ILC2) activation during infection and IL-33 activated ILC2s are sufficient to prevent disease. Furthermore, intestinal IL-33 expression is regulated by the microbiota as fecal microbiota transplantation (FMT) rescues antibiotic-associated depletion of IL-33. Lastly, dysregulated IL-33 signaling via the decoy receptor, sST2, predicts C. difficile-associated mortality in human patients. Thus, IL-33 signaling to ILC2s is an important mechanism of defense from C. difficile colitis.},
}

Adolescent
Adult
Aged
Aged, 80 and over
Animals
Anti-Bacterial Agents/adverse effects
Bacterial Toxins/immunology/metabolism
Clostridium difficile/*immunology/pathogenicity
Colon/cytology/immunology/microbiology/pathology
Disease Models, Animal
Enterocolitis, Pseudomembranous/*immunology/microbiology/mortality/therapy
Fecal Microbiota Transplantation
Female
Gastrointestinal Microbiome/drug effects/immunology
Gene Expression Profiling
Humans
*Immunity, Innate
Interleukin-33/immunology/*metabolism
Lymphocytes/*immunology/metabolism
Male
Mice, Inbred C57BL
Mice, Knockout
Middle Aged
Up-Regulation/drug effects/immunology
Virulence/immunology
Young Adult

@article {pmid31220424,
year = {2019},
author = {D'Haens, GR and Jobin, C},
title = {Fecal Microbial Transplantation For Diseases Beyond Recurrent Clostridium Difficile Infection.},
journal = {Gastroenterology},
volume = {},
number = {},
pages = {},
doi = {10.1053/j.gastro.2019.04.053},
pmid = {31220424},
issn = {1528-0012},
abstract = {As microbiome research has moved from associative to mechanistic studies, the activities of specific microbes and their products have been investigated in development of inflammatory bowel diseases, cancer, metabolic syndrome, and neuropsychiatric disorders. Findings from microbiome research have already been applied to the clinic, such as in fecal microbiota transplantation (FMT) for treatment of recurrent Clostridium difficile infection. We review the evidence for associations between alterations in the intestinal microbiome and gastrointestinal diseases and findings from clinical trials of FMT. We discuss opportunities for treatment of other diseases with FMT, based on findings from small clinical and preclinical studies.},
}

@article {pmid31218940,
year = {2019},
author = {Jagessar, SAR and Long, C and Cui, B and Zhang, F},
title = {Improvement of Good's syndrome by fecal microbiota transplantation: the first case report.},
journal = {The Journal of international medical research},
volume = {},
number = {},
pages = {300060519854913},
doi = {10.1177/0300060519854913},
pmid = {31218940},
issn = {1473-2300},
}

@article {pmid31212833,
year = {2019},
author = {Foligné, B and Plé, C and Titécat, M and Dendooven, A and Pagny, A and Daniel, C and Singer, E and Pottier, M and Bertin, B and Neut, C and Deplanque, D and Dubuquoy, L and Desreumaux, P and Capron, M and Standaert, A},
title = {Contribution of the Gut Microbiota in P28GST-Mediated Anti-Inflammatory Effects: Experimental and Clinical Insights.},
journal = {Cells},
volume = {8},
number = {6},
pages = {},
doi = {10.3390/cells8060577},
pmid = {31212833},
issn = {2073-4409},
support = {ANR-11-RPIB-0021//Agence Nationale de la Recherche/ ; IMITATION//SFR3I/ ; },
abstract = {An original immuno-regulatory strategy against inflammatory bowel diseases based on the use of 28 kDa glutathione S-transferase (P28GST), a unique schistosome protein, was recently proposed. Improvement of intestinal inflammation occurs through restoration of the immunological balance between pro-inflammatory T-helper 1 (Th1) responses and both T-helper 2 (Th2) and regulatory responses. However, detailed mechanisms explaining how P28GST prevents colitis and promotes gut homeostasis remain unknown. Considering the complex interplay between the adaptive and innate immune system and the intestinal microbiota, we raised the question of the possible role of the microbial ecosystem in the anti-inflammatory effects mediated by the helminth-derived P28GST protein. We first analyzed, by 16S rRNA sequencing, the bacterial profiles of mice fecal microbiota at several time points of the P28GST-immunomodulation period prior to trinitrobenzene sulfonic acid (TNBS)-colitis. The influence of gut microbiota in the P28GST-mediated anti-inflammatory effects was then assessed by fecal microbiota transplantation experiments from P28GST-immunized mice to either conventional or microbiota depleted naïve recipient mice. Finally, the experimental data were supplemented by the temporal fecal microbiota compositions of P28GST-treated Crohn's disease patients from a pilot clinical study (NCT02281916). The P28GST administration slightly modulated the diversity and composition of mouse fecal microbiota while it significantly reduced experimental colitis in mice. Fecal microbiota transplantation experiments failed to restore the P28GST-induced anti-inflammatory effects. In Crohn's disease patients, P28GST also induced slight changes in their overall fecal bacterial composition. Collectively, these results provide key elements in both the anti-inflammatory mechanisms and the safe therapeutic use of immunomodulation with such promising helminth-derived molecules.},
}

@article {pmid31212328,
year = {2019},
author = {Reisinger, EC and Ebbers, M and Löbermann, M},
title = {[Clostridium Difficile: Monoclonal Antibody Therapy and Vaccines].},
journal = {Deutsche medizinische Wochenschrift (1946)},
volume = {144},
number = {12},
pages = {842-849},
doi = {10.1055/a-0882-7530},
pmid = {31212328},
issn = {1439-4413},
abstract = {Hospital-acquired Clostridium difficile infections have become much more frequent in recent years. Besides treatment with antibiotics and fecal microbiota transplant, new preventive strategies are available now. Bezlotoxumab is an antibody against toxin B and may reduce the risk of relapse by roughly 10 %. Several vaccine candidates against toxins A and B and surface-associated antigens were immunogenic and are tested in clinical trials to investigate the efficacy and safety.},
}

@article {pmid31208713,
year = {2019},
author = {Kalinkovich, A and Livshits, G},
title = {A cross talk between dysbiosis and gut-associated immune system governs the development of inflammatory arthropathies.},
journal = {Seminars in arthritis and rheumatism},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.semarthrit.2019.05.007},
pmid = {31208713},
issn = {1532-866X},
abstract = {BACKGROUND: Emerging evidence suggests that dysbiosis, imbalanced gut microbial community, might be a key player in the development of various diseases, including inflammatory arthropathies, such as rheumatoid arthritis, spondyloarthritis (mainly, ankylosing spondylitis and psoriatic arthritis), and osteoarthritis. Yet, the underlying mechanisms and corresponding interactions remain poorly understood.

METHODS: We conducted a critical and extensive literature review to explore the association between dysbiosis and the development of inflammatory arthropathies. We also reviewed the literature to assess the perspectives that ameliorate inflammatory arthropathies by manipulating the microbiota with probiotics, prebiotics or fecal microbiota transplantation.

RESULTS: Some bacterial species (e.g. Prevotella, Citrobacter rodentium, Collinsella aerofaciens, Segmented filamentous bacteria) participate in the creation of the pro-inflammatory immune status, presumably via epitope mimicry, modification of self-antigens, enhanced cell apoptosis mechanisms, and destruction of tight junction proteins and intestinal barrier integrity, all leading to the development and maintainance of inflammatory arthropathies. Whether dysbiosis is an epiphenomenon or is an active driver of these disorders remains unclear, yet, recent observations clearly suggest that dysbiosis precedes and triggers their development implying a causative relationship between dysbiosis and inflammatory arthropathies. The underlying mechanisms include dysbiosis-mediated changes in the functional activity of the intestinal immune cell subsets, such as innate lymphoid cells, mucosa-associated invariant T cells, invariant natural killer T cells, T-follicular helper and T-regulatory cells. In turn, disturbed functionality of the gut-associated immune system is shown to promote the overgrowth of many bacteria, thus establishing a detrimental vicious circle of actively maintaining arthritis.

CONCLUSIONS: Analysis of the data described in the review supports the notion that a close, dynamic and tightly regulated cross talk between dysbiosis and the gut-associated immune system governs the development of inflammatory arthropathies.},
}

@article {pmid31205136,
year = {2019},
author = {Ahamed, R and Philips, CA and Augustine, P},
title = {Fecal Microbiota Transplantation for Primary Sclerosing Cholangitis-A Beautiful but Incomplete Story.},
journal = {The American journal of gastroenterology},
volume = {},
number = {},
pages = {},
doi = {10.14309/ajg.0000000000000294},
pmid = {31205136},
issn = {1572-0241},
}

@article {pmid31205129,
year = {2019},
author = {Khoruts, A and Brandt, LJ},
title = {Fecal Microbiota Transplant: A Rose by Any Other Name.},
journal = {The American journal of gastroenterology},
volume = {114},
number = {7},
pages = {1176},
doi = {10.14309/ajg.0000000000000286},
pmid = {31205129},
issn = {1572-0241},
}

@article {pmid31204469,
year = {2019},
author = {Wang, B and Zhang, L and Zhu, SW and Zhang, JD and Duan, LP},
title = {Short chain fatty acids contribute to gut microbiota-induced promotion of colonic melatonin receptor expression.},
journal = {Journal of biological regulators and homeostatic agents},
volume = {33},
number = {3},
pages = {763-771},
pmid = {31204469},
issn = {0393-974X},
}

@article {pmid31204202,
year = {2019},
author = {Smirnova, DV and Zalomova, LV and Zagainova, AV and Makarov, VV and Mezhevikina, LM and Fesenko, EE and Yudin, SM},
title = {Cryopreservation of the human gut microbiota: Current state and perspectives.},
journal = {International journal of medical microbiology : IJMM},
volume = {309},
number = {5},
pages = {259-269},
doi = {10.1016/j.ijmm.2019.06.001},
pmid = {31204202},
issn = {1618-0607},
abstract = {The human intestinal microbiota is a complex ecosystem that consists of thousands of bacterial species that are responsible for human health and disease. The intestinal microbiota is a natural resource for production of therapeutic and preventive medicals, such as probiotics and fecal transplants. Modern lifestyles have resulted in the extinction of evolutionally selected microbial populations upon exposure to environmental factors. Therefore, it is very important to preserve the human gut microbiota to have the opportunity for timely restoration with minimal safety risks. Cryopreservation techniques that are suitable for the preservation of viable, mixed microbial communities and a biobanking approach are currently under development in different countries. However, the number of studies in this area is very limited. The variety of morphological and physiological characteristics of microbes in the microbiota, the different cryopreservation goals, and the criteria for the evaluation of cryopreservation effectiveness are the main challenges in the creation of a universal and standardized cryopreservation protocol. In this review, we summarized the current progress of the main cryopreservation techniques for gut microbiota communities and the methods for the assessment of the effectiveness of these techniques in the context of practical application.},
}

@article {pmid31201994,
year = {2019},
author = {Baron, SA and Cassir, N and Mékidèche, T and Mlaga, KD and Brouqui, P and Rolain, JM},
title = {Successful treatment and digestive decolonization of a patient with osteitis caused by a Carbapenemase-producing Klebsiella pneumoniae isolate harboring both NDM-1 and OXA-48 enzymes.},
journal = {Journal of global antimicrobial resistance},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jgar.2019.06.001},
pmid = {31201994},
issn = {2213-7173},
abstract = {OBJECTIVES: Carbapenem resistance in Klebsiella pneumoniae (CRKP) is an increasing problem worldwide and infections caused by this bacterium can be difficult to treat. Here we reported the case of a patient from Romania hospitalized in Bulgaria after an accident trauma that came in France for the treatment of an osteitis caused by a K. pneumoniae carrying both blaNDM-1 and blaOXA-48.

METHOD: The resistome of this extremely-drug-resistant bacterium was analyzed both with phenotypic (large antibiotic susceptibility testing) and genomic method (genome sequencing). The genetic environment of the two carbapenemases was studied.

RESULTS: K. pneumoniae ST307 carrying both a blaNDM-1 gene and a blaOXA-48 gene located on two different plasmids, an Inc L/M and an IncFII. Patient was successfully treated by a combination of intravenous colistin (9 MUI, then 4.5 MUI 2 times/day), intravenous fosfomycin (4 g 3 times/day) and oral doxycycline (100 mg 2 times/day) for 3 months. Fecal microbiota transplantation was successfully conducted for a stool carriage.

CONCLUSION: The ST307 type is becoming endemic in hospital environment and is frequently associated with carbapenem resistance. Treatment of infection caused by multi-drug resistant bacteria are a clinical challenge and the use of old antibiotics associated with a screening and decolonization of the reservoirs can be an efficient therapeutic alternative.},
}

@article {pmid31201141,
year = {2019},
author = {Wortelboer, K and Nieuwdorp, M and Herrema, H},
title = {Fecal microbiota transplantation beyond Clostridioides difficile infections.},
journal = {EBioMedicine},
volume = {44},
number = {},
pages = {716-729},
doi = {10.1016/j.ebiom.2019.05.066},
pmid = {31201141},
issn = {2352-3964},
abstract = {The importance of the commensal microbiota to human health and well-being has become increasingly evident over the past decades. From a therapeutic perspective, the popularity of fecal microbiota transplantation (FMT) to restore a disrupted microbiota and amend imbalances has increased. To date, most clinical experience with FMT originates from the treatment of recurrent or refractory Clostridioides difficile infections (rCDI), with resolution rates up to 90%. In addition to CDI, a role for the intestinal microbiome has been implicated in several disorders. FMT has been tested in several randomized controlled trials for the treatment of inflammatory bowel disease, irritable bowel disease and constipation with mixed results. FMT has also been explored for extra-gastrointestinal disorders such as metabolic syndrome, hepatic encephalopathy and graft-versus-host disease. With the exception of recurrent CDI, FMT is currently used in experimental settings only and should not yet be offered as standard care. In addition, it is critical to further standardize and optimize procedures for FMT preparation. This includes determination of active components of FMT to develop (personalized) approaches to treat disease.},
}

@article {pmid31197926,
year = {2019},
author = {Wang, JW and Wang, YK and Zhang, F and Su, YC and Wang, JY and Wu, DC and Hsu, WH},
title = {Initial experience of fecal microbiota transplantation in gastrointestinal disease: A case series.},
journal = {The Kaohsiung journal of medical sciences},
volume = {},
number = {},
pages = {},
doi = {10.1002/kjm2.12094},
pmid = {31197926},
issn = {2410-8650},
support = {MOHW107-TDU-B-212-113006//Ministry of Health and Welfare, Taiwan/ ; KMU105-5M01//Kaohsiung Medical University Hospital/ ; MOST108-2321-B-037-001//Ministry of Science and Technology/ ; },
abstract = {Current studies have proven the strong association between gut microbiota dysbiosis and the pathogenesis of gastrointestinal diseases. Fecal microbiota transplantation (FMT) from a healthy donor is a promising therapeutic strategy to change and restore composition of the recipient's gut microbiota. Rapidly increasing clinical literatures confirmed the truth of the benefits of FMT on recurrent Clostridium difficile infection (rCDI) and inflammatory bowel disease. This article retrospectively reviewed nine cases (four cases had ulcerative colitis [UC], five cases had rCDI) who received FMT in Kaohsiung Medical University Hospital from April 2016 to November 2018. We summarized the procedure including donor selection, fecal materials preparation, transplantation delivery methods, and clinical outcomes. All of the four UC cases got clinical improvement and four rCDI cases achieved clinical remission after FMT. The other one rCDI case remained positive stool Toxin A+B result after FMT, and got remission after salvage treatment with fidaxomicin. FMT is considered to be a well-tolerated adjuvant treatment for UC and effective salvage treatment for rCDI in our initial experience. Multiple infusions of FMT in UC and rCDI might have exceptional clinical efficiency, and enteral tube insertion could be a useful method to reach this goal and make multiple sessions of FMT easier.},
}

@article {pmid31195433,
year = {2019},
author = {Na, SY and Moon, W},
title = {Perspectives on Current and Novel Treatments for Inflammatory Bowel Disease.},
journal = {Gut and liver},
volume = {},
number = {},
pages = {},
doi = {10.5009/gnl19019},
pmid = {31195433},
issn = {2005-1212},
abstract = {New therapeutic strategies in inflammatory bowel disease (IBD) have shifted from symptom control towards treat-totarget algorithms in order to optimize treatment results. The treatment of IBD has evolved with the development of tumor necrosis factor-α inhibitors beyond the conventional therapies. In spite of their long-term effectiveness, many patients do not respond to or cannot sustain treatment with these drugs, which have various side effects. Therefore, the development of new drugs targeting specific pathways in the pathogenesis of IBD has become necessary. Some novel biologics and small molecule drugs have shown potential in IBD clinical trials, providing safe and effective results. In addition, clinicians are now trying to target the dysbiotic microbiome of patients with IBD using fecal microbiota transplantation. New tools such as stem cells have also been developed. The available therapeutic options for IBD are expanding rapidly. In the next few years, physicians will face an unprecedented number of options when choosing the best treatments for patients with IBD. This review provides an overview of recent advances in IBD treatment options.},
}

@article {pmid31190948,
year = {2019},
author = {Ilan, Y},
title = {Why targeting the microbiome is not so successful: can randomness overcome the adaptation that occurs following gut manipulation?.},
journal = {Clinical and experimental gastroenterology},
volume = {12},
number = {},
pages = {209-217},
doi = {10.2147/CEG.S203823},
pmid = {31190948},
issn = {1178-7023},
abstract = {The microbiome is explored as a potential target for therapy of bowel and systemic diseases. Fecal microbiota transplantation (FMT) has demonstrated efficacy in Clostridium difficile infection. However, clinical results regarding other diseases are modest, despite the abundant research on the microbiome over the last decade. Both high rate variability of the microbiome and adaptation to gut manipulations may underlie the lack of ultimate effects of FMT, probiotics, prebiotics, synbiotics, and antibiotics, which are aimed at restoring a healthier microbiome. The present review discusses the inherent variability of the microbiome and multiple factors that affect its diversity, as possible causes of the adaptation of the gut microbiome to chronic manipulation. The potential use of randomness is proposed, as a means of overcoming the adaptation and of restoring some of the inherent variability, with the goal of improving the long-term efficacy of these therapies.},
}

@article {pmid31190584,
year = {2019},
author = {Mazzawi, T and Hausken, T and Hov, JR and Valeur, J and Sangnes, DA and El-Salhy, M and Gilja, OH and Hatlebakk, JG and Lied, GA},
title = {Clinical response to fecal microbiota transplantation in patients with diarrhea-predominant irritable bowel syndrome is associated with normalization of fecal microbiota composition and short-chain fatty acid levels.},
journal = {Scandinavian journal of gastroenterology},
volume = {},
number = {},
pages = {1-10},
doi = {10.1080/00365521.2019.1624815},
pmid = {31190584},
issn = {1502-7708},
abstract = {Objectives: Irritable bowel syndrome (IBS) may be associated with disturbances in gut microbiota composition and functions. We recently performed a study of fecal microbiota transplantation (FMT) in diarrhea-predominant IBS (IBS-D) and found that IBS symptoms improved and the gut microbiota profile changed following FMT. We now aimed to explore the effects of FMT on the gut microenvironment in further detail by using 16S rRNA sequencing for more extended microbiota profiling and analyzing bacterial fermentation products (SCFAs: short chain fatty acids). Materials and methods: The study included 13 patients (four females and nine males) with IBS-D according to Rome III criteria and 13 healthy donors. Freshly donated feces were administered into duodenum via gastroscopy. The patients completed symptom and quality of life (QoL) questionnaires and delivered feces before and 1, 3, 12 and 20/28 weeks after FMT. Microbiota analysis was performed by sequencing 16S rRNA gene with Illumina Miseq technology. Fecal concentrations of SCFAs were analyzed by vacuum distillation followed by gas chromatography. Results: Several gut microbiota taxa and SCFAs were significantly different in the patients at baseline compared to their donors. These differences normalized by the third week following FMT in parallel with significant improvement in symptoms and QoL. Responders had different gut microbiota profile and SCFAs than nonresponders. Significant correlations were found between the gut microenvironment and IBS symptoms. No adverse effects were reported. Conclusions: FMT restores alterations of the gut microenvironment in IBS-D patients during the first 3 weeks and improves their symptoms for up to 28 weeks. ClinicalTrials.gov ID: NCT03333291.},
}

@article {pmid31184735,
year = {2019},
author = {Costello, SP and Conlon, MA and Andrews, JM},
title = {Fecal Microbiota Transplantation for Ulcerative Colitis-Reply.},
journal = {JAMA},
volume = {321},
number = {22},
pages = {2240-2241},
doi = {10.1001/jama.2019.3950},
pmid = {31184735},
issn = {1538-3598},
mesh = {*Colitis, Ulcerative ; Fecal Microbiota Transplantation ; Feces ; *Gastrointestinal Microbiome ; Humans ; },
}

*Colitis, Ulcerative
Fecal Microbiota Transplantation
Feces
*Gastrointestinal Microbiome
Humans

@article {pmid31184729,
year = {2019},
author = {Benech, N and Kapel, N and Sokol, H},
title = {Fecal Microbiota Transplantation for Ulcerative Colitis.},
journal = {JAMA},
volume = {321},
number = {22},
pages = {2240},
doi = {10.1001/jama.2019.3946},
pmid = {31184729},
issn = {1538-3598},
mesh = {*Colitis, Ulcerative ; Fecal Microbiota Transplantation ; Feces ; *Gastrointestinal Microbiome ; Humans ; },
}

*Colitis, Ulcerative
Fecal Microbiota Transplantation
Feces
*Gastrointestinal Microbiome
Humans

@article {pmid31183574,
year = {2019},
author = {Smibert, O and Satlin, MJ and Nellore, A and Peleg, AY},
title = {Carbapenem-Resistant Enterobacteriaceae in Solid Organ Transplantation: Management Principles.},
journal = {Current infectious disease reports},
volume = {21},
number = {7},
pages = {26},
doi = {10.1007/s11908-019-0679-4},
pmid = {31183574},
issn = {1523-3847},
abstract = {PURPOSE OF REVIEW: Carbapenem-resistant Enterobacteriaceae (CRE) have emerged as a worldwide problem. Given their degree of immunosuppression and the level of contact with the healthcare system, solid organ transplant (SOT) recipients are at a disproportionately higher risk of acquisition, colonization, and infection with CRE, and outcomes from infection tend to be worse compared to non-transplant patients. Therapeutic options are limited for CRE infections although several newer agents have recently been approved for use. How well these agents perform in the setting of immunosuppression and SOT is unclear. We sought to review the epidemiology of CRE in SOT and the management principles.

RECENT FINDINGS: CRE infections are becoming an increasing problem in SOT, and donor-derived infections present a challenge in the peri-transplant period. Newer treatments for CRE are emerging that are less toxic and potentially more effective than prior CRE-active agents, but supportive clinical data are limited. Newer beta-lactamase inhibitors have good activity against KPC carbapenemases, but they lack activity against metallo-beta-lactamases (e.g., NDM). Promising data is emerging with newer agents that have activity against most carbapenemases, but, again, clinical data is needed. Combination therapy in addition to optimal pharmacokinetic and pharmacodynamics may go some way to improve outcomes against these difficult-to-treat organisms. Other novel therapies that prevent the emergence of resistance (oral beta-lactamase inhibitors) and eradication of resistant Gram-negative colonization (fecal microbiota transplant) may eventually become part of a bundle approach to reduce CRE infections in the future. As in non-transplant patients, CRE infections in the transplant setting are challenging to treat and prevent. Infection prevention and control remains crucial to prevent widespread dissemination, and unique challenges exist with donor-derived CRE and how best to manage recipients in the peri-transplant period. Newer treatments are now in early-phase clinical studies, and in vitro activity data are supportive for several agents providing hope for improved outcomes with these typically difficult-to-treat and highly morbid infections in transplant recipients.},
}

@article {pmid31178906,
year = {2019},
author = {Lam, WC and Zhao, C and Ma, WJ and Yao, L},
title = {The Clinical and Steroid-Free Remission of Fecal Microbiota Transplantation to Patients with Ulcerative Colitis: A Meta-Analysis.},
journal = {Gastroenterology research and practice},
volume = {2019},
number = {},
pages = {1287493},
doi = {10.1155/2019/1287493},
pmid = {31178906},
issn = {1687-6121},
abstract = {Background and Purpose: Since the first case of fecal microbiota transplantation for the treatment of ulcerative colitis was described in the year 1989, there have been an increment of case reports, case series, cohort studies, and randomized controlled trials (RCTs). In this study, we were going to investigate general clinical remission, clinical response, and steroid-free remission of fecal microbiota transplantation.

Methods: We searched Ovid Medline, Ovid EMBASE, and Cochrane Library, focusing prospective studies including randomized controlled trials and cohort studies. The outcomes were clinical remission, clinical response, steroid-free remission, and serious adverse events. We used RevMan 5.3 software for meta-analyses.

Key Results: A total of 4 RCTs and 2 cohort studies (340 cases from 5 countries) were included. We found that FMT might be more effective than placebo on clinical remission (OR, 3.85 [2.21, 6.7]; P < 0.001; I2 = 0%) and clinical response (OR, 2.75 [1.33, 5.67]; P = 0.006; I2 = 49%), but no statistical difference on steroid-free remission (OR, 2.08 [0.41, 10.5]; P = 0.37; I2 = 69%) and serious adverse events (OR, 2.0 [0.17, 22.97]; P = 0.44; I2 = 0%).

Conclusions and Inferences: Fecal microbiota transplantations were associated with significant clinical remission and response in ulcerative colitis patients while there was no significant difference found between FMT and placebo in steroid-free remission. Moreover, a common consensus on the route, volume, timing, preferred donor characteristics, and frequency of fecal administration is necessary to achieve remission.},
}

@article {pmid31178437,
year = {2019},
author = {Lui, RN and Wong, SH and Lau, LHS and Chan, TT and Cheung, KCY and Li, A and Chin, ML and Tang, W and Ching, JYL and Lam, KLY and Chan, PKS and Wu, JCY and Sung, JJY and Chan, FKL and Ng, SC},
title = {Faecal microbiota transplantation for treatment of recurrent or refractory Clostridioides difficile infection in Hong Kong.},
journal = {Hong Kong medical journal = Xianggang yi xue za zhi},
volume = {25},
number = {3},
pages = {178-182},
doi = {10.12809/hkmj197855},
pmid = {31178437},
issn = {1024-2708},
abstract = {INTRODUCTION: Clostridioides difficile infection (CDI) is a leading cause of healthcare-associated infection globally, causing significant morbidity and mortality. Faecal microbiota transplantation (FMT) has emerged as a promising option for recurrent and refractory CDI. This study aimed to assess the safety, efficacy, and feasibility of FMT for CDI in Hong Kong.

METHODS: We conducted a single-centre, retrospective study for all consecutive cases of recurrent or refractory CDI who underwent FMT from 2013 to 2018. Clinical demographics, outcome, and safety parameters were collected.

RESULTS: A total of 24 patients with recurrent or refractory CDI (median age 70 years, interquartile range=45.0-78.3 years; 67% male) were included. Over 80% had been recently hospitalised or were long-term care facility residents. Faecal microbiota transplantation was delivered by feeding tube in 11 (45.8%), oesophagogastroduodenoscopy in eight (33.3%), and colonoscopy in six (25%) of the patients. Resolution of diarrhoea without relapse within 8 weeks was achieved in 21 out of 24 patients (87.5%) after FMT. No deaths occurred within 30 days. The FMT was well tolerated and no serious adverse events attributable to FMT were reported.

CONCLUSION: Our results confirm that FMT is a safe, efficacious, and feasible intervention for patients with refractory or recurrent CDI in Hong Kong. Given the increasing disease burden and the lack of effective alternatives in Hong Kong for difficult-to-treat cases of CDI, we recommend that a territory-wide FMT service be established to address increasing demand for this treatment.},
}

@article {pmid31173991,
year = {2019},
author = {Borody, TJ and Eslick, GD and Clancy, RL},
title = {Fecal microbiota transplantation as a new therapy: from Clostridioides difficile infection to inflammatory bowel disease, irritable bowel syndrome, and colon cancer.},
journal = {Current opinion in pharmacology},
volume = {49},
number = {},
pages = {43-51},
doi = {10.1016/j.coph.2019.04.017},
pmid = {31173991},
issn = {1471-4973},
abstract = {Fecal microbiota transplantation (FMT) represents the most effective means of therapeutically manipulating the gastrointestinal microbiome. Originally employed as a treatment of last-resort in patients with life-threatening Clostridioides difficile infection (CDI), FMT gained widespread acceptance during the CDI epidemic, where it achieved resolution rates approaching 100%. Following our newfound appreciation for the role of the gut microbiome in both health and disease and owing to FMT's unique mechanism/s of action, FMT is rapidly advancing as an effective treatment for a number of conditions in which the gastrointestinal microbiome is thought to play a role. We review the role of FMT from its beginnings in CDI to its expansion into inflammatory bowel disease, irritable bowel syndrome, and colon cancer.},
}

@article {pmid31172007,
year = {2019},
author = {Herfarth, H and Barnes, EL and Long, MD and Isaacs, KL and Leith, T and Silverstein, M and Gerardin, Y and Kassam, Z},
title = {Combined Endoscopic and Oral Fecal Microbiota Transplantation in Patients with Antibiotic-Dependent Pouchitis: Low Clinical Efficacy due to Low Donor Microbial Engraftment.},
journal = {Inflammatory intestinal diseases},
volume = {4},
number = {1},
pages = {1-6},
doi = {10.1159/000497042},
pmid = {31172007},
issn = {2296-9365},
abstract = {Background and Objective: A significant number of pouch patients develop antibiotic-dependent pouchitis (ADP). Microbial dysbiosis is thought to be a major driver of clinical symptoms in ADP. The objective of this proof of concept study was to evaluate safety, efficacy, and donor microbial engraftment of an intensified fecal microbiota transplant (FMT) consisting of a single endoscopic FMT followed by daily oral FMT for 2 weeks in patients with ADP.

Methods: We performed a prospective placebo-controlled double-blind FMT trial in patents with established ADP and planned to enroll 20 patients in this proof of concept study. In case of non-response, patients were offered an optional open label active FMT treatment. The endpoints were safety, clinical remission without need for antibiotics during 16 weeks of follow-up, quantitative changes of fecal calprotectin (FCP), and engraftment of donor FMT as determined by metagenomic sequencing of the V4 region of the 16S rRNA gene.

Results: Due to a lower than expected clinical remission rate and low FMT engraftment, enrollment in the study was stopped prematurely after 6 patients were included. All 6 patients enrolled in the placebo-controlled portion failed to respond and needed antibiotic rescue therapy shortly after FMT. FCP increased in the majority of patients in the setting of relapse after FMT. In the active open label FMT extension study 1 out of 5 patients achieved antibiotic-free clinical remission. FMT engraftment after active FMT was observed only in this single patient, whereas engraftment of donor FMT occurred in none of the other patients receiving active FMT, paralleling the lack of clinical response.

Conclusions: Low donor FMT engraftment resulted in low clinical efficacy of FMT in patients with ADP. Before embarking on larger clinical trials with FMT in patients with ADP or other forms of pouchitis, it is mandatory to explore approaches for superior FMT engraftment.},
}

@article {pmid31171823,
year = {2019},
author = {Martínez, N and Hidalgo-Cantabrana, C and Delgado, S and Margolles, A and Sánchez, B},
title = {Filling the gap between collection, transport and storage of the human gut microbiota.},
journal = {Scientific reports},
volume = {9},
number = {1},
pages = {8327},
doi = {10.1038/s41598-019-44888-8},
pmid = {31171823},
issn = {2045-2322},
abstract = {Stool collection devices minimizing the exposure of gut bacteria to oxygen are critical for the standardization of further microbiota-based studies, analysis and developments. The aim of this work was to evidence that keeping anaerobiosis has a deep impact on the viability and diversity of the fecal microbiota that is recovered in the laboratory. Recovering certain microbial populations, such as obligate anaerobic bacteria, is particularly critical if the purpose of the study is to envisage personalized therapeutic purposes, such as autologous Fecal Microbiota Transplant. In this study the same fecal specimens were sampled in conventional stool containers and GutAlive, a disposable device that minimizes exposure of the gut microbiota to oxygen. Samples from five healthy donors were analysed and 150 differential colonies were recovered and identified by 16S rRNA gene sequencing. Globally, GutAlive maintained extremely oxygen sensitive (EOS) populations that were lost in conventional stool containers, and thus viability of species such as as Akkermansia muciniphila, Faecalibacterium prausnitzii and a novel member of the Clostridiales order was kept. These obligate anaerobes were not recovered using the conventional stool collection device. In conclusion, the use of GutAlive for stool collection and transport optimized the viability and recovery of EOS bacteria in the lab by diminishing oxygen toxicity.},
}

@article {pmid31169545,
year = {2019},
author = {Gurram, B and Sue, PK},
title = {Fecal microbiota transplantation in children: current concepts.},
journal = {Current opinion in pediatrics},
volume = {},
number = {},
pages = {},
doi = {10.1097/MOP.0000000000000787},
pmid = {31169545},
issn = {1531-698X},
abstract = {PURPOSE OF REVIEW: Administration of fecal material into the gastrointestinal tract, termed fecal microbiota transplantation (FMT), is increasingly recognized as an effective treatment option for recurrent Clostridium difficile infection (RCDI). The impact of FMT on host microbial communities and subsequent disease states has also been explored in recent years for conditions as varied as inflammatory bowel disease especially ulcerative colitis, metabolic diseases, such as diabetes, graft-versus-host disease in hematopoietic stem cell transplant recipients, and autism and autism spectrum disorders. The purpose of this article is to review the evidence for FMT as a treatment option in various pediatric illnesses.

RECENT FINDINGS: The rate of C. difficile infection is rising among children, and is associated with significant morbidity and disease, with recurrence in up to 20% of pediatric patients. Several randomized controlled trials evaluating the utility of FMT in RCDI in comparison to vancomycin have been published and demonstrate high rates of efficacy between 70 and 100%. In addition, the safety of FMT in the treatment of RCDI has been well described in the adult population, with several pediatric case series demonstrating similar rates of tolerability and adverse events. FMT in ulcerative colitis appears promising, especially with multiple infusions administered via the lower gastrointestinal tract. However, there are several limitations, including the lack of uniformity of protocols used, source of FMT, route of administration and the lack of standardization of concomitant therapies. The data on usage of FMT for other indications are preliminary and limited.

SUMMARY: FMT is recognized as an effective treatment option for RCDI and is increasing sought by parents. Although limited, pediatric studies to date on the use of FMT for RCDI demonstrate similar efficacy rates as in the adult population. FMT has been proposed as a treatment option for an increasing number of pediatric conditions, and additional studies are needed to delineate the efficacy of FMT outside of RCDI, as well as its short and long-term impacts on human health.},
}

@article {pmid31165961,
year = {2019},
author = {Lee, CH and Chai, J and Hammond, K and Jeon, SR and Patel, Y and Goldeh, C and Kim, P},
title = {Long-term durability and safety of fecal microbiota transplantation for recurrent or refractory Clostridioides difficile infection with or without antibiotic exposure.},
journal = {European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s10096-019-03602-2},
pmid = {31165961},
issn = {1435-4373},
abstract = {Fecal microbiota transplant (FMT) is a safe and effective treatment for recurrent or refractory Clostridioides (Clostridium) difficile infection (RCDI) in the short term. However, there are a paucity of data on long-term durability and safety of FMT. The aim of this study is to determine the long-term efficacy and safety of FMT for RCDI. Ninety-four patients underwent FMT via retention enema for RCDI between 2008 and 2012 and completed a follow-up questionnaire 4 to 8 years following the last FMT. Of these, 32 were unreachable and 37 were deceased; 23 of the remaining 25 participants completed the survey. No CDI recurrences were reported in patients treated with FMT; 12 of the 23 participants (52.2%) received at least one course of non-CDI antibiotic(s). Nine participants (40.9%) received probiotics and 4 (17.4%) received both non-CDI antibiotics and probiotics. All 23 participants rated their overall health compared with pre-FMT. Current health was considered "much better" in 17 patients (73.9%); "somewhat better" in 3 patients (13.0%); and "about the same" in 3 patients (13.0%). A total of 11 participants (47.8%) reported an increase in weight of more than 5 kg (kg) post-FMT and 9 participants (39.1%) reported no change in weight (± 5 kg). Four of the 23 participants (17.4%) reported improvement or resolution (undifferentiated colitis, n = 1; Crohn's disease, n = 2; ulcerative colitis, n = 1) of pre-existing gastrointestinal condition following FMT. Eight of 23 participants (34.8%) experienced new medical condition(s) post-FMT. The long-term efficacy (48-96 months) of FMT for RCDI appears to be durable even after non-CDI antibiotic use. Thirty percent had improvement of their pre-existing medical conditions following FMT; 73.9% reported "much better" overall health following FMT.},
}

@article {pmid31164642,
year = {2019},
author = {Stebegg, M and Silva-Cayetano, A and Innocentin, S and Jenkins, TP and Cantacessi, C and Gilbert, C and Linterman, MA},
title = {Heterochronic faecal transplantation boosts gut germinal centres in aged mice.},
journal = {Nature communications},
volume = {10},
number = {1},
pages = {2443},
doi = {10.1038/s41467-019-10430-7},
pmid = {31164642},
issn = {2041-1723},
support = {675395//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/International ; BBS/E/B/000C0407//RCUK | Biotechnology and Biological Sciences Research Council (BBSRC)/International ; 637801//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/International ; BBS/E/B/000C0407//Biotechnology and Biological Sciences Research Council/United Kingdom ; BBS/E/B/000C0427//RCUK | Biotechnology and Biological Sciences Research Council (BBSRC)/International ; },
mesh = {Aging/*immunology ; Animals ; Cholera Toxin/immunology ; Dysbiosis/*immunology ; *Fecal Microbiota Transplantation ; Female ; Gastrointestinal Microbiome/*immunology ; Germinal Center/*immunology ; Immunization ; Immunoglobulin A/immunology ; Mice ; Nitrophenols/immunology ; Peyer's Patches/*immunology ; Phenylacetates/immunology ; },
abstract = {Ageing is a complex multifactorial process associated with a plethora of disorders, which contribute significantly to morbidity worldwide. One of the organs significantly affected by age is the gut. Age-dependent changes of the gut-associated microbiome have been linked to increased frailty and systemic inflammation. This change in microbial composition with age occurs in parallel with a decline in function of the gut immune system; however, it is not clear whether there is a causal link between the two. Here we report that the defective germinal centre reaction in Peyer's patches of aged mice can be rescued by faecal transfers from younger adults into aged mice and by immunisations with cholera toxin, without affecting germinal centre reactions in peripheral lymph nodes. This demonstrates that the poor germinal centre reaction in aged animals is not irreversible, and that it is possible to improve this response in older individuals by providing appropriate stimuli.},
}

Aging/*immunology
Animals
Cholera Toxin/immunology
Dysbiosis/*immunology
*Fecal Microbiota Transplantation
Female
Gastrointestinal Microbiome/*immunology
Germinal Center/*immunology
Immunization
Immunoglobulin A/immunology
Mice
Nitrophenols/immunology
Peyer's Patches/*immunology
Phenylacetates/immunology

@article {pmid31154727,
year = {2019},
author = {Yin, GF and Li, B and Fan, XM},
title = {[Effects and mechanism of fecal transplantation on acute lung injury induced by lipopolysaccharide in rats].},
journal = {Zhonghua yi xue za zhi},
volume = {99},
number = {20},
pages = {1582-1587},
doi = {10.3760/cma.j.issn.0376-2491.2019.20.013},
pmid = {31154727},
issn = {0376-2491},
mesh = {*Acute Lung Injury ; Animals ; *Fecal Microbiota Transplantation ; Lipopolysaccharides ; Lung ; NF-kappa B ; Phosphatidylinositol 3-Kinases ; Rats ; Rats, Sprague-Dawley ; Tumor Necrosis Factor-alpha ; },
abstract = {Objective: To investigate the effect of fecal microbiota transplantation (FMT) on acute lung injury (ALI) induced by lipopolysaccharide (LPS) and its regulatory mechanism. Methods: Fifteen rats were divided into control group, LPS group and LPS+FMT group by random number table method. LPS group and LPS+FMT group were intraperitoneally injected with LPS to generate rat ALI model. After 24 h of modeling, feces (10 ml/kg) were given to the LPS+FMT group twice a day, and the control group and LPS group were given the same amount of normal saline. The intervention lasted for 2 days. After 24 h of the last fecal microbiota transplantation, arterial blood gas analysis was performed in each group. Then rats were sacrificed and enzyme-linked immunosorbent (ELISA) method was used to detect intercellular adhesion molecule 1 (ICAM-1) content in the serum and bronchoalveolar lavage fluid (BALF). The lung wet-dry weight ratio (W/D) was evaluated; HE staining and lung tissue pathology scoring, immunohistochemical detection of nuclear factor-kappa B (NF-κB) predominate nuclear expression and expression of ICAM-1 of alveolar epithelial cells were conducted; Western blot was used to detect the expression of proteins related to the intracellular phosphatidylinositol kinase (PI3K)/protein kinase (AKT) signaling pathway. Samples of rat feces were collected and DNA was extracted. Polymerase chain reaction (PCR) products of the V3 and V4 regions of the 16S ribosomal RNA gene (16SrDNA) were sequenced at high throughput, and bioinformatics analysis was conducted on the microbial community based on the operational classification unit. Results: The lung W/D and lung histopathological score of the LPS group were significantly higher than those of the control group, while the arterial partial oxygen pressure (PaO(2)) of the LPS group was significantly lower than that of the control group [(79.2±5.89 vs 95.2±2.77) mmHg, 1 mmHg=0.133 kPa](all P<0.05). The results of intestinal flora sequencing revealed that the diversity index of LPS group was significantly higher than that of the control group, while the lactobacillus of LPS group rats was significantly lower than that of the control group. The content of ICAM-1 in serum, BALF and its relative expression on the cell membrane in the LPS group was significantly higher than that in the control group [(8.64±0.87) vs (7.40±0.32) ng/L; (0.941±0.035) vs (0.739±0.079) ng/L; (0.250±0.010) vs (0.076±0.010)] (all P<0.05). Moreover, the relative expression levels of phosphorylated P65 (p-P65), p-PI3K and p-AKT nucleoprotein in the LPS group were significantly higher than those in the control group (4.89±0.27 vs 3.28±0.13, 0.265±0.030 vs 0.036±0.013 and 0.444±0.040 vs 0.109±0.016) (all P<0.05). The above injury effect was reduced after fecal fungus transplantation. The lung W/D and lung pathological score of LPS+FMT group were significantly lower than those of LPS group, and PaO(2) of LPS+FMT group was significantly higher than that of LPS group [(88.0±3.53) mmHg]. The results of intestinal flora sequencing revealed that the diversity index of LPS+FMT group was significantly lower than that of LPS group, and the lactobacillus genus of LPS+FMT group was significantly higher than that of LPS group. ICAM-1 in the blood serum ((7.44±0.46) ng/L), BALF (0.834±0.040) ng/L) and its relative expression on alveolar epithelial cell membrane (0.173±0.030), the relative expression of p-P65, p-PI3K and p-AKT protein of NF-κB in alveolar epithelial cells was down-regulated ((2.99±0.28, 0.090±0.013 and 0.206±0.018) in LPS+FMT group than those of LPS group, the differences were statistically significant (all P<0.05). Conclusion: Fecal transplantation can alleviate lipopolysaccharide-induced acute lung injury in rats, and its regulatory effect may be related to inhibiting the activation of PI3K/AKT/NF-κB signaling pathway and reducing the expression of inflammatory factor ICAM-1.},
}

*Acute Lung Injury
Animals
*Fecal Microbiota Transplantation
Lipopolysaccharides
Lung
NF-kappa B
Phosphatidylinositol 3-Kinases
Rats
Rats, Sprague-Dawley
Tumor Necrosis Factor-alpha

@article {pmid31154629,
year = {2019},
author = {Kim, KO and Schwartz, MA and Lin, OST and Chiorean, MV and Gluck, M},
title = {Reducing Cost and Complexity of Fecal Microbiota Transplantation Using Universal Donors for Recurrent Clostridium difficile Infection.},
journal = {Advances in therapy},
volume = {},
number = {},
pages = {},
doi = {10.1007/s12325-019-00974-x},
pmid = {31154629},
issn = {1865-8652},
abstract = {INTRODUCTION: Fecal microbiota transplantation resolves recurrent Clostridium difficile infections in greater than 82% of patients. Highly screened, processed universal donor fecal material is available. We compared cost and scheduling efficiency of fecal microbiota transplantation by universal donors to patient-directed donors.

METHODS: Medical records from a prospectively maintained database of recurrent C. difficile patients who underwent fecal microbiota transplantation between 2012 and 2017 were reviewed retrospectively. Patient-directed donor stool was prepared in our microbiology laboratory using protocol-based screening. We transitioned to purchasing and using universal donor fecal material in 2015. Clinical outcomes, adverse events, time between consult to infusion, consultation fees, and material costs were compared. This was a retrospective comparison of two historical cohorts.

RESULTS: A total of 111 fecal microbiota transplantations were performed on 105 patients (56 from patient-directed donors and 55 from universal donors). Median recipient age was 66 years (18-96) with male to female ratio of 1:2.7, equivalent in both cohorts. Total consultation fees were significantly lower in the universal donor group owing to fewer infectious disease consultations. Costs for donor screening and stool preparation were lower in the universal donor cohort ($485.0 vs. $1189.90 ± 541.4, p < 0.001, 95% CI 559.9-849.9). Time from consultations to infusion was shorter in the universal donor cohort (18.9 ± 19.1 vs. 36.4 ± 23.3 days, p < 0.001, 95% CI 9.521-25.591). Recurrences within 8 weeks after fecal microbiota transplantation were equivalent (p = 0.354). Adverse events were equivalent.

CONCLUSIONS: Fecal microbiota transplantation using universal donors versus patient-directed donors for recurrent C. difficile showed comparable efficacy and short-term complications. The use of universal donors resulted in significant cost savings and scheduling efficiency.},
}

@article {pmid31145641,
year = {2019},
author = {Ji, J and Ge, X and Chen, Y and Zhu, B and Wu, Q and Zhang, J and Shan, J and Cheng, H and Shi, L},
title = {Daphnetin ameliorates experimental colitis by modulating microbiota composition and Treg/Th17 balance.},
journal = {FASEB journal : official publication of the Federation of American Societies for Experimental Biology},
volume = {},
number = {},
pages = {fj201802659RR},
doi = {10.1096/fj.201802659RR},
pmid = {31145641},
issn = {1530-6860},
abstract = {Inflammatory bowel diseases (IBDs) are characterized by chronic pathologies associated with extensive gut dysbiosis and intestinal inflammation. Hence, endeavors to improve the inflammatory pathology by manipulating gut microbiota are ongoing. Daphnetin (DAPH) is a coumarin derivative extracted from Daphne odora var with anti-inflammatory and immune-regulatory properties that has been widely used in treating inflammatory disorders. Herein, we showed that DAPH remarkably alleviated experimental colitis by reducing colonic inflammation, improving colonic integrity, and reestablishing immune and metabolic homeostasis in the inflicted intestines. Our analysis showed that DAPH modified the composition of gut microbiota and altered the metabolic profiles in dextran sulfate sodium-treated mice. In particular, this agent significantly elevated the abundance of short-chain fatty acid (SCFA)-producing gut microbiota, causatively related with the enhanced development of Treg cells and the reduced proinflammatory Th17 cell differentiation. More critically, the protective effect of DAPH was shown to be transmissible among colitic mice through cohousing or fecal microbiota transplantation, further substantiating the importance of SCFA-producing gut microbiota in DAPH action. We thus for the first time reveal the potential of DAPH in resetting the gut microbiome and reestablishing immune homeostasis in colitic mice, which may have clinical implications for treating IBD.-Ji, J., Ge, X., Chen, Y., Zhu, B., Wu, Q., Zhang, J., Shan, J., Cheng, H., Shi, L. Daphnetin ameliorates experimental colitis by modulating microbiota composition and Treg/Th17 balance.},
}

@article {pmid31143780,
year = {2019},
author = {Zeng, W and Shen, J and Bo, T and Peng, L and Xu, H and Nasser, MI and Zhuang, Q and Zhao, M},
title = {Cutting Edge: Probiotics and Fecal Microbiota Transplantation in Immunomodulation.},
journal = {Journal of immunology research},
volume = {2019},
number = {},
pages = {1603758},
doi = {10.1155/2019/1603758},
pmid = {31143780},
issn = {2314-7156},
abstract = {Probiotics are commensal or nonpathogenic microbes that confer beneficial effects on the host through several mechanisms such as competitive exclusion, antibacterial effects, and modulation of immune responses. Some probiotics have been found to regulate immune responses via immune regulatory mechanisms. T regulatory (Treg) cells, T helper cell balances, dendritic cells, macrophages, B cells, and natural killer (NK) cells can be considered as the most determinant dysregulated mediators in immunomodulatory status. Recently, fecal microbiota transplantation (FMT) has been defined as the transfer of distal gut microbial communities from a healthy individual to a patient's intestinal tract to cure some immune disorders (mainly inflammatory bowel diseases). The aim of this review was followed through the recent literature survey on immunomodulatory effects and mechanisms of probiotics and FMT and also efficacy and safety of probiotics and FMT in clinical trials and applications.},
}

@article {pmid31142049,
year = {2019},
author = {Burrello, C and Giuffrè, MR and Macandog, AD and Diaz-Basabe, A and Cribiù, FM and Lopez, G and Borgo, F and Nezi, L and Caprioli, F and Vecchi, M and Facciotti, F},
title = {Fecal Microbiota Transplantation Controls Murine Chronic Intestinal Inflammation by Modulating Immune Cell Functions and Gut Microbiota Composition.},
journal = {Cells},
volume = {8},
number = {6},
pages = {},
doi = {10.3390/cells8060517},
pmid = {31142049},
issn = {2073-4409},
support = {14378//Associazione Italiana per la Ricerca sul Cancro/ ; GR-2016-02361741//Ministero della Salute/ ; 5X1000//Fondazione IRCCS Policlinico Maggiore Milano/ ; },
abstract = {Different gastrointestinal disorders, including inflammatory bowel diseases (IBD), have been linked to alterations of the gut microbiota composition, namely dysbiosis. Fecal microbiota transplantation (FMT) is considered an encouraging therapeutic approach for ulcerative colitis patients, mostly as a consequence of normobiosis restoration. We recently showed that therapeutic effects of FMT during acute experimental colitis are linked to functional modulation of the mucosal immune system and of the gut microbiota composition. Here we analysed the effects of therapeutic FMT administration during chronic experimental colitis, a condition more similar to that of IBD patients, on immune-mediated mucosal inflammatory pathways. Mucus and feces from normobiotic donors were orally administered to mice with established chronic Dextran Sodium Sulphate (DSS)-induced colitis. Immunophenotypes and functions of infiltrating colonic immune cells were evaluated by cytofluorimetric analysis. Compositional differences in the intestinal microbiome were analyzed by 16S rRNA sequencing. Therapeutic FMT in mice undergoing chronic intestinal inflammation was capable to decrease colonic inflammation by modulating the expression of pro-inflammatory genes, antimicrobial peptides, and mucins. Innate and adaptive mucosal immune cells manifested a reduced pro-inflammatory profile in FMT-treated mice. Finally, restoration of a normobiotic core ecology contributed to the resolution of inflammation. Thus, FMT is capable of controlling chronic intestinal experimental colitis by inducing a concerted activation of anti-inflammatory immune pathways, mechanistically supporting the positive results of FMT treatment reported in ulcerative colitis patients.},
}

@article {pmid31133692,
year = {2019},
author = {Aagaard, K and Hohmann, E},
title = {Regulating microbiome manipulation.},
journal = {Nature medicine},
volume = {25},
number = {6},
pages = {874-876},
doi = {10.1038/s41591-019-0451-1},
pmid = {31133692},
issn = {1546-170X},
mesh = {Drug Approval/legislation & jurisprudence ; Fecal Microbiota Transplantation/adverse effects ; Humans ; Legislation, Medical ; *Microbiota ; Risk Factors ; Safety/legislation & jurisprudence ; United States ; United States Food and Drug Administration/legislation & jurisprudence ; },
}

Drug Approval/legislation & jurisprudence
Fecal Microbiota Transplantation/adverse effects
Humans
Legislation, Medical
*Microbiota
Risk Factors
Safety/legislation & jurisprudence
United States
United States Food and Drug Administration/legislation & jurisprudence

@article {pmid31127327,
year = {2019},
author = {Alagna, L and Haak, BW and Gori, A},
title = {Fecal microbiota transplantation in the ICU: perspectives on future implementations.},
journal = {Intensive care medicine},
volume = {45},
number = {7},
pages = {998-1001},
doi = {10.1007/s00134-019-05645-7},
pmid = {31127327},
issn = {1432-1238},
}

@article {pmid31125783,
year = {2019},
author = {Cavuoto, KM and Banerjee, S and Galor, A},
title = {Relationship between the microbiome and ocular health.},
journal = {The ocular surface},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jtos.2019.05.006},
pmid = {31125783},
issn = {1937-5913},
support = {I01 CX001089/CX/CSRD VA/United States ; L30 EY019842/EY/NEI NIH HHS/United States ; R01 EY026174/EY/NEI NIH HHS/United States ; },
abstract = {The microbiome is important to the host as a whole, both in maintenance of health and in the pathophysiology of disease. The purpose of this review is to explore the relationship between the gut, ocular microbiome, and ocular disease states. We will also discuss how the microbiome can serve as a potential target for treatment, by methods such as modulation of diet, probiotics and fecal microbiota transplantation. The information discussed in the review has been gathered using literature published from 2004 to November 2018, as indexed in PubMed.},
}

@article {pmid31124558,
year = {2019},
author = {Sharpton, SR and Maraj, B and Harding-Theobald, E and Vittinghoff, E and Terrault, NA},
title = {Gut microbiome-targeted therapies in nonalcoholic fatty liver disease: a systematic review, meta-analysis, and meta-regression.},
journal = {The American journal of clinical nutrition},
volume = {},
number = {},
pages = {},
doi = {10.1093/ajcn/nqz042},
pmid = {31124558},
issn = {1938-3207},
abstract = {BACKGROUND: Preclinical evidence suggests that modulation of the gut microbiome could represent a new therapeutic target in nonalcoholic fatty liver disease (NAFLD).

OBJECTIVES: The aim of this study was to evaluate the most current evidence for liver-specific and metabolic effects of microbiome-targeted therapies (MTTs) in persons with NAFLD.

METHODS: We searched multiple electronic databases for randomized controlled trials (RCTs) published from January 1, 2005 to December 1, 2018 that enrolled persons with NAFLD who received MTT rather than placebo or usual care. MTT was defined as antibiotics, probiotics, synbiotics, or fecal microbiota transplantation (FMT). Clinical outcomes were pooled with the use of random-effects models and heterogeneity was assessed with the I2 statistic. A random-effects meta-regression was performed to determine sources of heterogeneity in prevalence estimates between studies.

RESULTS: Twenty-one RCTs (1252 participants) were included; 9 evaluated probiotics and 12 evaluated synbiotics, with treatment duration ranging from 8 to 28 wk. No RCTs examined the efficacy of antibiotics or FMT. Probiotics/synbiotics were associated with a significant reduction in alanine aminotransferase activity [ALT, weighted mean difference (WMD): -11.23 IU/L; 95% CI: -15.02, -7.44 IU/L] and liver stiffness measurement (LSM) by elastography (reflecting inflammation and fibrosis) (WMD: -0.70 kPa; 95% CI: -1.00, -0.40 kPa), although analyses showed heterogeneity (I2 = 90.6% and I2 = 93.4%, respectively). Probiotics/synbiotics were also associated with increased odds of improvement in hepatic steatosis, as graded by ultrasound (OR: 2.40; 95% CI: 1.50, 3.84; I2 = 22.4%). No RCTs examined sequential liver biopsy findings. Probiotics (WMD: -1.84; 95% CI: -3.30, -0.38; I2 = 23.6%), but not synbiotics (WMD: -0.85; 95% CI: -2.17, 0.47; I2 = 96.6%), were associated with a significant reduction in body mass index.

CONCLUSIONS: The use of probiotics/synbiotics was associated with improvement in liver-specific markers of hepatic inflammation, LSM, and steatosis in persons with NAFLD. Although promising, given the heterogeneity in pooled analyses, additional well-designed RCTs are needed to define the efficacy of probiotics/synbiotics for treatment of NAFLD. This study was registered with PROSPERO as CRD42018091455.},
}

@article {pmid31124390,
year = {2019},
author = {Li, N and Wang, Q and Wang, Y and Sun, A and Lin, Y and Jin, Y and Li, X},
title = {Fecal microbiota transplantation from chronic unpredictable mild stress mice donors affects anxiety-like and depression-like behavior in recipient mice via the gut microbiota-inflammation-brain axis.},
journal = {Stress (Amsterdam, Netherlands)},
volume = {},
number = {},
pages = {1-11},
doi = {10.1080/10253890.2019.1617267},
pmid = {31124390},
issn = {1607-8888},
abstract = {Recent studies have demonstrated that there are significant changes in the gut microbiota (GM) of humans with depression and animal models of depression and chronic stress. In our present study, we determined whether an alteration in GM is a decisive factor in anxiety-like and depression-like behavior and its impact on brain neurochemistry. An antibiotic cocktail was used to deplete the GM of mice before they were colonized, via fecal microbiota transplantation (FMT), by the GM of control mice or mice that had been exposed to chronic unpredictable mild stress (CUMS donors). The CUMS-donor group of mice and the mice that were colonized by their microbiota (the CUMS-recipient group) both showed higher levels of anxiety- and depression-like behavior compared to the controls. The GM community of the CUMS-donor and CUMS-recipient was distinctively different from the controls, with the CUMS group characterized by a lower relative abundance of Lactobacillus and a higher relative abundance of Akkermansia. Interestingly, FMT affected both behavior and neuroinflammation. Mice given the CUMS microbiota had significant elevations of interferon-γ (IFN-γ) and the tumor necrosis factor-alpha (TNF-α) in the hippocampus, which were accompanied by upregulated indoleamine 2,3-dioxygenase 1 (IDO1) in the hippocampus. These results suggest that GM modulates pro-inflammatory cytokines in the hippocampus through dysfunctional microbiota-gut-brain axis, exacerbating anxiety- and depression-like phenotypes. Key Points Chronic unpredictable mild stress increased anxiety- and depression-like behavior in mice. Mice colonized with gut microbiota (GM) from stressed mice showed similar behaviors. The GM composition of the donor and recipient mice was also comparable. Their relative pattern of two bacteria has been tied to neuroinflammatory activity. The results suggest a link between GM, brain function, and anxiety and depression.},
}

@article {pmid31123874,
year = {2019},
author = {Yousi, F and Kainan, C and Junnan, Z and Chuanxing, X and Lina, F and Bangzhou, Z and Jianlin, R and Baishan, F},
title = {Evaluation of the effects of four media on human intestinal microbiota culture in vitro.},
journal = {AMB Express},
volume = {9},
number = {1},
pages = {69},
doi = {10.1186/s13568-019-0790-9},
pmid = {31123874},
issn = {2191-0855},
support = {81770558//National Natural Science Foundation of China/ ; },
abstract = {The human intestinal microbiota has an important role in the maintenance of human health and disease pathogenesis. The aim of this research was to investigate the impact of four media on human intestinal microbiota metabolite and composition changes, we performed in vitro batch culture using intestinal microbiota samples from three fecal microbiota transplantation (FMT) donors. After 48 h culture, gut microbiota medium (GMM) had the highest production of acetic acid (73.00 ± 7.56 mM) and propionic acid (16.79 ± 1.59 mM), bacterial growth media (BGM) had the highest production of butyric acid (13.39 ± 0.56 mM). In addition, brain heart infusion (BHI) promoted (p < 0.05) the growth of Bacteroidetes, especially Bacteroides after 48 h, GMM resulted in a significant increase (p < 0.05) in Actinobacteria and increased the beneficial genus Bifidobacterium, fastidious anaerobe broth (FAB) increased Firmicutes population, and BGM promoted the growth of Escherichia-Shigella and Akkermansia. The results suggest that four media had different effects on the human intestinal microbiota metabolism and composition in vitro. These results may facilitate the culture of bacteria from the human intestinal microbiota.},
}

@article {pmid31123221,
year = {2019},
author = {Yu, F and Han, W and Zhan, G and Li, S and Xiang, S and Zhu, B and Jiang, X and Yang, L and Luo, A and Hua, F and Yang, C},
title = {Abnormal gut microbiota composition contributes to cognitive dysfunction in streptozotocin-induced diabetic mice.},
journal = {Aging},
volume = {11},
number = {10},
pages = {3262-3279},
doi = {10.18632/aging.101978},
pmid = {31123221},
issn = {1945-4589},
abstract = {Both diabetes and Alzheimer's disease are age-related disorders, and numerous studies have demonstrated that patients with diabetes are at an increased risk of cognitive dysfunction (CD) and Alzheimer's disease, suggesting shared or interacting pathomechanisms. The present study investigated the role of abnormal gut microbiota in diabetes-induced CD and the potential underlying mechanisms. An intraperitoneal injection of streptozotocin administered for 5 consecutive days was used for establishing a diabetic animal model. Hierarchical cluster analysis of Morris water maze (MWM) performance indices (escape latency and target quadrant crossing) was adopted to classify the diabetic model mice into CD and Non-CD phenotypes. Both β-diversity and relative abundance of several gut bacteria significantly differed between the CD and Non-CD groups. Further, fecal bacteria transplantation from Non-CD mice, but not from CD mice, into the gut of pseudo-germ-free mice significantly improved host MWM performance, an effect associated with alterations in β-diversity and relative abundance of host gut bacteria. Collectively, these findings suggest that abnormal gut microbiota composition contributes to the onset of diabetes-induced CD and that improving gut microbiota composition is a potential therapeutic strategy for diabetes and related comorbidities.},
}

@article {pmid31122134,
year = {2019},
author = {McSweeney, B and Allegretti, JR and Fischer, M and Xu, H and Goodman, KJ and Monaghan, T and McLeod, C and Mullish, BH and Petrof, EO and Phelps, EL and Chis, R and Edmison, A and Juby, A and Ennis-Davis, R and Roach, B and Wong, K and Kao, D},
title = {In search of stool donors: a multicenter study of prior knowledge, perceptions, motivators, and deterrents among potential donors for fecal microbiota transplantation.},
journal = {Gut microbes},
volume = {},
number = {},
pages = {1-12},
doi = {10.1080/19490976.2019.1611153},
pmid = {31122134},
issn = {1949-0984},
abstract = {Fecal microbiota transplantation (FMT) is a highly effective therapy for recurrent Clostridioides difficile infection. Stool donors are essential, but difficult to recruit and retain. We aimed to identify factors influencing willingness to donate stool. This multi-center study with a 32-item questionnaire targeted young adults and health care workers via social media and university email lists in Edmonton and Kingston, Canada; London and Nottingham, England; and Indianapolis and Boston, USA. Items included baseline demographics and FMT knowledge and perception. Investigated motivators and deterrents included economic compensation, screening process, time commitment, and stool donation logistics. Logistic regression and linear regression models estimated associations of study variables with self-assessed willingness to donate stool. 802 respondents completed our questionnaire: 387 (48.3%) age 21-30 years, 573 (71.4%) female, 323 (40%) health care workers. Country of residence, age and occupation were not associated with willingness to donate stool. Factors increasing willingness to donate were: already a blood donor (OR 1.64), male, altruism, economic benefit, knowledge of how FMT can help patients (OR 1.32), and positive attitudes towards FMT (OR 1.39). Factors decreasing willingness to donate were: stool collection unpleasant (OR 0.92), screening process invasive (OR 0.92), higher stool donation frequency, negative social perception of stool, and logistics of collection/transporting feces. We conclude that 1) blood donors and males are more willing to consider stool donation; 2) altruism, economic compensation, and positive feedback are motivators; and 3) screening process, high donation frequency, logistics of collection/transporting feces, lack of public awareness, and negative social perception are deterrents. Considering these variables could maximize donor recruitment and retention.},
}

@article {pmid31119397,
year = {2019},
author = {Contreras, GA and Munita, JM and Arias, CA},
title = {Novel Strategies for the Management of Vancomycin-Resistant Enterococcal Infections.},
journal = {Current infectious disease reports},
volume = {21},
number = {7},
pages = {22},
doi = {10.1007/s11908-019-0680-y},
pmid = {31119397},
issn = {1523-3847},
abstract = {PURPOSE OF REVIEW: Vancomycin-resistant enterococci (VRE) are important nosocomial pathogens that commonly affect critically ill patients. VRE have a remarkable genetic plasticity allowing them to acquire genes associated with antimicrobial resistance. Therefore, the treatment of deep-seated infections due to VRE has become a challenge for the clinician. The purpose of this review is to assess the current and future strategies for the management of recalcitrant deep-seated VRE infections and efforts for infection control in the hospital setting.

RECENT FINDINGS: Preventing colonization and decolonization of multidrug-resistant bacteria are becoming the most promising novel strategies to control and eradicate VRE from the hospital environment. Fecal microbiota transplantation (FMT) has shown remarkable results on treating colonization and infection due to Clostridiodes difficille and VRE, as well as to recover the integrity of the gut microbiota under antibiotic pressure. Initial reports have shown the efficacy of FMT on reestablishing patient microbiota diversity in the gut and reducing the dominance of VRE in the gastrointestinal tract. In addition, the use of bacteriophages may be a promising strategy in eradicating VRE from the gut of patients. Until these strategies become widely available in the hospital setting, the implementation of infection control measures and stewardship programs are paramount for the control of this pathogen and each program should provide recommendations for the proper use of antibiotics and develop strategies that help to detect populations at risk of VRE colonization, prevent and control nosocomial transmission of VRE, and develop educational programs for all healthcare workers addressing the epidemiology of VRE and the potential impact of these pathogens on the cost and outcomes of patients. In terms of antibiotic strategies, daptomycin has become the standard of care for the management of deep-seated infections due to VRE. However, recent evidence indicates that the efficacy of this antibiotic is limited, and higher (10-12 mg/kg) doses and/or combination with β-lactams is needed for therapeutic success. Clinical data to support the best use of daptomycin against VRE are urgently needed. This review provides an overview of recent developments regarding the prevention, treatment, control, and eradication of VRE in the hospital setting. We aim to provide an update of the most recent therapeutic strategies to treat deep-seated infections due to VRE.},
}

@article {pmid31117340,
year = {2019},
author = {Cho, JM and Pestana, L and Pardi, R and Pardi, DS and Khanna, S},
title = {Fecal microbiota transplant via colonoscopy may be preferred due to intraprocedure findings.},
journal = {Intestinal research},
volume = {},
number = {},
pages = {},
doi = {10.5217/ir.2019.00056},
pmid = {31117340},
issn = {1598-9100},
}

@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 = {32},
number = {4},
pages = {307-313},
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 {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 {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 {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 {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 {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 {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 = {114},
number = {7},
pages = {1032-1033},
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 {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 {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},
support = {20181A011007//Guangzhou General Science and Technology Project of Health and Family Planning/ ; 201707010275//Guangzhou Planned Project of Science and Technology/ ; 201904010132//Guangzhou Planned Project of Science and Technology/ ; 2018A030313676//Natural Science Foundation of Guangdong Province/ ; },
abstract = {OBJECTIVE: To evaluate the efficacy and safety of fecal microbiota transplantation (FMT) for refractory irritable bowel syndrome (IBS).

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

RESULTS: FMT improved IBS gastrointestinal symptoms and alleviated depression and anxiety, as shown by the improved IBS-QOL, IBS-SSS, GSRS, HAMA and HAMD scores at 1 month and 3 months after FMT. A total adverse event rate of FMT was 6.7% (2/30). Gut microbiota analysis revealed that FMT responders had a significantly higher Shannon diversity index before FMT than non-responders. In addition, analysis of differences in bacterial composition before and after FMT in responders showed specific abundance of the phyla Verrucomincrobia and Euryarchaeota at 1 month after FMT. At the genus level, Methanobrevibacter and Akkermansia were the most abundant fecal microbiota 1 month after FMT compared with those before FMT.

CONCLUSIONS: FMT may be an effective and safe therapeutic strategy for treating IBS that achieves a sustained clinical response 3-6 months after the first procedure. Changes in the diversity and dominant flora may contribute to its therapeutic effect.},
}

@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},
mesh = {*Clostridium Infections/therapy ; *Colitis, Ulcerative ; *Fecal Microbiota Transplantation ; Feces ; *Gastrointestinal Microbiome ; Humans ; *Metabolic Diseases/therapy ; Treatment Outcome ; },
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.},
}

*Clostridium Infections/therapy
*Colitis, Ulcerative
*Fecal Microbiota Transplantation
Feces
*Gastrointestinal Microbiome
Humans
*Metabolic Diseases/therapy
Treatment Outcome

@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},
support = {P30 CA016672/CA/NCI NIH HHS/United States ; S10 OD012304/OD/NIH HHS/United States ; },
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 = {Preexisting Commensal Dysbiosis Is a Host-Intrinsic Regulator of Tissue Inflammation and Tumor Cell Dissemination in Hormone Receptor-Positive Breast Cancer.},
journal = {Cancer research},
volume = {79},
number = {14},
pages = {3662-3675},
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 cross-talk 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 preestablished 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 nonabsorbable 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 preexisting, host-intrinsic regulator of tissue inflammation, myeloid recruitment, fibrosis, and dissemination of tumor cells in HR+ breast cancer. SIGNIFICANCE: Identification of commensal dysbiosis as a host-intrinsic factor mediating evolution of metastatic breast cancer allows for development of interventions or diagnostic tools for patients at highest risk for developing metastatic disease.See related commentary by Ingman, p. 3539.},
}

@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 {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 {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 {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 = {16},
number = {3},
pages = {204-213},
doi = {10.1007/s11904-019-00441-w},
pmid = {31037552},
issn = {1548-3576},
support = {Z99 AI999999/NULL/Intramural NIH HHS/United States ; },
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 {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 {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 = {35},
number = {6},
pages = {327-331},
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/ ; MOST108-2321-B-037-001//Ministry of Science and Technology/ ; },
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.},
}