Search

Recent work has underscored the importance of the microbiome in human health, and has largely attributed differences in phenotype to differences in the species present among individuals (1-5). However, mobile [...]

Author(s): I. L. Brito; S. Yilmaz; K. Huang; L. Xu; S. D. Jupiter; A. P. Jenkins; W. Naisilisili; M. Tamminen; C. S. Smillie; J. R. Wortman; B. W. Birren; R. [...]

The usefulness of rpoA, recA, and pyrH gene sequences for the identification of vibrios is analyzed. It is concluded that strains of the same species will have at least 98, 94, and 94% rpoA, recA, and pyrH gene sequence similarity, respectively.

Ketoconazole (100 mg, orally, once daily) was investigated in nine patients with extensive dermatophyte infections. After treatment ranging between one week and three months, clinical cures (healing of lesions and negative cultures) were observed in all cases. In vitro growth of Trichophyton rubrum, T. mentagrophytes, and T. verrucosum isolated from infected skin scales were completely inhibited by concentrations of ketoconazole of 10 μg/ml and above. No evidence for the development of drug resistance was obtained from regular in vitro sensitivity tests. [ABSTRACT FROM AUTHOR]

2 case reports are given of patients with positive patch test reactions to clobetasol propionate. One of the patients also reacted to clobetasone butyrate. 30 other steroids that were chemically very closely related to these two 21-chloro-9-α-fluoro-corticosteroids, were patch test negative. The literature on contact dermatitis reactions to corticosteroids is reviewed. [ABSTRACT FROM AUTHOR]

The tumor microenvironment of colorectal carcinoma is a complex community of genomically altered cancer cells, nonneoplastic cells, and a diverse collection of microorganisms. Each of these components may contribute to carcinogenesis; however, the role of the microbiota is the least well understood. We have characterized the composition of the microbiota in colorectal carcinoma using whole genome sequences from nine tumor/normal pairs. Fusobacterium sequences were enriched in carcinomas, confirmed by quantitative PCR and 16S rDNA sequence analysis of 95 carcinoma/normal DNA pairs, while the Bacteroidetes and Firmicutes phyla were depleted in tumors. Fusobacteria were also visualized within colorectal tumors using FISH. These findings reveal alterations in the colorectal cancer microbiota; however, the precise role of Fusobacteria in colorectal carcinoma pathogenesis requires further investigation.

The enterococci are low-GC Gram-positive bacteria that have emerged as leading causes of hospital-acquired infection. They are also commensals of the gastrointestinal tract of healthy humans and most other animals with gastrointestinal flora and are important for food fermentations. Here we report the availability of draft genome sequences for 28 enterococcal strains of diverse origin, including the species Enterococcus faecalis, E. faecium, E. casseliflavus, and E. gallinarum.

Abstract Background While most gamma proteobacteria have a single circular chromosome, Vibrionales have two circular chromosomes. Horizontal gene transfer is common among Vibrios, and in light of this genetic mobility, it is an open question to what extent the two chromosomes themselves share a common history since their formation. Results Single copy genes from each chromosome (142 genes from chromosome I and 42 genes from chromosome II) were identified from 19 sequenced Vibrionales genomes and their phylogenetic comparison suggests consistent phylogenies for each chromosome. Additionally, study of the gene organization and phylogeny of the respective origins of replication confirmed the shared history. Conclusions Thus, while elements within the chromosomes may have experienced significant genetic mobility, the backbones share a common history. This allows conclusions based on multilocus sequence analysis (MLSA) for one chromosome to be applied equally to both chromosomes.

Abstract Background Biological nitrogen fixation is a prokaryotic process that plays an essential role in the global nitrogen cycle. Azorhizobium caulinodans ORS571 has the dual capacity to fix nitrogen both as free-living organism and in a symbiotic interaction with Sesbania rostrata. The host is a fast-growing, submergence-tolerant tropical legume on which A. caulinodans can efficiently induce nodule formation on the root system and on adventitious rootlets located on the stem. Results The 5.37-Mb genome consists of a single circular chromosome with an overall average GC of 67% and numerous islands with varying GC contents. Most nodulation functions as well as a putative type-IV secretion system are found in a distinct symbiosis region. The genome contains a plethora of regulatory and transporter genes and many functions possibly involved in contacting a host. It potentially encodes 4717 proteins of which 96.3% have homologs and 3.7% are unique for A. caulinodans. Phylogenetic analyses show that the diazotroph Xanthobacter autotrophicus is the closest relative among the sequenced genomes, but the synteny between both genomes is very poor. Conclusion The genome analysis reveals that A. caulinodans is a diazotroph that acquired the capacity to nodulate most probably through horizontal gene transfer of a complex symbiosis island. The genome contains numerous genes that reflect a strong adaptive and metabolic potential. These combined features and the availability of the annotated genome make A. caulinodans an attractive organism to explore symbiotic biological nitrogen fixation beyond leguminous plants.

The article presents a case of contact dermatitis caused due to antirheumatic gel containing etofenamate. A 20-year-old woman was admitted to a clinic with a vesicular weeping eczema on her right ankle. Etofenaznate, an ingredient of Bay-d-1107, has antipyretic and analgesic properties. It is marketed in Germany under the name of Rheumon-gel. According to dermatologist Bayer Leverkusen, no cases of contact allergic reactions to etofenamate have been reported up to this time, but reactions to isopropanol, another ingredient of Bay-d-1107 have occurred.

Several studies have documented the significant impact of methodological choices in microbiome analyses. The myriad of methodological options available complicate the replication of results and generally limit the comparability of findings between independent studies that use differing techniques and measurement pipelines. Here we describe the Mosaic Standards Challenge (MSC), an international interlaboratory study designed to assess the impact of methodological variables on the results. The MSC did not prescribe methods but rather asked participating labs to analyze 7 shared reference samples (5 × human stool samples and 2 × mock communities) using their standard laboratory methods. To capture the array of methodological variables, each participating lab completed a metadata reporting sheet that included 100 different questions regarding the details of their protocol. The goal of this study was to survey the methodological landscape for microbiome metagenomic sequencing (MGS) analyses and the impact of methodological decisions on metagenomic sequencing results. A total of 44 labs participated in the MSC by submitting results (16S or WGS) along with accompanying metadata; thirty 16S rRNA gene amplicon datasets and 14 WGS datasets were collected. The inclusion of two types of reference materials (human stool and mock communities) enabled analysis of both MGS measurement variability between different protocols using the biologically-relevant stool samples, and MGS bias with respect to ground truth values using the DNA mixtures. Owing to the compositional nature of MGS measurements, analyses were conducted on the ratio of Firmicutes: Bacteroidetes allowing us to directly apply common statistical methods. The resulting analysis demonstrated that protocol choices have significant effects, including both bias of the MGS measurement associated with a particular methodological choices, as well as effects on measurement robustness as observed through the spread of results between labs making similar methodological choices. In the analysis of the DNA mock communities, MGS measurement bias was observed even when there was general consensus among the participating laboratories. This study was the result of a collaborative effort that included academic, commercial, and government labs. In addition to highlighting the impact of different methodological decisions on MGS result comparability, this work also provides insights for consideration in future microbiome measurement study design., (© 2024. This is a U.S. Government work and not under copyright protection in the US; foreign copyright protection may apply.)

The human gut microbiome contributes crucial bioactive metabolites that support human health and is sensitive to perturbations from the ingestion of alcohol and antibiotics. We interrogated the response and recovery of human gut microbes after acute alcohol or broad-spectrum antibiotic administration in a gut model simulating the luminal and mucosal colonic environment with an inoculated human microbiome. Both alcohol and antibiotic treatments reduced the production of major short-chain fatty acids (SCFAs) (acetate, propionate, and butyrate), which are established modulators of human health. Treatment with a microbial synbiotic restored and enhanced gut function. Butyrate and acetate production increased by up to 29.7% and 18.6%, respectively, relative to untreated, dysbiotic samples. In parallel, treatment led to increases in the relative abundances of beneficial commensal organisms not found in the synbiotic (e.g., Faecalibacterium prausnitzii and the urolithin-producing organism Gordonibacter pamelaeae) as well as species present in the synbiotic (e.g., Bifidobacterium infantis), suggesting synergistic interactions between supplemented and native microorganisms. These results lead us to conclude that functional shifts in the microbiome, evaluated by both metabolite production and specific taxonomic compositional changes, are an appropriate metric to assess microbiome "recovery" following a dysbiosis-inducing disruption. Overall, these findings support the execution of randomized clinical studies to determine whether a microbial synbiotic can help restore microbiome function after a disruption. IMPORTANCE The human gut microbiome is sensitive to disruptions by common stressors such as alcohol consumption and antibiotic treatment. In this study, we used an in vitro system modeling the gut microbiome to investigate whether treatment with a microbial synbiotic can help restore microbiome function after stress. We find that a complex gut community treated with alcohol or antibiotics showed reduced levels of production of short-chain fatty acids, which are critical beneficial molecules produced by a healthy gut microbiota. Treatment of stressed communities with a microbial synbiotic resulted in the recovery of SCFA production as well as an increase in the abundance of beneficial commensal organisms. Our results suggest that treatment with a microbial synbiotic has the potential to restore healthy gut microbiome function after stress and merits further investigation in clinical studies.

Suitable instruments for measuring Food Parenting Practices (FPP) among adolescents and their parents that also measure the perception of adolescents about their parent's FPP are rare. The current study describes the development and preliminary testing of a short 16-item Adolescent Food Parenting Questionnaire (AFPQ) for parents (AFPQ-p) and adolescents (AFPQ-a) that may enable future large-scale research on potentially eminent parent-child FPP discrepancy. Participants included 381 parents (73.8 % mothers; M age 45.9, 26.2% fathers; M age 49.1) and their adolescent children (aged 12-16) who participated in the Dutch "G(F)OOD together" study. Most parents finished higher professional education (mothers: 44.3 %; fathers: 34.4 %) and performed a paid job of 32 h per week or more (mothers: 22.1 %; fathers: 60.0 %). The theoretical framework of Vaughn (2016) was leading in the development of the AFPQ. Exploratory factor analysis (EFA) was performed on a random split sample of parent-adolescent dyads and confirmatory factor analysis (CFA) was performed on the other half. The EFA in both parent and adolescent samples resulted in a clear 5 factor solution explaining 61.6 % (AFPQ-p) and 64.2 % (AFPQ-a) of the variance respectively, representing the factors Autonomy Support (α = 0.79/.82), Coercive Control (α = 0.85/.83), Snack Structure (α = 0.79/75), Healthy Structure (α = 0.78/74) and Modelling (α = 0.69/85). CFA confirmed good model fit for the AFPQ-p and the AFPQ-a. Associations with adolescent self-reported food intake were in the expected direction, confirming the preliminary convergent validity of the instrument among a moderate to highly educated group of parent-adolescent dyads. Although the AFPQ provides a promising short instrument, future research in more diverse samples is needed to build evidence on the instrument's psychometric characteristics in other groups., (Copyright © 2021 The Authors. Published by Elsevier Ltd.. All rights reserved.)

Fecal microbiota transplantation (FMT) has been successfully applied to treat recurrent Clostridium difficile infection in humans, but a precise method to measure which bacterial strains stably engraft in recipients and evaluate their association with clinical outcomes is lacking. We assembled a collection of >1,000 different bacterial strains that were cultured from the fecal samples of 22 FMT donors and recipients. Using our strain collection combined with metagenomic sequencing data from the same samples, we developed a statistical approach named Strainer for the detection and tracking of bacterial strains from metagenomic sequencing data. We applied Strainer to evaluate a cohort of 13 FMT longitudinal clinical interventions and detected stable engraftment of 71% of donor microbiota strains in recipients up to 5 years post-FMT. We found that 80% of recipient gut bacterial strains pre-FMT were eliminated by FMT and that post-FMT the strains present persisted up to 5 years later, together with environmentally acquired strains. Quantification of donor bacterial strain engraftment in recipients independently explained (precision 100%, recall 95%) the clinical outcomes (relapse or success) after initial and repeat FMT. We report a compendium of bacterial species and strains that consistently engraft in recipients over time that could be used in defined live biotherapeutic products as an alternative to FMT. Our analytical framework and Strainer can be applied to systematically evaluate either FMT or defined live bacterial therapeutic studies by quantification of strain engraftment in recipients., (© 2021. The Author(s), under exclusive licence to Springer Nature Limited.)

The building evidence for the contribution of microbiota to human disease has spurred an effort to develop therapies that target the gut microbiota. This is particularly evident in inflammatory bowel diseases (IBDs), where clinical trials of fecal microbiota transplantation have shown some efficacy. To aid the development of novel microbiota-targeted therapies and to better understand the biology underpinning such treatments, we have used gnotobiotic mice to model microbiota manipulations in the context of microbiotas from humans with inflammatory bowel disease. Mice colonized with IBD donor-derived microbiotas exhibit a stereotypical set of phenotypes, characterized by abundant mucosal Th17 cells, a deficit in the tolerogenic RORγt + regulatory T (Treg) cell subset, and susceptibility to disease in colitis models. Transplanting healthy donor-derived microbiotas into mice colonized with human IBD microbiotas led to induction of RORγt + Treg cells, which was associated with an increase in the density of the microbiotas following transplant. Microbiota transplant reduced gut Th17 cells in mice colonized with a microbiota from a donor with Crohn's disease. By culturing strains from this microbiota and screening them in vivo, we identified a specific strain that potently induces Th17 cells. Microbiota transplants reduced the relative abundance of this strain in the gut microbiota, which was correlated with a reduction in Th17 cells and protection from colitis., Competing Interests: Competing interest statement: L.S.M., A.B., A.D. and D.G. are employees of Janssen Research and Development. G.B. is a former employee of Janssen Research and Development. G.J.B. and J.J.F. have filed patents related to the work published in this paper. T.J.B. has an interest in the Centre for Digestive Diseases, where fecal microbiota transplantation is a treatment option for patients, and has filed patents in this field. J.-F.C. has served as consultant, advisory board member, or speaker for AbbVie, Amgen, Boehringer-Ingelheim, Celgene Corporation, Celltrion, Enterome, Ferring, Genentech, Janssen, Lilly, Medimmune, Merck & Co., Pfizer, PPM Services, Protagonist, Second Genome, Seres, Shire, Takeda, Theradiag, and Theravance Biopharma, has stock options in Intestinal Biotech Development and Genfit and research grants from AbbVie, Takeda, and Janssen. M.C.D. has served as a consultant for Janssen. A.G. has received lecture fees from Merck and Takeda. J.J.F. has served as consultant, advisory board member, or speaker for Vedanta Biosciences and Janssen and has research grants from Janssen. The remaining authors declare no competing interests., (Copyright © 2020 the Author(s). Published by PNAS.)

The 'Healthy Primary School of the Future' (HPSF) aims to integrate health and well-being within the whole school system. This study examined the two-year effects of HPSF on children's dietary and physical activity (PA) behaviours at school and at home and investigated whether child characteristics or the home context moderated these effects. This study ( n = 1676 children) has a quasi-experimental design with four intervention schools, i.e., two full HPSF (focus: nutrition and PA), two partial HPSF (focus: PA), and four control schools. Measurements consisted of accelerometry (Actigraph GT3X+) and questionnaires. Favourable effects on children's dietary and PA behaviours at school were found in the full HPSF; in the partial HPSF, only on PA behaviours. Children in the full HPSF did not compensate at home for the improved health behaviours at school, while in the partial HPSF, the children became less active at home. In both the full and partial HPSF, less favourable effects at school were found for younger children. At home, less favourable effects were found for children with a lower socioeconomic status. Overall, the effect of the full HPSF on children's dietary and PA behaviours was larger and more equally beneficial for all children than that of the partial HPSF.

The intestinal microbiota is a dynamic community of bacteria, fungi, and viruses that mediates mucosal homeostasis and physiology. Imbalances in the microbiome and aberrant immune responses to gut bacteria can disrupt homeostasis and are associated with inflammatory bowel diseases (IBDs) in humans and colitis in mice. We review genetic variants associated with IBD and their effects on the intestinal microbiome, the immune response, and disease pathogenesis. The intestinal microbiome, which includes microbial antigens, adjuvants, and metabolic products, affects the development and function of the intestinal mucosa, influencing inflammatory responses in the gut. Therefore, strategies to manipulate the microbiome might be used in treatment of IBD. We review microbe-based therapies for IBD and the potential to engineer patients' intestinal microbiota. We discuss how studies of patients with IBD and mouse models have advanced our understanding of the interactions between genetic factors and the gut microbiome, and challenges to the development of microbe-based therapies for IBD., (Copyright © 2019 AGA Institute. Published by Elsevier Inc. All rights reserved.)

The human microbiome, described as an accessory organ because of the crucial functions it provides, is composed of species that are uniquely found in humans 1,2 . Yet, surprisingly little is known about the impact of routine interpersonal contacts in shaping microbiome composition. In a relatively 'closed' cohort of 287 people from the Fiji Islands, where common barriers to bacterial transmission are absent, we examine putative bacterial transmission in individuals' gut and oral microbiomes using strain-level data from both core single-nucleotide polymorphisms and flexible genomic regions. We find a weak signal of transmission, defined by the inferred sharing of genotypes, across many organisms that, in aggregate, reveals strong transmission patterns, most notably within households and between spouses. We were unable to determine the directionality of transmission nor whether it was direct. We further find that women harbour strains more closely related to those harboured by their familial and social contacts than men, and that transmission patterns of oral-associated and gut-associated microbiota need not be the same. Using strain-level data alone, we are able to confidently predict a subset of spouses, highlighting the role of shared susceptibilities, behaviours or social interactions that distinguish specific links in the social network.

Microbiota are thought to influence the development and progression of inflammatory bowel disease (IBD), but determining generalizable effects of microbiota on IBD etiology requires larger-scale functional analyses. We colonized germ-free mice with intestinal microbiotas from 30 healthy and IBD donors and determined the homeostatic intestinal T cell response to each microbiota. Compared to microbiotas from healthy donors, transfer of IBD microbiotas into germ-free mice increased numbers of intestinal Th17 cells and Th2 cells and decreased numbers of RORγt + Treg cells. Colonization with IBD microbiotas exacerbated disease in a model where colitis is induced upon transfer of naive T cells into Rag1 -/- mice. The proportions of Th17 and RORγt + Treg cells induced by each microbiota were predictive of human disease status and accounted for disease severity in the Rag1 -/- colitis model. Thus, an impact on intestinal Th17 and RORγt + Treg cell compartments emerges as a unifying feature of IBD microbiotas, suggesting a general mechanism for microbial contribution to IBD pathogenesis., (Copyright © 2018 Elsevier Inc. All rights reserved.)