Mobile genes in the human microbiome are structured from global to individual scales.

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. However, mobile genes can confer profoundly different phenotypes on different strains of the same species. Little is known about the function and distribution of mobile genes in the human microbiome, and in particular whether the gene pool is globally homogenous or constrained by human population structure. Here, we investigate this question by comparing the mobile genes found in the microbiomes of 81 metropolitan North Americans with those of 172 agrarian Fiji islanders using a combination of single-cell genomics and metagenomics. We find large differences in mobile gene content between the Fijian and North American microbiomes, with functional variation that mirrors known dietary differences such as the excess of plant-based starch degradation genes found in Fijian individuals. Notably, we also observed differences between the mobile gene pools of neighbouring Fijian villages, even though microbiome composition across villages is similar. Finally, we observe high rates of recombination leading to individual-specific mobile elements, suggesting that the abundance of some genes may reflect environmental selection rather than dispersal limitation. Together, these data support the hypothesis that human activities and behaviours provide selective pressures that shape mobile gene pools, and that acquisition of mobile genes is important for colonizing specific human populations.

Characterization of Intestinal Microbiota in Ulcerative Colitis Patients with and without Primary Sclerosing Cholangitis.

BACKGROUND AND AIMS: There is an unexplained association between ulcerative colitis [UC] and primary sclerosing cholangitis [PSC], with the intestinal microbiota implicated as an important factor. The study aim was to compare the structure of the intestinal microbiota of patients with UC with and without PSC. METHODS: UC patients with PSC [PSC-UC] and without PSC [UC] were identified from biobanks at Oslo University Hospital, Foothills Hospital Calgary and Mount Sinai Hospital Toronto. Microbial DNA was extracted from colonic tissue and sequencing performed of the V4 region of the 16S rRNA gene on Illumina MiSeq. Sequences were assigned to operational taxonomic units [OTUs] using Quantitative Insights Into Microbial Ecology [QIIME]. Microbial alpha diversity, beta diversity, and relative abundance were compared between PSC-UC and UC phenotypes. RESULTS: In all, 31 PSC-UC patients and 56 UC patients were included. Principal coordinate analysis [PCoA] demonstrated that city of sample collection was the strongest determinant of taxonomic profile. In the Oslo cohort, Chao 1 index was modestly decreased in PSC-UC compared with UC [p = 0.04] but did not differ significantly in the Calgary cohort. No clustering by PSC phenotype was observed using beta diversity measures. For multiple microbial genera there were nominally significant differences between UC and PSC-UC, but results were not robust to false-discovery rate correction. CONCLUSIONS: No strong PSC-specific microbial associations in UC patients consistent across different cohorts were identified. Recruitment centre had a strong effect on microbial composition. Future studies should include larger cohorts to increase power and the ability to control for confounding factors.

Clarifying concepts of food parenting practices. A Delphi study with an application to snacking behavior.

Inconsistencies in measurements of food parenting practices continue to exist. Fundamental to this problem is the lack of clarity about what is understood by different concepts of food parenting practices. The purpose of this study was to clarify food parenting practice concepts related to snacking. A three round Delphi study among an international group of experts (n = 63) was conducted. In the first round, an open-ended survey was used to collect food parenting practice descriptions and concept labels associated with those practices. In the second round, participants were asked to match up descriptions with the appropriate concept labels. The third and final round allowed participants to reconsider how descriptions and concept labels were matched, taking into account the opinions expressed in round two. Round one produced 408 descriptions of food parenting practices and 110 different concept names. Round two started with 116 descriptions of food parenting practices and 20 concept names. On 40 descriptions, consensus regarding the underlying concept name was reached in round two. Of the remaining 76 descriptions, consensus on 47 descriptions regarding the underlying concept name was reached in round three. The present study supports the essential process of consensus development with respect to food parenting practices concepts.

The intestinal microbiome in type 1 diabetes.

Few concepts in recent years have garnered more disease research attention than that of the intestinal (i.e. 'gut') microbiome. This emerging interest has included investigations of the microbiome's role in the pathogenesis of a variety of autoimmune disorders, including type 1 diabetes (T1D). Indeed, a growing number of recent studies of patients with T1D or at varying levels of risk for this disease, as well as in animal models of the disorder, lend increasing support to the notion that alterations in the microbiome precede T1D onset. Herein, we review these investigations, examining the mechanisms by which the microbiome may influence T1D development and explore how multi-disciplinary analysis of the microbiome and the host immune response may provide novel biomarkers and therapeutic options for prevention of T1D.

Identification of lactic acid bacteria in Moroccan raw milk and traditionally fermented skimmed milk 'lben'.

AIMS: To identify lactic acid bacteria (LAB) present in Moroccan dairy products to establish and preserve their microbial species diversity. METHODS AND RESULTS: Thirty-seven samples were collected from different farms. A total of 146 LAB were isolated and subjected to (GTG)(5)-PCR analysis. Comparison of the profiles with data available at the Moroccan Coordinated Collections of Micro-organisms allowed identification of 85 isolates. The remaining 61 were subjected to SDS-PAGE analysis of whole cell proteins. Comparison of the profiles with data available at the Belgian Coordinated Collections of Micro-organisms allowed identification of 43 isolates. Several of the remaining 18 isolates exhibited identical protein electrophoretic fingerprints. Therefore, eight representatives of them were subjected to partial pheS gene sequencing which allowed identification of all remaining isolates. In raw milk, six genera were found while in 'lben', three were found. This is the first report of Leuconostoc kimchii in dairy products. CONCLUSIONS: LAB diversity was established using a stepwise polyphasic identification approach. It used the expertise of both research bodies involved in this study and proved to be cost-effective for the identification of all isolates. SIGNIFICANCE AND IMPACT OF THE STUDY: To establish LAB diversity in Moroccan dairy products which could be a source of strains with specific properties.

Phylogeny and molecular identification of vibrios on the basis of multilocus sequence analysis.

We analyzed the usefulness of rpoA, recA, and pyrH gene sequences for the identification of vibrios. We sequenced fragments of these loci from a collection of 208 representative strains, including 192 well-documented Vibrionaceae strains and 16 presumptive Vibrio isolates associated with coral bleaching. In order to determine the intraspecies variation among the three loci, we included several representative strains per species. The phylogenetic trees constructed with the different genetic loci were roughly in agreement with former polyphasic taxonomic studies, including the 16S rRNA-based phylogeny of vibrios. The families Vibrionaceae, Photobacteriaceae, Enterovibrionaceae, and Salinivibrionaceae were all differentiated on the basis of each genetic locus. Each species clearly formed separated clusters with at least 98, 94, and 94% rpoA, recA, and pyrH gene sequence similarity, respectively. The genus Vibrio was heterogeneous and polyphyletic, with Vibrio fischeri, V. logei, and V. wodanis grouping closer to the Photobacterium genus. V. halioticoli-, V. harveyi-, V. splendidus-, and V. tubiashii-related species formed groups within the genus Vibrio. Overall, the three genetic loci were more discriminatory among species than were 16S rRNA sequences. In some cases, e.g., within the V. splendidus and V. tubiashii group, rpoA gene sequences were slightly less discriminatory than recA and pyrH sequences. In these cases, the combination of several loci will yield the most robust identification. We can conclude that strains of the same species will have at least 98, 94, and 94% rpoA, recA, and pyrH gene sequence similarity, respectively.

Phylogeny and identification of Enterococci by atpA gene sequence analysis.

The relatedness among 91 Enterococcus strains representing all validly described species was investigated by comparing a 1,102-bp fragment of atpA, the gene encoding the alpha subunit of ATP synthase. The relationships observed were in agreement with the phylogeny inferred from 16S rRNA gene sequence analysis. However, atpA gene sequences were much more discriminatory than 16S rRNA for species differentiation. All species were differentiated on the basis of atpA sequences with, at a maximum, 92% similarity. Six members of the Enterococcus faecium species group (E. faecium, E. hirae, E. durans, E. villorum, E. mundtii, and E. ratti) showed > 99% 16S rRNA gene sequence similarity, but the highest value of atpA gene sequence similarity was only 89.9%. The intraspecies atpA sequence similarities for all species except E. faecium strains varied from 98.6 to 100%; the E. faecium strains had a lower atpA sequence similarity of 96.3%. Our data clearly show that atpA provides an alternative tool for the phylogenetic study and identification of enterococci.

Screening of bacterial contamination during gelatine production by means of denaturing gradient gel electrophoresis, focussed on Bacillus and related endospore-forming genera.

AIMS: To screen for bacterial contamination during gelatine production by means of denaturing gradient gel electrophoresis (DGGE). As members of Bacillus and related genera were found to persist in the final product, this study focussed on these taxa. METHODS AND RESULTS: Template DNA was extracted from gelatine samples at five crucial points of a gelatine production process. A primer specific for Bacillus and related genera was designed and used in a selective PCR, followed by a nested DGGE-PCR targeting the V9 region of the 16S rDNA. DGGE analysis of the resulting amplicons, and sequence analysis of selected bands, showed high sequence similarities of these bands with Bacillus fumarioli, B. licheniformis, B. coagulans and Clostridium perfringens. When the selective PCR was omitted, primarily Lactobacillus bands were retrieved. CONCLUSIONS: PCR-DGGE analysis of gelatine extracts can be used for tracing and screening of bacterial contamination during gelatine production. A selective PCR, nested with DGGE-PCR, gave much more accurate information about endospore-forming contaminants than did the direct DGGE procedure alone. SIGNIFICANCE AND IMPACT OF THE STUDY: Use of this nested DGGE-PCR protocol may provide important information about possible hazards to the final microbiological quality and/or safety of gelatine, so allowing production parameters and/or remediation procedures may be adjusted on-line.

Applicability of rep-PCR fingerprinting for identification of Lactobacillus species.

PCR amplification of repetitive bacterial DNA elements fingerprinting using the (GTG)(5) primer ((GTG)(5)-PCR) was proven to be useful for differentiation of a wide range of lactobacilli (i.e. 26 different (sub)species) at the species, subspecies and potentially up to the strain level. Using this rapid and reproducible genotypic technique, new Lactobacillus isolates recovered from different types of fermented dry sausage could be reliable identified at the (sub)species level. In conclusion, (GTG)(5)-PCR was found to be a promising genotypic tool for rapid and reliable speciation and typing of lactobacilli and other lactic acid bacteria important in food-fermentation industries.

Comparison of the antimicrobial tolerance of oxytetracycline-resistant heterotrophic bacteria isolated from hospital sewage and freshwater fishfarm water in Belgium.

The aim of this study was to investigate the relationship between antimicrobial tolerance and taxonomic diversity among the culturable oxytetracycline-resistant (Ot(r)) heterotrophic bacterial population in two Belgian aquatic sites receiving wastewater either from human medicine or from aquaculture. The study of Ot(r) heterotrophs and mesophilic Aeromonas spp. allowed comparison of tolerance data at the intergenus as well as at the intragenus level. In total, 354 independently obtained Ot(r) isolates were subjected to antimicrobial tolerance testing and identified by GLC analysis of their cellular fatty acid methyl esters (FAMEs), by API 20E profiling and/or by Fluorescent Amplified Fragment Length Polymorphism (FAFLP) DNA fingerprinting. In general, Ot(r) hospital heterotrophs displayed a higher frequency (84%) of ampicillin (Amp) tolerance compared to the Ot(r) heterotrophs from the freshwater fishfarm site (22%). FAME results indicated that this effect was linked to the predominance of intrinsically ampicillin-resistant Ot(r) Aeromonas strains over representatives of Acinetobacter and Escherichia coli within the hospital strain set. Among the Ot(r) mesophilic Aeromonas strain set, the global tolerance profiles of the two sites only differed in a higher number of kanamycin (Kan) -tolerant strains (43%) for hospital aeromonads in comparison with the fishfarm aeromonads (8%). To some extent, this finding was correlated with the specific presence of Aeromonas caviae DNA hybridisation group (HG) 4. Collectively, these results suggest that the profiles for Amp and Kan tolerance observed in both sites arose from taxonomic differences in the culturable Ot(r) bacterial population at the generic or subgeneric level. In addition, our identification data also revealed that Enterobacter sp., Stenotrophomonas maltophilia, and A. veronii biovar sobria HG8 may be considered potential indicator organisms to assess microbial tolerance in various compartments of the aquatic environment.

Isolation and identification of tetracycline resistant lactic acid bacteria from pre-packed sliced meat products.

In recent years, the food chain has been recognised as one of the main routes for transmission of antibiotic resistant bacteria between the animal and human population. In this regard, the current study aimed to investigate if tetracycline resistant (tetR) lactic acid bacteria (LAB) are present in ready-to-eat modified atmosphere packed (MAP) sliced meat products including fermented dry sausage, cooked chicken breast meat and cooked ham. From population graphs based on doubling tetracycline concentrations between 0 and 256 microg ml(-1), only fermented dry sausage was shown to contain a high-level retR LAB population (5.10(1) - 2,23.10(4) CFU/g), and this in four out of ten examined sausages. From these four positive sausages, a total of 100 strains were isolated on de Man, Rogosa and Sharpe-sorbic acid (MRS-S) agar without tetracycline (n = 45) and on MRS-S agar supplemented with a tetracycline breakpoint concentration of 64 microg ml(-1) (n = 55). Using resistance histograms derived from the disc diffusion method, all these strains were grouped as sensitive to rifampicin, erythromycin and ampicillin. All strains from the tetracycline-containing MRS-S plates were resistant to tetracycline. Identification with whole-cell protein profiling revealed that the total strain set represented four different species: Pediococcus pentosaceus, Lactobacillus plantarum, Lactobacillus sakei subsp. carnosus and Lactobacillus curvatus. All species are commonly associated with fermented dry sausage, either as starter culture or as natural contaminants. The latter three species were found to comprise all tetracycline resistant strains. To our knowledge, this is the first report providing evidence for the presence of tetR LAB in final ready-to-eat pre-packed fermented dry sausages.

[The risk of developing osteoporosis in rheumatic diseases]. / Risk razvitiia osteoporoza pri revmaticheskikh zabolevaniiakh.

Although osteoporosis is frequently associated with rheumatic diseases, at present it is not clear if osteoporosis is due to local factors as for example disease and inflammation, or to a systemic factor related to the rheumatic condition. In this review the present stage of knowledge on the inverse relationship between primary osteoarthritis and primary osteoporosis, bone metabolism in rheumatoid arthritis, the effect of corticosteroids on bone in rheumatoid arthritis, and preventive and curative therapy for osteoporosis is discussed.

Contact dermatitis caused by airborne agents. A review and case reports.

A general review is given of airborne-induced contact dermatoses, particularly of the irritant and allergenic types. Because the reports in the literature often omit the term airborne, 12 volumes of Contact Dermatitis (January 1975-July 1985) were screened, and the cases cited were classified in function of the anamnesis, lesion locations, causative irritants and allergens, and other factors. The present article also discusses differential diagnoses, in particular with regard to contact dermatitis of the face, ears, and neck. Finally, seven case reports of occupational and nonoccupational contact dermatitis problems caused by airborne agents are presented. In some of the cases the allergens have not been mentioned in published literature previously.

Allergic contact dermatitis to topical corticosteroids: clobetasol propionate and clobetasone butyrate.

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-alpha-fluoro-corticosteroids, were patch test negative. The literature on contact dermatitis reactions to corticosteroids is reviewed.

Ketoconazole (R 41 400) in the treatment of dermatophyte infections: a clinical, mycological, and morphological study.

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 microgram/ml and above. No evidence for the development of drug resistance was obtained from regular in vitro sensitivity tests.