Special issue : The Human Intestinal Microbiota

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16S rRNA gene-based profiling of the human infant gut microbiota is strongly influenced by sample processing and PCR primer choice

Acknowledgements The authors acknowledge the assistance of Grietje Holtrop (RINH-BioSS) with the statistical analysis of the data and the Wellcome Trust Sanger Institute’s 454 pyrosequencing team for generating 16S rRNA gene data. AWW, PS and JP received core funding support from the Wellcome Trust [grant number 098051]. AWW, JCM, HJF and KPS are funded by the Scottish Government (SG-RESAS).Peer reviewedPublisher PD

Pro-inflammatory flagellin proteins of prevalent motile commensal bacteria are variably abundant in the intestinal microbiome of elderly humans

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Polysaccharide utilization loci and nutritional specialization in a dominant group of butyrate-producing human colonic Firmicutes

Acknowledgements The Rowett Institute of Nutrition and Health (University of Aberdeen) receives financial support from the Scottish Government Rural and Environmental Sciences and Analytical Services (RESAS). POS is a PhD student supported by the Scottish Government (RESAS) and the Science Foundation Ireland, through a centre award to the APC Microbiome Institute, Cork, Ireland. Data Summary The high-quality draft genomes generated in this work were deposited at the European Nucleotide Archive under the following accession numbers: 1. Eubacterium rectale T1-815; CVRQ01000001–CVRQ0100 0090: http://www.ebi.ac.uk/ena/data/view/PRJEB9320 2. Roseburia faecis M72/1; CVRR01000001–CVRR010001 01: http://www.ebi.ac.uk/ena/data/view/PRJEB9321 3. Roseburia inulinivorans L1-83; CVRS01000001–CVRS0 100 0151: http://www.ebi.ac.uk/ena/data/view/PRJEB9322Peer reviewedPublisher PD

Heterologous gene expression in the human gut bacteria Eubacterium rectale and Roseburia inulinivorans by means of conjugative plasmids

Acknowledgements The Rowett Institute (University of Aberdeen) receives financial support from the Scottish Government Rural and Environmental Sciences and Analytical Services (RESAS). POS was a PhD student supported by the Scottish Government (RESAS) and the Science Foundation Ireland, through a centre award (12/RC/2273) to APC Microbiome Ireland, Cork, Ireland.Peer reviewedPostprin

Alveolar soft part sarcoma of the uterine cervix

Alveolar soft part sarcoma is a histologically distinctive neoplasm of uncertain histogenesis. Since its initial description in 1952, more than 200 cases have been reported. The extremities are most often the sites of involvement; the tongue, bones, and the orbit have been less commonly involved. The present paper describes a case of alveolar soft part sarcoma which was present only within the uterine cervix of a 37-year-old woman. Histologically, the tumor cells were arranged in the characteristic alveolar pattern; diagnostic PAS-positive diastase-resistant needle-shaped crystals were observed within the cytoplasm of the tumor cells. After the initial biopsy, the patient underwent a radical hysterectomy and pelvic lymph node dissection. Although no residual tumor was found within the cervix, a microscopic focus of tumor was detected in an obturator lymph node. The patient is at present clinically free of disease.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/25551/1/0000093.pd

UV Screening in Native and Non-native Plant Species in the Tropical Alpine: Implications for Climate Change-Driven Migration of Species to Higher Elevations

Ongoing changes in Earth’s climate are shifting the elevation ranges of many plant species with non-native species often experiencing greater expansion into higher elevations than native species. These climate change-induced shifts in distributions inevitably expose plants to novel biotic and abiotic environments, including altered solar ultraviolet (UV)-B (280–315 nm) radiation regimes. Do the greater migration potentials of non-native species into higher elevations imply that they have more effective UV-protective mechanisms than native species? In this study, we surveyed leaf epidermal UV-A transmittance (TUVA) in a diversity of plant species representing different growth forms to test whether native and non-native species growing above 2800 m elevation on Mauna Kea, Hawaii differed in their UV screening capabilities. We further compared the degree to which TUVA varied along an elevation gradient in the native shrub Vaccinium reticulatum and the introduced forb Verbascum thapsus to evaluate whether these species differed in their abilities to adjust their levels of UV screening in response to elevation changes in UV-B. For plants growing in the Mauna Kea alpine/upper subalpine, we found that adaxial TUVA, measured with a UVA-PAM fluorometer, varied significantly among species but did not differ between native (mean = 6.0%; n = 8) and non-native (mean = 5.8%; n = 11) species. When data were pooled across native and non-native taxa, we also found no significant effect of growth form on TUVA, though woody plants (shrubs and trees) were represented solely by native species whereas herbaceous growth forms (grasses and forbs) were dominated by non-native species. Along an elevation gradient spanning 2600–3800 m, TUVA was variable (mean range = 6.0–11.2%) and strongly correlated with elevation and relative biologically effective UV-B in the exotic V. thapsus; however, TUVA was consistently low (3%) and did not vary with elevation in the native V. reticulatum. Results indicate that high levels of UV protection occur in both native and non-native species in this high UV-B tropical alpine environment, and that flexibility in UV screening is a mechanism employed by some, but not all species to cope with varying solar UV-B exposures along elevation gradients. © 2017 Barnes, Ryel and Flint

Distribution, organization and expression of genes concerned with anaerobic lactate utilization in human intestinal bacteria

Lactate accumulation in the human gut is linked to a range of deleterious health impacts. However, lactate is consumed and converted to the beneficial short-chain fatty acids butyrate and propionate by indigenous lactate-utilizing bacteria. To better understand the underlying genetic basis for lactate utilization, transcriptomic analyses were performed for two prominent lactate-utilizing species from the human gut, Anaerobutyricum soehngenii and Coprococcus catus , during growth on lactate, hexose sugar or hexose plus lactate. In A. soehngenii L2-7 six genes of the lactate utilization (lct) cluster, including NAD-independent d-lactate dehydrogenase (d-iLDH), were co-ordinately upregulated during growth on equimolar d- and l-lactate (dl-lactate). Upregulated genes included an acyl-CoA dehydrogenase related to butyryl-CoA dehydrogenase, which may play a role in transferring reducing equivalents between reduction of crotonyl-CoA and oxidation of lactate. Genes upregulated in C. catus GD/7 included a six-gene cluster (lap) encoding propionyl CoA-transferase, a putative lactoyl-CoA epimerase, lactoyl-CoA dehydratase and lactate permease, and two unlinked acyl-CoA dehydrogenase genes that are candidates for acryloyl-CoA reductase. A d-iLDH homologue in C. catus is encoded by a separate, partial lct, gene cluster, but not upregulated on lactate. While C. catus converts three mols of dl-lactate via the acrylate pathway to two mols propionate and one mol acetate, some of the acetate can be re-used with additional lactate to produce butyrate. A key regulatory difference is that while glucose partially repressed lct cluster expression in A. soehngenii , there was no repression of lactate-utilization genes by fructose in the non-glucose utilizer C. catus . This suggests that these species could occupy different ecological niches for lactate utilization in the gut, which may be important factors to consider when developing lactate-utilizing bacteria as novel candidate probiotics

Impact of carbohydrate substrate complexity on the diversity of the human colonic microbiota.

The diversity of the colonic microbial community has been linked with health in adults and diet composition is one possible determinant of diversity. We used carefully controlled conditions in vitro to determine how the complexity and multiplicity of growth substrates influence species diversity of the human colonic microbiota. In each experiment, five parallel anaerobic fermenters that received identical faecal inocula were supplied continuously with single carbohydrates (either arabinoxylan-oligosaccharides (AXOS), pectin or inulin) or with a '3-mix' of all three carbohydrates, or with a '6-mix' that additionally contained resistant starch, β-glucan and galactomannan as energy sources. Inulin supported less microbial diversity over the first 6 d than the other two single substrates or the 3- and 6-mixes, showing that substrate complexity is key to influencing microbiota diversity. The communities enriched in these fermenters did not differ greatly at the phylum and family level, but were markedly different at the species level. Certain species were promoted by single substrates, whilst others (such as Bacteroides ovatus, LEfSe P = 0.001) showed significantly greater success with the mixed substrate. The complex polysaccharides such as pectin and arabinoxylan-oligosaccharides promoted greater diversity than simple homopolymers, such as inulin. These findings suggest that dietary strategies intended to achieve health benefits by increasing gut microbiota diversity should employ complex non-digestible substrates and substrate mixtures

Plant responses to fluctuating UV environments

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