Dataset Information

Polyphasic analysis of a middle ages coprolite microbiota, Belgium.

ABSTRACT: Paleomicrobiological investigations of a 14(th)-century coprolite found inside a barrel in Namur, Belgium were done using microscopy, a culture-dependent approach and metagenomics. Results were confirmed by ad hoc PCR--sequencing. Investigations yielded evidence for flora from ancient environment preserved inside the coprolite, indicated by microscopic observation of amoebal cysts, plant fibers, seeds, pollens and mold remains. Seventeen different bacterial species were cultured from the coprolite, mixing organisms known to originate from the environment and organisms known to be gut inhabitants. Metagenomic analyses yielded 107,470 reads, of which known sequences (31.9%) comprised 98.98% bacterial, 0.52% eukaryotic, 0.44% archaeal and 0.06% viral assigned reads. Most abundant bacterial phyla were Proteobacteria, Gemmatimonadetes, Actinobacteria and Bacteroidetes. The 16 S rRNA gene dataset yielded 132,000 trimmed reads and 673 Operational Taxonomic Units. Most abundant bacterial phyla observed in the 16 S rRNA gene dataset belonged to Proteobacteria, Firmicutes, Actinobacteria and Chlamydia. The Namur coprolite yielded typical gut microbiota inhabitants, intestinal parasites Trichuris and Ascaris and systemic pathogens Bartonella and Bordetella. This study adds knowledge to gut microbiota in medieval times.

SUBMITTER: Appelt S

PROVIDER: S-EPMC3938422 | biostudies-literature | 2014

REPOSITORIES: biostudies-literature

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Polyphasic analysis of a middle ages coprolite microbiota, Belgium.

Appelt Sandra S Armougom Fabrice F Le Bailly Matthieu M Robert Catherine C Drancourt Michel M

PloS one 20140228 2

Paleomicrobiological investigations of a 14(th)-century coprolite found inside a barrel in Namur, Belgium were done using microscopy, a culture-dependent approach and metagenomics. Results were confirmed by ad hoc PCR--sequencing. Investigations yielded evidence for flora from ancient environment preserved inside the coprolite, indicated by microscopic observation of amoebal cysts, plant fibers, seeds, pollens and mold remains. Seventeen different bacterial species were cultured from the coproli ...[more]

PMID: 24586319

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Project description:BACKGROUND:Mycobacterium indicus pranii (MIP), popularly known as Mw, is a cultivable, non-pathogenic organism, which, based on its growth and metabolic properties, is classified in Runyon Group IV along with M. fortuitum, M. smegmatis and M. vaccae. The novelty of this bacterium was accredited to its immunological ability to undergo antigen driven blast transformation of leukocytes and delayed hypersensitivity skin test in leprosy patients, a disease endemic in the Indian sub-continent. Consequently, MIP has been extensively evaluated for its biochemical and immunological properties leading to its usage as an immunomodulator in leprosy and tuberculosis patients. However, owing to advances in sequencing and culture techniques, the citing of new strains with almost 100% similarity in the sequences of marker genes like 16S rRNA, has compromised the identity of MIP as a novel species. Hence, to define its precise taxonomic position, we have carried out polyphasic taxonomic studies on MIP that integrate its phenotypic, chemotaxonomic and molecular phylogenetic attributes. METHODOLOGY/PRINCIPAL FINDINGS:The comparative analysis of 16S rRNA sequence of MIP by using BLAST algorithm at NCBI (nr database) revealed a similarity of > or =99% with M. intracellulare, M. arosiense, M. chimaera, M. seoulense, M. avium subsp. hominissuis, M. avium subsp. paratuberculosis and M. bohemicum. Further analysis with other widely used markers like rpoB and hsp65 could resolve the phylogenetic relationship between MIP and other closely related mycobacteria apart from M. intracellulare and M. chimaera, which shares > or =99% similarity with corresponding MIP orthologues. Molecular phylogenetic analysis, based on the concatenation of candidate orthologues of 16S rRNA, hsp65 and rpoB, also substantiated its distinctiveness from all the related organisms used in the analysis excluding M. intracellulare and M. chimaera with which it exhibited a close proximity. This necessitated further analysis of MIP with more sensitive and segregating parameters to ascertain its precise taxonomic position as a new species. The analysis of MIP and its comparison with other mycobacterial reference strains based on cellular and biochemical features, growth characteristics and chemotaxonomic studies like FAME profiling confirmed that MIP is uniquely endowed with diverse metabolic attributes that effectively distinguishes it from all the closely related mycobacteria including M. intracellulare and M. chimaera. CONCLUSION:The results presented in this study coupled with the non-pathogenic nature and different biochemical and immunomodulatory properties of MIP affirm it as a distinct species belonging to M. avium complex (MAC). It is further proposed to use an earlier suggested name Mycobacterium indicus pranii for this newly established mycobacterial species. This study also exemplifies the growing need for a uniform, consensus based broader polyphasic frame work for the purpose of taxonomy and speciation, particularly in the genus Mycobacterium.

Project description:Importance:Noncognitive life skills are patterns of behavior, thoughts, and feelings that complement cognitive ability in promoting positive economic and educational outcomes. These positive attributes have been associated with favorable social and health outcomes at older ages, but their combined association with survival is not known. Objectives:To evaluate the association of the combination of 5 noncognitive life skills with mortality, and to explore the role of sociodemographic, health, cognitive, and behavioral factors in explaining associations. Design, Setting, and Participants:This cohort study used data from wave 5 of the English Longitudinal Study of Ageing, conducted in 2010. Participants included adults 52 years and older. Associations of scores on 5 noncognitive life skills, including conscientiousness, perseverance, emotional stability, optimism, and control, with all-cause mortality were analyzed for a mean (SD) of 7.2 (1.3) years. Data analyses were completed in November 2019. Exposures:Response to wave 5 of the English Longitudinal Study of Ageing. Main Outcomes and Measures:Noncognitive life skills scores, including conscientiousness, perseverance, emotional stability, optimism, and control, were measured by questionnaire. The main outcome was all-cause mortality, and the associations with noncognitive life skills scores were analyzed using Cox proportional hazards regressions models to estimate hazard ratios per 1-SD increase in score. Results:A total of 7850 participants (mean [SD] age, 66.5 [9.0] years; 4333 [55.2%] women) were included. Combined life skill score was positively associated with survival, with a hazard ratio of 0.81 (95% CI, 0.72-0.90) per 1-SD increase in positive attributes after adjustment for age, sex, race/ethnicity, childhood socioeconomic status, educational attainment, baseline chronic disease, depressive symptoms, cognitive function, mobility impairment, social isolation, smoking, physical activity, alcohol intake, and fruit and vegetable consumption (P?<?.001). Excluding deaths during 24 months after baseline as a check for reverse causation showed the same pattern (adjusted hazard ratio, 0.79; 95% CI, 0.70-0.89; P?<?.001). Associations were maintained after each life skill was omitted in turn from the aggregate score, indicating that no single positive attribute accounted for the protective association. Conclusions and Relevance:These findings suggest that noncognitive life skills are associated with survival at older ages. Whether training and education programs could enhance these attributes and influence mortality risk is not known, but fostering and maintaining life skills may be important in later life.

Dataset Information

Polyphasic analysis of a middle ages coprolite microbiota, Belgium.

Publications

Polyphasic analysis of a middle ages coprolite microbiota, Belgium.

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