Human methanogen diversity and incidence in healthy and diseased colonic groups using mcrA gene analysis

<p>Abstract</p> <p>Background</p> <p>The incidence and diversity of human methanogens are insufficiently characterised in the gastrointestinal tract of both health and disease. A PCR and clone library methodology targeting the <it>mcrA </it>gene was adopted to facilitate the two-fold aim of surveying the relative incidence of methanogens in health and disease groups and also to provide an overview of methanogen diversity in the human gastrointestinal tract.</p> <p>Results</p> <p>DNA faecal extracts (207 in total) from a group of healthy controls and five gastrointestinal disease groups were investigated. Colorectal cancer, polypectomised, irritable bowel syndrome and the control group had largely equivalent numbers of individuals positive for methanogens (range 45–50%). Methanogen incidence in the inflammatory bowel disease groups was reduced, 24% for ulcerative colitis and 30% for Crohn's disease. Four unique <it>mcrA </it>gene restriction fragment length polymorphism profiles were identified and bioinformatic analyses revealed that the majority of all sequences (94%) retrieved from libraries were 100% identical to <it>Methanobrevibacter smithii mcrA </it>gene. In addition, <it>mcrA </it>gene sequences most closely related to <it>Methanobrevibacter oralis </it>and members of the order <it>Methanosarcinales </it>were also recovered.</p> <p>Conclusion</p> <p>The <it>mcrA </it>gene serves as a useful biomarker for methanogen detection in the human gut and the varying trends of methanogen incidence in the human gut could serve as important indicators of intestinal function. Although <it>Methanobrevibacter smithii </it>is the dominant methanogen in both the distal colon of individuals in health and disease, the diversity of methanogens is greater than previously reported. In conclusion, the low incidence of methanogens in Inflammatory Bowel Disease, the functionality of the methanogens and impact of methane production in addition to competitive interactions between methanogens and other microbial groups in the human gastrointestinal tract warrants further investigation.</p

Moving beyond DNA: towards functional analysis of the vaginal microbiome by non-sequencing-based methods

Over the last two decades, sequencing-based methods have revolutionised our understanding of niche-specific microbial complexity. In the lower female reproductive tract, these approaches have enabled identification of bacterial compositional structures associated with health and disease. Application of metagenomics and metatranscriptomics strategies have provided insight into the putative function of these communities but it is increasingly clear that direct measures of microbial and host cell function are required to understand the contribution of microbe–host interactions to pathophysiology. Here we explore and discuss current methods and approaches, many of which rely upon mass-spectrometry, being used to capture functional insight into the vaginal mucosal interface. In addition to improving mechanistic understanding, these methods offer innovative solutions for the development of diagnostic and therapeutic strategies designed to improve women’s health

Gamma-ray emission revealed at the western edge of SNR G344.7-0.1

We report on the investigation of a very high energy (VHE), Galactic gamma-ray source recently discovered at >50GeV using the Large Area Telescope (LAT) on board the Fermi Gamma-Ray Space Telescope. This object, 2FHL J1703.4-4145, displays a very hard >50GeV spectrum with a photon index ~1.2 in the 2FHL catalog and, as such, is one of the most extreme sources in the 2FHL sub-sample of Galactic objects. A detailed analysis of the available multi-wavelength data shows that this source is located on the western edge of the supernova remnant (SNR) G344.7--0.1, along with extended TeV source, HESS J1702-420. The observations and the spectral energy distribution modeling support a scenario where this gamma-ray source is the byproduct of the interaction between the SNR shock and the dense surrounding medium, with escaping cosmic rays (CRs) diffusing into the dense environment and interacting with a large local cloud, generating the observed TeV emission. If confirmed, an interaction between the SNR CRs and a nearby cloud would make 2FHL J1703.4-4145 another promising candidate for efficient particle acceleration of the 2FHL Galactic sample, following the first candidate from our previous investigation of a likely shock-cloud interaction occurring on the West edge of the Vela SNR.Comment: 9 pages, 7 figures, Submitted to ApJ June 15, 2020. Accepted for publication Oct 2, 202

Combined metagenomic and phenomic approaches identify a novel salt tolerance gene from the human gut microbiome

In the current study, a number of salt-tolerant clones previously isolated from a human gut metagenomic library were screened using Phenotype MicroArray (PM) technology to assess their functional capacity. One clone, SMG 9, was found to be positive for utilisation/transport of L-carnitine (a well-characterised osmoprotectant) in the presence of 6% w/v sodium chloride (NaCl). Subsequent experiments revealed a significant growth advantage in minimal media containing NaCl and L-carnitine. Fosmid sequencing revealed putative candidate genes responsible for the phenotype. Subsequent cloning of two genes did not replicate the L-carnitine-associated phenotype, although one of the genes, a σ54-dependent transcriptional regulator, did confer salt tolerance to Escherichia coli when expressed in isolation. The original clone, SMG 9, was subsequently found to have lost the original observed phenotype upon further investigation. Nevertheless, this study demonstrates the usefulness of a phenomic approach to assign a functional role to metagenome-derived clones

Metagenomic Identification of a Novel Salt Tolerance Gene from the Human Gut Microbiome Which Encodes a Membrane Protein with Homology to a brp/blh-Family beta-Carotene 15,15\u27-Monooxygenase

The human gut microbiome consists of at least 3 million non-redundant genes, 150 times that of the core human genome. Herein, we report the identification and characterisation of a novel stress tolerance gene from the human gut metagenome. The locus, assigned brpA, encodes a membrane protein with homology to a brp/blh-family β-carotene monooxygenase. Cloning and heterologous expression of brpA in Escherichia coli confers a significant salt tolerance phenotype. Furthermore, when cultured in the presence of exogenous β-carotene, cell pellets adopt a red/orange pigmentation indicating the incorporation of carotenoids in the cell membrane

Are bullies more productive? Empirical study of affectiveness vs. issue fixing time

Human Affectiveness, i.e., The emotional state of a person, plays a crucial role in many domains where it can make or break a team's ability to produce successful products. Software development is a collaborative activity as well, yet there is little information on how affectiveness impacts software productivity. As a first measure of this impact, this paper analyzes the relation between sentiment, emotions and politeness of developers in more than 560K Jira comments with the time to fix a Jira issue. We found that the happier developers are (expressing emotions such as JOY and LOVE in their comments), the shorter the issue fixing time is likely to be. In contrast, negative emotions such as SADNESS, are linked with longer issue fixing time. Politeness plays a more complex role and we empirically analyze its impact on developers' productivity

Dissimilarity of the gut-lung axis and dysbiosis of the lower airways in ventilated preterm infants.

BACKGROUND: Chronic lung disease of prematurity (CLD), also called bronchopulmonary dysplasia, is a major consequence of preterm birth but the role of the microbiome in its development remains unclear. We, therefore, assessed the progression of the bacterial community in ventilated preterm infants over time in the upper and lower airways, and assessed the gut-lung axis by comparing the upper and lower airways bacterial communities with the stool findings. Finally, we assessed if the bacterial communities were associated with lung inflammation to suggest dysbiosis. METHODS: We serially sampled multiple anatomical sites including the upper airway (nasopharyngeal aspirates, NPA), lower airways (tracheal aspirate fluid, TAF, and bronchoalveolar lavage fluid, BAL) and the gut (stool) of ventilated preterm-born infants. Bacterial DNA load was measured in all samples and sequenced using the V3-V4 region of the 16S rRNA gene RESULTS: From 1102 (539 NPA, 276 TAF, 89 BAL, 198 stool) samples from 55 preterm infants, 352 (32%) amplified suitably for 16 s RNA gene sequencing. Bacterial load was low at birth, quickly increased with time but was associated with predominant operational taxonomic units (OTUs) in all sample types. There was dissimilarity in bacterial communities between the upper and lower airways and the gut with a separate dysbiotic inflammatory process occurring in the lower airways of infants. Individual OTUs were associated with increased inflammatory markers. CONCLUSIONS: Taken together, these findings suggest that targeted treatment of the predominant organisms, including those not routinely treated such as Ureaplasma spp., may decrease the development of CLD in preterm-born infants

Bifunctional Paramagnetic and Luminescent Clays Obtained by Incorporation of Gd3+and Eu3+Ions in the Saponite Framework

A novel bifunctional saponite clay incorporating gadolinium (Gd3+) and europium (Eu3+) in the inorganic framework was prepared by one-pot hydrothermal synthesis. The material exhibited interesting luminescent and paramagnetic features derived from the co-presence of the lanthanide ions in equivalent structural positions. Relaxometry and photoluminescence spectroscopy shed light on the chemical environment surrounding the metal sites, the emission properties of Eu3+, and the dynamics of interactions between Gd3+ and the inner-sphere water placed in the saponite gallery. The optical and paramagnetic properties of this solid make it an attractive nanoplatform for bimodal diagnostic applications

The properties of the AGN torus as revealed from a set of unbiased NuSTAR observations

The obscuration observed in active galactic nuclei (AGN) is mainly caused by dust and gas distributed in a torus-like structure surrounding the supermassive black hole (SMBH). However, properties of the obscuring torus of the AGN in X-ray have not been fully investigated yet due to the lack of high-quality data and proper models. In this work, we perform a broadband X-ray spectral analysis of a large, unbiased sample of obscured AGN (with line-of-sight column density 23$\le$log(NH)$\le$24) in the nearby universe which has high-quality archival NuSTAR data. The source spectra are analyzed using the recently developed borus02 model, which enables us to accurately characterize the physical and geometrical properties of AGN obscuring tori. We also compare our results obtained from the unbiased Compton thin AGN with those of Compton-thick AGN. We find that Compton thin and Compton-thick AGN may possess similar tori, whose average column density is Compton thick (N$\rm _{H,tor,ave}$ $\sim$1.4$\times$10$^{24}$ cm$^{-2}$), but they are observed through different (under-dense or over-dense) regions of the tori. We also find that the obscuring torus medium is significantly inhomogeneous, with the torus average column densities significantly different from their line-of-sight column densities (for most of the sources in the sample). The average torus covering factor of sources in our unbiased sample is c$_f$=0.67, suggesting that the fraction of unobscured AGN is $\sim$33%. We develop a new method to measure the intrinsic line-of-sight column density distribution of AGN in the nearby universe, which we find the result is in good agreement with the constraints from recent population synthesis models.Comment: 16 pages, 14 figures, 7 tables; accepted by A&