The gut microbiome is widely accepted to have a significant impact on human health yet, despite years of research on this complex ecosystem, the contributions of different forces driving microbial ...population structure remain to be fully elucidated. The viral component of the human gut microbiome is dominated by bacteriophage, which are known to play crucial roles in shaping microbial composition, driving bacterial diversity, and facilitating horizontal gene transfer. Bacteriophage are also one of the most poorly understood components of the human gut microbiome, with the vast majority of viral sequences sharing little to no homology to reference databases. If we are to understand the dynamics of bacteriophage populations, their interaction with the human microbiome and ultimately their influence on human health, we will depend heavily on sequence based approaches and
tools. This is complicated by the fact that, as with any research field in its infancy, methods of analyses vary and this can impede our ability to compare the outputs of different studies. Here, we discuss the major findings to date regarding the human virome and reflect on our current understanding of how gut bacteriophage shape the microbiome. We consider whether or not the virome field is built on unstable foundations and if so, how can we provide a solid basis for future experimentation. The virome is a challenging yet crucial piece of the human microbiome puzzle. In order to develop our understanding, we will discuss the need to underpin future studies with robust research methods and suggest some solutions to existing challenges.
Although we are nearing a consensus that most ultraluminous X-ray sources (ULXs) below 1041 erg s−1 represent stellar mass black holes accreting in a super-Eddington 'ultraluminous' accretion state, ...little is yet established of the physics of this extreme accretion mode. Here, we use a combined X-ray spectral and timing analysis of an XMM-Newton sample of ULXs to investigate this new accretion regime. We start by suggesting an empirical classification scheme that separates ULXs into three classes based on the spectral morphologies observed by Gladstone et al.: a singly peaked broadened disc class, and two-component hard ultraluminous and soft ultraluminous regimes, with the spectra of the latter two classes dominated by the harder and softer component, respectively. We find that at the lowest luminosities (L
X < 3 × 1039 erg s−1) the ULX population is dominated by sources with broadened disc spectra, whilst ULXs with two-component spectra are seen almost exclusively at higher luminosities, suggestive of a distinction between ∼Eddington and super-Eddington accretion modes. We find high levels of fractional variability are limited to ULXs with soft ultraluminous spectra, and a couple of the broadened disc sources. Furthermore, the variability in these sources is strongest at high energies, suggesting it originates in the harder of the two spectral components. We argue that these properties are consistent with current models of super-Eddington emission, where a massive radiatively driven wind forms a funnel-like geometry around the central regions of the accretion flow. As the wind provides the soft spectral component this suggests that inclination is the key determinant in the observed two-component X-ray spectra, which is very strongly supported by the variability results if this originates due to clumpy material at the edge of the wind intermittently obscuring our line-of-sight to the spectrally hard central regions of the ULX. The pattern of spectral variability with luminosity in two ULXs that straddle the hard/soft ultraluminous regime boundary is consistent with the wind increasing at higher accretion rates, and thus narrowing the opening angle of the funnel. Hence, this work suggests that most ULXs can be explained as stellar mass black holes accreting at and above the Eddington limit, with their observed characteristics dominated by two variables: accretion rate and inclination.
The relationships of major arthropod clades have long been contentious, but refinements in molecular phylogenetics underpin an emerging consensus. Nevertheless, molecular phylogenies have recovered ...topologies that morphological phylogenies have not, including the placement of hexapods within a paraphyletic Crustacea, and an alliance between myriapods and chelicerates. Here we show enhanced congruence between molecular and morphological phylogenies based on 753 morphological characters for 309 fossil and Recent panarthropods. We resolve hexapods within Crustacea, with remipedes as their closest extant relatives, and show that the traditionally close relationship between myriapods and hexapods is an artefact of convergent character acquisition during terrestrialisation. The inclusion of fossil morphology mitigates long-branch artefacts as exemplified by pycnogonids: when fossils are included, they resolve with euchelicerates rather than as a sister taxon to all other euarthropods.
Jet ejection by accreting black holes is a mass invariant mechanism unifying stellar and supermassive black holes (SMBHs) that should also apply for intermediate-mass black holes (IMBHs), which are ...thought to be the seeds from which SMBHs form. We present the detection of an off-nuclear IMBH of ∼5 × 104 M⊙ located in an unusual spiral arm of the galaxy NGC 2276 based on quasi-simultaneous Chandra X-ray observations and European VLBI Network (EVN) radio observations. The IMBH, NGC2276-3c, possesses a 1.8 pc radio jet that is oriented in the same direction as large-scale (∼650 pc) radio lobes and whose emission is consistent with flat to optically thin synchrotron emission between 1.6 and 5 GHz. Its jet kinetic power (4 × 1040 erg s−1) is comparable to its radiative output and its jet efficiency (≥46 per cent) is as large as that of SMBHs. A region of ∼300 pc along the jet devoid of young stars could provide observational evidence of jet feedback from an IMBH. The discovery confirms that the accretion physics is mass invariant and that seed IMBHs in the early Universe possibly had powerful jets that were an important source of feedback.
Three-dimensional fossils, especially those preserving soft-part anatomy, are a rich source of palaeontological information; they can, however, be difficult to work with. Imaging of serial planes ...through an object (tomography) allows study of both the inside and outside of three-dimensional fossils. Tomography may be performed using physical grinding or sawing coupled with photography, through optical techniques of serial focusing, or using a variety of scanning technologies such as neutron tomography, magnetic resonance imaging and most usefully X-ray computed tomography. This latter technique is applicable at a variety of scales, and when combined with a synchrotron X-ray source can produce very high-quality data that may be augmented by phase-contrast information to enhance contrast. Tomographic data can be visualized in several ways, the most effective of which is the production of isosurface-based 'virtual fossils' that can be manipulated and dissected interactively.
Faecalibacterium prausnitzii is a ubiquitous member of the human gut microbiome, constituting up to 15% of the total bacteria in the human gut. Substantial evidence connects decreased levels of F. ...prausnitzii with the onset and progression of certain forms of inflammatory bowel disease, which has been attributed to its anti-inflammatory potential. Two phylogroups of F. prausnitzii have been identified, with a decrease in phylogroup I being a more sensitive marker of intestinal inflammation. Much of the genomic and physiological data available to date was collected using phylogroup II strains. Little analysis of F. prausnitzii genomes has been performed so far and genetic differences between phylogroups I and II are poorly understood.
In this study we sequenced 11 additional F. prausnitzii genomes and performed comparative genomics to investigate intraspecies diversity, functional gene complement and the mobilome of 31 high-quality draft and complete genomes. We reveal a very low level of average nucleotide identity among F. prausnitzii genomes and a high level of genome plasticity. Two genomogroups can be separated based on differences in functional gene complement, albeit that this division does not fully agree with separation based on conserved gene phylogeny, highlighting the importance of horizontal gene transfer in shaping F. prausnitzii genomes. The difference between the two genomogroups is mainly in the complement of genes associated with catabolism of carbohydrates (such as a predicted sialidase gene in genomogroup I) and amino acids, as well as defense mechanisms.
Based on the combination of ANI of genomic sequences, phylogenetic analysis of core proteomes and functional differences we propose to separate the species F. prausnitzii into two new species level taxa: F. prausnitzii sensu stricto (neotype strain A2-165
= DSM 17677
= JCM 31915
) and F. moorei sp. nov. (type strain ATCC 27768
= NCIMB 13872
).
Abstract
In recent work with high-resolution reflection grating spectrometers (RGS) aboard XMM–Newton, Pinto et al. have discovered that two bright and archetypal ultraluminous X-ray sources (ULXs) ...have strong relativistic winds in agreement with theoretical predictions of high accretion rates. It has been proposed that such winds can become optically thick enough to block and reprocess the disc X-ray photons almost entirely, making the source appear as a soft thermal emitter or ultraluminous supersoft X-ray source (ULS). To test this hypothesis, we have studied a ULX where the wind is strong enough to cause significant absorption of the hard X-ray continuum: NGC 55 ULX. The RGS spectrum of NGC 55 ULX shows a wealth of emission and absorption lines blueshifted by significant fractions of the light speed (0.01–0.20)c indicating the presence of a powerful wind. The wind has a complex dynamical structure with the ionization state increasing with the outflow velocity, which may indicate launching from different regions of the accretion disc. The comparison with other ULXs such as NGC 1313 X-1 and NGC 5408 X-1 suggests that NGC 55 ULX is being observed at higher inclination. The wind partly absorbs the source flux above 1 keV, generating a spectral drop similar to that observed in ULSs. The softening of the spectrum at lower (∼ Eddington) luminosities and the detection of a soft lag agree with the scenario of wind clumps crossing the line of sight, partly absorbing and reprocessing the hard X-rays from the innermost region.
We conducted a systematic review of guidelines on the management of low back pain (LBP) to assess their methodological quality and guide care. We synthesized guidelines on the management of LBP ...published from 2005 to 2014 following best evidence synthesis principles. We searched MEDLINE, EMBASE, CINAHL, PsycINFO, Cochrane, DARE, National Health Services Economic Evaluation Database, Health Technology Assessment Database, Index to Chiropractic Literature and grey literature. Independent reviewers critically appraised eligible guidelines using AGREE II criteria. We screened 2504 citations; 13 guidelines were eligible for critical appraisal, and 10 had a low risk of bias. According to high‐quality guidelines: (1) all patients with acute or chronic LBP should receive education, reassurance and instruction on self‐management options; (2) patients with acute LBP should be encouraged to return to activity and may benefit from paracetamol, nonsteroidal anti‐inflammatory drugs (NSAIDs), or spinal manipulation; (3) the management of chronic LBP may include exercise, paracetamol or NSAIDs, manual therapy, acupuncture, and multimodal rehabilitation (combined physical and psychological treatment); and (4) patients with lumbar disc herniation with radiculopathy may benefit from spinal manipulation. Ten guidelines were of high methodological quality, but updating and some methodological improvements are needed. Overall, most guidelines target nonspecific LBP and recommend education, staying active/exercise, manual therapy, and paracetamol or NSAIDs as first‐line treatments. The recommendation to use paracetamol for acute LBP is challenged by recent evidence and needs to be revisited.
Significance
Most high‐quality guidelines recommend education, staying active/exercise, manual therapy and paracetamol/NSAIDs as first‐line treatments for LBP. Recommendation of paracetamol for acute LBP is challenged by recent evidence and needs updating.
Several members of the order Mucorales (subphylum Mucoromycotina) are important agents of severe human infections. The identification of these fungi by using standard mycologic methods is often ...difficult and time consuming. Frequently, the etiological agent in clinical cases is reported either as a Mucor sp., which is not the most frequent genus of zygomycetes, or only as a member of the MUCORALES: For this reason, the actual spectrum of species of zygomycetes and their incidences in the clinical setting is not well known. The goals of this study were to compare the results of the molecular identification of an important set of clinical isolates, received in a mycological reference center from different regions of the United States, with those obtained by using the traditional morphological methods and to determine the spectrum of species involved. We tested 190 isolates morphologically identified as zygomycetes by using sequencing of the internal transcribed spacer (ITS) region of the ribosomal DNA. Molecular identification revealed that Rhizopus oryzae represented approximately half (44.7%) of these isolates. The remainder was identified as Rhizopus microsporus (22.1%), Mucor circinelloides (9.5%), Mycocladus corymbifer (formerly Absidia corymbifera) (5.3%), Rhizomucor pusillus (3.7%), Cunninghamella bertholletiae (3.2%), Mucor indicus (2.6%), Cunninghamella echinulata (1%), and Apophysomyces elegans (0.5%). The most common anatomic sites for clinically significant zygomycetes, as determined by isolates sent to the Fungus Testing Laboratory for identification and/or susceptibility testing and included in this study, were the sinuses, lungs, and various cutaneous locations, at 25.8%, 26.8%, and 28%, respectively. These sites represented approximately 80% of the isolates evaluated. A high level of correlation (92.6%) between morphological and molecular identifications was found.
The taxonomy of the coelomycetes has undergone dramatic changes in recent years, but remains controversial due to the high number of taxa involved, their poor morphological differentiation, the rare ...occurrence of the sexual morphs, and rapid loss of fertility in vitro. In the present study, we revisited the families Cucurbitariaceae and Didymellaceae (Pleosporales, Dothideomycetes), which include numerous plant pathogens, endophytic species associated with a wide host range, and saprobes. The taxonomy of two of the most relevant genera, i.e. Phoma and Pyrenochaeta, remains ambiguous after several phylogenetic studies, and needs further revision. We have studied a total of 143 strains of coelomycetes from clinical or environmental origin, by combining the LSU, ITS, tub2 and rpb2 sequences for a multi-locus analysis and a detailed morphological comparison. The resulting phylogenetic tree revealed that some fungi previously considered as members of Cucurbitariaceae represented five different families, and four of them, Neopyrenochaetaceae, Parapyrenochaetaceae, Pseudopyrenochaetaceae and Pyrenochaetopsidaceae, are proposed here as new. Furthermore, 13 new genera, 28 new species, and 20 new combinations are proposed within the Pleosporineae. Moreover, four new typifications are introduced to stabilise the taxonomy of these fungi.
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