Fungi in the healthy human gastrointestinal tract

Many species of fungi have been detected in the healthy human gut; however, nearly half of all taxa reported have only been found in one sample or one study. Fungi capable of growing in and colonizing the gut are limited to a small number of species, mostly Candida yeasts and yeasts in the family Dipodascaceae (Galactomyces, Geotrichum, Saprochaete). Malassezia and the filamentous fungus Cladosporium are potential colonizers; more work is needed to clarify their role. Other commonly-detected fungi come from the diet or environment but either cannot or do not colonize (Penicillium and Debaryomyces species, which are common on fermented foods but cannot grow at human body temperature), while still others have dietary or environmental sources (Saccharomyces cerevisiae, a fermentation agent and sometime probiotic; Aspergillus species, ubiquitous molds) yet are likely to impact gut ecology. The gut mycobiome appears less stable than the bacterial microbiome, and is likely subject to environmental factors

The human gut mycobiome: pitfalls and potentials — a mycologist\u27s perspective

We have entered the Age of the Microbiome, with new studies appearing constantly and whole journals devoted to the human microbiome. While bacteria outnumber other gut microbes by orders of magnitude, eukaryotes are consistently found in the human gut, and are represented primarily by the fungi. Compiling 36 studies spanning from 1917 to 2015, we found at least 267 distinct fungal taxa have been reported from the human gut, and seemingly every new study includes one or more fungi not previously described from this niche. This diversity, while impressive, is illusory. If we examine gut fungi, we will quickly observe a division between a small number of commonly detected species (Candida yeasts, Saccharomyces and yeasts in the Dipodascaceae, and Malassezia species), and a long tail of taxa which have only been reported once. Furthermore, an investigation into the ecology of these rare species reveals that many of them are incapable of colonization or long-term persistence in the gut. This paper examines what we know and have yet to learn about the fungal component of the gut microbiome, or “mycobiome”, and an overview of methods. We address the potential of the field while introducing some caveats, and argue for the necessity of including mycologists in mycobiome studies

Fungi in the healthy human gastrointestinal tract

Many species of fungi have been detected in the healthy human gut; however, nearly half of all taxa reported have only been found in one sample or one study. Fungi capable of growing in and colonizing the gut are limited to a small number of species, mostly Candida yeasts and yeasts in the family Dipodascaceae (Galactomyces, Geotrichum, Saprochaete). Malassezia and the filamentous fungus Cladosporium are potential colonizers; more work is needed to clarify their role. Other commonly-detected fungi come from the diet or environment but either cannot or do not colonize (Penicillium and Debaryomyces species, which are common on fermented foods but cannot grow at human body temperature), while still others have dietary or environmental sources (Saccharomyces cerevisiae, a fermentation agent and sometime probiotic; Aspergillus species, ubiquitous molds) yet are likely to impact gut ecology. The gut mycobiome appears less stable than the bacterial microbiome, and is likely subject to environmental factors

Sequence-based Methods for Detecting and Evaluating the Human Gut Mycobiome

We surveyed the fungal microbiota in 16 fecal samples from healthy humans with a vegetarian diet. Fungi were identified using molecular cloning, 454 pyrosequencing and a Luminex analyte specific reagent (ASR) assay, all targeting the ITS region of the rRNA genes. Fungi were detected in each fecal sample and at least 46 distinct fungal operational taxonomic units (OTUs) were detected, from two phyla — Ascomycota and Basidiomycota. Fusarium was the most abundant genus, followed by Malassezia, Penicillium, Aspergillus, and Candida. Commonly detected fungi such as Aspergillus and Penicillium, as well as known dietary fungi Agaricus bisporus and Ophiocordyceps sinensis, are presumed to be transient, allochthonous members due to their abundance in the environment or dietary associations. No single method identified the full diversity of fungi in all samples; pyrosequencing detected more distinct OTUs than the other methods, but failed to detect OTUs in some samples that were detected by cloning and/or ASR assays. ASRs were limited by the commercially available assays, but the potential to design new, optimized assays, coupled with speed and cost, makes the ASR method worthy of further study

Coping and resilience in adults: a cross-sectional network analysis

Background and objectives: Coping and resilience, how we deal with problems and difficulties and recover from misfortune or change, are two well-known interrelated conce

Commensurate and Incommensurate Vortex States in Superconductors with Periodic Pinning Arrays

As a function of applied field, we find a rich variety of ordered and partially-ordered vortex lattice configurations in systems with square or triangular arrays of pinning sites. We present formulas that predict the matching fields at which commensurate vortex configurations occur and the vortex lattice orientation with respect to the pinning lattice. Our results are in excellent agreement with recent imaging experiments on square pinning arrays [K. Harada et al., Science 274, 1167 (1996)].Comment: 9 pages, 3 figures. Accepted to Physical Review

Anastral spindle assembly and γ-tubulin in Drosophila oocytes

<p>Abstract</p> <p>Background</p> <p>Anastral spindles assemble by a mechanism that involves microtubule nucleation and growth from chromatin. It is still uncertain whether γ-tubulin, a microtubule nucleator essential for mitotic spindle assembly and maintenance, plays a role. Not only is the requirement for γ-tubulin to form anastral <it>Drosophila </it>oocyte meiosis I spindles controversial, but its presence in oocyte meiosis I spindles has not been demonstrated and is uncertain.</p> <p>Results</p> <p>We show, for the first time, using a bright GFP fusion protein and live imaging, that the <it>Drosophila </it>maternally-expressed γTub37C is present at low levels in oocyte meiosis I spindles. Despite this, we find that formation of bipolar meiosis I spindles does not require functional γTub37C, extending previous findings by others. Fluorescence photobleaching assays show rapid recovery of γTub37C in the meiosis I spindle, similar to the cytoplasm, indicating weak binding by γTub37C to spindles, and fits of a new, potentially more accurate model for fluorescence recovery yield kinetic parameters consistent with transient, diffusional binding.</p> <p>Conclusions</p> <p>The FRAP results, together with its mutant effects late in meiosis I, indicate that γTub37C may perform a role subsequent to metaphase I, rather than nucleating microtubules for meiosis I spindle formation. Weak binding to the meiosis I spindle could stabilize pre-existing microtubules or position γ-tubulin for function during meiosis II spindle assembly, which follows rapidly upon oocyte activation and completion of the meiosis I division.</p

Changes in knee kinematics reflect the articular geometry after arthroplasty

We hypothesized changes in rotations and translations after TKA with a fixed-bearing anterior cruciate ligament (ACL)-sacrificing but posterior cruciate ligament (PCL)-retaining design with equal-sized, circular femoral condyles would reflect the changes of articular geometry. Using 8 cadaveric knees, we compared the kinematics of normal knees and TKA in a standardized navigated position with defined loads. The quadriceps was tensed and moments and drawer forces applied during knee flexion-extension while recording the kinematics with the navigation system. TKA caused loss of the screw-home; the flexed tibia remained at the externally rotated position of normal full knee extension with considerably increased external rotation from 63° to 11° extension. The range of internal-external rotation was shifted externally from 30° to 20° extension. There was a small tibial posterior translation from 40° to 90° flexion. The varus-valgus alignment and laxity did not change after TKA. Thus, navigated TKA provided good coronal plane alignment but still lost some aspects of physiologic motion. The loss of tibial screw-home was related to the symmetric femoral condyles, but the posterior translation in flexion was opposite the expected change after TKA with the PCL intact and the ACL excised. Thus, the data confirmed our hypothesis for rotations but not for translations. It is not known whether the standard navigated position provides the best match to physiologic kinematics