Characterisation of the octogenarians presenting to the diagnostic heart failure clinic: SHEAF registry.

Introduction: Heart failure (HF) incidence is increasing in older adults with high hospitalisation and mortality rates. Treatment is complicated by side effects and comorbidities. We investigated the clinical characteristics of octogenarians presenting to the HF clinic.

Investigation of machine learning algorithms for taxonomic classification of marine metagenomes.

Taxonomic profiling of microbial communities is essential to model microbial interactions and inform habitat conservation. This work develops approaches in constructing training/testing data sets from publicly available marine metagenomes and evaluates the performance of machine learning (ML) approaches in read-based taxonomic classification of marine metagenomes. Predictions from two models are used to test accuracy in metagenomic classification and to guide improvements in ML approaches.

Extraction Free RT-PCR Surveillance Testing and Reporting for SARS-CoV-2.

The COVID-19 pandemic necessitated sensitive, fast and inexpensive testing for the virus on university campuses across the nation in 2020 prior to the widespread availability of vaccines. Early testing efforts were limited by bottlenecks on reagents, low throughput testing options and slow return of test results. In this paper we detail the testing pipeline we established at the University of Wisconsin-Madison for rapid, inexpensive and sensitive surveillance testing for SARS-CoV-2 and highlight the strengths of the platform that would allow it to be applied to other disease surveillance projects, SARS-CoV-2 variant testing or future pandemics.

Decoding dissolved information: environmental DNA sequencing at global scale to monitor a changing ocean.

The use of environmental DNA (eDNA) technology for environmental monitoring is rapidly expanding, with applications for fisheries, coral reefs, harmful algal blooms, invasive and endangered species, and biodiversity monitoring. By enabling detection of species over space and time, eDNA fulfills a fundamental need of environmental surveys. Traditional surveys are expensive, require significant capital expenditure, and can be destructive; eDNA offers promise for cheaper, less invasive, and higher-resolution (i.

Novel Application of Large Bore Aspiration in the Treatment of COVID-19 Associated Acute Limb Ischemia Using the Penumbra CAT 12 Lightning Aspiration System.

COVID-19 associated cardiovascular complications have been well documented throughout the pandemic and are associated with higher rates of morbidity and mortality. Hypercoagulable states resulting from systemic inflammation have been associated with increasing incidences of acute myocardial infarctions (AMI) and acute limb ischemia (ALI). Herein, we present a case of AMI complicated by ALI in a patient with COVID-19 in which aspiration thrombectomy using the Penumbra CAT 12 thrombectomy catheter was used in the management of acute popliteal artery occlusion.

Standardized multi-omics of Earth's microbiomes reveals microbial and metabolite diversity.

Despite advances in sequencing, lack of standardization makes comparisons across studies challenging and hampers insights into the structure and function of microbial communities across multiple habitats on a planetary scale. Here we present a multi-omics analysis of a diverse set of 880 microbial community samples collected for the Earth Microbiome Project. We include amplicon (16S, 18S, ITS) and shotgun metagenomic sequence data, and untargeted metabolomics data (liquid chromatography-tandem mass spectrometry and gas chromatography mass spectrometry).

Tourmaline: A containerized workflow for rapid and iterable amplicon sequence analysis using QIIME 2 and Snakemake.

Background: Amplicon sequencing (metabarcoding) is a common method to survey diversity of environmental communities whereby a single genetic locus is amplified and sequenced from the DNA of whole or partial organisms, organismal traces (e.g., skin, mucus, feces), or microbes in an environmental sample.

Dominance of in Metagenomes Associated with the Methane Ice Worm (Sirsoe methanicola).

Sirsoe methanicola, commonly known as the methane ice worm, is the only macrofaunal species known to inhabit the Gulf of Mexico methane hydrates. Little is known about this elusive marine polychaete that can colonize rich carbon and energy reserves. Metagenomic analysis of gut contents and worm fragments predicted diverse metabolic capabilities with the ability to utilize a range of nitrogen, sulfur, and organic carbon compounds through microbial taxa affiliated with , , , , , and .

Novel Use of the Penumbra CAT 12 Lightning Aspiration System for the Treatment of a Complex Thrombus.

Debulking procedures using aspiration devices have been previously described in the literature to treat vegetations or thrombi on intracardiac structures such as the tricuspid valve. Transcatheter therapy has also been shown to be an effective alternative to surgical treatment for managing high risk or non-surgical patients. Furthermore, aspiration procedures can help identify the unique etiologies of intracardiac masses which can greatly impact differing treatment modalities.

Subsurface automated samplers for eDNA (SASe) for biological monitoring and research.

Sampling of environmental DNA (eDNA) in seawater is an increasingly common approach to non-invasively assess marine biodiversity, detect cryptic or invasive species, and monitor specific groups of organisms. Despite this remarkable utility, collection and filtration of eDNA samples in the field still requires considerable time and effort. Recent advancements in automated water samplers have standardized the eDNA collection process, allowing researchers to collect eDNA day or night, sample in locations that are difficult to access, and remove the need for highly trained personnel to perform sampling.

Microbiome Metadata Standards: Report of the National Microbiome Data Collaborative's Workshop and Follow-On Activities.

Microbiome samples are inherently defined by the environment in which they are found. Therefore, data that provide context and enable interpretation of measurements produced from biological samples, often referred to as metadata, are critical. Important contributions have been made in the development of community-driven metadata standards; however, these standards have not been uniformly embraced by the microbiome research community.

Two hundred and fifty-four metagenome-assembled bacterial genomes from the bank vole gut microbiota.

Vertebrate gut microbiota provide many essential services to their host. To better understand the diversity of such services provided by gut microbiota in wild rodents, we assembled metagenome shotgun sequence data from a small mammal, the bank vole Myodes glareolus (Rodentia, Cricetidae). We were able to identify 254 metagenome assembled genomes (MAGs) that were at least 50% (n = 133 MAGs), 80% (n = 77 MAGs) or 95% (n = 44 MAGs) complete.

Author Correction: Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Red Sea SAR11 and Single-Cell Genomes Reflect Globally Distributed Pangenomes.

Evidence suggests many marine bacteria are cosmopolitan, with widespread but sparse strains poised to seed abundant populations under conducive growth conditions. However, studies supporting this "microbial seed bank" hypothesis have analyzed taxonomic marker genes rather than whole genomes/metagenomes, leaving open the possibility that disparate ocean regions harbor endemic gene content. The Red Sea is isolated geographically from the rest of the ocean and has a combination of high irradiance, high temperature, and high salinity that is unique among the oceans; we therefore asked whether it harbors endemic gene content.

A Novel Sparse Compositional Technique Reveals Microbial Perturbations.

The central aims of many host or environmental microbiome studies are to elucidate factors associated with microbial community compositions and to relate microbial features to outcomes. However, these aims are often complicated by difficulties stemming from high-dimensionality, non-normality, sparsity, and the compositional nature of microbiome data sets. A key tool in microbiome analysis is beta diversity, defined by the distances between microbial samples.

Species-level functional profiling of metagenomes and metatranscriptomes.

Functional profiles of microbial communities are typically generated using comprehensive metagenomic or metatranscriptomic sequence read searches, which are time-consuming, prone to spurious mapping, and often limited to community-level quantification. We developed HUMAnN2, a tiered search strategy that enables fast, accurate, and species-resolved functional profiling of host-associated and environmental communities. HUMAnN2 identifies a community's known species, aligns reads to their pangenomes, performs translated search on unclassified reads, and finally quantifies gene families and pathways.

The genome of a novel isolate of Prochlorococcus from the Red Sea contains transcribed genes for compatible solute biosynthesis.

Marine microbes possess genomic and physiological adaptations to cope with varying environmental conditions. So far, the effects of high salinity on the most abundant marine photoautotrophic organism, Prochlorococcus, in marine oligotrophic environments, are mostly unknown. Here, we report the isolation of a new Prochlorococcus strain (RSP50) belonging to high-light (HL) clade II from the Red Sea, one of the warmest and most saline bodies of water in the global oceans.

Evolutionary trends in host physiology outweigh dietary niche in structuring primate gut microbiomes.

Over the past decade several studies have reported that the gut microbiomes of mammals with similar dietary niches exhibit similar compositional and functional traits. However, these studies rely heavily on samples from captive individuals and often confound host phylogeny, gut morphology, and diet. To more explicitly test the influence of host dietary niche on the mammalian gut microbiome we use 16S rRNA gene amplicon sequencing and shotgun metagenomics to compare the gut microbiota of 18 species of wild non-human primates classified as either folivores or closely related non-folivores, evenly distributed throughout the primate order and representing a range of gut morphological specializations.

Environmental radiation alters the gut microbiome of the bank vole Myodes glareolus.

Gut microbiota composition depends on many factors, although the impact of environmental pollution is largely unknown. We used amplicon sequencing of bacterial 16S rRNA genes to quantify whether anthropogenic radionuclides at Chernobyl (Ukraine) impact the gut microbiome of the bank vole Myodes glareolus. Exposure to elevated levels of environmental radionuclides had no detectable effect on the gut community richness but was associated with an almost two-fold increase in the Firmicutes:Bacteroidetes ratio.

American Gut: an Open Platform for Citizen Science Microbiome Research.

Although much work has linked the human microbiome to specific phenotypes and lifestyle variables, data from different projects have been challenging to integrate and the extent of microbial and molecular diversity in human stool remains unknown. Using standardized protocols from the Earth Microbiome Project and sample contributions from over 10,000 citizen-scientists, together with an open research network, we compare human microbiome specimens primarily from the United States, United Kingdom, and Australia to one another and to environmental samples. Our results show an unexpected range of beta-diversity in human stool microbiomes compared to environmental samples; demonstrate the utility of procedures for removing the effects of overgrowth during room-temperature shipping for revealing phenotype correlations; uncover new molecules and kinds of molecular communities in the human stool metabolome; and examine emergent associations among the microbiome, metabolome, and the diversity of plants that are consumed (rather than relying on reductive categorical variables such as veganism, which have little or no explanatory power).