KatharoSeq Enables High-Throughput Microbiome Analysis from Low-Biomass Samples

Minich JJ, Zhu Q, Janssen S, et al. KatharoSeq Enables High-Throughput Microbiome Analysis from Low-Biomass Samples. mSystems. 2018;3(3):e00218-17

Hitomi (ASTRO-H) X-ray Astronomy Satellite

The Hitomi (ASTRO-H) mission is the sixth Japanese x-ray astronomy satellite developed by a large international collaboration, including Japan, USA, Canada, and Europe. The mission aimed to provide the highest energy resolution ever achieved at E  >  2  keV, using a microcalorimeter instrument, and to cover a wide energy range spanning four decades in energy from soft x-rays to gamma rays. After a successful launch on February 17, 2016, the spacecraft lost its function on March 26, 2016, but the commissioning phase for about a month provided valuable information on the onboard instruments and the spacecraft system, including astrophysical results obtained from first light observations. The paper describes the Hitomi (ASTRO-H) mission, its capabilities, the initial operation, and the instruments/spacecraft performances confirmed during the commissioning operations for about a month

The James Webb Space Telescope Mission

Twenty-six years ago a small committee report, building on earlier studies, expounded a compelling and poetic vision for the future of astronomy, calling for an infrared-optimized space telescope with an aperture of at least $4m$. With the support of their governments in the US, Europe, and Canada, 20,000 people realized that vision as the $6.5m$ James Webb Space Telescope. A generation of astronomers will celebrate their accomplishments for the life of the mission, potentially as long as 20 years, and beyond. This report and the scientific discoveries that follow are extended thank-you notes to the 20,000 team members. The telescope is working perfectly, with much better image quality than expected. In this and accompanying papers, we give a brief history, describe the observatory, outline its objectives and current observing program, and discuss the inventions and people who made it possible. We cite detailed reports on the design and the measured performance on orbit.Comment: Accepted by PASP for the special issue on The James Webb Space Telescope Overview, 29 pages, 4 figure

Instructional Models for Course-Based Research Experience (CRE) Teaching

The course-based research experience (CRE) with its documented educational benefits is increasingly being implemented in science, technology, engineering, and mathematics education. This article reports on a study that was done over a period of 3 years to explicate the instructional processes involved in teaching an undergraduate CRE. One hundred and two instructors from the established and large multi-institutional SEA-PHAGES program were surveyed for their understanding of the aims and practices of CRE teaching. This was followed by large-scale feedback sessions with the cohort of instructors at the annual SEA Faculty Meeting and subsequently with a small focus group of expert CRE instructors. Using a qualitative content analysis approach, the survey data were analyzed for the aims of inquiry instruction and pedagogical practices used to achieve these goals. The results characterize CRE inquiry teaching as involving three instructional models: 1) being a scientist and generating data; 2) teaching procedural knowledge; and 3) fostering project ownership. Each of these models is explicated and visualized in terms of the specific pedagogical practices and their relationships. The models present a complex picture of the ways in which CRE instruction is conducted on a daily basis and can inform instructors and institutions new to CRE teaching

KatharoSeq Enables High-Throughput Microbiome Analysis from Low-Biomass Samples.

Microbiome analyses of low-biomass samples are challenging because of contamination and inefficiencies, leading many investigators to employ low-throughput methods with minimal controls. We developed a new automated protocol, KatharoSeq (from the Greek katharos [clean]), that outperforms single-tube extractions while processing at least five times as fast. KatharoSeq incorporates positive and negative controls to reveal the whole bacterial community from inputs of as few as 50 cells and correctly identifies 90.6% (standard error, 0.013%) of the reads from 500 cells. To demonstrate the broad utility of KatharoSeq, we performed 16S rRNA amplicon and shotgun metagenome analyses of the Jet Propulsion Laboratory spacecraft assembly facility (SAF; n = 192, 96), 52 rooms of a neonatal intensive care unit (NICU; n = 388, 337), and an endangered-abalone-rearing facility (n = 192, 123), obtaining spatially resolved, unique microbiomes reproducible across hundreds of samples. The SAF, our primary focus, contains 32 sOTUs (sub-OTUs, defined as exact sequence matches) and their inferred variants identified by the deblur algorithm, with four (Acinetobacter lwoffii, Paracoccus marcusii, Mycobacterium sp., and Novosphingobium) being present in >75% of the samples. According to microbial spatial topography, the most abundant cleanroom contaminant, A. lwoffii, is related to human foot traffic exposure. In the NICU, we have been able to discriminate environmental exposure related to patient infectious disease, and in the abalone facility, we show that microbial communities reflect the marine environment rather than human input. Consequently, we demonstrate the feasibility and utility of large-scale, low-biomass metagenomic analyses using the KatharoSeq protocol. IMPORTANCE Various indoor, outdoor, and host-associated environments contain small quantities of microbial biomass and represent a niche that is often understudied because of technical constraints. Many studies that attempt to evaluate these low-biomass microbiome samples are riddled with erroneous results that are typically false positive signals obtained during the sampling process. We have investigated various low-biomass kits and methods to determine the limit of detection of these pipelines. Here we present KatharoSeq, a high-throughput protocol combining laboratory and bioinformatic methods that can differentiate a true positive signal in samples with as few as 50 to 500 cells. We demonstrate the application of this method in three unique low-biomass environments, including a SAF, a hospital NICU, and an abalone-rearing facility

Changes to the ACGME Common Program Requirements and Their Potential Impact on Emergency Medicine Core Faculty Protected Time.

The Accreditation Council for Graduate Medical Education (ACGME), which regulates residency and fellowship training in the United States, recently revised the minimum standards for all training programs. These standards are codified and published as the Common Program Requirements. Recent specific revisions, particularly removing the requirement ensuring protected time for core faculty, are poised to have a substantial impact on emergency medicine training programs. A group of representatives and relevant stakeholders from national emergency medicine (EM) organizations was convened to assess the potential effects of these changes on core faculty and the training of emergency physicians. We reviewed the literature and results of surveys conducted by EM organizations to examine the role of core faculty protected time. Faculty nonclinical activities contribute greatly to the academic missions of EM training programs. Protected time and reduced clinical hours allow core faculty to engage in education and research, which are two of the three core pillars of academic EM. Loss of core faculty protected time is expected to have detrimental impacts on training programs and on EM generally. We provide consensus recommendations regarding EM core faculty clinical work hour limitations to maintain protected time for educational activities and scholarship and preserve the quality of academic EM

Multiomic Analyses of Nascent Preterm Infant Microbiomes Differentiation Suggest Opportunities for Targeted Intervention

The first week after birth is a critical time for the establishment of microbial communities for infants. Preterm infants face unique environmental impacts on their newly acquired microbiomes, including increased incidence of cesarean section delivery and exposure to antibiotics as well as delayed enteral feeding and reduced human interaction during their intensive care unit stay. Using contextualized paired metabolomics and 16S sequencing data, the development of the gut, skin, and oral microbiomes of infants is profiled daily for the first week after birth, and it is found that the skin microbiome appears robust to early life perturbation, while direct exposure of infants to antibiotics, rather than presumed maternal transmission, delays microbiome development and prevents the early differentiation based on body site regardless of delivery mode. Metabolomic analyses identify the development of all gut metabolomes of preterm infants toward full‐term infant profiles, but a significant increase of primary bile acid metabolism only in the non‐antibiotic treated vaginally birthed late preterm infants. This study provides a framework for future multi‐omic, multibody site analyses on these high‐risk preterm infant populations and suggests opportunities for monitoring and intervention, with infant antibiotic exposure as the primary driver of delays in microbiome development.Daily, multibody‐site microbiome sampling for the first week of life reveals that preterm infant antibiotic exposure delays the differentiation of body‐site specific microbiomes. Primary bile acid metabolism in the gut metabolome is also present only in the non‐antibiotic‐treated, vaginally birthed preterm infants, further highlighting the disruptive impact of antibiotics. This study provides a framework for future studies of infant microbiome development.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/174837/1/adbi202101313.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/174837/2/adbi202101313-sup-0001-SuppMat.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/174837/3/adbi202101313_am.pd

Changes to the ACGME Common Program Requirements and Their Potential Impact on Emergency Medicine Core Faculty Protected Time

The Accreditation Council for Graduate Medical Education (ACGME), which regulates residency and fellowship training in the United States, recently revised the minimum standards for all training programs. These standards are codified and published as the Common Program Requirements (CPRs). Recent specific revisions, particularly removing the requirement ensuring protected time for core faculty, are poised to have a substantial impact on emergency medicine training programs. A group of representatives and relevant stakeholders from national emergency medicine organizations was convened to assess the potential effects of these changes on core faculty and the training of emergency physicians. We reviewed the literature and results of surveys conducted by emergency medicine organizations to examine the role of core faculty protected time. Faculty nonclinical activities contribute greatly to the academic missions of emergency medicine training programs. Protected time and reduced clinical hours allow core faculty to engage in education and research, which are two of the three core pillars of academic emergency medicine. Loss of core faculty protected time is expected to have detrimental impacts on training programs and on emergency medicine generally. We provide consensus recommendations regarding emergency medicine core faculty clinical work hour limitations to maintain protected time for educational activities and scholarship and preserve the quality of academic emergency medicine